pax_global_header00006660000000000000000000000064125656476210014530gustar00rootroot0000000000000052 comment=dfcb2ff01b4c234fb6974cce3c181640a4fc5f64 libsis-jhdf5-java-14.12.1/000077500000000000000000000000001256564762100151005ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/000077500000000000000000000000001256564762100164005ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/c/000077500000000000000000000000001256564762100166225ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/c/COPYING000066400000000000000000000110321256564762100176520ustar00rootroot00000000000000Copyright Notice and Statement for NCSA Hierarchical Data Format (HDF) Java Software Library and Utilities NCSA Hierarchical Data Format (HDF) Software Library and Utilities Copyright 1988-2004, the Board of Trustees of the University of Illinois. Copyright 2007-2009, Center for Information Sciences and Databases, ETH Zurich, Switzerland. All rights reserved. Contributors to the library: National Center for Supercomputing Applications (NCSA) at the University of Illinois, Lawrence Livermore Nationall Laboratory (LLNL), Sandia National Laboratories (SNL), Los Alamos National Laboratory (LANL). Fortner Software, Unidata Program Center (netCDF), The Independent JPEG Group (JPEG), Jean-loup Gailly and Mark Adler (gzip), and Digital Equipment Corporation (DEC). Macintosh support contributed by Gregory L. Guerin. The package 'glguerin': Copyright 1998, 1999 by Gregory L. Guerin. Redistribute or reuse only as described below. These files are from the MacBinary Toolkit for Java: and are redistributed by NCSA with permission of the author. This work was supported in part by a Cooperative Agreement with NASA under NASA grant NAG 5-2040 and NAG NCC5-599. Redistribution and use in source and binary forms, with or without modification, are permitted for any purpose (including commercial purposes) provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or materials provided with the distribution. 3. In addition, redistributions of modified forms of the source or binary code must carry prominent notices stating that the original code was changed and the date of the change. 4. All publications or advertising materials mentioning features or use of this software must acknowledge that it was developed by the National Center for Supercomputing Applications at the University of Illinois, and credit the Contributors. 5. Neither the name of the University nor the names of the Contributors may be used to endorse or promote products derived from this software without specific prior written permission from the University or the Contributors. 6. THIS SOFTWARE IS PROVIDED BY THE UNIVERSITY AND THE CONTRIBUTORS "AS IS" WITH NO WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED. In no event shall the University or the Contributors be liable for any damages suffered by the users arising out of the use of this software, even if advised of the possibility of such damage. -------------------------------------------------------------------------- Portions of HDF5 were developed with support from the University of California, Lawrence Livermore National Laboratory (UC LLNL). The following statement applies to those portions of the product and must be retained in any redistribution of source code, binaries, documentation, and/or accompanying materials: This work was partially produced at the University of California, Lawrence Livermore National Laboratory (UC LLNL) under contract no. W-7405-ENG-48 (Contract 48) between the U.S. Department of Energy (DOE) and The Regents of the University of California (University) for the operation of UC LLNL. DISCLAIMER: This work was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor the University of California nor any of their employees, makes any warranty, express or implied, or assumes any liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately- owned rights. Reference herein to any specific commercial products, process, or service by trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or the University of California. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or the University of California, and shall not be used for advertising or product endorsement purposes. -------------------------------------------------------------------------- libsis-jhdf5-java-14.12.1/source/c/compile_hdf5_gcc.sh000077500000000000000000000011601256564762100223310ustar00rootroot00000000000000#! /bin/bash source version.sh PLATFORM="$1" PATCHES="$2" if [ "$PLATFORM" != "i386" -a "$PLATFORM" != "x86" -a "$PLATFORM" != "amd64" -a "$PLATFORM" != "x86_64" -a "$PLATFORM" != "armv6l" ]; then echo "Syntax: compile_hdf5.sh " echo "where is one of i386, x86, amd64, or x86_64" exit 1 fi tar xvf hdf5-$VERSION.tar cd hdf5-$VERSION if [ -n "$PATCHES" ]; then for p in $PATCHES; do patch -p0 < ../$p done fi CFLAGS=$CFLAGS ./configure --prefix=/opt/hdf5-$VERSION-$PLATFORM --enable-debug=none --enable-production $ADDITIONAL &> configure.log make &> make.log make test &> test.log libsis-jhdf5-java-14.12.1/source/c/compile_hdf5_linux_amd64.sh000077500000000000000000000001451256564762100237310ustar00rootroot00000000000000#! /bin/bash CFLAGS='-fPIC -m64' ./compile_hdf5_gcc.sh amd64 "gcc-4.678-optimizations-config.patch" libsis-jhdf5-java-14.12.1/source/c/compile_hdf5_linux_arm.sh000077500000000000000000000000531256564762100235730ustar00rootroot00000000000000#! /bin/bash ./compile_hdf5_gcc.sh armv6l libsis-jhdf5-java-14.12.1/source/c/compile_hdf5_linux_i386.sh000077500000000000000000000001361256564762100235070ustar00rootroot00000000000000#! /bin/bash CFLAGS='-m32' ./compile_hdf5_gcc.sh i386 "gcc-4.678-optimizations-config.patch" libsis-jhdf5-java-14.12.1/source/c/compile_hdf5_macosx_i386.sh000077500000000000000000000001211256564762100236340ustar00rootroot00000000000000#! /bin/bash CFLAGS='-m32 -mmacosx-version-min=10.6' ./compile_hdf5_gcc.sh i386 libsis-jhdf5-java-14.12.1/source/c/compile_hdf5_macosx_x86_64.sh000077500000000000000000000001231256564762100241030ustar00rootroot00000000000000#! /bin/bash CFLAGS='-m64 -mmacosx-version-min=10.6' ./compile_hdf5_gcc.sh x86_64 libsis-jhdf5-java-14.12.1/source/c/compile_hdf5_sunstudio_64.sh000077500000000000000000000005651256564762100241530ustar00rootroot00000000000000#! /bin/bash PATH=/opt/SUNWspro/bin:/usr/local/bin:/opt/csw/bin:/usr/sbin:/usr/bin:/usr/openwin/bin:/usr/ccs/bin:/usr/ucb export PATH source version.sh tar xf hdf5-$VERSION.tar cd hdf5-$VERSION CFLAGS='-fast -m64 -KPIC' ./configure --prefix=/opt/hdf5-$VERSION-64 --enable-shared --enable-debug=none --enable-production make > make.log 2>&1 make test > test.log 2>&1 libsis-jhdf5-java-14.12.1/source/c/compile_hdf5_sunstudio_sparc32.sh000077500000000000000000000006471256564762100252000ustar00rootroot00000000000000#! /bin/bash PATH=/opt/SUNWspro/bin:/usr/local/bin:/opt/csw/bin:/usr/sbin:/usr/bin:/usr/openwin/bin:/usr/ccs/bin:/usr/ucb export PATH source version.sh tar xf hdf5-$VERSION.tar cd hdf5-$VERSION CPPFLAGS='-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE' ./configure --prefix=/opt/hdf5-$VERSION-32 --enable-shared --enable-debug=none --enable-production make > make.log 2>&1 make test > test.log 2>&1 libsis-jhdf5-java-14.12.1/source/c/compile_hdf5_sunstudio_x86.sh000077500000000000000000000006661256564762100243510ustar00rootroot00000000000000#! /bin/bash PATH=/opt/SUNWspro/bin:/usr/local/bin:/opt/csw/bin:/usr/sbin:/usr/bin:/usr/openwin/bin:/usr/ccs/bin:/usr/ucb export PATH source version.sh tar xf hdf5-$VERSION.tar cd hdf5-$VERSION CPPFLAGS='-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE' CFLAGS='-KPIC' ./configure --prefix=/opt/hdf5-$VERSION-32 --enable-shared --enable-debug=none --enable-production make > make.log 2>&1 make test > test.log 2>&1 libsis-jhdf5-java-14.12.1/source/c/compile_linux_amd64.sh000077500000000000000000000005321256564762100230230ustar00rootroot00000000000000#! /bin/bash source version.sh gcc -shared -O3 -floop-interchange -floop-strip-mine -floop-block -fgraphite-identity -mtune=corei7 -fPIC -Wl,--exclude-libs,ALL jhdf5/*.c hdf-java/*.c -I/opt/hdf5-${VERSION}-amd64/include -I/usr/java/jdk1.6.0/include -I/usr/java/jdk1.6.0/include/linux /opt/hdf5-${VERSION}-amd64/lib/libhdf5.a -o libjhdf5.so -lz libsis-jhdf5-java-14.12.1/source/c/compile_linux_arm.sh000077500000000000000000000004021256564762100226630ustar00rootroot00000000000000#! /bin/bash source version.sh gcc -shared -O3 -Wl,--exclude-libs,ALL jhdf5/*.c hdf-java/*.c -I/opt/hdf5-${VERSION}-armv6l/include -I/usr/java/jdk1.7.0/include -I/usr/java/jdk1.7.0/include/linux /opt/hdf5-${VERSION}-armv6l/lib/libhdf5.a -o libjhdf5.so -lz libsis-jhdf5-java-14.12.1/source/c/compile_linux_i386.sh000077500000000000000000000005271256564762100226050ustar00rootroot00000000000000#! /bin/bash source version.sh gcc -m32 -shared -O3 -floop-interchange -floop-strip-mine -floop-block -fgraphite-identity -mtune=corei7 -Wl,--exclude-libs,ALL jhdf5/*.c hdf-java/*.c -I/opt/hdf5-${VERSION}-i386/include -I/usr/java/jdk1.6.0/include -I/usr/java/jdk1.6.0/include/linux /opt/hdf5-${VERSION}-i386/lib/libhdf5.a -o libjhdf5.so -lz libsis-jhdf5-java-14.12.1/source/c/compile_macosx_i386.sh000077500000000000000000000004211256564762100227310ustar00rootroot00000000000000#! /bin/bash source version.sh gcc -m32 -mmacosx-version-min=10.6 -bundle -O3 jhdf5/*.c hdf-java/*.c -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -I/opt/hdf5-${VERSION}-i386/include /opt/hdf5-${VERSION}-i386/lib/libhdf5.a -lz -o libjhdf5.jnilib libsis-jhdf5-java-14.12.1/source/c/compile_macosx_x86_64.sh000077500000000000000000000004311256564762100231770ustar00rootroot00000000000000#! /bin/bash source version.sh gcc -m64 -mmacosx-version-min=10.6 -dynamiclib -O3 jhdf5/*.c hdf-java/*.c -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -I/opt/hdf5-${VERSION}-x86_64/include /opt/hdf5-${VERSION}-x86_64/lib/libhdf5.a -lz -o libjhdf5.jnilib libsis-jhdf5-java-14.12.1/source/c/compile_solaris_64.sh000077500000000000000000000003321256564762100226540ustar00rootroot00000000000000#! /bin/bash source version.sh cc -G -KPIC -fast -m64 jhdf5/*.c hdf-java/*.c -I/opt/hdf5-${VERSION}-64/include -I/usr/java/include -I/usr/java/include/solaris /opt/hdf5-${VERSION}-64/lib/libhdf5.a -lz -o libjhdf5.so libsis-jhdf5-java-14.12.1/source/c/compile_solaris_sparc32.sh000077500000000000000000000004121256564762100236770ustar00rootroot00000000000000#! /bin/bash source version.sh cc -G -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE jhdf5/*.c hdf-java/*.c -I/opt/hdf5-${VERSION}-32/include -I/usr/java/include -I/usr/java/include/solaris /opt/hdf5-${VERSION}-32/lib/libhdf5.a -lz -o libjhdf5.so libsis-jhdf5-java-14.12.1/source/c/compile_solaris_x86.sh000066400000000000000000000004261256564762100230510ustar00rootroot00000000000000#! /bin/bash source version.sh cc -G -KPIC -fast -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE jhdf5/*.c hdf-java/*.c -I/opt/hdf5-${VERSION}-32/include -I/usr/java/include -I/usr/java/include/solaris /opt/hdf5-${VERSION}-32/lib/libhdf5.a -lz -o libjhdf5.so libsis-jhdf5-java-14.12.1/source/c/compile_windows_i386.mak000066400000000000000000000253741256564762100233020ustar00rootroot00000000000000#============================================================================ # # Makefile to compile HDF Java Native C Source # Usage: nmake /f compile_windows_i386.mak # #============================================================================ # Visual C++ directory, for example VCPPDIR=C:\Program Files\Microsoft Visual Studio 9.0\VC # Directory where JDK is installed (We require JDK 1.6) JAVADIR=C:\Program Files\Java\jdk1.6.0_37 # Common parent directory HDFPARENTDIR=C:\JHDF5 # Directory of the HDF Java Products, for example HDFJAVADIR=$(HDFPARENTDIR)\jhdf5_src\ # The directory where HDF5 has been compiled HDFDIR=$(HDFPARENTDIR)\hdf5\hdf5-1.8.14 # The directory where HDF library is located HDFBUILDDIR=$(HDFDIR)\build # The directory where HDF library is located HDFLIBDIR=$(HDFBUILDDIR)\bin\Release # The directory where HDF header files are located HDFINCDIR=$(HDFDIR)\src # the JPEG library, for example #JPEGLIB=E:\Work\MyHDFstuff\lib-external\jpeg\libjpeg.lib JPEGLIB= # the GZIP library, for example #GZIPLIB=E:\Work\MyHDFstuff\lib-external\zlib\bin\windows\zlib114\lib\zlib.lib GZIPLIB=$(HDFLIBDIR)\zlibstatic.lib # SZIP library, for example #SZIPLIB=E:\Work\MyHDFstuff\lib-external\szip\bin\windows\szip-msvc++\lib\szlib.lib SZIPLIB= #=========================================================================== # Do not make any change below this line unless you know what you do #=========================================================================== PATH=$(PATH);$(VCPPDIR)\BIN SRCDIR1=$(HDFJAVADIR)\jhdf5 SRCDIR2=$(HDFJAVADIR)\hdf-java VALID_PATH_SET=YES #------------------------------------------------------- # Test if all path is valid !IF EXISTS("$(VCPPDIR)") !ELSE !MESSAGE ERROR: Visual C++ directory $(VCPPDIR) does not exist VALID_PATH_SET=NO !ENDIF !IF EXISTS("$(JAVADIR)") !ELSE !MESSAGE ERROR: JDK directory $(JAVADIR) does not exist VALID_PATH_SET=NO !ENDIF !IF EXISTS("$(SRCDIR1)") !ELSE !MESSAGE ERROR: C source directory $(SRCDIR1) does not exist VALID_PATH_SET=NO !ENDIF !IF EXISTS("$(SRCDIR2)") !ELSE !MESSAGE ERROR: C source directory $(SRCDIR2) does not exist VALID_PATH_SET=NO !ENDIF !IF EXISTS("$(HDFBUILDDIR)") !ELSE !MESSAGE ERROR: HDF build directory $(HDFBUILDDIR) does not exist VALID_PATH_SET=NO !ENDIF !IF EXISTS("$(HDFLIBDIR)") !ELSE !MESSAGE ERROR: HDF library directory $(HDFLIBDIR) does not exist VALID_PATH_SET=NO !ENDIF !IF EXISTS("$(HDFINCDIR)") !ELSE !MESSAGE ERROR: HDF header directory $(HDFINCDIR) does not exist VALID_PATH_SET=NO !ENDIF #!IF EXISTS("$(JPEGLIB)") #!ELSE #!MESSAGE ERROR: JPEG library does not exist #VALID_PATH_SET=NO #!ENDIF !IF EXISTS("$(GZIPLIB)") !ELSE !MESSAGE ERROR: GZIP library does not exist VALID_PATH_SET=NO !ENDIF #!IF EXISTS("$(SZIPLIB)") #!ELSE #!MESSAGE ERROR: SZIP library does not exist #VALID_PATH_SET=NO #!ENDIF #------------------------------------------------------- !IF "$(VALID_PATH_SET)" == "YES" !IF "$(OS)" == "Windows_NT" NULL= !ELSE NULL=nul !ENDIF INTDIR=.\jhdf5\Release OUTDIR=$(HDFJAVADIR)\lib\win ALL : "$(OUTDIR)\jhdf5.dll" "$(INTDIR)" : if not exist "$(INTDIR)/$(NULL)" mkdir "$(INTDIR)" "$(OUTDIR)" : if not exist "$(OUTDIR)/$(NULL)" mkdir "$(OUTDIR)" CPP=cl.exe CPP_PROJ=/nologo /W3 /EHsc /O2 /I "$(HDFINCDIR)" /I "$(HDFBUILDDIR)" /I "$(JAVADIR)\include" /I "$(JAVADIR)\include\win32" /D "WIN32" /D "NDEBUG" /D "_WINDOWS" /Fp"$(INTDIR)\jhdf5.pch" /Fo"$(INTDIR)\\" /Fd"$(INTDIR)\\" /FD /c .c{$(INTDIR)}.obj:: $(CPP) @<< $(CPP_PROJ) $< << .cpp{$(INTDIR)}.obj:: $(CPP) @<< $(CPP_PROJ) $< << .cxx{$(INTDIR)}.obj:: $(CPP) @<< $(CPP_PROJ) $< << .c{$(INTDIR)}.sbr:: $(CPP) @<< $(CPP_PROJ) $< << .cpp{$(INTDIR)}.sbr:: $(CPP) @<< $(CPP_PROJ) $< << .cxx{$(INTDIR)}.sbr:: $(CPP) @<< $(CPP_PROJ) $< << MTL=midl.exe MTL_PROJ=/nologo /D "NDEBUG" /mktyplib203 /win32 RSC=rc.exe BSC32=bscmake.exe BSC32_FLAGS=/nologo /o"$(INTDIR)\jhdf5.bsc" BSC32_SBRS= \ LINK32=link.exe LINK32_FLAGS=$(HDFLIBDIR)\libhdf5.lib $(SZIPLIB) $(GZIPLIB) /nologo /dll /nodefaultlib:msvcrt /incremental:no /pdb:"$(INTDIR)\jhdf5.pdb" /machine:I386 /out:"$(OUTDIR)\jhdf5.dll" /implib:"$(INTDIR)\jhdf5.lib" LINK32_OBJS= \ "$(INTDIR)\exceptionImpJHDF5.obj" \ "$(INTDIR)\h5aImpJHDF5.obj" \ "$(INTDIR)\h5ConstantsJHDF5.obj" \ "$(INTDIR)\h5dImpJHDF5.obj" \ "$(INTDIR)\h5fImpJHDF5.obj" \ "$(INTDIR)\h5gImpJHDF5.obj" \ "$(INTDIR)\h5iImpJHDF5.obj" \ "$(INTDIR)\h5ImpJHDF5.obj" \ "$(INTDIR)\h5lImpJHDF5.obj" \ "$(INTDIR)\h5oImpJHDF5.obj" \ "$(INTDIR)\h5pImpJHDF5.obj" \ "$(INTDIR)\h5rImpJHDF5.obj" \ "$(INTDIR)\h5sImpJHDF5.obj" \ "$(INTDIR)\h5tImpJHDF5.obj" \ "$(INTDIR)\h5utilJHDF5.obj" \ "$(INTDIR)\h5zImpJHDF5.obj" \ "$(INTDIR)\strcpyJHDF5.obj" \ "$(INTDIR)\h5aImp.obj" \ "$(INTDIR)\h5Constants.obj" \ "$(INTDIR)\h5dImp.obj" \ "$(INTDIR)\h5eImp.obj" \ "$(INTDIR)\h5fImp.obj" \ "$(INTDIR)\h5gImp.obj" \ "$(INTDIR)\h5iImp.obj" \ "$(INTDIR)\h5Imp.obj" \ "$(INTDIR)\h5lImp.obj" \ "$(INTDIR)\h5oImp.obj" \ "$(INTDIR)\h5pImp.obj" \ "$(INTDIR)\h5rImp.obj" \ "$(INTDIR)\h5sImp.obj" \ "$(INTDIR)\h5tImp.obj" \ "$(INTDIR)\h5util.obj" \ "$(INTDIR)\h5zImp.obj" \ "$(INTDIR)\nativeData.obj" "$(OUTDIR)\jhdf5.dll" : "$(OUTDIR)" $(DEF_FILE) $(LINK32_OBJS) $(LINK32) @<< $(LINK32_FLAGS) $(LINK32_OBJS) << SOURCE=$(SRCDIR1)\exceptionImpJHDF5.c 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libsis-jhdf5-java-14.12.1/source/c/compile_windows_x64.mak000066400000000000000000000254101256564762100232210ustar00rootroot00000000000000#============================================================================ # # Makefile to compile HDF Java Native C Source # Usage: nmake /f compile_windows_i386.mak # #============================================================================ # Visual C++ directory, for example VCPPDIR=C:\Program Files (x86)\Microsoft Visual Studio 9.0\VC # Directory where JDK is installed (We require JDK 1.6) JAVADIR=C:\Program Files\Java\jdk1.6.0_37 # Common parent directory HDFPARENTDIR=C:\JHDF5 # Directory of the HDF Java Products, for example HDFJAVADIR=$(HDFPARENTDIR)\jhdf5_src\ # The directory where HDF5 has been compiled HDFDIR=$(HDFPARENTDIR)\hdf5\hdf5-1.8.14 # The directory where HDF library is located HDFBUILDDIR=$(HDFDIR)\build # The directory where HDF library is located HDFLIBDIR=$(HDFBUILDDIR)\bin\Release # The directory where HDF header files are located HDFINCDIR=$(HDFDIR)\src # the JPEG library, for example #JPEGLIB=E:\Work\MyHDFstuff\lib-external\jpeg\libjpeg.lib JPEGLIB= # the GZIP library, for example #GZIPLIB=E:\Work\MyHDFstuff\lib-external\zlib\bin\windows\zlib114\lib\zlib.lib GZIPLIB=$(HDFLIBDIR)\zlibstatic.lib # SZIP library, for example #SZIPLIB=E:\Work\MyHDFstuff\lib-external\szip\bin\windows\szip-msvc++\lib\szlib.lib SZIPLIB= #=========================================================================== # Do not make any change below this line unless you know what you do #=========================================================================== PATH=$(PATH);$(VCPPDIR)\BIN SRCDIR1=$(HDFJAVADIR)\jhdf5 SRCDIR2=$(HDFJAVADIR)\hdf-java VALID_PATH_SET=YES #------------------------------------------------------- # Test if all path is valid !IF EXISTS("$(VCPPDIR)") !ELSE !MESSAGE ERROR: Visual C++ directory $(VCPPDIR) does not exist VALID_PATH_SET=NO !ENDIF !IF EXISTS("$(JAVADIR)") !ELSE !MESSAGE ERROR: JDK directory $(JAVADIR) does not exist VALID_PATH_SET=NO !ENDIF !IF EXISTS("$(SRCDIR1)") !ELSE !MESSAGE ERROR: C source directory $(SRCDIR1) does not exist VALID_PATH_SET=NO !ENDIF !IF EXISTS("$(SRCDIR2)") !ELSE !MESSAGE ERROR: C source directory $(SRCDIR2) does not exist VALID_PATH_SET=NO !ENDIF !IF EXISTS("$(HDFBUILDDIR)") !ELSE !MESSAGE ERROR: HDF build directory $(HDFBUILDDIR) does not exist VALID_PATH_SET=NO !ENDIF !IF EXISTS("$(HDFLIBDIR)") !ELSE !MESSAGE ERROR: HDF library directory $(HDFLIBDIR) does not exist VALID_PATH_SET=NO !ENDIF !IF EXISTS("$(HDFINCDIR)") !ELSE !MESSAGE ERROR: HDF header directory $(HDFINCDIR) does not exist VALID_PATH_SET=NO !ENDIF #!IF EXISTS("$(JPEGLIB)") #!ELSE #!MESSAGE ERROR: JPEG library does not exist #VALID_PATH_SET=NO #!ENDIF !IF EXISTS("$(GZIPLIB)") !ELSE !MESSAGE ERROR: GZIP library does not exist VALID_PATH_SET=NO !ENDIF #!IF EXISTS("$(SZIPLIB)") #!ELSE #!MESSAGE ERROR: SZIP library does not exist #VALID_PATH_SET=NO #!ENDIF #------------------------------------------------------- !IF "$(VALID_PATH_SET)" == "YES" !IF "$(OS)" == "Windows_NT" NULL= !ELSE NULL=nul !ENDIF INTDIR=.\jhdf5\Release OUTDIR=$(HDFJAVADIR)\lib\win ALL : "$(OUTDIR)\jhdf5.dll" "$(INTDIR)" : if not exist "$(INTDIR)/$(NULL)" mkdir "$(INTDIR)" "$(OUTDIR)" : if not exist "$(OUTDIR)/$(NULL)" mkdir "$(OUTDIR)" CPP=cl.exe CPP_PROJ=/nologo /W3 /EHsc /O2 /I "$(HDFINCDIR)" /I "$(HDFBUILDDIR)" /I "$(JAVADIR)\include" /I "$(JAVADIR)\include\win32" /D "WIN32" /D "NDEBUG" /D "_WINDOWS" /Fp"$(INTDIR)\jhdf5.pch" /Fo"$(INTDIR)\\" /Fd"$(INTDIR)\\" /FD /c .c{$(INTDIR)}.obj:: $(CPP) @<< $(CPP_PROJ) $< << .cpp{$(INTDIR)}.obj:: $(CPP) @<< $(CPP_PROJ) $< << .cxx{$(INTDIR)}.obj:: $(CPP) @<< $(CPP_PROJ) $< << .c{$(INTDIR)}.sbr:: $(CPP) @<< $(CPP_PROJ) $< << .cpp{$(INTDIR)}.sbr:: $(CPP) @<< $(CPP_PROJ) $< << .cxx{$(INTDIR)}.sbr:: $(CPP) @<< $(CPP_PROJ) $< << MTL=midl.exe MTL_PROJ=/nologo /D "NDEBUG" /mktyplib203 /win32 RSC=rc.exe BSC32=bscmake.exe BSC32_FLAGS=/nologo /o"$(INTDIR)\jhdf5.bsc" BSC32_SBRS= \ LINK64=link.exe LINK64_FLAGS=$(HDFLIBDIR)\libhdf5.lib $(SZIPLIB) $(GZIPLIB) /nologo /dll /nodefaultlib:msvcrt /incremental:no /pdb:"$(INTDIR)\jhdf5.pdb" /machine:x64 /out:"$(OUTDIR)\jhdf5.dll" /implib:"$(INTDIR)\jhdf5.lib" LINK64_OBJS= \ "$(INTDIR)\exceptionImpJHDF5.obj" \ "$(INTDIR)\h5aImpJHDF5.obj" \ "$(INTDIR)\h5ConstantsJHDF5.obj" \ "$(INTDIR)\h5dImpJHDF5.obj" \ "$(INTDIR)\h5fImpJHDF5.obj" \ "$(INTDIR)\h5gImpJHDF5.obj" \ "$(INTDIR)\h5iImpJHDF5.obj" \ "$(INTDIR)\h5ImpJHDF5.obj" \ "$(INTDIR)\h5lImpJHDF5.obj" \ "$(INTDIR)\h5oImpJHDF5.obj" \ "$(INTDIR)\h5pImpJHDF5.obj" \ "$(INTDIR)\h5rImpJHDF5.obj" \ "$(INTDIR)\h5sImpJHDF5.obj" \ "$(INTDIR)\h5tImpJHDF5.obj" \ "$(INTDIR)\h5utilJHDF5.obj" \ "$(INTDIR)\h5zImpJHDF5.obj" \ "$(INTDIR)\strcpyJHDF5.obj" \ "$(INTDIR)\h5aImp.obj" \ "$(INTDIR)\h5Constants.obj" \ "$(INTDIR)\h5dImp.obj" \ "$(INTDIR)\h5eImp.obj" \ "$(INTDIR)\h5fImp.obj" \ "$(INTDIR)\h5gImp.obj" \ "$(INTDIR)\h5iImp.obj" \ "$(INTDIR)\h5Imp.obj" \ "$(INTDIR)\h5lImp.obj" \ "$(INTDIR)\h5oImp.obj" \ "$(INTDIR)\h5pImp.obj" \ "$(INTDIR)\h5rImp.obj" \ "$(INTDIR)\h5sImp.obj" \ "$(INTDIR)\h5tImp.obj" \ "$(INTDIR)\h5util.obj" \ "$(INTDIR)\h5zImp.obj" \ "$(INTDIR)\nativeData.obj" "$(OUTDIR)\jhdf5.dll" : "$(OUTDIR)" $(DEF_FILE) $(LINK64_OBJS) $(LINK64) @<< $(LINK64_FLAGS) $(LINK64_OBJS) << SOURCE=$(SRCDIR1)\exceptionImpJHDF5.c "$(INTDIR)\exceptionImpJHDF5.obj" : $(SOURCE) "$(INTDIR)" $(CPP) $(CPP_PROJ) $(SOURCE) SOURCE=$(SRCDIR1)\h5aImpJHDF5.c "$(INTDIR)\h5aImpJHDF5.obj" : $(SOURCE) "$(INTDIR)" $(CPP) $(CPP_PROJ) $(SOURCE) SOURCE=$(SRCDIR1)\h5ConstantsJHDF5.c "$(INTDIR)\h5ConstantsJHDF5.obj" : $(SOURCE) "$(INTDIR)" $(CPP) $(CPP_PROJ) $(SOURCE) SOURCE=$(SRCDIR1)\h5dImpJHDF5.c "$(INTDIR)\h5dImpJHDF5.obj" : $(SOURCE) "$(INTDIR)" $(CPP) $(CPP_PROJ) $(SOURCE) SOURCE=$(SRCDIR1)\h5fImpJHDF5.c "$(INTDIR)\h5fImpJHDF5.obj" : $(SOURCE) "$(INTDIR)" $(CPP) $(CPP_PROJ) $(SOURCE) SOURCE=$(SRCDIR1)\h5gImpJHDF5.c 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SOURCE=$(SRCDIR2)\nativeData.c "$(INTDIR)\nativeData.obj" : $(SOURCE) "$(INTDIR)" $(CPP) $(CPP_PROJ) $(SOURCE) CLEAN : -@erase "$(INTDIR)\exceptionImpJHDF5.obj" -@erase "$(INTDIR)\h5aImpJHDF5.obj" -@erase "$(INTDIR)\h5ConstantsJHDF5.obj" -@erase "$(INTDIR)\h5dImpJHDF5.obj" -@erase "$(INTDIR)\h5fImpJHDF5.obj" -@erase "$(INTDIR)\h5gImpJHDF5.obj" -@erase "$(INTDIR)\h5iImpJHDF5.obj" -@erase "$(INTDIR)\h5lImpJHDF5.obj" -@erase "$(INTDIR)\h5ImpJHDF5.obj" -@erase "$(INTDIR)\h5pImpJHDF5.obj" -@erase "$(INTDIR)\h5rImpJHDF5.obj" -@erase "$(INTDIR)\h5sImpJHDF5.obj" -@erase "$(INTDIR)\h5tImpJHDF5.obj" -@erase "$(INTDIR)\h5oImpJHDF5.obj" -@erase "$(INTDIR)\h5zImpJHDF5.obj" -@erase "$(INTDIR)\h5utilJHDF5.obj" -@erase "$(INTDIR)\strcpyJHDF5.obj" -@erase "$(INTDIR)\h5aImp.obj" -@erase "$(INTDIR)\h5Constants.obj" -@erase "$(INTDIR)\h5dImp.obj" -@erase "$(INTDIR)\h5eImp.obj" -@erase "$(INTDIR)\h5fImp.obj" -@erase "$(INTDIR)\h5gImp.obj" -@erase "$(INTDIR)\h5iImp.obj" -@erase "$(INTDIR)\h5lImp.obj" -@erase "$(INTDIR)\h5Imp.obj" -@erase "$(INTDIR)\h5pImp.obj" -@erase "$(INTDIR)\h5rImp.obj" -@erase "$(INTDIR)\h5sImp.obj" -@erase "$(INTDIR)\h5tImp.obj" -@erase "$(INTDIR)\h5oImp.obj" -@erase "$(INTDIR)\h5zImp.obj" -@erase "$(INTDIR)\h5util.obj" -@erase "$(INTDIR)\nativeData.obj" -@erase "$(INTDIR)\vc90.idb" -@erase "$(INTDIR)\jhdf5.exp" -@erase "$(INTDIR)\jhdf5.lib" -@erase "$(OUTDIR)\jhdf5.dll" !ENDIF libsis-jhdf5-java-14.12.1/source/c/create_win_zip.sh000077500000000000000000000012311256564762100221600ustar00rootroot00000000000000#! /bin/bash source version.sh rm -f hdf5-$VERSION-win.zip rm -fR hdf5-$VERSION tar xf hdf5-$VERSION.tar cd hdf5-$VERSION patch -s -p0 < ../hdf5_win_compile.diff find . -name "*.orig" -exec rm {} \; cp -f config/cmake/UserMacros/Windows_MT.cmake UserMacros.cmake fgres "option (BUILD_STATIC_CRT_LIBS \"Build With Static CRT Libraries\" OFF)" "option (BUILD_STATIC_CRT_LIBS \"Build With Static CRT Libraries\" ON)" UserMacros.cmake grep -q -F 'option (BUILD_STATIC_CRT_LIBS "Build With Static CRT Libraries" ON)' UserMacros.cmake || echo "Patching UserMacros.cmake for static build FAILED" cd .. zip -rq hdf5-$VERSION-win.zip hdf5-$VERSION rm -fR hdf5-$VERSION libsis-jhdf5-java-14.12.1/source/c/gcc-4.678-optimizations-config.patch000066400000000000000000000026601256564762100252410ustar00rootroot00000000000000diff -ruN hdf5-1.8.13.orig/config/gnu-flags hdf5-1.8.13/config/gnu-flags --- config/gnu-flags 2014-05-06 04:13:21.000000000 +0200 +++ config/gnu-flags 2014-06-06 15:36:09.318183153 +0200 @@ -260,6 +260,9 @@ # (Strictly speaking this isn't really a "warning" flag, so it's added to # the debugging flags) #DEBUG_CFLAGS="$DEBUG_CFLAGS -Wstack-protector -fstack-protector-all" + + # Enable some additional optimization settings + PROD_CFLAGS="$PROD_CFLAGS -floop-interchange -floop-strip-mine -floop-block -fgraphite-identity -fuse-linker-plugin -flto -mtune=corei7" ;; gcc-4.7*) @@ -331,6 +334,9 @@ # (Strictly speaking this isn't really a "warning" flag, so it's added to # the debugging flags) #DEBUG_CFLAGS="$DEBUG_CFLAGS -Wstack-protector -fstack-protector-all" + + # Enable some additional optimization settings + PROD_CFLAGS="$PROD_CFLAGS -floop-interchange -floop-strip-mine -floop-block -fgraphite-identity -fuse-linker-plugin -flto -mtune=corei7" ;; gcc-4.6*) @@ -395,6 +401,9 @@ # (Strictly speaking this isn't really a "warning" flag, so it's added to # the debugging flags) #DEBUG_CFLAGS="$DEBUG_CFLAGS -Wstack-protector -fstack-protector-all" + + # Enable some additional optimization settings + PROD_CFLAGS="$PROD_CFLAGS -floop-interchange -floop-strip-mine -floop-block -fgraphite-identity -fuse-linker-plugin -flto -mtune=corei7" ;; gcc-4.5*) libsis-jhdf5-java-14.12.1/source/c/hdf-java/000077500000000000000000000000001256564762100203025ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/c/hdf-java/h5Constants.c000077500000000000000000002270431256564762100226720ustar00rootroot00000000000000/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF Java Products. The full HDF Java copyright * * notice, including terms governing use, modification, and redistribution, * * is contained in the file, COPYING. COPYING can be found at the root of * * the source code distribution tree. You can also access it online at * * http://www.hdfgroup.org/products/licenses.html. If you do not have * * access to the file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #ifdef __cplusplus extern "C" { #endif #include #include "hdf5.h" JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5_1QUARTER_1HADDR_1MAX(JNIEnv *env, jclass cls) { return (hsize_t)HADDR_MAX/4; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5_1SZIP_1ALLOW_1K13_1OPTION_1MASK(JNIEnv *env, jclass cls) { return H5_SZIP_ALLOW_K13_OPTION_MASK; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5_1SZIP_1CHIP_1OPTION_1MASK(JNIEnv *env, jclass cls) { return H5_SZIP_CHIP_OPTION_MASK; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5_1SZIP_1EC_1OPTION_1MASK(JNIEnv *env, jclass cls) { return H5_SZIP_EC_OPTION_MASK; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5_1SZIP_1MAX_1PIXELS_1PER_1BLOCK(JNIEnv *env, jclass cls) { return H5_SZIP_MAX_PIXELS_PER_BLOCK; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5_1SZIP_1NN_1OPTION_1MASK(JNIEnv *env, jclass cls) { return H5_SZIP_NN_OPTION_MASK; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5_1INDEX_1UNKNOWN(JNIEnv *env, jclass cls) { return H5_INDEX_UNKNOWN; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5_1INDEX_1NAME(JNIEnv *env, jclass cls) { return H5_INDEX_NAME; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5_1INDEX_1CRT_1ORDER(JNIEnv *env, jclass cls) { return H5_INDEX_CRT_ORDER; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5_1INDEX_1N(JNIEnv *env, jclass cls) { return H5_INDEX_N; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5_1ITER_1UNKNOWN(JNIEnv *env, jclass cls) { return H5_ITER_UNKNOWN; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5_1ITER_1INC(JNIEnv *env, jclass cls) { return H5_ITER_INC; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5_1ITER_1DEC(JNIEnv *env, jclass cls) { return H5_ITER_DEC; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5_1ITER_1NATIVE(JNIEnv *env, jclass cls) { return H5_ITER_NATIVE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5_1ITER_1N(JNIEnv *env, jclass cls) { return H5_ITER_N; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5AC_1CURR_1CACHE_1CONFIG_1VERSION(JNIEnv *env, jclass cls) { return H5AC__CURR_CACHE_CONFIG_VERSION; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5AC_1MAX_1TRACE_1FILE_1NAME_1LEN(JNIEnv *env, jclass cls) { return H5AC__MAX_TRACE_FILE_NAME_LEN; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5AC_1METADATA_1WRITE_1STRATEGY_1PROCESS_1ZERO_1ONLY(JNIEnv *env, jclass cls) { #if (H5_VERS_RELEASE >= 6) return H5AC_METADATA_WRITE_STRATEGY__PROCESS_0_ONLY; #else return 0; #endif } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5AC_1METADATA_1WRITE_1STRATEGY_1DISTRIBUTED(JNIEnv *env, jclass cls) { #if (H5_VERS_RELEASE >= 6) return H5AC_METADATA_WRITE_STRATEGY__DISTRIBUTED; #else return 0; #endif } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5C_1incr_1off(JNIEnv *env, jclass cls) { return H5C_incr__off; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5C_1incr_1threshold(JNIEnv *env, jclass cls) { return H5C_incr__threshold; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5C_1flash_1incr_1off(JNIEnv *env, jclass cls) { return H5C_flash_incr__off; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5C_1flash_1incr_1add_1space(JNIEnv *env, jclass cls) { return H5C_flash_incr__add_space; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5C_1decr_1off(JNIEnv *env, jclass cls) { return H5C_decr__off; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5C_1decr_1threshold(JNIEnv *env, jclass cls) { return H5C_decr__threshold; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5C_1decr_1age_1out(JNIEnv *env, jclass cls) { return H5C_decr__age_out; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5C_1decr_1age_1out_1with_1threshold(JNIEnv *env, jclass cls) { return H5C_decr__age_out_with_threshold; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5D_1CHUNK_1BTREE(JNIEnv *env, jclass cls) { return H5D_CHUNK_BTREE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5D_1ALLOC_1TIME_1DEFAULT(JNIEnv *env, jclass cls) { return H5D_ALLOC_TIME_DEFAULT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5D_1ALLOC_1TIME_1EARLY(JNIEnv *env, jclass cls) { return H5D_ALLOC_TIME_EARLY; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5D_1ALLOC_1TIME_1ERROR(JNIEnv *env, jclass cls) { return H5D_ALLOC_TIME_ERROR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5D_1ALLOC_1TIME_1INCR(JNIEnv *env, jclass cls) { return H5D_ALLOC_TIME_INCR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5D_1ALLOC_1TIME_1LATE(JNIEnv *env, jclass cls) { return H5D_ALLOC_TIME_LATE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5D_1FILL_1TIME_1ERROR(JNIEnv *env, jclass cls) { return H5D_FILL_TIME_ERROR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5D_1FILL_1TIME_1ALLOC(JNIEnv *env, jclass cls) { return H5D_FILL_TIME_ALLOC; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5D_1FILL_1TIME_1NEVER(JNIEnv *env, jclass cls) { return H5D_FILL_TIME_NEVER; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5D_1FILL_1TIME_1IFSET(JNIEnv *env, jclass cls) { return H5D_FILL_TIME_IFSET; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5D_1FILL_1VALUE_1DEFAULT(JNIEnv *env, jclass cls) { return H5D_FILL_VALUE_DEFAULT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5D_1FILL_1VALUE_1ERROR(JNIEnv *env, jclass cls) { return H5D_FILL_VALUE_ERROR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5D_1FILL_1VALUE_1UNDEFINED(JNIEnv *env, jclass cls) { return H5D_FILL_VALUE_UNDEFINED; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5D_1FILL_1VALUE_1USER_1DEFINED(JNIEnv *env, jclass cls) { return H5D_FILL_VALUE_USER_DEFINED; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5D_1LAYOUT_1ERROR(JNIEnv *env, jclass cls) { return H5D_LAYOUT_ERROR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5D_1CHUNKED(JNIEnv *env, jclass cls) { return H5D_CHUNKED; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5D_1COMPACT(JNIEnv *env, jclass cls) { return H5D_COMPACT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5D_1CONTIGUOUS(JNIEnv *env, jclass cls) { return H5D_CONTIGUOUS; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5D_1NLAYOUTS(JNIEnv *env, jclass cls) { return H5D_NLAYOUTS; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5D_1SPACE_1STATUS_1ALLOCATED(JNIEnv *env, jclass cls) { return H5D_SPACE_STATUS_ALLOCATED; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5D_1SPACE_1STATUS_1ERROR(JNIEnv *env, jclass cls) { return H5D_SPACE_STATUS_ERROR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5D_1SPACE_1STATUS_1NOT_1ALLOCATED(JNIEnv *env, jclass cls) { return H5D_SPACE_STATUS_NOT_ALLOCATED; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5D_1SPACE_1STATUS_1PART_1ALLOCATED(JNIEnv *env, jclass cls) { return H5D_SPACE_STATUS_PART_ALLOCATED; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1ALIGNMENT(JNIEnv *env, jclass cls) { return H5E_ALIGNMENT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1ALREADYEXISTS(JNIEnv *env, jclass cls) { return H5E_ALREADYEXISTS; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1ALREADYINIT(JNIEnv *env, jclass cls) { return H5E_ALREADYINIT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1ARGS(JNIEnv *env, jclass cls) { return H5E_ARGS; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1ATOM(JNIEnv *env, jclass cls) { return H5E_ATOM; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1ATTR(JNIEnv *env, jclass cls) { return H5E_ATTR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1BADATOM(JNIEnv *env, jclass cls) { return H5E_BADATOM; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1BADFILE(JNIEnv *env, jclass cls) { return H5E_BADFILE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1BADGROUP(JNIEnv *env, jclass cls) { return H5E_BADGROUP; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1BADMESG(JNIEnv *env, jclass cls) { return H5E_BADMESG; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1BADRANGE(JNIEnv *env, jclass cls) { return H5E_BADRANGE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1BADSELECT(JNIEnv *env, jclass cls) { return H5E_BADSELECT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1BADSIZE(JNIEnv *env, jclass cls) { return H5E_BADSIZE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1BADTYPE(JNIEnv *env, jclass cls) { return H5E_BADTYPE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1BADVALUE(JNIEnv *env, jclass cls) { return H5E_BADVALUE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1BTREE(JNIEnv *env, jclass cls) { return H5E_BTREE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CACHE(JNIEnv *env, jclass cls) { return H5E_CACHE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CALLBACK(JNIEnv *env, jclass cls) { return H5E_CALLBACK; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CANAPPLY(JNIEnv *env, jclass cls) { return H5E_CANAPPLY; } /*JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CANTALLOC(JNIEnv *env, jclass cls) { return H5E_CANTALLOC; }*/ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CANTCLIP(JNIEnv *env, jclass cls) { return H5E_CANTCLIP; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CANTCLOSEFILE(JNIEnv *env, jclass cls) { return H5E_CANTCLOSEFILE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CANTCONVERT(JNIEnv *env, jclass cls) { return H5E_CANTCONVERT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CANTCOPY(JNIEnv *env, jclass cls) { return H5E_CANTCOPY; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CANTCOUNT(JNIEnv *env, jclass cls) { return H5E_CANTCOUNT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CANTCREATE(JNIEnv *env, jclass cls) { return H5E_CANTCREATE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CANTDEC(JNIEnv *env, jclass cls) { return H5E_CANTDEC; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CANTDECODE(JNIEnv *env, jclass cls) { return H5E_CANTDECODE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CANTDELETE(JNIEnv *env, jclass cls) { return H5E_CANTDELETE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CANTENCODE(JNIEnv *env, jclass cls) { return H5E_CANTENCODE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CANTFLUSH(JNIEnv *env, jclass cls) { return H5E_CANTFLUSH; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CANTFREE(JNIEnv *env, jclass cls) { return H5E_CANTFREE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CANTGET(JNIEnv *env, jclass cls) { return H5E_CANTGET; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CANTINC(JNIEnv *env, jclass cls) { return H5E_CANTINC; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CANTINIT(JNIEnv *env, jclass cls) { return H5E_CANTINIT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CANTINSERT(JNIEnv *env, jclass cls) { return H5E_CANTINSERT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CANTLIST(JNIEnv *env, jclass cls) { return H5E_CANTLIST; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CANTLOAD(JNIEnv *env, jclass cls) { return H5E_CANTLOAD; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CANTLOCK(JNIEnv *env, jclass cls) { return H5E_CANTLOCK; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CANTNEXT(JNIEnv *env, jclass cls) { return H5E_CANTNEXT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CANTOPENFILE(JNIEnv *env, jclass cls) { return H5E_CANTOPENFILE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CANTOPENOBJ(JNIEnv *env, jclass cls) { return H5E_CANTOPENOBJ; } /*JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CANTRECV(JNIEnv *env, jclass cls) { return H5E_CANTRECV; }*/ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CANTREGISTER(JNIEnv *env, jclass cls) { return H5E_CANTREGISTER; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CANTRELEASE(JNIEnv *env, jclass cls) { return H5E_CANTRELEASE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CANTSELECT(JNIEnv *env, jclass cls) { return H5E_CANTSELECT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CANTSET(JNIEnv *env, jclass cls) { return H5E_CANTSET; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CANTSPLIT(JNIEnv *env, jclass cls) { return H5E_CANTSPLIT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CANTUNLOCK(JNIEnv *env, jclass cls) { return H5E_CANTUNLOCK; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1CLOSEERROR(JNIEnv *env, jclass cls) { return H5E_CLOSEERROR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1COMPLEN(JNIEnv *env, jclass cls) { return H5E_COMPLEN; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1DATASET(JNIEnv *env, jclass cls) { return H5E_DATASET; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1DATASPACE(JNIEnv *env, jclass cls) { return H5E_DATASPACE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1DATATYPE(JNIEnv *env, jclass cls) { return H5E_DATATYPE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1DEFAULT(JNIEnv *env, jclass cls) { return H5E_DEFAULT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1DUPCLASS(JNIEnv *env, jclass cls) { return H5E_DUPCLASS; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1EFL(JNIEnv *env, jclass cls) { return H5E_EFL; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1EXISTS(JNIEnv *env, jclass cls) { return H5E_EXISTS; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1FCNTL(JNIEnv *env, jclass cls) { return H5E_FCNTL; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1FILE(JNIEnv *env, jclass cls) { return H5E_FILE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1FILEEXISTS(JNIEnv *env, jclass cls) { return H5E_FILEEXISTS; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1FILEOPEN(JNIEnv *env, jclass cls) { return H5E_FILEOPEN; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1FUNC(JNIEnv *env, jclass cls) { return H5E_FUNC; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1HEAP(JNIEnv *env, jclass cls) { return H5E_HEAP; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1INTERNAL(JNIEnv *env, jclass cls) { return H5E_INTERNAL; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1IO(JNIEnv *env, jclass cls) { return H5E_IO; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1LINK(JNIEnv *env, jclass cls) { return H5E_LINK; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1LINKCOUNT(JNIEnv *env, jclass cls) { return H5E_LINKCOUNT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1MAJOR(JNIEnv *env, jclass cls) { return H5E_MAJOR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1MINOR(JNIEnv *env, jclass cls) { return H5E_MINOR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1MOUNT(JNIEnv *env, jclass cls) { return H5E_MOUNT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1MPI(JNIEnv *env, jclass cls) { return H5E_MPI; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1MPIERRSTR(JNIEnv *env, jclass cls) { return H5E_MPIERRSTR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1NOFILTER(JNIEnv *env, jclass cls) { return H5E_NOFILTER; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1NOIDS(JNIEnv *env, jclass cls) { return H5E_NOIDS; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1NONE_1MAJOR(JNIEnv *env, jclass cls) { return H5E_NONE_MAJOR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1NONE_1MINOR(JNIEnv *env, jclass cls) { return H5E_NONE_MINOR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1NOSPACE(JNIEnv *env, jclass cls) { return H5E_NOSPACE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1NOTCACHED(JNIEnv *env, jclass cls) { return H5E_NOTCACHED; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1NOTFOUND(JNIEnv *env, jclass cls) { return H5E_NOTFOUND; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1NOTHDF5(JNIEnv *env, jclass cls) { return H5E_NOTHDF5; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1OHDR(JNIEnv *env, jclass cls) { return H5E_OHDR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1OVERFLOW(JNIEnv *env, jclass cls) { return H5E_OVERFLOW; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1PLINE(JNIEnv *env, jclass cls) { return H5E_PLINE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1PLIST(JNIEnv *env, jclass cls) { return H5E_PLIST; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1PROTECT(JNIEnv *env, jclass cls) { return H5E_PROTECT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1READERROR(JNIEnv *env, jclass cls) { return H5E_READERROR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1REFERENCE(JNIEnv *env, jclass cls) { return H5E_REFERENCE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1RESOURCE(JNIEnv *env, jclass cls) { return H5E_RESOURCE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1RS(JNIEnv *env, jclass cls) { return H5E_RS; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1SEEKERROR(JNIEnv *env, jclass cls) { return H5E_SEEKERROR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1SETLOCAL(JNIEnv *env, jclass cls) { return H5E_SETLOCAL; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1STORAGE(JNIEnv *env, jclass cls) { return H5E_STORAGE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1SYM(JNIEnv *env, jclass cls) { return H5E_SYM; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1TRUNCATED(JNIEnv *env, jclass cls) { return H5E_TRUNCATED; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1TST(JNIEnv *env, jclass cls) { return H5E_TST; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1UNINITIALIZED(JNIEnv *env, jclass cls) { return H5E_UNINITIALIZED; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1UNSUPPORTED(JNIEnv *env, jclass cls) { return H5E_UNSUPPORTED; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1VERSION(JNIEnv *env, jclass cls) { return H5E_VERSION; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1VFL(JNIEnv *env, jclass cls) { return H5E_VFL; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1WALK_1DOWNWARD(JNIEnv *env, jclass cls) { return H5E_WALK_DOWNWARD; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1WALK_1UPWARD(JNIEnv *env, jclass cls) { return H5E_WALK_UPWARD; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5E_1WRITEERROR(JNIEnv *env, jclass cls) { return H5E_WRITEERROR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5F_1ACC_1CREAT(JNIEnv *env, jclass cls) { return H5F_ACC_CREAT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5F_1ACC_1DEBUG(JNIEnv *env, jclass cls) { return H5F_ACC_DEBUG; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5F_1ACC_1EXCL(JNIEnv *env, jclass cls) { return H5F_ACC_EXCL; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5F_1ACC_1RDONLY(JNIEnv *env, jclass cls) { return H5F_ACC_RDONLY; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5F_1ACC_1RDWR(JNIEnv *env, jclass cls) { return H5F_ACC_RDWR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5F_1ACC_1TRUNC(JNIEnv *env, jclass cls) { return H5F_ACC_TRUNC; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5F_1ACC_1DEFAULT(JNIEnv *env, jclass cls) { return H5F_ACC_DEFAULT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5F_1CLOSE_1DEFAULT(JNIEnv *env, jclass cls) { return H5F_CLOSE_DEFAULT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5F_1CLOSE_1SEMI(JNIEnv *env, jclass cls) { return H5F_CLOSE_SEMI; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5F_1CLOSE_1STRONG(JNIEnv *env, jclass cls) { return H5F_CLOSE_STRONG; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5F_1CLOSE_1WEAK(JNIEnv *env, jclass cls) { return H5F_CLOSE_WEAK; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5F_1LIBVER_1EARLIEST(JNIEnv *env, jclass cls){return H5F_LIBVER_EARLIEST;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5F_1LIBVER_1LATEST(JNIEnv *env, jclass cls){return H5F_LIBVER_LATEST;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5F_1OBJ_1ALL(JNIEnv *env, jclass cls) { return H5F_OBJ_ALL; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5F_1OBJ_1ATTR(JNIEnv *env, jclass cls) { return H5F_OBJ_ATTR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5F_1OBJ_1DATASET(JNIEnv *env, jclass cls) { return H5F_OBJ_DATASET; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5F_1OBJ_1DATATYPE(JNIEnv *env, jclass cls) { return H5F_OBJ_DATATYPE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5F_1OBJ_1FILE(JNIEnv *env, jclass cls) { return H5F_OBJ_FILE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5F_1OBJ_1GROUP(JNIEnv *env, jclass cls) { return H5F_OBJ_GROUP; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5F_1OBJ_1LOCAL(JNIEnv *env, jclass cls) { return H5F_OBJ_LOCAL; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5F_1SCOPE_1GLOBAL(JNIEnv *env, jclass cls) { return H5F_SCOPE_GLOBAL; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5F_1SCOPE_1LOCAL(JNIEnv *env, jclass cls) { return H5F_SCOPE_LOCAL; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5F_1UNLIMITED(JNIEnv *env, jclass cls) { return (jint)H5F_UNLIMITED; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1CORE(JNIEnv *env, jclass cls) { return H5FD_CORE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1DIRECT(JNIEnv *env, jclass cls) { #ifdef H5_HAVE_DIRECT return H5FD_DIRECT; #else return -1; #endif } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1FAMILY(JNIEnv *env, jclass cls) { return H5FD_FAMILY; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1LOG(JNIEnv *env, jclass cls) { return H5FD_LOG; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1MPIO(JNIEnv *env, jclass cls) { return H5FD_MPIO; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1MULTI(JNIEnv *env, jclass cls) { return H5FD_MULTI; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1SEC2(JNIEnv *env, jclass cls) { return H5FD_SEC2; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1STDIO(JNIEnv *env, jclass cls) { return H5FD_STDIO; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1WINDOWS(JNIEnv *env, jclass cls) { #ifdef H5_HAVE_WINDOWS return H5FD_DIRECT; #else return -1; #endif } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1LOG_1LOC_1READ(JNIEnv *env, jclass cls) { return H5FD_LOG_LOC_READ; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1LOG_1LOC_1WRITE(JNIEnv *env, jclass cls) { return H5FD_LOG_LOC_WRITE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1LOG_1LOC_1SEEK(JNIEnv *env, jclass cls) { return H5FD_LOG_LOC_SEEK; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1LOG_1LOC_1IO(JNIEnv *env, jclass cls) { return H5FD_LOG_LOC_IO; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1LOG_1FILE_1READ(JNIEnv *env, jclass cls) { return H5FD_LOG_FILE_READ; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1LOG_1FILE_1WRITE(JNIEnv *env, jclass cls) { return H5FD_LOG_FILE_WRITE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1LOG_1FILE_1IO(JNIEnv *env, jclass cls) { return H5FD_LOG_FILE_IO; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1LOG_1FLAVOR(JNIEnv *env, jclass cls) { return H5FD_LOG_FLAVOR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1LOG_1NUM_1READ(JNIEnv *env, jclass cls) { return H5FD_LOG_NUM_READ; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1LOG_1NUM_1WRITE(JNIEnv *env, jclass cls) { return H5FD_LOG_NUM_WRITE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1LOG_1NUM_1SEEK(JNIEnv *env, jclass cls) { return H5FD_LOG_NUM_SEEK; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1LOG_1NUM_1TRUNCATE(JNIEnv *env, jclass cls) { #if (H5_VERS_RELEASE > 6) /* H5_VERSION_GE(1,8,7) */ return H5FD_LOG_NUM_TRUNCATE; #else return 0; #endif } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1LOG_1NUM_1IO(JNIEnv *env, jclass cls) { return H5FD_LOG_NUM_IO; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1LOG_1TIME_1OPEN(JNIEnv *env, jclass cls) { return H5FD_LOG_TIME_OPEN; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1LOG_1TIME_1STAT(JNIEnv *env, jclass cls) { #if (H5_VERS_RELEASE > 6) /* H5_VERSION_GE(1,8,7) */ return H5FD_LOG_TIME_STAT; #else return 0; #endif } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1LOG_1TIME_1READ(JNIEnv *env, jclass cls) { return H5FD_LOG_TIME_READ; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1LOG_1TIME_1WRITE(JNIEnv *env, jclass cls) { return H5FD_LOG_TIME_WRITE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1LOG_1TIME_1SEEK(JNIEnv *env, jclass cls) { return H5FD_LOG_TIME_SEEK; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1LOG_1TIME_1CLOSE(JNIEnv *env, jclass cls) { return H5FD_LOG_TIME_CLOSE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1LOG_1TIME_1IO(JNIEnv *env, jclass cls) { return H5FD_LOG_TIME_IO; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1LOG_1ALLOC(JNIEnv *env, jclass cls) { return H5FD_LOG_ALLOC; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1LOG_1ALL(JNIEnv *env, jclass cls) { return H5FD_LOG_ALL; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1MEM_1NOLIST(JNIEnv *env, jclass cls) { return H5FD_MEM_NOLIST; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1MEM_1DEFAULT(JNIEnv *env, jclass cls) { return H5FD_MEM_DEFAULT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1MEM_1SUPER(JNIEnv *env, jclass cls) { return H5FD_MEM_SUPER; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1MEM_1BTREE(JNIEnv *env, jclass cls) { return H5FD_MEM_BTREE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1MEM_1DRAW(JNIEnv *env, jclass cls) { return H5FD_MEM_DRAW; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1MEM_1GHEAP(JNIEnv *env, jclass cls) { return H5FD_MEM_GHEAP; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1MEM_1LHEAP(JNIEnv *env, jclass cls) { return H5FD_MEM_LHEAP; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1MEM_1OHDR(JNIEnv *env, jclass cls) { return H5FD_MEM_OHDR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1MEM_1NTYPES(JNIEnv *env, jclass cls) { return H5FD_MEM_NTYPES; } JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5FD_1DEFAULT_1HADDR_1SIZE(JNIEnv *env, jclass cls) { return (hsize_t)HADDR_MAX/H5FD_MEM_NTYPES; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5G_1DATASET(JNIEnv *env, jclass cls) { return H5G_DATASET; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5G_1GROUP(JNIEnv *env, jclass cls) { return H5G_GROUP; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5G_1LINK(JNIEnv *env, jclass cls) { return H5G_LINK; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5G_1UDLINK(JNIEnv *env, jclass cls) { return H5G_UDLINK; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5G_1LINK_1ERROR(JNIEnv *env, jclass cls) { return H5G_LINK_ERROR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5G_1LINK_1HARD(JNIEnv *env, jclass cls) { return H5G_LINK_HARD; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5G_1LINK_1SOFT(JNIEnv *env, jclass cls) { return H5G_LINK_SOFT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5G_1NLIBTYPES(JNIEnv *env, jclass cls) { return H5G_NLIBTYPES; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5G_1NTYPES(JNIEnv *env, jclass cls) { return H5G_NTYPES; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5G_1NUSERTYPES(JNIEnv *env, jclass cls) { return H5G_NUSERTYPES; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5G_1RESERVED_15(JNIEnv *env, jclass cls) { return H5G_RESERVED_5; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5G_1RESERVED_16(JNIEnv *env, jclass cls) { return H5G_RESERVED_6; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5G_1RESERVED_17(JNIEnv *env, jclass cls) { return H5G_RESERVED_7; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5G_1SAME_1LOC(JNIEnv *env, jclass cls) { return H5G_SAME_LOC; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5G_1STORAGE_1TYPE_1UNKNOWN(JNIEnv *env, jclass cls){ return H5G_STORAGE_TYPE_UNKNOWN; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5G_1STORAGE_1TYPE_1SYMBOL_1TABLE(JNIEnv *env, jclass cls){ return H5G_STORAGE_TYPE_SYMBOL_TABLE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5G_1STORAGE_1TYPE_1COMPACT(JNIEnv *env, jclass cls){ return H5G_STORAGE_TYPE_COMPACT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5G_1STORAGE_1TYPE_1DENSE(JNIEnv *env, jclass cls){ return H5G_STORAGE_TYPE_DENSE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5G_1TYPE(JNIEnv *env, jclass cls) { return H5G_TYPE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5G_1UNKNOWN(JNIEnv *env, jclass cls) { return H5G_UNKNOWN; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5I_1ATTR(JNIEnv *env, jclass cls) { return H5I_ATTR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5I_1BADID(JNIEnv *env, jclass cls) { return H5I_BADID; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5I_1DATASET(JNIEnv *env, jclass cls) { return H5I_DATASET; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5I_1DATASPACE(JNIEnv *env, jclass cls) { return H5I_DATASPACE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5I_1DATATYPE(JNIEnv *env, jclass cls) { return H5I_DATATYPE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5I_1FILE(JNIEnv *env, jclass cls) { return H5I_FILE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5I_1GENPROP_1CLS(JNIEnv *env, jclass cls) { return H5I_GENPROP_CLS; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5I_1GENPROP_1LST(JNIEnv *env, jclass cls) { return H5I_GENPROP_LST; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5I_1GROUP(JNIEnv *env, jclass cls) { return H5I_GROUP; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5I_1INVALID_1HID(JNIEnv *env, jclass cls) { return H5I_INVALID_HID; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5I_1REFERENCE(JNIEnv *env, jclass cls) { return H5I_REFERENCE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5I_1VFL(JNIEnv *env, jclass cls) { return H5I_VFL; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5L_1TYPE_1ERROR(JNIEnv *env, jclass cls) { return H5L_TYPE_ERROR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5L_1TYPE_1HARD(JNIEnv *env, jclass cls) { return H5L_TYPE_HARD; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5L_1TYPE_1SOFT(JNIEnv *env, jclass cls) { return H5L_TYPE_SOFT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5L_1TYPE_1EXTERNAL(JNIEnv *env, jclass cls) { return H5L_TYPE_EXTERNAL; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5L_1TYPE_1MAX(JNIEnv *env, jclass cls) { return H5L_TYPE_MAX; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5O_1COPY_1SHALLOW_1HIERARCHY_1FLAG(JNIEnv *env, jclass cls){return H5O_COPY_SHALLOW_HIERARCHY_FLAG; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5O_1COPY_1EXPAND_1SOFT_1LINK_1FLAG(JNIEnv *env, jclass cls){return H5O_COPY_EXPAND_SOFT_LINK_FLAG; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5O_1COPY_1EXPAND_1EXT_1LINK_1FLAG(JNIEnv *env, jclass cls){return H5O_COPY_EXPAND_EXT_LINK_FLAG; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5O_1COPY_1EXPAND_1REFERENCE_1FLAG(JNIEnv *env, jclass cls){return H5O_COPY_EXPAND_REFERENCE_FLAG; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5O_1COPY_1WITHOUT_1ATTR_1FLAG(JNIEnv *env, jclass cls){return H5O_COPY_WITHOUT_ATTR_FLAG; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5O_1COPY_1PRESERVE_1NULL_1FLAG(JNIEnv *env, jclass cls){return H5O_COPY_PRESERVE_NULL_FLAG; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5O_1SHMESG_1NONE_1FLAG(JNIEnv *env, jclass cls){return H5O_SHMESG_NONE_FLAG; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5O_1SHMESG_1SDSPACE_1FLAG(JNIEnv *env, jclass cls){return H5O_SHMESG_SDSPACE_FLAG; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5O_1SHMESG_1DTYPE_1FLAG(JNIEnv *env, jclass cls){return H5O_SHMESG_DTYPE_FLAG; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5O_1SHMESG_1FILL_1FLAG(JNIEnv *env, jclass cls){return H5O_SHMESG_FILL_FLAG; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5O_1SHMESG_1PLINE_1FLAG(JNIEnv *env, jclass cls){return H5O_SHMESG_PLINE_FLAG; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5O_1SHMESG_1ATTR_1FLAG(JNIEnv *env, jclass cls){return H5O_SHMESG_ATTR_FLAG; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5O_1SHMESG_1ALL_1FLAG(JNIEnv *env, jclass cls){return H5O_SHMESG_ALL_FLAG; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5O_1TYPE_1UNKNOWN(JNIEnv *env, jclass cls) { return H5O_TYPE_UNKNOWN; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5O_1TYPE_1GROUP(JNIEnv *env, jclass cls) { return H5O_TYPE_GROUP; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5O_1TYPE_1DATASET(JNIEnv *env, jclass cls) { return H5O_TYPE_DATASET; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5O_1TYPE_1NAMED_1DATATYPE(JNIEnv *env, jclass cls) { return H5O_TYPE_NAMED_DATATYPE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5O_1TYPE_1NTYPES(JNIEnv *env, jclass cls) { return H5O_TYPE_NTYPES; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1ROOT(JNIEnv *env, jclass cls){return H5P_ROOT;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1OBJECT_1CREATE(JNIEnv *env, jclass cls){return H5P_OBJECT_CREATE;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1FILE_1CREATE(JNIEnv *env, jclass cls){return H5P_FILE_CREATE;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1FILE_1ACCESS(JNIEnv *env, jclass cls){return H5P_FILE_ACCESS;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1DATASET_1CREATE(JNIEnv *env, jclass cls){return H5P_DATASET_CREATE;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1DATASET_1ACCESS(JNIEnv *env, jclass cls){return H5P_DATASET_ACCESS;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1DATASET_1XFER(JNIEnv *env, jclass cls){return H5P_DATASET_XFER;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1FILE_1MOUNT(JNIEnv *env, jclass cls){return H5P_FILE_MOUNT;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1GROUP_1CREATE(JNIEnv *env, jclass cls){return H5P_GROUP_CREATE;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1GROUP_1ACCESS(JNIEnv *env, jclass cls){return H5P_GROUP_ACCESS;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1DATATYPE_1CREATE(JNIEnv *env, jclass cls){return H5P_DATATYPE_CREATE;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1DATATYPE_1ACCESS(JNIEnv *env, jclass cls){return H5P_DATATYPE_ACCESS;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1STRING_1CREATE(JNIEnv *env, jclass cls){return H5P_STRING_CREATE;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1ATTRIBUTE_1CREATE(JNIEnv *env, jclass cls){return H5P_ATTRIBUTE_CREATE;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1OBJECT_1COPY(JNIEnv *env, jclass cls){return H5P_OBJECT_COPY;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1LINK_1CREATE(JNIEnv *env, jclass cls){return H5P_LINK_CREATE;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1LINK_1ACCESS(JNIEnv *env, jclass cls){return H5P_LINK_ACCESS;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1FILE_1CREATE_1DEFAULT(JNIEnv *env, jclass cls){return H5P_FILE_CREATE_DEFAULT;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1FILE_1ACCESS_1DEFAULT(JNIEnv *env, jclass cls){return H5P_FILE_ACCESS_DEFAULT;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1DATASET_1CREATE_1DEFAULT(JNIEnv *env, jclass cls){return H5P_DATASET_CREATE_DEFAULT;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1DATASET_1ACCESS_1DEFAULT(JNIEnv *env, jclass cls){return H5P_DATASET_ACCESS_DEFAULT;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1DATASET_1XFER_1DEFAULT(JNIEnv *env, jclass cls){return H5P_DATASET_XFER_DEFAULT;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1FILE_1MOUNT_1DEFAULT(JNIEnv *env, jclass cls){return H5P_FILE_MOUNT_DEFAULT;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1GROUP_1CREATE_1DEFAULT(JNIEnv *env, jclass cls){return H5P_GROUP_CREATE_DEFAULT;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1GROUP_1ACCESS_1DEFAULT(JNIEnv *env, jclass cls){return H5P_GROUP_ACCESS_DEFAULT;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1DATATYPE_1CREATE_1DEFAULT(JNIEnv *env, jclass cls){return H5P_DATATYPE_CREATE_DEFAULT;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1DATATYPE_1ACCESS_1DEFAULT(JNIEnv *env, jclass cls){return H5P_DATATYPE_ACCESS_DEFAULT;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1ATTRIBUTE_1CREATE_1DEFAULT(JNIEnv *env, jclass cls){return H5P_ATTRIBUTE_CREATE_DEFAULT;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1OBJECT_1COPY_1DEFAULT(JNIEnv *env, jclass cls){return H5P_OBJECT_COPY_DEFAULT;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1LINK_1CREATE_1DEFAULT(JNIEnv *env, jclass cls){return H5P_LINK_CREATE_DEFAULT;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1LINK_1ACCESS_1DEFAULT(JNIEnv *env, jclass cls){return H5P_LINK_ACCESS_DEFAULT;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1CRT_1ORDER_1TRACKED(JNIEnv *env, jclass cls){return H5P_CRT_ORDER_TRACKED;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1CRT_1ORDER_1INDEXED(JNIEnv *env, jclass cls){return H5P_CRT_ORDER_INDEXED;} JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1DEFAULT(JNIEnv *env, jclass cls) { return H5P_DEFAULT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5P_1NO_1CLASS(JNIEnv *env, jclass cls) { return H5P_NO_CLASS; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5R_1BADTYPE(JNIEnv *env, jclass cls) { return H5R_BADTYPE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5R_1MAXTYPE(JNIEnv *env, jclass cls) { return H5R_MAXTYPE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5R_1OBJ_1REF_1BUF_1SIZE(JNIEnv *env, jclass cls) { return H5R_OBJ_REF_BUF_SIZE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5R_1DSET_1REG_1REF_1BUF_1SIZE(JNIEnv *env, jclass cls) { return H5R_DSET_REG_REF_BUF_SIZE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5R_1OBJECT(JNIEnv *env, jclass cls) { return H5R_OBJECT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5R_1DATASET_1REGION(JNIEnv *env, jclass cls) { return H5R_DATASET_REGION; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5S_1ALL(JNIEnv *env, jclass cls) { return H5S_ALL; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5S_1MAX_1RANK(JNIEnv *env, jclass cls) { return H5S_MAX_RANK; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5S_1NO_1CLASS(JNIEnv *env, jclass cls) { return H5S_NO_CLASS; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5S_1NULL(JNIEnv *env, jclass cls) { return H5S_NULL; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5S_1SCALAR(JNIEnv *env, jclass cls) { return H5S_SCALAR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5S_1SEL_1ALL(JNIEnv *env, jclass cls) { return H5S_SEL_ALL; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5S_1SEL_1ERROR(JNIEnv *env, jclass cls) { return H5S_SEL_ERROR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5S_1SEL_1HYPERSLABS(JNIEnv *env, jclass cls) { return H5S_SEL_HYPERSLABS; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5S_1SEL_1N(JNIEnv *env, jclass cls) { return H5S_SEL_N; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5S_1SEL_1NONE(JNIEnv *env, jclass cls) { return H5S_SEL_NONE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5S_1SEL_1POINTS(JNIEnv *env, jclass cls) { return H5S_SEL_POINTS; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5S_1SELECT_1AND(JNIEnv *env, jclass cls) { return H5S_SELECT_AND; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5S_1SELECT_1APPEND(JNIEnv *env, jclass cls) { return H5S_SELECT_APPEND; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5S_1SELECT_1INVALID(JNIEnv *env, jclass cls) { return H5S_SELECT_INVALID; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5S_1SELECT_1NOOP(JNIEnv *env, jclass cls) { return H5S_SELECT_NOOP; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5S_1SELECT_1NOTA(JNIEnv *env, jclass cls) { return H5S_SELECT_NOTA; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5S_1SELECT_1NOTB(JNIEnv *env, jclass cls) { return H5S_SELECT_NOTB; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5S_1SELECT_1OR(JNIEnv *env, jclass cls) { return H5S_SELECT_OR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5S_1SELECT_1PREPEND(JNIEnv *env, jclass cls) { return H5S_SELECT_PREPEND; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5S_1SELECT_1SET(JNIEnv *env, jclass cls) { return H5S_SELECT_SET; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5S_1SELECT_1XOR(JNIEnv *env, jclass cls) { return H5S_SELECT_XOR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5S_1SIMPLE(JNIEnv *env, jclass cls) { return H5S_SIMPLE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5S_1UNLIMITED(JNIEnv *env, jclass cls) { return (jint)H5S_UNLIMITED; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1ALPHA_1B16(JNIEnv *env, jclass cls) { return H5T_ALPHA_B16; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1ALPHA_1B32(JNIEnv *env, jclass cls) { return H5T_ALPHA_B32; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1ALPHA_1B64(JNIEnv *env, jclass cls) { return H5T_ALPHA_B64; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1ALPHA_1B8(JNIEnv *env, jclass cls) { return H5T_ALPHA_B8; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1ALPHA_1F32(JNIEnv *env, jclass cls) { return H5T_ALPHA_F32; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1ALPHA_1F64(JNIEnv *env, jclass cls) { return H5T_ALPHA_F64; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1ALPHA_1I16(JNIEnv *env, jclass cls) { return H5T_ALPHA_I16; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1ALPHA_1I32(JNIEnv *env, jclass cls) { return H5T_ALPHA_I32; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1ALPHA_1I64(JNIEnv *env, jclass cls) { return H5T_ALPHA_I64; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1ALPHA_1I8(JNIEnv *env, jclass cls) { return H5T_ALPHA_I8; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1ALPHA_1U16(JNIEnv *env, jclass cls) { return H5T_ALPHA_U16; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1ALPHA_1U32(JNIEnv *env, jclass cls) { return H5T_ALPHA_U32; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1ALPHA_1U64(JNIEnv *env, jclass cls) { return H5T_ALPHA_U64; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1ALPHA_1U8(JNIEnv *env, jclass cls) { return H5T_ALPHA_U8; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1ARRAY(JNIEnv *env, jclass cls) { return H5T_ARRAY; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1BITFIELD(JNIEnv *env, jclass cls) { return H5T_BITFIELD; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1BKG_1NO(JNIEnv *env, jclass cls) { return H5T_BKG_NO; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1BKG_1YES(JNIEnv *env, jclass cls) { return H5T_BKG_YES; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1C_1S1(JNIEnv *env, jclass cls) { return H5T_C_S1; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1COMPOUND(JNIEnv *env, jclass cls) { return H5T_COMPOUND; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1CONV_1CONV(JNIEnv *env, jclass cls) { return H5T_CONV_CONV; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1CONV_1FREE(JNIEnv *env, jclass cls) { return H5T_CONV_FREE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1CONV_1INIT(JNIEnv *env, jclass cls) { return H5T_CONV_INIT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1CSET_1ERROR(JNIEnv *env, jclass cls) { return H5T_CSET_ERROR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1CSET_1ASCII(JNIEnv *env, jclass cls) { return H5T_CSET_ASCII; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1CSET_1UTF8(JNIEnv *env, jclass cls) { return H5T_CSET_UTF8; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1CSET_1RESERVED_110(JNIEnv *env, jclass cls) { return H5T_CSET_RESERVED_10; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1CSET_1RESERVED_111(JNIEnv *env, jclass cls) { return H5T_CSET_RESERVED_11; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1CSET_1RESERVED_112(JNIEnv *env, jclass cls) { return H5T_CSET_RESERVED_12; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1CSET_1RESERVED_113(JNIEnv *env, jclass cls) { return H5T_CSET_RESERVED_13; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1CSET_1RESERVED_114(JNIEnv *env, jclass cls) { return H5T_CSET_RESERVED_14; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1CSET_1RESERVED_115(JNIEnv *env, jclass cls) { return H5T_CSET_RESERVED_15; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1CSET_1RESERVED_12(JNIEnv *env, jclass cls) { return H5T_CSET_RESERVED_2; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1CSET_1RESERVED_13(JNIEnv *env, jclass cls) { return H5T_CSET_RESERVED_3; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1CSET_1RESERVED_14(JNIEnv *env, jclass cls) { return H5T_CSET_RESERVED_4; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1CSET_1RESERVED_15(JNIEnv *env, jclass cls) { return H5T_CSET_RESERVED_5; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1CSET_1RESERVED_16(JNIEnv *env, jclass cls) { return H5T_CSET_RESERVED_6; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1CSET_1RESERVED_17(JNIEnv *env, jclass cls) { return H5T_CSET_RESERVED_7; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1CSET_1RESERVED_18(JNIEnv *env, jclass cls) { return H5T_CSET_RESERVED_8; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1CSET_1RESERVED_19(JNIEnv *env, jclass cls) { return H5T_CSET_RESERVED_9; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1DIR_1ASCEND(JNIEnv *env, jclass cls) { return H5T_DIR_ASCEND; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1DIR_1DEFAULT(JNIEnv *env, jclass cls) { return H5T_DIR_DEFAULT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1DIR_1DESCEND(JNIEnv *env, jclass cls) { return H5T_DIR_DESCEND; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1ENUM(JNIEnv *env, jclass cls) { return H5T_ENUM; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1FLOAT(JNIEnv *env, jclass cls) { return H5T_FLOAT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1FORTRAN_1S1(JNIEnv *env, jclass cls) { return H5T_FORTRAN_S1; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1IEEE_1F32BE(JNIEnv *env, jclass cls) { return H5T_IEEE_F32BE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1IEEE_1F32LE(JNIEnv *env, jclass cls) { return H5T_IEEE_F32LE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1IEEE_1F64BE(JNIEnv *env, jclass cls) { return H5T_IEEE_F64BE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1IEEE_1F64LE(JNIEnv *env, jclass cls) { return H5T_IEEE_F64LE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1INTEGER(JNIEnv *env, jclass cls) { return H5T_INTEGER; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1INTEL_1B16(JNIEnv *env, jclass cls) { return H5T_INTEL_B16; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1INTEL_1B32(JNIEnv *env, jclass cls) { return H5T_INTEL_B32; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1INTEL_1B64(JNIEnv *env, jclass cls) { return H5T_INTEL_B64; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1INTEL_1B8(JNIEnv *env, jclass cls) { return H5T_INTEL_B8; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1INTEL_1F32(JNIEnv *env, jclass cls) { return H5T_INTEL_F32; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1INTEL_1F64(JNIEnv *env, jclass cls) { return H5T_INTEL_F64; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1INTEL_1I16(JNIEnv *env, jclass cls) { return H5T_INTEL_I16; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1INTEL_1I32(JNIEnv *env, jclass cls) { return H5T_INTEL_I32; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1INTEL_1I64(JNIEnv *env, jclass cls) { return H5T_INTEL_I64; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1INTEL_1I8(JNIEnv *env, jclass cls) { return H5T_INTEL_I8; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1INTEL_1U16(JNIEnv *env, jclass cls) { return H5T_INTEL_U16; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1INTEL_1U32(JNIEnv *env, jclass cls) { return H5T_INTEL_U32; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1INTEL_1U64(JNIEnv *env, jclass cls) { return H5T_INTEL_U64; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1INTEL_1U8(JNIEnv *env, jclass cls) { return H5T_INTEL_U8; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1MIPS_1B16(JNIEnv *env, jclass cls) { return H5T_MIPS_B16; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1MIPS_1B32(JNIEnv *env, jclass cls) { return H5T_MIPS_B32; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1MIPS_1B64(JNIEnv *env, jclass cls) { return H5T_MIPS_B64; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1MIPS_1B8(JNIEnv *env, jclass cls) { return H5T_MIPS_B8; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1MIPS_1F32(JNIEnv *env, jclass cls) { return H5T_MIPS_F32; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1MIPS_1F64(JNIEnv *env, jclass cls) { return H5T_MIPS_F64; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1MIPS_1I16(JNIEnv *env, jclass cls) { return H5T_MIPS_I16; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1MIPS_1I32(JNIEnv *env, jclass cls) { return H5T_MIPS_I32; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1MIPS_1I64(JNIEnv *env, jclass cls) { return H5T_MIPS_I64; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1MIPS_1I8(JNIEnv *env, jclass cls) { return H5T_MIPS_I8; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1MIPS_1U16(JNIEnv *env, jclass cls) { return H5T_MIPS_U16; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1MIPS_1U32(JNIEnv *env, jclass cls) { return H5T_MIPS_U32; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1MIPS_1U64(JNIEnv *env, jclass cls) { return H5T_MIPS_U64; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1MIPS_1U8(JNIEnv *env, jclass cls) { return H5T_MIPS_U8; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1B16(JNIEnv *env, jclass cls) { return H5T_NATIVE_B16; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1B32(JNIEnv *env, jclass cls) { return H5T_NATIVE_B32; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1B64(JNIEnv *env, jclass cls) { return H5T_NATIVE_B64; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1B8(JNIEnv *env, jclass cls) { return H5T_NATIVE_B8; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1CHAR(JNIEnv *env, jclass cls) { return H5T_NATIVE_CHAR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1DOUBLE(JNIEnv *env, jclass cls) { return H5T_NATIVE_DOUBLE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1FLOAT(JNIEnv *env, jclass cls) { return H5T_NATIVE_FLOAT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1HADDR(JNIEnv *env, jclass cls) { return H5T_NATIVE_HADDR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1HBOOL(JNIEnv *env, jclass cls) { return H5T_NATIVE_HBOOL; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1HERR(JNIEnv *env, jclass cls) { return H5T_NATIVE_HERR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1HSIZE(JNIEnv *env, jclass cls) { return H5T_NATIVE_HSIZE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1HSSIZE(JNIEnv *env, jclass cls) { return H5T_NATIVE_HSSIZE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1INT(JNIEnv *env, jclass cls) { return H5T_NATIVE_INT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1INT_1FAST16(JNIEnv *env, jclass cls) { return H5T_NATIVE_INT_FAST16; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1INT_1FAST32(JNIEnv *env, jclass cls) { return H5T_NATIVE_INT_FAST32; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1INT_1FAST64(JNIEnv *env, jclass cls) { return H5T_NATIVE_INT_FAST64; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1INT_1FAST8(JNIEnv *env, jclass cls) { return H5T_NATIVE_INT_FAST8; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1INT_1LEAST16(JNIEnv *env, jclass cls) { return H5T_NATIVE_INT_LEAST16; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1INT_1LEAST32(JNIEnv *env, jclass cls) { return H5T_NATIVE_INT_LEAST32; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1INT_1LEAST64(JNIEnv *env, jclass cls) { return H5T_NATIVE_INT_LEAST64; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1INT_1LEAST8(JNIEnv *env, jclass cls) { return H5T_NATIVE_INT_LEAST8; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1INT16(JNIEnv *env, jclass cls) { return H5T_NATIVE_INT16; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1INT32(JNIEnv *env, jclass cls) { return H5T_NATIVE_INT32; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1INT64(JNIEnv *env, jclass cls) { return H5T_NATIVE_INT64; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1INT8(JNIEnv *env, jclass cls) { return H5T_NATIVE_INT8; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1LDOUBLE(JNIEnv *env, jclass cls) { return H5T_NATIVE_LDOUBLE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1LLONG(JNIEnv *env, jclass cls) { return H5T_NATIVE_LLONG; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1LONG(JNIEnv *env, jclass cls) { return H5T_NATIVE_LONG; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1OPAQUE(JNIEnv *env, jclass cls) { return H5T_NATIVE_OPAQUE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1SCHAR(JNIEnv *env, jclass cls) { return H5T_NATIVE_SCHAR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1SHORT(JNIEnv *env, jclass cls) { return H5T_NATIVE_SHORT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1UCHAR(JNIEnv *env, jclass cls) { return H5T_NATIVE_UCHAR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1UINT(JNIEnv *env, jclass cls) { return H5T_NATIVE_UINT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1UINT_1FAST16(JNIEnv *env, jclass cls) { return H5T_NATIVE_UINT_FAST16; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1UINT_1FAST32(JNIEnv *env, jclass cls) { return H5T_NATIVE_UINT_FAST32; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1UINT_1FAST64(JNIEnv *env, jclass cls) { return H5T_NATIVE_UINT_FAST64; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1UINT_1FAST8(JNIEnv *env, jclass cls) { return H5T_NATIVE_UINT_FAST8; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1UINT_1LEAST16(JNIEnv *env, jclass cls) { return H5T_NATIVE_UINT_LEAST16; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1UINT_1LEAST32(JNIEnv *env, jclass cls) { return H5T_NATIVE_UINT_LEAST32; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1UINT_1LEAST64(JNIEnv *env, jclass cls) { return H5T_NATIVE_UINT_LEAST64; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1UINT_1LEAST8(JNIEnv *env, jclass cls) { return H5T_NATIVE_UINT_LEAST8; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1UINT16(JNIEnv *env, jclass cls) { return H5T_NATIVE_UINT16; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1UINT32(JNIEnv *env, jclass cls) { return H5T_NATIVE_UINT32; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1UINT64(JNIEnv *env, jclass cls) { return H5T_NATIVE_UINT64; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1UINT8(JNIEnv *env, jclass cls) { return H5T_NATIVE_UINT8; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1ULLONG(JNIEnv *env, jclass cls) { return H5T_NATIVE_ULLONG; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1ULONG(JNIEnv *env, jclass cls) { return H5T_NATIVE_ULONG; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NATIVE_1USHORT(JNIEnv *env, jclass cls) { return H5T_NATIVE_USHORT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NCLASSES(JNIEnv *env, jclass cls) { return H5T_NCLASSES; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NO_1CLASS(JNIEnv *env, jclass cls) { return H5T_NO_CLASS; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NORM_1ERROR(JNIEnv *env, jclass cls) { return H5T_NORM_ERROR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NORM_1IMPLIED(JNIEnv *env, jclass cls) { return H5T_NORM_IMPLIED; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NORM_1MSBSET(JNIEnv *env, jclass cls) { return H5T_NORM_MSBSET; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NORM_1NONE(JNIEnv *env, jclass cls) { return H5T_NORM_NONE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NPAD(JNIEnv *env, jclass cls) { return H5T_NPAD; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1NSGN(JNIEnv *env, jclass cls) { return H5T_NSGN; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1OPAQUE(JNIEnv *env, jclass cls) { return H5T_OPAQUE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1OPAQUE_1TAG_1MAX(JNIEnv *env, jclass cls) { return H5T_OPAQUE_TAG_MAX; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1ORDER_1BE(JNIEnv *env, jclass cls) { return H5T_ORDER_BE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1ORDER_1ERROR(JNIEnv *env, jclass cls) { return H5T_ORDER_ERROR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1ORDER_1LE(JNIEnv *env, jclass cls) { return H5T_ORDER_LE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1ORDER_1NONE(JNIEnv *env, jclass cls) { return H5T_ORDER_NONE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1ORDER_1VAX(JNIEnv *env, jclass cls) { return H5T_ORDER_VAX; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1PAD_1BACKGROUND(JNIEnv *env, jclass cls) { return H5T_PAD_BACKGROUND; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1PAD_1ERROR(JNIEnv *env, jclass cls) { return H5T_PAD_ERROR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1PAD_1ONE(JNIEnv *env, jclass cls) { return H5T_PAD_ONE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1PAD_1ZERO(JNIEnv *env, jclass cls) { return H5T_PAD_ZERO; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1PERS_1DONTCARE(JNIEnv *env, jclass cls) { return H5T_PERS_DONTCARE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1PERS_1HARD(JNIEnv *env, jclass cls) { return H5T_PERS_HARD; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1PERS_1SOFT(JNIEnv *env, jclass cls) { return H5T_PERS_SOFT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1REFERENCE(JNIEnv *env, jclass cls) { return H5T_REFERENCE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1SGN_12(JNIEnv *env, jclass cls) { return H5T_SGN_2; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1SGN_1ERROR(JNIEnv *env, jclass cls) { return H5T_SGN_ERROR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1SGN_1NONE(JNIEnv *env, jclass cls) { return H5T_SGN_NONE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STD_1B16BE(JNIEnv *env, jclass cls) { return H5T_STD_B16BE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STD_1B16LE(JNIEnv *env, jclass cls) { return H5T_STD_B16LE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STD_1B32BE(JNIEnv *env, jclass cls) { return H5T_STD_B32BE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STD_1B32LE(JNIEnv *env, jclass cls) { return H5T_STD_B32LE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STD_1B64BE(JNIEnv *env, jclass cls) { return H5T_STD_B64BE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STD_1B64LE(JNIEnv *env, jclass cls) { return H5T_STD_B64LE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STD_1B8BE(JNIEnv *env, jclass cls) { return H5T_STD_B8BE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STD_1B8LE(JNIEnv *env, jclass cls) { return H5T_STD_B8LE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STD_1I16BE(JNIEnv *env, jclass cls) { return H5T_STD_I16BE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STD_1I16LE(JNIEnv *env, jclass cls) { return H5T_STD_I16LE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STD_1I32BE(JNIEnv *env, jclass cls) { return H5T_STD_I32BE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STD_1I32LE(JNIEnv *env, jclass cls) { return H5T_STD_I32LE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STD_1I64BE(JNIEnv *env, jclass cls) { return H5T_STD_I64BE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STD_1I64LE(JNIEnv *env, jclass cls) { return H5T_STD_I64LE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STD_1I8BE(JNIEnv *env, jclass cls) { return H5T_STD_I8BE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STD_1I8LE(JNIEnv *env, jclass cls) { return H5T_STD_I8LE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STD_1REF_1DSETREG(JNIEnv *env, jclass cls) { return H5T_STD_REF_DSETREG; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STD_1REF_1OBJ(JNIEnv *env, jclass cls) { return H5T_STD_REF_OBJ; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STD_1U16BE(JNIEnv *env, jclass cls) { return H5T_STD_U16BE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STD_1U16LE(JNIEnv *env, jclass cls) { return H5T_STD_U16LE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STD_1U32BE(JNIEnv *env, jclass cls) { return H5T_STD_U32BE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STD_1U32LE(JNIEnv *env, jclass cls) { return H5T_STD_U32LE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STD_1U64BE(JNIEnv *env, jclass cls) { return H5T_STD_U64BE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STD_1U64LE(JNIEnv *env, jclass cls) { return H5T_STD_U64LE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STD_1U8BE(JNIEnv *env, jclass cls) { return H5T_STD_U8BE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STD_1U8LE(JNIEnv *env, jclass cls) { return H5T_STD_U8LE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STR_1ERROR(JNIEnv *env, jclass cls) { return H5T_STR_ERROR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STR_1NULLPAD(JNIEnv *env, jclass cls) { return H5T_STR_NULLPAD; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STR_1NULLTERM(JNIEnv *env, jclass cls) { return H5T_STR_NULLTERM; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STR_1RESERVED_110(JNIEnv *env, jclass cls) { return H5T_STR_RESERVED_10; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STR_1RESERVED_111(JNIEnv *env, jclass cls) { return H5T_STR_RESERVED_11; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STR_1RESERVED_112(JNIEnv *env, jclass cls) { return H5T_STR_RESERVED_12; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STR_1RESERVED_113(JNIEnv *env, jclass cls) { return H5T_STR_RESERVED_13; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STR_1RESERVED_114(JNIEnv *env, jclass cls) { return H5T_STR_RESERVED_14; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STR_1RESERVED_115(JNIEnv *env, jclass cls) { return H5T_STR_RESERVED_15; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STR_1RESERVED_13(JNIEnv *env, jclass cls) { return H5T_STR_RESERVED_3; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STR_1RESERVED_14(JNIEnv *env, jclass cls) { return H5T_STR_RESERVED_4; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STR_1RESERVED_15(JNIEnv *env, jclass cls) { return H5T_STR_RESERVED_5; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STR_1RESERVED_16(JNIEnv *env, jclass cls) { return H5T_STR_RESERVED_6; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STR_1RESERVED_17(JNIEnv *env, jclass cls) { return H5T_STR_RESERVED_7; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STR_1RESERVED_18(JNIEnv *env, jclass cls) { return H5T_STR_RESERVED_8; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STR_1RESERVED_19(JNIEnv *env, jclass cls) { return H5T_STR_RESERVED_9; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STR_1SPACEPAD(JNIEnv *env, jclass cls) { return H5T_STR_SPACEPAD; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1STRING(JNIEnv *env, jclass cls) { return H5T_STRING; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1TIME(JNIEnv *env, jclass cls) { return H5T_TIME; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1UNIX_1D32BE(JNIEnv *env, jclass cls) { return H5T_UNIX_D32BE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1UNIX_1D32LE(JNIEnv *env, jclass cls) { return H5T_UNIX_D32LE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1UNIX_1D64BE(JNIEnv *env, jclass cls) { return H5T_UNIX_D64BE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1UNIX_1D64LE(JNIEnv *env, jclass cls) { return H5T_UNIX_D64LE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1VARIABLE(JNIEnv *env, jclass cls) { return (int)H5T_VARIABLE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5T_1VLEN(JNIEnv *env, jclass cls) { return H5T_VLEN; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1CB_1CONT(JNIEnv *env, jclass cls) { return H5Z_CB_CONT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1CB_1ERROR(JNIEnv *env, jclass cls) { return H5Z_CB_ERROR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1CB_1FAIL(JNIEnv *env, jclass cls) { return H5Z_CB_FAIL; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1CB_1NO(JNIEnv *env, jclass cls) { return H5Z_CB_NO; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1DISABLE_1EDC(JNIEnv *env, jclass cls) { return H5Z_DISABLE_EDC; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1ENABLE_1EDC(JNIEnv *env, jclass cls) { return H5Z_ENABLE_EDC; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1ERROR_1EDC(JNIEnv *env, jclass cls) { return H5Z_ERROR_EDC; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1FILTER_1CONFIG_1DECODE_1ENABLED(JNIEnv *env, jclass cls) { return H5Z_FILTER_CONFIG_DECODE_ENABLED; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1FILTER_1CONFIG_1ENCODE_1ENABLED(JNIEnv *env, jclass cls) { return H5Z_FILTER_CONFIG_ENCODE_ENABLED; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1FILTER_1DEFLATE(JNIEnv *env, jclass cls) { return H5Z_FILTER_DEFLATE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1FILTER_1ERROR(JNIEnv *env, jclass cls) { return H5Z_FILTER_ERROR; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1FILTER_1FLETCHER32(JNIEnv *env, jclass cls) { return H5Z_FILTER_FLETCHER32; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1FILTER_1MAX(JNIEnv *env, jclass cls) { return H5Z_FILTER_MAX; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1FILTER_1NBIT(JNIEnv *env, jclass cls) {return H5Z_FILTER_NBIT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1FILTER_1NONE(JNIEnv *env, jclass cls) { return H5Z_FILTER_NONE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1FILTER_1RESERVED(JNIEnv *env, jclass cls) { return H5Z_FILTER_RESERVED; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1FILTER_1SCALEOFFSET(JNIEnv *env, jclass cls){ return H5Z_FILTER_SCALEOFFSET; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1FILTER_1SHUFFLE(JNIEnv *env, jclass cls) { return H5Z_FILTER_SHUFFLE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1FILTER_1SZIP(JNIEnv *env, jclass cls) { return H5Z_FILTER_SZIP; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1FLAG_1DEFMASK(JNIEnv *env, jclass cls) { return H5Z_FLAG_DEFMASK; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1FLAG_1INVMASK(JNIEnv *env, jclass cls) { return H5Z_FLAG_INVMASK; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1FLAG_1MANDATORY(JNIEnv *env, jclass cls) { return H5Z_FLAG_MANDATORY; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1FLAG_1OPTIONAL(JNIEnv *env, jclass cls) { return H5Z_FLAG_OPTIONAL; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1FLAG_1REVERSE(JNIEnv *env, jclass cls) { return H5Z_FLAG_REVERSE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1FLAG_1SKIP_1EDC(JNIEnv *env, jclass cls) { return H5Z_FLAG_SKIP_EDC; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1MAX_1NFILTERS(JNIEnv *env, jclass cls) { return H5Z_MAX_NFILTERS; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1NO_1EDC(JNIEnv *env, jclass cls) { return H5Z_NO_EDC; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1SO_1INT_1MINBITS_1DEFAULT(JNIEnv *env, jclass cls) { return H5Z_SO_INT_MINBITS_DEFAULT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1SO_1FLOAT_1DSCALE(JNIEnv *env, jclass cls){return H5Z_SO_FLOAT_DSCALE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1SO_1FLOAT_1ESCALE(JNIEnv *env, jclass cls){return H5Z_SO_FLOAT_ESCALE; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1SO_1INT(JNIEnv *env, jclass cls){return H5Z_SO_INT; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1SHUFFLE_1USER_1NPARMS(JNIEnv *env, jclass cls) { return H5Z_SHUFFLE_USER_NPARMS; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1SHUFFLE_1TOTAL_1NPARMS(JNIEnv *env, jclass cls) { return H5Z_SHUFFLE_TOTAL_NPARMS; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1SZIP_1USER_1NPARMS(JNIEnv *env, jclass cls) { return H5Z_SZIP_USER_NPARMS; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1SZIP_1TOTAL_1NPARMS(JNIEnv *env, jclass cls) { return H5Z_SZIP_TOTAL_NPARMS; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1SZIP_1PARM_1MASK(JNIEnv *env, jclass cls) { return H5Z_SZIP_PARM_MASK; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1SZIP_1PARM_1PPB(JNIEnv *env, jclass cls) { return H5Z_SZIP_PARM_PPB; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1SZIP_1PARM_1BPP(JNIEnv *env, jclass cls) { return H5Z_SZIP_PARM_BPP; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1SZIP_1PARM_1PPS(JNIEnv *env, jclass cls) { return H5Z_SZIP_PARM_PPS; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1NBIT_1USER_1NPARMS(JNIEnv *env, jclass cls) { return H5Z_NBIT_USER_NPARMS; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1SCALEOFFSET_1USER_1NPARMS(JNIEnv *env, jclass cls) { return H5Z_SCALEOFFSET_USER_NPARMS; } JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_HDF5Constants_H5Z_1FILTER_1ALL(JNIEnv *env, jclass cls) { return H5Z_FILTER_ALL; } #ifdef __cplusplus } #endif libsis-jhdf5-java-14.12.1/source/c/hdf-java/h5Imp.c000077500000000000000000000125111256564762100214330ustar00rootroot00000000000000/**************************************************************************** * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF Java Products. The full HDF Java copyright * * notice, including terms governing use, modification, and redistribution, * * is contained in the file, COPYING. COPYING can be found at the root of * * the source code distribution tree. You can also access it online at * * http://www.hdfgroup.org/products/licenses.html. If you do not have * * access to the file, you may request a copy from help@hdfgroup.org. * ****************************************************************************/ #ifdef __cplusplus extern "C" { #endif /* * This code is the C-interface called by Java programs to access the * general library functions of the HDF5 library. * * Each routine wraps a single HDF entry point, generally with the * analogous arguments and return codes. * * For details of the HDF libraries, see the HDF Documentation at: * http://hdf.ncsa.uiuc.edu/HDF5/doc/ * */ #include "hdf5.h" #include #include "h5jni.h" /* #include */ /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5open * Signature: ()I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5open (JNIEnv *env, jclass clss) { herr_t retVal = -1; retVal = H5open(); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5close * Signature: ()I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5close (JNIEnv *env, jclass clss) { herr_t retVal = -1; retVal = H5close(); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5dont_atexit * Signature: ()I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5dont_1atexit (JNIEnv *env, jclass clss) { int retVal = H5dont_atexit(); if (retVal < 0) { h5libraryError(env); } return retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5get_libversion * Signature: ([I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5get_1libversion (JNIEnv *env, jclass clss, jintArray libversion) { unsigned *theArray = NULL; jboolean isCopy; int status; if (libversion == NULL) { h5nullArgument( env, "H5get_version: libversion is NULL"); return -1; } theArray = (unsigned *)ENVPTR->GetIntArrayElements(ENVPAR libversion,&isCopy); if (theArray == NULL) { h5JNIFatalError( env, "H5get_libversion: input not pinned"); return -1; } status = H5get_libversion(&(theArray[0]), &(theArray[1]), &(theArray[2])); if (status < 0) { ENVPTR->ReleaseIntArrayElements(ENVPAR libversion,(jint *)theArray,JNI_ABORT); h5libraryError(env); } else { ENVPTR->ReleaseIntArrayElements(ENVPAR libversion,(jint *)theArray,0); } return (jint)status; } #ifdef notdef /* struct sigaction { int sa_flags; void (*sa_handler)(); sigset_t sa_mask; void (*sa_sigaction)(int, siginfo_t *, void *); }; int sigaction(int sig, struct sigaction *act, struct sigaction *oact); */ void catch_abrt() { /* Raise Java exception */ printf("raise exception....\n"); } #endif /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5check_version * Signature: (III)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5check_1version (JNIEnv *env, jclass clss, jint majnum, jint minnum, jint relnum) { int status; /* * In principle, we want to catch the 'abort' signal, and * do something other than crash. * Look up how to do this portably. */ /* int res; struct sigaction ctchit; struct sigaction old; ctchit.sa_handler = catch_abrt; */ /* res = sigaction(SIGABRT, &ctchit, &old); if (res != 0) { printf("sigaction failed\n"); return(-1); } */ /* catch the signal? */ status = H5check_version((unsigned)majnum, (unsigned)minnum, (unsigned)relnum); /* res = sigaction(SIGABRT, &old, 0); if (res != 0) { printf("sigaction failed\n"); return(-1); } */ return status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5garbage_collect * Signature: ()I * */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5garbage_1collect (JNIEnv *env, jclass clss) { herr_t retVal = -1; retVal = H5garbage_collect(); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5set_free_list_limits * Signature: (IIIIII)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5set_1free_1list_1limits (JNIEnv *env, jclass clss, jint reg_global_lim, jint reg_list_lim, jint arr_global_lim, jint arr_list_lim, jint blk_global_lim, jint blk_list_lim ) { int retVal = H5set_free_list_limits((int)reg_global_lim, (int)reg_list_lim, (int)arr_global_lim, (int)arr_list_lim, (int)blk_global_lim, (int)blk_list_lim); if (retVal < 0) { h5libraryError(env); } return retVal; } #ifdef __cplusplus } #endif libsis-jhdf5-java-14.12.1/source/c/hdf-java/h5aImp.c000077500000000000000000001161351256564762100216030ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ /* * This code is the C-interface called by Java programs to access the * Attribute API Functions of the HDF5 library. * * Each routine wraps a single HDF entry point, generally with the * analogous arguments and return codes. * * For details of the HDF libraries, see the HDF Documentation at: * http://hdf.ncsa.uiuc.edu/HDF5/doc/ * */ #ifdef __cplusplus extern "C" { #endif #include "hdf5.h" #include "h5util.h" #include #include #include #include "h5jni.h" herr_t H5AreadVL_str (JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf); herr_t H5AreadVL_num (JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf); herr_t H5AreadVL_comp (JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf); herr_t H5AwriteVL_str (JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf); herr_t H5AwriteVL_num (JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf); herr_t H5AwriteVL_comp (JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Acreate * Signature: (ILjava/lang/String;III)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Acreate (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint type_id, jint space_id, jint create_plist) { hid_t status; char* aName; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Acreate: name is NULL"); return -1; } aName = (char *)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (aName == NULL) { h5JNIFatalError( env, "H5Acreate: aName is not pinned"); return -1; } status = H5Acreate2((hid_t)loc_id, aName, (hid_t)type_id, (hid_t)space_id, (hid_t)create_plist, (hid_t)H5P_DEFAULT ); ENVPTR->ReleaseStringUTFChars(ENVPAR name,aName); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Aopen_name * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Aopen_1name (JNIEnv *env, jclass clss, jint loc_id, jstring name) { hid_t status; char* aName; jboolean isCopy; if (name == NULL) { h5nullArgument( env,"H5Aopen_name: name is NULL"); return -1; } aName = (char *)ENVPTR->GetStringUTFChars(ENVPAR name,&isCopy); if (aName == NULL) { h5JNIFatalError( env,"H5Aopen_name: name is not pinned"); return -1; } status = H5Aopen_name((hid_t)loc_id, aName); ENVPTR->ReleaseStringUTFChars(ENVPAR name,aName); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Aopen_idx * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Aopen_1idx (JNIEnv *env, jclass clss, jint loc_id, jint idx) { hid_t retVal = -1; retVal = H5Aopen_idx((hid_t)loc_id, (unsigned int) idx ); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Awrite * Signature: (II[B)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Awrite (JNIEnv *env, jclass clss, jint attr_id, jint mem_type_id, jbyteArray buf) { herr_t status; jbyte *byteP; jboolean isCopy; if (buf == NULL) { h5nullArgument( env,"H5Awrite: buf is NULL"); return -1; } byteP = ENVPTR->GetByteArrayElements(ENVPAR buf,&isCopy); if (byteP == NULL) { h5JNIFatalError( env,"H5Awrite: buf is not pinned"); return -1; } status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, byteP); ENVPTR->ReleaseByteArrayElements(ENVPAR buf, byteP,JNI_ABORT); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5AwriteVL * Signature: (II[Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5AwriteVL (JNIEnv *env, jclass clss, jint attr_id, jint mem_type_id, jobjectArray buf) { herr_t status; if (buf == NULL) { h5nullArgument( env,"H5AwriteVL: buf is NULL"); return -1; } if (H5Tis_variable_str((hid_t)mem_type_id) > 0) { status = H5AwriteVL_str (env, (hid_t)attr_id, (hid_t)mem_type_id, buf); } else if (H5Tget_class((hid_t)mem_type_id) == H5T_COMPOUND) { status = H5AwriteVL_comp (env, (hid_t)attr_id, (hid_t)mem_type_id, buf); } else if (H5Tget_class((hid_t)mem_type_id) == H5T_ARRAY) { status = H5AwriteVL_comp (env, (hid_t)attr_id, (hid_t)mem_type_id, buf); } else { status = H5AwriteVL_num (env, (hid_t)attr_id, (hid_t)mem_type_id, buf); } return (jint)status; } herr_t H5AwriteVL_num (JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf) { herr_t status; h5unimplemented(env, "H5AwriteVL_num: not implemented"); status = -1; return status; } herr_t H5AwriteVL_comp (JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf) { herr_t status; h5unimplemented(env, "H5AwriteVL_comp: not implemented"); status = -1; return status; } herr_t H5AwriteVL_str (JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf) { herr_t status = -1; char **wdata; jsize size; jint i; size = ENVPTR->GetArrayLength(ENVPAR (jarray) buf); wdata = (char**)malloc(size * sizeof (char*)); if (!wdata) { h5JNIFatalError(env, "H5AwriteVL_str: cannot allocate buffer"); return -1; } memset(wdata, 0, size * sizeof(char*)); for (i = 0; i < size; ++i) { jstring obj = (jstring) ENVPTR->GetObjectArrayElement(ENVPAR (jobjectArray) buf, i); if (obj != 0) { jsize length = ENVPTR->GetStringUTFLength(ENVPAR obj); const char *utf8 = ENVPTR->GetStringUTFChars(ENVPAR obj, 0); if (utf8) { wdata[i] = (char*)malloc(length + 1); if (wdata[i]) { memset(wdata[i], 0, (length + 1)); strncpy(wdata[i], utf8, length); } } ENVPTR->ReleaseStringUTFChars(ENVPAR obj, utf8); ENVPTR->DeleteLocalRef(ENVPAR obj); } } /*for (i = 0; i < size; ++i) */ status = H5Awrite((hid_t)aid, (hid_t)tid, wdata); // now free memory for (i = 0; i < size; i++) { if(wdata[i]) { free(wdata[i]); } } free(wdata); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Aread * Signature: (II[B)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Aread (JNIEnv *env, jclass clss, jint attr_id, jint mem_type_id, jbyteArray buf) { herr_t status; jbyte *byteP; jboolean isCopy; if (buf == NULL) { h5nullArgument( env,"H5Aread: buf is NULL"); return -1; } byteP = ENVPTR->GetByteArrayElements(ENVPAR buf,&isCopy); if (byteP == NULL) { h5JNIFatalError( env,"H5Aread: buf is not pinned"); return -1; } status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, byteP); if (status < 0) { ENVPTR->ReleaseByteArrayElements(ENVPAR buf,byteP,JNI_ABORT); h5libraryError(env); } else { ENVPTR->ReleaseByteArrayElements(ENVPAR buf,byteP,0); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Aget_space * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Aget_1space (JNIEnv *env, jclass clss, jint attr_id) { hid_t retVal = -1; retVal = H5Aget_space((hid_t)attr_id); if (retVal < 0) { /* throw exception */ h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Aget_type * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Aget_1type (JNIEnv *env, jclass clss, jint attr_id) { hid_t retVal = -1; retVal = H5Aget_type((hid_t)attr_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Aget_name * Signature: (IJ[Ljava/lang/String;)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Aget_1name (JNIEnv *env, jclass clss, jint attr_id, jlong buf_size, jobjectArray name) { char *aName; jstring str; hssize_t size; long bs; if (buf_size==0 && name == NULL) return (jlong) H5Aget_name((hid_t)attr_id, 0, NULL); bs = (long)buf_size; if (bs <= 0) { h5badArgument( env, "H5Aget_name: buf_size <= 0"); return -1; } aName = (char*)malloc(sizeof(char)*bs); if (aName == NULL) { h5outOfMemory( env, "H5Aget_name: malloc failed"); return -1; } size = H5Aget_name((hid_t)attr_id, (size_t)buf_size, aName); if (size < 0) { free(aName); h5libraryError(env); return -1; /* exception, returns immediately */ } /* successful return -- save the string; */ str = ENVPTR->NewStringUTF(ENVPAR aName); if (str == NULL) { free(aName); h5JNIFatalError( env,"H5Aget_name: return string failed"); return -1; } free(aName); /* Note: throws ArrayIndexOutOfBoundsException, ArrayStoreException */ ENVPTR->SetObjectArrayElement(ENVPAR name,0,str); return (jlong)size; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Aget_num_attrs * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Aget_1num_1attrs (JNIEnv *env, jclass clss, jint loc_id) { int retVal = -1; retVal = H5Aget_num_attrs((hid_t)loc_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Adelete * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Adelete (JNIEnv *env, jclass clss, jint loc_id, jstring name) { herr_t status; char* aName; jboolean isCopy; if (name == NULL) { h5nullArgument( env,"H5Adelete: name is NULL"); return -1; } aName = (char *)ENVPTR->GetStringUTFChars(ENVPAR name,&isCopy); if (aName == NULL) { h5JNIFatalError( env,"H5Adelete: name is not pinned"); return -1; } status = H5Adelete((hid_t)loc_id, aName ); ENVPTR->ReleaseStringUTFChars(ENVPAR name,aName); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Aclose * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Aclose (JNIEnv *env, jclass clss, jint attr_id) { herr_t retVal = 0; if (attr_id > 0) retVal = H5Aclose((hid_t)attr_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5AreadVL * Signature: (II[Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5AreadVL (JNIEnv *env, jclass clss, jint attr_id, jint mem_type_id, jobjectArray buf) { htri_t isStr; if ( buf == NULL ) { h5nullArgument( env, "H5AreadVL: buf is NULL"); return -1; } isStr = H5Tis_variable_str((hid_t)mem_type_id); if (H5Tis_variable_str((hid_t)mem_type_id) > 0) { return (jint) H5AreadVL_str (env, (hid_t)attr_id, (hid_t)mem_type_id, buf); } else if (H5Tget_class((hid_t)mem_type_id) == H5T_COMPOUND) { return (jint) H5AreadVL_comp (env, (hid_t)attr_id, (hid_t)mem_type_id, buf); } else if (H5Tget_class((hid_t)mem_type_id) == H5T_ARRAY) { return (jint) H5AreadVL_comp (env, (hid_t)attr_id, (hid_t)mem_type_id, buf); } else { return (jint) H5AreadVL_num (env, (hid_t)attr_id, (hid_t)mem_type_id, buf); } } herr_t H5AreadVL_num (JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf) { herr_t status; int i; int n; size_t max_len = 0; h5str_t h5str; jstring jstr; hvl_t *rdata = NULL; size_t size; hid_t sid; hsize_t dims[H5S_MAX_RANK]; n = ENVPTR->GetArrayLength(ENVPAR buf); rdata = (hvl_t *)calloc(n+1, sizeof(hvl_t)); if (rdata == NULL) { h5JNIFatalError( env, "H5AreadVL_num: failed to allocate buff for read"); return -1; } status = H5Aread(aid, tid, rdata); dims[0] = n; sid = H5Screate_simple(1, dims, NULL); if (status < 0) { H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, rdata); H5Sclose(sid); free(rdata); h5JNIFatalError(env, "H5AreadVL_num: failed to read data"); return -1; } for (i = 0; i < n; i++) { if ((rdata +i)->len > max_len) max_len = (rdata + i)->len; } size = H5Tget_size(tid); memset((void *)&h5str, (int)0, (size_t)sizeof(h5str_t)); h5str_new(&h5str, 4*size); if (h5str.s == NULL) { H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, rdata); H5Sclose(sid); free(rdata); h5JNIFatalError(env, "H5AreadVL_num: failed to allocate strng buf"); return -1; } for (i = 0; i < n; i++) { h5str.s[0] = '\0'; h5str_sprintf(&h5str, aid, tid, rdata + i, 0); jstr = ENVPTR->NewStringUTF(ENVPAR h5str.s); ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr); } h5str_free(&h5str); H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, rdata); H5Sclose(sid); free(rdata); return status; } herr_t H5AreadVL_comp (JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf) { herr_t status; int i; int n; size_t max_len = 0; h5str_t h5str; jstring jstr; char *rdata; size_t size; hid_t p_type; p_type = H5Tget_native_type(tid, H5T_DIR_DEFAULT); size = (((H5Tget_size(tid))>(H5Tget_size(p_type))) ? (H5Tget_size(tid)) : (H5Tget_size(p_type))); H5Tclose(p_type); n = ENVPTR->GetArrayLength(ENVPAR buf); rdata = (char *)malloc(n * size); if (rdata == NULL) { h5JNIFatalError(env, "H5AreadVL_comp: failed to allocate buff for read"); return -1; } status = H5Aread(aid, tid, rdata); if (status < 0) { free(rdata); h5JNIFatalError(env, "H5AreadVL_comp: failed to read data"); return -1; } memset(&h5str, 0, sizeof(h5str_t)); h5str_new(&h5str, 4 * size); if (h5str.s == NULL) { free(rdata); h5JNIFatalError(env, "H5AreadVL_comp: failed to allocate string buf"); return -1; } for (i = 0; i < n; i++) { h5str.s[0] = '\0'; h5str_sprintf(&h5str, aid, tid, rdata + i * size, 0); jstr = ENVPTR->NewStringUTF(ENVPAR h5str.s); ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr); } h5str_free(&h5str); free(rdata); return status; } herr_t H5AreadVL_str (JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf) { herr_t status=-1; jstring jstr; char **strs; int i, n; hid_t sid; hsize_t dims[H5S_MAX_RANK]; n = ENVPTR->GetArrayLength(ENVPAR buf); strs =(char **)malloc(n*sizeof(char *)); if (strs == NULL) { h5JNIFatalError( env, "H5AreadVL_str: failed to allocate buff for read variable length strings"); return -1; } status = H5Aread(aid, tid, strs); if (status < 0) { dims[0] = n; sid = H5Screate_simple(1, dims, NULL); H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, strs); H5Sclose(sid); free(strs); h5JNIFatalError(env, "H5AreadVL_str: failed to read variable length strings"); return -1; } for (i=0; iNewStringUTF(ENVPAR strs[i]); ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr); free (strs[i]); } /* for repeatedly reading an attribute with a large number of strs (e.g., 1,000,000 strings, H5Dvlen_reclaim() may crash on Windows because the Java GC will not be able to collect free space in time. Instead, use "free(strs[i])" to free individual strings after it is done. H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, strs); */ if (strs) free(strs); return status; } /* * Copies the content of one dataset to another dataset * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Acopy * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Acopy (JNIEnv *env, jclass clss, jint src_id, jint dst_id) { jbyte *buf; herr_t retVal = -1; hid_t src_did = (hid_t)src_id; hid_t dst_did = (hid_t)dst_id; hid_t tid=-1; hid_t sid=-1; hsize_t total_size = 0; sid = H5Aget_space(src_did); if (sid < 0) { h5libraryError(env); return -1; } tid = H5Aget_type(src_did); if (tid < 0) { H5Sclose(sid); h5libraryError(env); return -1; } total_size = H5Sget_simple_extent_npoints(sid) * H5Tget_size(tid); H5Sclose(sid); buf = (jbyte *)malloc( (int) (total_size * sizeof(jbyte))); if (buf == NULL) { H5Tclose(tid); h5outOfMemory( env, "H5Acopy: malloc failed"); return -1; } retVal = H5Aread(src_did, tid, buf); H5Tclose(tid); if (retVal < 0) { free(buf); h5libraryError(env); return (jint)retVal; } tid = H5Aget_type(dst_did); if (tid < 0) { free(buf); h5libraryError(env); return -1; } retVal = H5Awrite(dst_did, tid, buf); H5Tclose(tid); free(buf); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Acreate2 * Signature: (ILjava/lang/String;IIII)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Acreate2 (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint type_id, jint space_id, jint create_plist, jint access_plist) { hid_t status; char* aName; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Acreate2: name is NULL"); return -1; } aName = (char *)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (aName == NULL) { h5JNIFatalError( env, "H5Acreate2: aName is not pinned"); return -1; } status = H5Acreate2((hid_t)loc_id, aName, (hid_t)type_id, (hid_t)space_id, (hid_t)create_plist, (hid_t)access_plist ); ENVPTR->ReleaseStringUTFChars(ENVPAR name,aName); if (status < 0) { h5libraryError(env); } return (jint)status; } /********************************************************************** * * * New functions release 1.8.0 * * * **********************************************************************/ /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Acreate2 * Signature: (ILjava/lang/String;IIII)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Acreate2 (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint type_id, jint space_id, jint create_plist, jint access_plist) { hid_t status; char* aName; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Acreate2: name is NULL"); return -1; } aName = (char *)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (aName == NULL) { h5JNIFatalError( env, "H5Acreate2: aName is not pinned"); return -1; } status = H5Acreate2((hid_t)loc_id, aName, (hid_t)type_id, (hid_t)space_id, (hid_t)create_plist, (hid_t)access_plist ); ENVPTR->ReleaseStringUTFChars(ENVPAR name,aName); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Aopen * Signature: (ILjava/lang/String;I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Aopen (JNIEnv *env, jclass clss, jint obj_id, jstring name, jint access_plist) { hid_t retVal; char* aName; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Aopen: name is NULL"); return -1; } aName = (char *)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (aName == NULL) { h5JNIFatalError( env, "H5Aopen: aName is not pinned"); return -1; } retVal = H5Aopen((hid_t)obj_id, aName, (hid_t)access_plist); ENVPTR->ReleaseStringUTFChars(ENVPAR name,aName); if (retVal< 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Aopen_by_idx * Signature: (ILjava/lang/String;IIIII)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Aopen_1by_1idx (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint idx_type, jint order, jlong n, jint aapl_id, jint lapl_id) { hid_t retVal; char* aName; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Aopen_by_idx: name is NULL"); return -1; } aName = (char *)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (aName == NULL) { h5JNIFatalError( env, "H5Aopen_by_idx: aName is not pinned"); return -1; } retVal = H5Aopen_by_idx((hid_t)loc_id, aName, (H5_index_t)idx_type, (H5_iter_order_t)order, (hsize_t)n, (hid_t)aapl_id, (hid_t)lapl_id); ENVPTR->ReleaseStringUTFChars(ENVPAR name,aName); if (retVal< 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Acreate_by_name * Signature: (ILjava/lang/String;Ljava/lang/String;IIIII)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Acreate_1by_1name (JNIEnv *env, jclass clss, jint loc_id, jstring obj_name, jstring attr_name, jint type_id, jint space_id, jint acpl_id, jint aapl_id, jint lapl_id) { hid_t retVal; char *aName, *attrName; jboolean isCopy; if (obj_name == NULL) { h5nullArgument( env, "H5Acreate_by_name: object name is NULL"); return -1; } if (attr_name == NULL) { h5nullArgument( env, "H5Acreate_by_name: attribute name is NULL"); return -1; } aName = (char *)ENVPTR->GetStringUTFChars(ENVPAR obj_name, &isCopy); if (aName == NULL) { h5JNIFatalError( env, "H5Acreate_by_name: aName is not pinned"); return -1; } attrName = (char *)ENVPTR->GetStringUTFChars(ENVPAR attr_name, &isCopy); if (attrName == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR obj_name,aName); h5JNIFatalError( env, "H5Acreate_by_name: attrName is not pinned"); return -1; } retVal = H5Acreate_by_name((hid_t)loc_id, aName, attrName, (hid_t)type_id, (hid_t)space_id, (hid_t)acpl_id, (hid_t)aapl_id, (hid_t)lapl_id); ENVPTR->ReleaseStringUTFChars(ENVPAR obj_name,aName); ENVPTR->ReleaseStringUTFChars(ENVPAR attr_name,attrName); if (retVal< 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Aexists_by_name * Signature: (ILjava/lang/String;Ljava/lang/String;I)Z */ JNIEXPORT jboolean JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Aexists_1by_1name (JNIEnv *env, jclass clss, jint loc_id, jstring obj_name, jstring attr_name, jint lapl_id) { htri_t retVal; char *aName, *attrName; jboolean isCopy; if (obj_name == NULL) { h5nullArgument( env, "H5Aexists_by_name: object name is NULL"); return -1; } if (attr_name == NULL) { h5nullArgument( env, "H5Aexists_by_name: attribute name is NULL"); return -1; } aName = (char *)ENVPTR->GetStringUTFChars(ENVPAR obj_name, &isCopy); if (aName == NULL) { h5JNIFatalError( env, "H5Aexists_by_name: aName is not pinned"); return -1; } attrName = (char *)ENVPTR->GetStringUTFChars(ENVPAR attr_name, &isCopy); if (attrName == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR obj_name,aName); h5JNIFatalError( env, "H5Aexists_by_name: attrName is not pinned"); return -1; } retVal = H5Aexists_by_name((hid_t)loc_id, aName, attrName, (hid_t)lapl_id); ENVPTR->ReleaseStringUTFChars(ENVPAR obj_name,aName); ENVPTR->ReleaseStringUTFChars(ENVPAR attr_name,attrName); if (retVal< 0) { h5libraryError(env); } return (jboolean)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Arename * Signature: (ILjava/lang/String;Ljava/lang/String)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Arename (JNIEnv *env, jclass clss, jint loc_id, jstring old_attr_name, jstring new_attr_name) { herr_t retVal; char *oName, *nName; jboolean isCopy; if (old_attr_name == NULL) { h5nullArgument( env, "H5Arename: old_attr_name is NULL"); return -1; } if (new_attr_name == NULL) { h5nullArgument( env, "H5Arename: new_attr_name is NULL"); return -1; } oName = (char *)ENVPTR->GetStringUTFChars(ENVPAR old_attr_name,&isCopy); if (oName == NULL) { h5JNIFatalError( env, "H5Arename: old_attr_name not pinned"); return -1; } nName = (char *)ENVPTR->GetStringUTFChars(ENVPAR new_attr_name,&isCopy); if (nName == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR old_attr_name,oName); h5JNIFatalError( env, "H5Arename: new_attr_name not pinned"); return -1; } retVal = H5Arename((hid_t)loc_id, oName, nName); ENVPTR->ReleaseStringUTFChars(ENVPAR old_attr_name,oName); ENVPTR->ReleaseStringUTFChars(ENVPAR new_attr_name,nName); if (retVal< 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Arename_by_name * Signature: (ILjava/lang/String;Ljava/lang/String;Ljava/lang/String;I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Arename_1by_1name (JNIEnv *env, jclass clss, jint loc_id, jstring obj_name, jstring old_attr_name, jstring new_attr_name, jint lapl_id) { herr_t retVal; char *aName, *oName, *nName; jboolean isCopy; if (obj_name == NULL) { h5nullArgument( env, "H5Arename_by_name: object name is NULL"); return -1; } if (old_attr_name == NULL) { h5nullArgument( env, "H5Arename_by_name: old_attr_name is NULL"); return -1; } if (new_attr_name == NULL) { h5nullArgument( env, "H5Arename_by_name: new_attr_name is NULL"); return -1; } aName = (char *)ENVPTR->GetStringUTFChars(ENVPAR obj_name, &isCopy); if (aName == NULL) { h5JNIFatalError( env, "H5Arename_by_name: object name is not pinned"); return -1; } oName = (char *)ENVPTR->GetStringUTFChars(ENVPAR old_attr_name,&isCopy); if (oName == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR obj_name,aName); h5JNIFatalError( env, "H5Arename_by_name: old_attr_name not pinned"); return -1; } nName = (char *)ENVPTR->GetStringUTFChars(ENVPAR new_attr_name,&isCopy); if (nName == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR obj_name,aName); ENVPTR->ReleaseStringUTFChars(ENVPAR old_attr_name,oName); h5JNIFatalError( env, "H5Arename_by_name: new_attr_name not pinned"); return -1; } retVal = H5Arename_by_name((hid_t)loc_id, aName, oName, nName, (hid_t)lapl_id); ENVPTR->ReleaseStringUTFChars(ENVPAR obj_name,aName); ENVPTR->ReleaseStringUTFChars(ENVPAR old_attr_name,oName); ENVPTR->ReleaseStringUTFChars(ENVPAR new_attr_name,nName); if (retVal< 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Aget_name_by_idx * Signature: (ILjava/lang/String;IIJI)Ljava/lang/String; */ JNIEXPORT jstring JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Aget_1name_1by_1idx (JNIEnv *env, jclass clss, jint loc_id, jstring obj_name, jint idx_type, jint order, jlong n, jint lapl_id) { size_t buf_size; char *aName; char *aValue; jboolean isCopy; jlong status_size; jstring str = NULL; if (obj_name == NULL) { h5nullArgument( env, "H5Aget_name_by_idx: object name is NULL"); return NULL; } aName = (char*)ENVPTR->GetStringUTFChars(ENVPAR obj_name, &isCopy); if (aName == NULL) { h5JNIFatalError( env, "H5Aget_name_by_idx: name not pinned"); return NULL; } /* get the length of the attribute name */ status_size = H5Aget_name_by_idx((hid_t)loc_id, aName, (H5_index_t)idx_type, (H5_iter_order_t) order, (hsize_t) n, (char*)NULL, (size_t)0, (hid_t)lapl_id); if(status_size < 0) { ENVPTR->ReleaseStringUTFChars(ENVPAR obj_name, aName); h5libraryError(env); return NULL; } buf_size = (size_t)status_size + 1;/* add extra space for the null terminator */ aValue = (char*)malloc(sizeof(char) * buf_size); if (aValue == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR obj_name, aName); h5outOfMemory( env, "H5Aget_name_by_idx: malloc failed "); return NULL; } status_size = H5Aget_name_by_idx((hid_t)loc_id, aName, (H5_index_t)idx_type, (H5_iter_order_t) order, (hsize_t) n, (char*)aValue, (size_t)buf_size, (hid_t)lapl_id); ENVPTR->ReleaseStringUTFChars(ENVPAR obj_name, aName); if (status_size < 0) { free(aValue); h5libraryError(env); return NULL; } /* may throw OutOfMemoryError */ str = ENVPTR->NewStringUTF(ENVPAR aValue); if (str == NULL) { /* exception -- fatal JNI error */ free(aValue); h5JNIFatalError( env, "H5Aget_name_by_idx: return string not created"); return NULL; } free(aValue); return str; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Aget_storage_size * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Aget_1storage_1size (JNIEnv *env, jclass clss, jint attr_id) { hsize_t retVal = (hsize_t)-1; retVal = H5Aget_storage_size((hid_t)attr_id); /* probably returns '0' if fails--don't do an exception if (retVal < 0) { h5libraryError(env); } */ return (jlong)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Aget_info * Signature: (I)Lncsa/hdf/hdf5lib/structs/H5A_info_t; */ JNIEXPORT jobject JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Aget_1info (JNIEnv *env, jclass clss, jint attr_id) { herr_t status; H5A_info_t ainfo; jclass cls; jmethodID constructor; jvalue args[4]; jobject ret_info_t = NULL; status = H5Aget_info((hid_t)attr_id, (H5A_info_t*)&ainfo); if (status < 0) { h5libraryError(env); return NULL; } // get a reference to your class if you don't have it already cls = ENVPTR->FindClass(ENVPAR "ncsa/hdf/hdf5lib/structs/H5A_info_t"); // get a reference to the constructor; the name is constructor = ENVPTR->GetMethodID(ENVPAR cls, "", "(ZJIJ)V"); args[0].z = ainfo.corder_valid; args[1].j = ainfo.corder; args[2].i = ainfo.cset; args[3].j = ainfo.data_size; ret_info_t = ENVPTR->NewObjectA(ENVPAR cls, constructor, args); return ret_info_t; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Aget_info_by_idx * Signature: (ILjava/lang/String;IIJI)Lncsa/hdf/hdf5lib/structs/H5A_info_t; */ JNIEXPORT jobject JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Aget_1info_1by_1idx (JNIEnv *env, jclass clss, jint loc_id, jstring obj_name, jint idx_type, jint order, jlong n, jint lapl_id) { char *aName; herr_t status; H5A_info_t ainfo; jboolean isCopy; jclass cls; jmethodID constructor; jvalue args[4]; jobject ret_info_t = NULL; if (obj_name == NULL) { h5nullArgument( env, "H5Aget_info_by_idx: obj_name is NULL"); return NULL; } aName = (char*)ENVPTR->GetStringUTFChars(ENVPAR obj_name, &isCopy); if (aName == NULL) { h5JNIFatalError( env, "H5Aget_info_by_idx: object name not pinned"); return NULL; } status = H5Aget_info_by_idx((hid_t)loc_id, (const char*)aName, (H5_index_t)idx_type, (H5_iter_order_t)order, (hsize_t)n, (H5A_info_t*)&ainfo, (hid_t)lapl_id); ENVPTR->ReleaseStringUTFChars(ENVPAR obj_name, aName); if (status < 0) { h5libraryError(env); return NULL; } // get a reference to your class if you don't have it already cls = ENVPTR->FindClass(ENVPAR "ncsa/hdf/hdf5lib/structs/H5A_info_t"); // get a reference to the constructor; the name is constructor = ENVPTR->GetMethodID(ENVPAR cls, "", "(ZJIJ)V"); args[0].z = ainfo.corder_valid; args[1].j = ainfo.corder; args[2].i = ainfo.cset; args[3].j = ainfo.data_size; ret_info_t = ENVPTR->NewObjectA(ENVPAR cls, constructor, args); return ret_info_t; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Aget_info_by_name * Signature: (ILjava/lang/String;Ljava/lang/String;I)Lncsa/hdf/hdf5lib/structs/H5A_info_t; */ JNIEXPORT jobject JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Aget_1info_1by_1name (JNIEnv *env, jclass clss, jint loc_id, jstring obj_name, jstring attr_name, jint lapl_id) { char *aName; char *attrName; herr_t status; H5A_info_t ainfo; jboolean isCopy; jclass cls; jmethodID constructor; jvalue args[4]; jobject ret_info_t = NULL; if (obj_name == NULL) { h5nullArgument( env, "H5Aget_info_by_name: obj_name is NULL"); return NULL; } if (attr_name == NULL) { h5nullArgument( env, "H5Aget_info_by_name: attr_name is NULL"); return NULL; } aName = (char*)ENVPTR->GetStringUTFChars(ENVPAR obj_name, &isCopy); if (aName == NULL) { h5JNIFatalError( env, "H5Aget_info_by_name: object name not pinned"); return NULL; } attrName = (char*)ENVPTR->GetStringUTFChars(ENVPAR attr_name, &isCopy); if (attrName == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR obj_name, aName); h5JNIFatalError( env, "H5Aget_info_by_name: Attribute name not pinned"); return NULL; } status = H5Aget_info_by_name((hid_t)loc_id, (const char*)aName, (const char*)attrName, (H5A_info_t*)&ainfo,(hid_t)lapl_id); ENVPTR->ReleaseStringUTFChars(ENVPAR obj_name, aName); ENVPTR->ReleaseStringUTFChars(ENVPAR attr_name, attrName); if (status < 0) { h5libraryError(env); return NULL; } // get a reference to your class if you don't have it already cls = ENVPTR->FindClass(ENVPAR "ncsa/hdf/hdf5lib/structs/H5A_info_t"); // get a reference to the constructor; the name is constructor = ENVPTR->GetMethodID(ENVPAR cls, "", "(ZJIJ)V"); args[0].z = ainfo.corder_valid; args[1].j = ainfo.corder; args[2].i = ainfo.cset; args[3].j = ainfo.data_size; ret_info_t = ENVPTR->NewObjectA(ENVPAR cls, constructor, args); return ret_info_t; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Adelete_by_name * Signature: (ILjava/lang/String;Ljava/lang/String;I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Adelete_1by_1name (JNIEnv *env, jclass clss, jint loc_id, jstring obj_name, jstring attr_name, jint lapl_id) { herr_t retVal; char *aName, *attrName; jboolean isCopy; if (obj_name == NULL) { h5nullArgument( env, "H5Adelete_by_name: object name is NULL"); return -1; } if (attr_name == NULL) { h5nullArgument( env, "H5Adelete_by_name: attribute name is NULL"); return -1; } aName = (char *)ENVPTR->GetStringUTFChars(ENVPAR obj_name, &isCopy); if (aName == NULL) { h5JNIFatalError( env, "H5Adelete_by_name: aName is not pinned"); return -1; } attrName = (char *)ENVPTR->GetStringUTFChars(ENVPAR attr_name, &isCopy); if (attrName == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR obj_name,aName); h5JNIFatalError( env, "H5Adelete_by_name: attrName is not pinned"); return -1; } retVal = H5Adelete_by_name((hid_t)loc_id, (const char*)aName, (const char*)attrName, (hid_t)lapl_id); ENVPTR->ReleaseStringUTFChars(ENVPAR obj_name,aName); ENVPTR->ReleaseStringUTFChars(ENVPAR attr_name,attrName); if (retVal< 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Aexists * Signature: (ILjava/lang/String;)Z */ JNIEXPORT jboolean JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Aexists (JNIEnv *env, jclass clss, jint obj_id, jstring attr_name) { char *aName; jboolean isCopy; htri_t bval = 0; if (attr_name == NULL) { h5nullArgument( env, "H5Aexists: attr_name is NULL"); return JNI_FALSE; } aName = (char*)ENVPTR->GetStringUTFChars(ENVPAR attr_name, &isCopy); if (aName == NULL) { h5JNIFatalError( env, "H5Aexists: attr_name not pinned"); return JNI_FALSE; } bval = H5Aexists((hid_t)obj_id, (const char*)aName); ENVPTR->ReleaseStringUTFChars(ENVPAR attr_name, aName); if (bval > 0) { return JNI_TRUE; } else if (bval == 0) { return JNI_FALSE; } else { h5libraryError(env); return JNI_FALSE; } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Adelete_by_idx * Signature: (ILjava/lang/String;IIJI)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Adelete_1by_1idx (JNIEnv *env, jclass clss, jint loc_id, jstring obj_name, jint idx_type, jint order, jlong n, jint lapl_id) { char *aName; herr_t status; jboolean isCopy; if (obj_name == NULL) { h5nullArgument( env, "H5Adelete_by_idx: obj_name is NULL"); return; } aName = (char*)ENVPTR->GetStringUTFChars(ENVPAR obj_name, &isCopy); if (aName == NULL) { h5JNIFatalError( env, "H5Adelete_by_idx: obj_name not pinned"); return; } status = H5Adelete_by_idx((hid_t)loc_id, (const char*)aName, (H5_index_t)idx_type, (H5_iter_order_t)order, (hsize_t)n, (hid_t)lapl_id); ENVPTR->ReleaseStringUTFChars(ENVPAR obj_name, aName); if (status < 0) { h5libraryError(env); return; } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Aopen_by_name * Signature: (ILjava/lang/String;Ljava/lang/String;II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Aopen_1by_1name (JNIEnv *env, jclass clss, jint loc_id, jstring obj_name, jstring attr_name, jint aapl_id, jint lapl_id) { hid_t status; char *aName, *oName; jboolean isCopy; if (obj_name == NULL) { h5nullArgument( env,"_H5Aopen_by_name: obj_name is NULL"); return -1; } if (attr_name == NULL) { h5nullArgument( env,"_H5Aopen_by_name: attr_name is NULL"); return -1; } oName = (char *)ENVPTR->GetStringUTFChars(ENVPAR obj_name,&isCopy); if (oName == NULL) { h5JNIFatalError( env,"_H5Aopen_by_name: obj_name is not pinned"); return -1; } aName = (char *)ENVPTR->GetStringUTFChars(ENVPAR attr_name,&isCopy); if (aName == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR obj_name,oName); h5JNIFatalError( env,"_H5Aopen_by_name: attr_name is not pinned"); return -1; } status = H5Aopen_by_name((hid_t)loc_id, oName, aName, (hid_t)aapl_id, (hid_t)lapl_id); ENVPTR->ReleaseStringUTFChars(ENVPAR obj_name,oName); ENVPTR->ReleaseStringUTFChars(ENVPAR attr_name,aName); if (status < 0) { h5libraryError(env); } return (jint)status; } #ifdef __cplusplus } #endif libsis-jhdf5-java-14.12.1/source/c/hdf-java/h5dImp.c000077500000000000000000001576361256564762100216210ustar00rootroot00000000000000/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF Java Products. The full HDF Java copyright * * notice, including terms governing use, modification, and redistribution, * * is contained in the file, COPYING. COPYING can be found at the root of * * the source code distribution tree. You can also access it online at * * http://www.hdfgroup.org/products/licenses.html. If you do not have * * access to the file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /* * This code is the C-interface called by Java programs to access the * Dataset Object API Functions of HDF5 library. * * Each routine wraps a single HDF entry point, generally with the * analogous arguments and return codes. * * For details of the HDF libraries, see the HDF Documentation at: * http://hdfdfgroup.org/HDF5/doc/ * */ #ifdef __cplusplus extern "C" { #endif #include #include #include #include #include "hdf5.h" #include "h5util.h" #include "h5jni.h" #include "h5dImp.h" #ifdef __cplusplus #ifdef _WINDOWS #include #endif #endif #ifdef _WINDOWS #define CHDIR _chdir #define GETCWD _getcwd #else #define CHDIR chdir #define GETCWD getcwd #endif #ifdef __cplusplus #define CBENVPTR (cbenv) #define CBENVPAR #define JVMPTR (jvm) #define JVMPAR #define JVMPAR2 #else #define CBENVPTR (*cbenv) #define CBENVPAR cbenv, #define JVMPTR (*jvm) #define JVMPAR jvm #define JVMPAR2 jvm, #endif herr_t H5DreadVL_str (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf); herr_t H5DreadVL_notstr (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf); #define PIN_BYTE_ARRAY() { \ if (isCriticalPinning) \ buffP = (jbyte*)ENVPTR->GetPrimitiveArrayCritical(ENVPAR buf, &isCopy); \ else \ buffP = ENVPTR->GetByteArrayElements(ENVPAR buf, &isCopy); \ } #define UNPIN_BYTE_ARRAY(mode) { \ if (isCriticalPinning) \ ENVPTR->ReleasePrimitiveArrayCritical(ENVPAR buf, buffP, mode); \ else \ ENVPTR->ReleaseByteArrayElements(ENVPAR buf, buffP, mode); \ } #define PIN_SHORT_ARRAY() { \ if (isCriticalPinning) \ buffP = (jshort*)ENVPTR->GetPrimitiveArrayCritical(ENVPAR buf, &isCopy); \ else \ buffP = ENVPTR->GetShortArrayElements(ENVPAR buf, &isCopy); \ } #define UNPIN_SHORT_ARRAY(mode) { \ if (isCriticalPinning) \ ENVPTR->ReleasePrimitiveArrayCritical(ENVPAR buf, buffP, mode); \ else \ ENVPTR->ReleaseShortArrayElements(ENVPAR buf, buffP, mode); \ } #define PIN_INT_ARRAY() { \ if (isCriticalPinning) \ buffP = (jint*)ENVPTR->GetPrimitiveArrayCritical(ENVPAR buf, &isCopy); \ else \ buffP = ENVPTR->GetIntArrayElements(ENVPAR buf, &isCopy); \ } #define UNPIN_INT_ARRAY(mode) { \ if (isCriticalPinning) \ ENVPTR->ReleasePrimitiveArrayCritical(ENVPAR buf, buffP, mode); \ else \ ENVPTR->ReleaseIntArrayElements(ENVPAR buf, buffP, mode); \ } #define PIN_LONG_ARRAY() { \ if (isCriticalPinning) \ buffP = (jlong*)ENVPTR->GetPrimitiveArrayCritical(ENVPAR buf, &isCopy); \ else \ buffP = ENVPTR->GetLongArrayElements(ENVPAR buf,&isCopy); \ } #define UNPIN_LONG_ARRAY(mode) { \ if (isCriticalPinning) \ ENVPTR->ReleasePrimitiveArrayCritical(ENVPAR buf, buffP, mode); \ else \ ENVPTR->ReleaseLongArrayElements(ENVPAR buf, buffP, mode); \ } #define PIN_FLOAT_ARRAY() { \ if (isCriticalPinning) \ buffP = (jfloat*)ENVPTR->GetPrimitiveArrayCritical(ENVPAR buf, &isCopy); \ else \ buffP = ENVPTR->GetFloatArrayElements(ENVPAR buf, &isCopy); \ } #define UNPIN_FLOAT_ARRAY(mode) { \ if (isCriticalPinning) \ ENVPTR->ReleasePrimitiveArrayCritical(ENVPAR buf, buffP, mode); \ else \ ENVPTR->ReleaseFloatArrayElements(ENVPAR buf, buffP, mode); \ } #define PIN_DOUBLE_ARRAY() { \ if (isCriticalPinning) \ buffP = (jdouble*)ENVPTR->GetPrimitiveArrayCritical(ENVPAR buf, &isCopy); \ else \ buffP = ENVPTR->GetDoubleArrayElements(ENVPAR buf, &isCopy); \ } #define UNPIN_DOUBLE_ARRAY(mode) { \ if (isCriticalPinning) \ ENVPTR->ReleasePrimitiveArrayCritical(ENVPAR buf, buffP, mode); \ else \ ENVPTR->ReleaseDoubleArrayElements(ENVPAR buf, buffP, mode); \ } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Dcreate * Signature: (ILjava/lang/String;III)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Dcreate (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint type_id, jint space_id, jint create_plist_id) { hid_t status; char *file; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Dcreate: name is NULL"); return -1; } file = (char*)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (file == NULL) { h5JNIFatalError( env, "H5Dcreate: file name not pinned"); return -1; } status = H5Dcreate2(loc_id, file, type_id, space_id, (hid_t)H5P_DEFAULT, (hid_t)create_plist_id, (hid_t)H5P_DEFAULT); ENVPTR->ReleaseStringUTFChars(ENVPAR name, file); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dchdir_ext * Signature: (Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dchdir_1ext (JNIEnv *env, jclass clss, jstring dir_name) { hid_t status; char *file; jboolean isCopy; if (dir_name == NULL) { h5nullArgument( env, "H5Dchdir_ext: dir_name is NULL"); return -1; } file = (char*)ENVPTR->GetStringUTFChars(ENVPAR dir_name, &isCopy); if (file == NULL) { h5JNIFatalError( env, "H5Dchdir_ext: file dir not pinned"); return -1; } status = CHDIR( file ); ENVPTR->ReleaseStringUTFChars(ENVPAR dir_name, file); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dgetdir_1ext * Signature: ([Ljava/lang/String;I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dgetdir_1ext (JNIEnv *env, jclass clss, jobjectArray dir_name, jint buf_size) { char *aName; jstring str; if (buf_size <= 0) { h5badArgument( env, "H5Dgetcwd: buf_size <= 0"); return -1; } aName = (char*)malloc(sizeof(char) * buf_size); if (aName == NULL) { h5outOfMemory( env, "H5Dgetcwd: malloc failed"); return -1; } GETCWD( (char*)aName, (size_t)buf_size); str = ENVPTR->NewStringUTF(ENVPAR aName); free(aName); if (str == NULL) { h5JNIFatalError( env,"H5Dgetcwd: return string failed"); return -1; } ENVPTR->SetObjectArrayElement(ENVPAR dir_name, 0, str); return 0; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Dopen * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Dopen (JNIEnv *env, jclass clss, jint loc_id, jstring name) { hid_t status; char *file; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Dopen: name is NULL"); return -1; } file = (char*)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (file == NULL) { h5JNIFatalError( env, "H5Dopen: file name not pinned"); return -1; } status = H5Dopen2((hid_t)loc_id, (const char*)file, (hid_t)H5P_DEFAULT); ENVPTR->ReleaseStringUTFChars(ENVPAR name, file); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Dget_space * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Dget_1space (JNIEnv *env, jclass clss, jint dataset_id) { hid_t retVal = -1; retVal = H5Dget_space((hid_t)dataset_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Dget_type * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Dget_1type (JNIEnv *env, jclass clss, jint dataset_id) { hid_t retVal = -1; retVal = H5Dget_type((hid_t)dataset_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Dget_create_plist * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Dget_1create_1plist (JNIEnv *env, jclass clss, jint dataset_id) { hid_t retVal = -1; retVal = H5Dget_create_plist((hid_t)dataset_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } htri_t H5Tdetect_variable_str(hid_t tid) { htri_t ret_val = 0; if (H5Tget_class(tid) == H5T_COMPOUND) { hid_t mtid = H5Tget_member_type(tid, 0); ret_val = H5Tdetect_variable_str(mtid); H5Tclose (mtid); } else ret_val = H5Tis_variable_str(tid); return ret_val; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dread * Signature: (IIIII[BZ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dread (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jbyteArray buf, jboolean isCriticalPinning) { herr_t status; jbyte *buffP; jboolean isCopy; htri_t data_class; /* recursive detect any vlen data values in type (compound, array ...) */ data_class = H5Tdetect_class(mem_type_id, H5T_VLEN); if((data_class == 1) || (data_class < 0)) { h5badArgument( env, "H5Dread: buf does not support variable length type"); return -1; } /* recursive detect any vlen string in type (compound, array ...) */ data_class = H5Tdetect_variable_str(mem_type_id); if((data_class == 1) || (data_class < 0)) { h5badArgument( env, "H5Dread: buf does not support variable length string type"); return -1; } if ( buf == NULL ) { h5nullArgument( env, "H5Dread: buf is NULL"); return -1; } PIN_BYTE_ARRAY(); if (buffP == NULL) { h5JNIFatalError( env, "H5Dread: buf not pinned"); return -1; } status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); if (status < 0) { UNPIN_BYTE_ARRAY(JNI_ABORT); h5libraryError(env); return -1; } UNPIN_BYTE_ARRAY(0); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dwrite * Signature: (IIIII[BZ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dwrite (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jbyteArray buf, jboolean isCriticalPinning) { herr_t status; jbyte *buffP; jboolean isCopy; if ( buf == NULL ) { h5nullArgument( env, "H5Dwrite: buf is NULL"); return -1; } PIN_BYTE_ARRAY(); if (buffP == NULL) { h5JNIFatalError( env, "H5Dwrite: buf not pinned"); return -1; } status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); UNPIN_BYTE_ARRAY(JNI_ABORT); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dextend * Signature: (I[B)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dextend (JNIEnv *env, jclass clss, jint dataset_id, jbyteArray size) { herr_t status; int i; int rank; hsize_t *sa; hsize_t *lp; jbyte *P; jboolean isCopy; jlong *jlp; if (size == NULL) { h5nullArgument( env, "H5Dextend: array of sizes is NULL"); return -1; } /* * Future: check that the array has correct * rank (same as dataset dataset_id) */ P = ENVPTR->GetByteArrayElements(ENVPAR size, &isCopy); if (P == NULL) { h5JNIFatalError( env, "H5Dextend: array not pinned"); return -1; } i = ENVPTR->GetArrayLength(ENVPAR size); rank = i / sizeof(jlong); sa = lp = (hsize_t*)malloc(rank * sizeof(hsize_t)); if (sa == NULL) { ENVPTR->ReleaseByteArrayElements(ENVPAR size, P, JNI_ABORT); h5JNIFatalError(env, "H5Dextend: size not converted to hsize_t"); return -1; } jlp = (jlong*)P; for (i = 0; i < rank; i++) { *lp = (hsize_t) * jlp; lp++; jlp++; } status = H5Dextend((hid_t)dataset_id, (hsize_t*)sa); ENVPTR->ReleaseByteArrayElements(ENVPAR size, P, JNI_ABORT); free(sa); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Dclose * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Dclose (JNIEnv *env, jclass clss, jint dataset_id) { hid_t retVal = 0; retVal = H5Dclose((hid_t)dataset_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dget_storage_size * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dget_1storage_1size (JNIEnv *env, jclass clss, jint dataset_id) { hsize_t retVal = (hsize_t)-1; if (dataset_id < 0) { h5badArgument(env, "H5Dget_storage_size: not a dataset"); } retVal = H5Dget_storage_size((hid_t)dataset_id ); return (jlong)retVal; } /* * Copies the content of one dataset to another dataset * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dcopy * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dcopy (JNIEnv *env, jclass clss, jint src_id, jint dst_id) { jbyte *buf; herr_t retVal = -1; hid_t src_did = (hid_t)src_id; hid_t dst_did = (hid_t)dst_id; hid_t tid = -1; hid_t sid = -1; hsize_t total_size = 0, total_allocated_size; total_allocated_size = H5Dget_storage_size(src_did); if (total_allocated_size <=0) return 0; // nothing to write; sid = H5Dget_space(src_did); if (sid < 0) { h5libraryError(env); return -1; } tid = H5Dget_type(src_did); if (tid < 0) { H5Sclose(sid); h5libraryError(env); return -1; } total_size = H5Sget_simple_extent_npoints(sid) * H5Tget_size(tid); H5Sclose(sid); buf = (jbyte*)malloc((int)(total_size * sizeof(jbyte))); if (buf == NULL) { H5Tclose(tid); h5outOfMemory(env, "H5Dcopy: malloc failed"); return -1; } retVal = H5Dread((hid_t)src_did, (hid_t)tid, (hid_t)H5S_ALL, (hid_t)H5S_ALL, (hid_t)H5P_DEFAULT, buf); H5Tclose(tid); if (retVal < 0) { free(buf); h5libraryError(env); return (jint)retVal; } tid = H5Dget_type(dst_did); if (tid < 0) { free(buf); h5libraryError(env); return -1; } retVal = H5Dwrite((hid_t)dst_did, (hid_t)tid, (hid_t)H5S_ALL, (hid_t)H5S_ALL, (hid_t)H5P_DEFAULT, buf); H5Tclose(tid); free(buf); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Copies the content of one dataset to another dataset * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dvlen_get_buf_size * Signature: (III[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dvlen_1get_1buf_1size (JNIEnv *env, jclass clss, jint dataset_id, jint type_id, jint space_id, jintArray size) { jint *P; jboolean isCopy; herr_t status; hsize_t sz; if ( size == NULL ) { h5nullArgument(env, "H5Dvlen_get_buf_size: size is NULL"); return -1; } P = ENVPTR->GetIntArrayElements(ENVPAR size, &isCopy); if (P == NULL) { h5JNIFatalError(env, "H5Dvlen_get_buf_size: array not pinned"); return -1; } status = (jint)H5Dvlen_get_buf_size((hid_t)dataset_id, (hid_t)type_id, (hid_t)space_id, (hsize_t*)&sz); if (status < 0) { ENVPTR->ReleaseIntArrayElements(ENVPAR size, P, JNI_ABORT); h5libraryError(env); return -1; } P[0] = (jint)sz; ENVPTR->ReleaseIntArrayElements(ENVPAR size, P, 0); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dvlen_reclaim * Signature: (III[B)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dvlen_1reclaim (JNIEnv *env, jclass clss, jint type_id, jint space_id, jint xfer_plist_id, jbyteArray buf) { herr_t status; jbyte *byteP; jboolean isCopy; if ( buf == NULL ) { h5nullArgument( env, "H5Dvlen_reclaim: buf is NULL"); return -1; } byteP = ENVPTR->GetByteArrayElements(ENVPAR buf, &isCopy); if (byteP == NULL) { h5JNIFatalError( env, "H5Dvlen_reclaim: buf not pinned"); return -1; } status = H5Dvlen_reclaim((hid_t)type_id, (hid_t)space_id, (hid_t)xfer_plist_id, byteP); ENVPTR->ReleaseByteArrayElements(ENVPAR buf, byteP, JNI_ABORT); if (status < 0) { h5libraryError(env); } return (jint)status; } /*************************************************************** * New APIs for HDF5.1.6 * ***************************************************************/ /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Dget_space_status * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Dget_1space_1status (JNIEnv *env, jclass clss, jint dset_id, jintArray status) { jint *theArray; jboolean isCopy; H5D_space_status_t space_status; herr_t retVal = -1; if (status == NULL) { /* exception ? */ h5nullArgument(env, "H5Dget_space_status: status is NULL"); return -1; } theArray = (jint*)ENVPTR->GetIntArrayElements(ENVPAR status, &isCopy); if (theArray == NULL) { h5JNIFatalError(env, "H5Dget_space_status: status not pinned"); return -1; } retVal = H5Dget_space_status((hid_t)dset_id, (H5D_space_status_t*)&space_status ); if (retVal < 0) { ENVPTR->ReleaseIntArrayElements(ENVPAR status, theArray, JNI_ABORT); h5libraryError(env); return -1; } theArray[0] = space_status; ENVPTR->ReleaseIntArrayElements(ENVPAR status, theArray, 0); return (jint)retVal; } /* //////////////////////////////////////////////////////////////////// // // // New APIs for read data from library // // Using H5Dread(..., Object buf) requires function calls // // theArray.emptyBytes() and theArray.arrayify( buf), which // // triples the actual memory needed by the data set. // // Using the following APIs solves the problem. // // // //////////////////////////////////////////////////////////////////// */ /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dread_short * Signature: (IIIII[S[Z)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dread_1short (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jshortArray buf, jboolean isCriticalPinning) { herr_t status; jshort *buffP; jboolean isCopy; htri_t data_class; /* recursive detect any vlen data values in type (compound, array ...) */ data_class = H5Tdetect_class(mem_type_id, H5T_VLEN); if((data_class == 1) || (data_class < 0)) { h5badArgument( env, "H5Dread_short: buf does not support variable length type"); return -1; } /* recursive detect any vlen string in type (compound, array ...) */ data_class = H5Tdetect_variable_str(mem_type_id); if((data_class == 1) || (data_class < 0)) { h5badArgument( env, "H5Dread_short: buf does not support variable length string type"); return -1; } if (buf == NULL) { h5nullArgument(env, "H5Dread_short: buf is NULL"); return -1; } PIN_SHORT_ARRAY(); if (buffP == NULL) { h5JNIFatalError(env, "H5Dread_short: buf not pinned"); return -1; } status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); if (status < 0) { UNPIN_SHORT_ARRAY(JNI_ABORT); h5libraryError(env); return -1; } UNPIN_SHORT_ARRAY(0); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dread_int * Signature: (IIIII[I[Z)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dread_1int (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jintArray buf, jboolean isCriticalPinning) { herr_t status; jint *buffP; jboolean isCopy; htri_t data_class; /* recursive detect any vlen data values in type (compound, array ...) */ data_class = H5Tdetect_class(mem_type_id, H5T_VLEN); if((data_class == 1) || (data_class < 0)) { h5badArgument( env, "H5Dread_int: buf does not support variable length type"); return -1; } /* recursive detect any vlen string in type (compound, array ...) */ data_class = H5Tdetect_variable_str(mem_type_id); if((data_class == 1) || (data_class < 0)) { h5badArgument( env, "H5Dread_int: buf does not support variable length string type"); return -1; } if (buf == NULL) { h5nullArgument(env, "H5Dread_int: buf is NULL"); return -1; } PIN_INT_ARRAY(); if (buffP == NULL) { h5JNIFatalError(env, "H5Dread_int: buf not pinned"); return -1; } status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); if (status < 0) { UNPIN_INT_ARRAY(JNI_ABORT); h5libraryError(env); return -1; } UNPIN_INT_ARRAY(0); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dread_long * Signature: (IIIII[J[Z)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dread_1long (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jlongArray buf, jboolean isCriticalPinning) { herr_t status; jlong *buffP; jboolean isCopy; htri_t data_class; /* recursive detect any vlen data values in type (compound, array ...) */ data_class = H5Tdetect_class(mem_type_id, H5T_VLEN); if((data_class == 1) || (data_class < 0)) { h5badArgument( env, "H5Dread_long: buf does not support variable length type"); return -1; } /* recursive detect any vlen string in type (compound, array ...) */ data_class = H5Tdetect_variable_str(mem_type_id); if((data_class == 1) || (data_class < 0)) { h5badArgument( env, "H5Dread_long: buf does not support variable length string type"); return -1; } if (buf == NULL) { h5nullArgument(env, "H5Dread_long: buf is NULL"); return -1; } PIN_LONG_ARRAY(); if (buffP == NULL) { h5JNIFatalError(env, "H5Dread_long: buf not pinned"); return -1; } status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); if (status < 0) { UNPIN_LONG_ARRAY(JNI_ABORT); h5libraryError(env); return -1; } UNPIN_LONG_ARRAY(0); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dread_float * Signature: (IIIII[F[Z)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dread_1float (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jfloatArray buf, jboolean isCriticalPinning) { herr_t status; jfloat *buffP; jboolean isCopy; htri_t data_class; /* recursive detect any vlen data values in type (compound, array ...) */ data_class = H5Tdetect_class(mem_type_id, H5T_VLEN); if((data_class == 1) || (data_class < 0)) { h5badArgument( env, "H5Dread_float: buf does not support variable length type"); return -1; } /* recursive detect any vlen string in type (compound, array ...) */ data_class = H5Tdetect_variable_str(mem_type_id); if((data_class == 1) || (data_class < 0)) { h5badArgument( env, "H5Dread_float: buf does not support variable length string type"); return -1; } if (buf == NULL) { h5nullArgument(env, "H5Dread_float: buf is NULL"); return -1; } PIN_FLOAT_ARRAY(); if (buffP == NULL) { h5JNIFatalError(env, "H5Dread_float: buf not pinned"); return -1; } status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); if (status < 0) { UNPIN_FLOAT_ARRAY(JNI_ABORT); h5libraryError(env); return -1; } UNPIN_FLOAT_ARRAY(0); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dread_double * Signature: (IIIII[D[Z)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dread_1double (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jdoubleArray buf, jboolean isCriticalPinning) { herr_t status; jdouble *buffP; jboolean isCopy; htri_t data_class; /* recursive detect any vlen data values in type (compound, array ...) */ data_class = H5Tdetect_class(mem_type_id, H5T_VLEN); if((data_class == 1) || (data_class < 0)) { h5badArgument( env, "H5Dread_double: buf does not support variable length type"); return -1; } /* recursive detect any vlen string in type (compound, array ...) */ data_class = H5Tdetect_variable_str(mem_type_id); if((data_class == 1) || (data_class < 0)) { h5badArgument( env, "H5Dread_double: buf does not support variable length string type"); return -1; } if (buf == NULL) { h5nullArgument(env, "H5Dread_double: buf is NULL"); return -1; } PIN_DOUBLE_ARRAY(); if (buffP == NULL) { h5JNIFatalError(env, "H5Dread_double: buf not pinned"); return -1; } status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); if (status < 0) { UNPIN_DOUBLE_ARRAY(JNI_ABORT); h5libraryError(env); return -1; } UNPIN_DOUBLE_ARRAY(0); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dread_string * Signature: (IIIII[Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dread_1string (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jobjectArray j_buf) { herr_t status; char *c_buf; char *cstr; size_t str_len; size_t i; size_t n; size_t pos; jstring jstr; c_buf = cstr = NULL; if (j_buf == NULL) { h5nullArgument(env, "H5Dread_string: buf is NULL"); return -1; } n = ENVPTR->GetArrayLength(ENVPAR j_buf); if (n <= 0) { h5nullArgument(env, "H5Dread_string: buf length <=0"); return -1; } if ((str_len = H5Tget_size((hid_t)mem_type_id)) <=0) { h5libraryError(env); return -1; } if ((cstr = (char*)malloc(str_len + 1)) == NULL) { h5JNIFatalError(env, "H5Dread_string: memory allocation failed."); return -1; } if ((c_buf = (char*)malloc(n * str_len)) == NULL) { if (cstr) free (cstr); cstr = NULL; h5JNIFatalError(env, "H5Dread_string: memory allocation failed."); return -1; } status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)xfer_plist_id, c_buf); if (status < 0) { if (cstr) free (cstr); cstr = NULL; if (c_buf) free (c_buf); c_buf = NULL; h5libraryError(env); return -1; } pos = 0; for (i=0; iNewStringUTF(ENVPAR cstr); ENVPTR->SetObjectArrayElement(ENVPAR j_buf, i, jstr); pos += str_len; } if (c_buf) free(c_buf); if (cstr) free (cstr); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dwrite_short * Signature: (IIIII[S[Z)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dwrite_1short (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jshortArray buf, jboolean isCriticalPinning) { herr_t status; jshort *buffP; jboolean isCopy; if (buf == NULL ) { h5nullArgument(env, "H5Dwrite_short: buf is NULL"); return -1; } PIN_SHORT_ARRAY(); if (buffP == NULL) { h5JNIFatalError(env, "H5Dwrite_short: buf not pinned"); return -1; } status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); UNPIN_SHORT_ARRAY(JNI_ABORT); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dwrite_int * Signature: (IIIII[I[Z)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dwrite_1int (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jintArray buf, jboolean isCriticalPinning) { herr_t status; jint *buffP; jboolean isCopy; if (buf == NULL) { h5nullArgument(env, "H5Dwrite_int: buf is NULL"); return -1; } PIN_INT_ARRAY(); if (buffP == NULL) { h5JNIFatalError(env, "H5Dwrite_int: buf not pinned"); return -1; } status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); UNPIN_INT_ARRAY(JNI_ABORT); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dwrite_long * Signature: (IIIII[J[Z)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dwrite_1long (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jlongArray buf, jboolean isCriticalPinning) { herr_t status; jlong *buffP; jboolean isCopy; if (buf == NULL) { h5nullArgument(env, "H5Dwrite_long: buf is NULL"); return -1; } PIN_LONG_ARRAY(); if (buffP == NULL) { h5JNIFatalError(env, "H5Dwrite_long: buf not pinned"); return -1; } status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); UNPIN_LONG_ARRAY(JNI_ABORT); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dwrite_float * Signature: (IIIII[F[Z)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dwrite_1float (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jfloatArray buf, jboolean isCriticalPinning) { herr_t status; jfloat *buffP; jboolean isCopy; if (buf == NULL) { h5nullArgument(env, "H5Dwrite_float: buf is NULL"); return -1; } PIN_FLOAT_ARRAY(); if (buffP == NULL) { h5JNIFatalError(env, "H5Dwrite_float: buf not pinned"); return -1; } status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); UNPIN_FLOAT_ARRAY(JNI_ABORT); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dwrite_double * Signature: (IIIII[D[Z)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dwrite_1double (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jdoubleArray buf, jboolean isCriticalPinning) { herr_t status; jdouble *buffP; jboolean isCopy; if (buf == NULL) { h5nullArgument(env, "H5Dwrite_double: buf is NULL"); return -1; } PIN_DOUBLE_ARRAY(); if (buffP == NULL) { h5JNIFatalError(env, "H5Dwrite_double: buf not pinned"); return -1; } status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); UNPIN_DOUBLE_ARRAY(JNI_ABORT); if (status < 0) { h5libraryError(env); } return (jint)status; } // Rosetta Biosoftware /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5DwriteString * Signature: (IIIII[Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5DwriteString (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jobjectArray buf) { herr_t status; char **wdata; jsize size; jint i; if (buf == NULL) { h5nullArgument(env, "H5DwriteString: buf is NULL"); return -1; } size = ENVPTR->GetArrayLength(ENVPAR (jarray) buf); wdata = (char**)malloc(size * sizeof (char*)); if (!wdata) { h5JNIFatalError(env, "H5DwriteString: cannot allocate buffer"); return -1; } memset(wdata, 0, size * sizeof(char*)); for (i = 0; i < size; ++i) { jstring obj = (jstring) ENVPTR->GetObjectArrayElement(ENVPAR (jobjectArray) buf, i); if (obj != 0) { jsize length = ENVPTR->GetStringUTFLength(ENVPAR obj); const char *utf8 = ENVPTR->GetStringUTFChars(ENVPAR obj, 0); if (utf8) { wdata[i] = (char*)malloc(length + 1); if (wdata[i]) { memset(wdata[i], 0, (length + 1)); strncpy(wdata[i], utf8, length); } } ENVPTR->ReleaseStringUTFChars(ENVPAR obj, utf8); ENVPTR->DeleteLocalRef(ENVPAR obj); } } /*for (i = 0; i < size; ++i) */ status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)xfer_plist_id, wdata); // now free memory for (i = 0; i < size; i++) { if(wdata[i]) { free(wdata[i]); } } free(wdata); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5DwriteNotString * Signature: (IIIII[BZ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5DwriteNotString (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jbyteArray buf, jboolean isCriticalPinning) { herr_t status; hvl_t *wdata; size_t size; jsize n; jbyte *buffP; jboolean isCopy; jint i; jint j; if (buf == NULL) { h5nullArgument(env, "H5DwriteNotString: buf is NULL"); return -1; } PIN_BYTE_ARRAY(); if (buffP == NULL) { h5JNIFatalError( env, "H5DwriteNotString: buf not pinned"); return -1; } /* rebuild VL structure */ n = ENVPTR->GetArrayLength(ENVPAR (jarray) buf); wdata = (hvl_t*)calloc(n, sizeof(hvl_t)); if (!wdata) { h5JNIFatalError(env, "H5DwriteNotString: cannot allocate buffer"); return -1; } size = H5Tget_size(mem_type_id); memset(wdata, 0, n * sizeof(hvl_t)); /* Allocate and initialize VL data to write */ // for (i = 0; i < n; i++) { // jbyte *obj = (jbyte *) ENVPTR->GetByteArrayElement(ENVPAR (jbyteArray) buf, i); // if (obj != 0) { // jsize length = ENVPTR->GetStringUTFLength(ENVPAR obj); // const char *utf8 = ENVPTR->GetStringUTFChars(ENVPAR obj, 0); // // if (utf8) { // wdata[i].p = malloc(length * size); // if (wdata[i].p == NULL) { // h5JNIFatalError(env, "H5DwriteNotString: cannot allocate memory for VL data!"); // return -1; // } /* end if */ // wdata[i].len = length; // for(j = 0; j < length; j++) // switch(mem_type_id) { // case float: // ((float *)wdata[i].p)[j] = (float)(utf8); // break; // } // } // // ENVPTR->ReleaseStringUTFChars(ENVPAR obj, utf8); // ENVPTR->ReleaseByteArrayElements(ENVPAR ref, refP, JNI_ABORT); // } // } /*for (i = 0; i < n; ++i) */ UNPIN_BYTE_ARRAY(0); status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)xfer_plist_id, wdata); // now free memory for (i = 0; i < n; i++) { if(wdata[i].p) { free(wdata[i].p); } } free(wdata); if (status < 0) { h5libraryError(env); } return (jint)status; } /** * Read VLEN data into array of arrays. * Object[] buf contains VL arrays of data points * Currently only deal with variable length of atomic data types */ /* old version */ /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5DreadVL * Signature: (IIIII[Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5DreadVL (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jobjectArray buf) { htri_t isStr=0, isComplex=0, isVlenStr=0; if (buf == NULL) { h5nullArgument(env, "H5DreadVL: buf is NULL"); return -1; } /* fixed bug 951 if (H5Tget_class((hid_t)mem_type_id) == H5T_COMPOUND) { hid_t nested_tid = H5Tget_member_type((hid_t)mem_type_id, 0); isStr = H5Tis_variable_str(nested_tid); H5Tclose(nested_tid); } else isStr = H5Tis_variable_str((hid_t)mem_type_id); */ /* fixed bug 2105, the following line does not detect array of vlen strings isStr = H5Tdetect_variable_str((hid_t)mem_type_id); */ isStr = H5Tdetect_class((hid_t)mem_type_id, H5T_STRING); /* fixed compound of vlen of compound */ if (H5Tget_class((hid_t)mem_type_id) == H5T_COMPOUND) { hid_t nested_tid = H5Tget_member_type((hid_t)mem_type_id, 0); isComplex = H5Tdetect_class((hid_t)nested_tid, H5T_COMPOUND) || H5Tdetect_class((hid_t)nested_tid, H5T_VLEN); H5Tclose(nested_tid); } else if (H5Tget_class((hid_t)mem_type_id) == H5T_VLEN) { isVlenStr = 1; /* strings created by H5Tvlen_create( H5T_C_S1) */ } if (isStr == 0 || isComplex>0 || isVlenStr) { return (jint) H5DreadVL_notstr (env, (hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)xfer_plist_id, buf); } if (isStr > 0) { return (jint) H5DreadVL_str (env, (hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)xfer_plist_id, buf); } return -1; } herr_t H5DreadVL_notstr (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf) { jint i; jint n; jstring jstr; herr_t status; h5str_t h5str; hvl_t *rdata; size_t size; size_t max_len = 0; n = ENVPTR->GetArrayLength(ENVPAR buf); rdata = (hvl_t*)calloc(n, sizeof(hvl_t)); if (rdata == NULL) { h5JNIFatalError(env, "H5DreadVL_notstr: failed to allocate buff for read"); return -1; } status = H5Dread(did, tid, mem_sid, file_sid, xfer_plist_id, rdata); if (status < 0) { H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, rdata); free(rdata); h5JNIFatalError(env, "H5DreadVL_notstr: failed to read data"); return -1; } max_len = 1; for (i=0; ilen > max_len) max_len = (rdata + i)->len; } size = H5Tget_size(tid) * max_len; memset(&h5str, 0, sizeof(h5str_t)); h5str_new(&h5str, 4 * size); if (h5str.s == NULL) { H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, rdata); free(rdata); h5JNIFatalError(env, "H5DreadVL_notstr: failed to allocate strng buf"); return -1; } for (i=0; iNewStringUTF(ENVPAR h5str.s); ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr); } h5str_free(&h5str); H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, rdata); free(rdata); return status; } herr_t H5DreadVL_str (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf) { char **strs; jstring jstr; jint i; jint n; herr_t status = -1; n = ENVPTR->GetArrayLength(ENVPAR buf); strs =(char**)calloc(n, sizeof(char*)); if (strs == NULL) { h5JNIFatalError(env, "H5DreadVL_str: failed to allocate buff for read variable length strings"); return -1; } status = H5Dread(did, tid, mem_sid, file_sid, xfer_plist_id, strs); if (status < 0) { H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, strs); free(strs); h5JNIFatalError(env, "H5DreadVL_str: failed to read variable length strings"); return -1; } for (i=0; iNewStringUTF(ENVPAR strs[i]); ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr); free (strs[i]); } /* for repeatedly reading a dataset with a large number of strs (e.g., 1,000,000 strings, H5Dvlen_reclaim() may crash on Windows because the Java GC will not be able to collect free space in time. Instead, use "free(strs[i])" above to free individual strings after it is done. H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, strs); */ free(strs); return status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dread_reg_ref * Signature: (IIIII[Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dread_1reg_1ref (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jobjectArray buf) { herr_t status; h5str_t h5str; size_t size; hdset_reg_ref_t *ref_data; jint i; jint n; jstring jstr; hid_t region = -1; hid_t did = (hid_t) dataset_id; hid_t tid = (hid_t) mem_type_id; hid_t mem_sid = (hid_t) mem_space_id; hid_t file_sid = (hid_t) file_space_id; n = ENVPTR->GetArrayLength(ENVPAR buf); size = sizeof(hdset_reg_ref_t); /*H5Tget_size(tid);*/ ref_data = (hdset_reg_ref_t*)malloc(size * n); if (ref_data == NULL) { h5JNIFatalError(env, "H5Dread_reg_ref: failed to allocate buff for read"); return -1; } status = H5Dread(did, tid, mem_sid, file_sid, xfer_plist_id, ref_data); if (status < 0) { free(ref_data); h5JNIFatalError(env, "H5Dread_reg_ref: failed to read data"); return -1; } memset(&h5str, 0, sizeof(h5str_t)); h5str_new(&h5str, 1024); for (i=0; iNewStringUTF(ENVPAR h5str.s); ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr); } h5str_free(&h5str); free(ref_data); return status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dread_reg_ref_data * Signature: (IIIII[Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dread_1reg_1ref_1data (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jobjectArray buf) { herr_t status; h5str_t h5str; size_t size; hdset_reg_ref_t *ref_data; jint i; jint n; jstring jstr; hid_t region_obj; H5S_sel_type region_type; hid_t region = -1; hid_t did = (hid_t) dataset_id; hid_t tid = (hid_t) mem_type_id; hid_t mem_sid = (hid_t) mem_space_id; hid_t file_sid = (hid_t) file_space_id; n = ENVPTR->GetArrayLength(ENVPAR buf); size = sizeof(hdset_reg_ref_t); /*H5Tget_size(tid);*/ ref_data = (hdset_reg_ref_t*)malloc(size * n); if (ref_data == NULL) { h5JNIFatalError(env, "H5Dread_reg_ref_data: failed to allocate buff for read"); return -1; } status = H5Dread(did, tid, mem_sid, file_sid, xfer_plist_id, ref_data); if (status < 0) { free(ref_data); h5JNIFatalError(env, "H5Dread_reg_ref_data: failed to read data"); return -1; } memset(&h5str, 0, sizeof(h5str_t)); h5str_new(&h5str, 1024); for (i=0; i= 0) { region = H5Rget_region(did, H5R_DATASET_REGION, ref_data[i]); if (region >= 0) { region_type = H5Sget_select_type(region); if(region_type==H5S_SEL_POINTS) { h5str_dump_region_points_data(&h5str, region, region_obj); } else { h5str_dump_region_blocks_data(&h5str, region, region_obj); } H5Sclose(region); } H5Dclose(region_obj); } jstr = ENVPTR->NewStringUTF(ENVPAR h5str.s); ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr); } h5str_free(&h5str); free(ref_data); return status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Dcreate2 * Signature: (ILjava/lang/String;IIIII)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Dcreate2 (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint type_id, jint space_id, jint link_plist_id, jint create_plist_id, jint access_plist_id) { hid_t status; char *file; jboolean isCopy; if (name == NULL) { h5nullArgument(env, "_H5Dcreate2: name is NULL"); return -1; } file = (char *)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (file == NULL) { h5JNIFatalError(env, "_H5Dcreate2: file name not pinned"); return -1; } status = H5Dcreate2((hid_t)loc_id, (const char*)file, (hid_t)type_id, (hid_t)space_id, (hid_t)link_plist_id, (hid_t)create_plist_id, (hid_t)access_plist_id); ENVPTR->ReleaseStringUTFChars(ENVPAR name, file); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Dopen2 * Signature: (ILjava/lang/String;I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Dopen2 (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint access_plist) { hid_t status; char *file; jboolean isCopy; if (name == NULL) { h5nullArgument(env, "_H5Dopen2: name is NULL"); return -1; } file = (char *)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (file == NULL) { h5JNIFatalError(env, "_H5Dopen2: file name not pinned"); return -1; } status = H5Dopen2((hid_t)loc_id, file, (hid_t)access_plist ); ENVPTR->ReleaseStringUTFChars(ENVPAR name, file); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Dcreate_anon * Signature: (IIIII)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Dcreate_1anon (JNIEnv *env, jclass clss, jint loc_id, jint type_id, jint space_id, jint dcpl_id, jint dapl_id) { hid_t status; status = H5Dcreate_anon((hid_t)loc_id, (hid_t)type_id, (hid_t)space_id, (hid_t)dcpl_id, (hid_t)dapl_id); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dget_space_status * Signature: (I)I; */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dget_1space_1status (JNIEnv *env, jclass clss, jint loc_id) { herr_t status; H5D_space_status_t space_status; status = H5Dget_space_status((hid_t)loc_id, (H5D_space_status_t*)&space_status); if (status < 0) { h5libraryError(env); } return (jint)space_status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dget_access_plist * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dget_1access_1plist (JNIEnv *env, jclass clss, jint loc_id) { hid_t status; status = H5Dget_access_plist((hid_t)loc_id); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dget_offset * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dget_1offset (JNIEnv *env, jclass clss, jint loc_id) { haddr_t offset; offset = H5Dget_offset((hid_t)loc_id); if (offset == HADDR_UNDEF) { h5libraryError(env); } return (jlong)offset; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dvlen_get_buf_size_long * Signature: (III)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dvlen_1get_1buf_1size_1long (JNIEnv *env, jclass clss, jint dataset_id, jint type_id, jint space_id) { herr_t status; hsize_t sz; status = (jint)H5Dvlen_get_buf_size((hid_t)dataset_id, (hid_t)type_id, (hid_t)space_id, (hsize_t*)&sz); if (status < 0) { h5libraryError(env); return -1; } return (jlong)sz; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dfill * Signature: ([BI[BII)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dfill (JNIEnv *env, jclass clss, jbyteArray fill, jint fill_type_id, jbyteArray buf, jint buf_type_id, jint space_id) { herr_t status; jbyte *fillP; jbyte *buffP; jboolean isCopy1; jboolean isCopy2; if(fill) { fillP = ENVPTR->GetByteArrayElements(ENVPAR fill, &isCopy1); if (fillP == NULL) { h5JNIFatalError( env, "H5Dfill: fill not pinned"); return; } } else fillP = NULL; if (buf == NULL) { h5nullArgument(env, "H5Dfill: buf is NULL"); return; } buffP = ENVPTR->GetByteArrayElements(ENVPAR buf, &isCopy2); if (buffP == NULL) { h5JNIFatalError(env, "H5Dfill: buf not pinned"); return; } status = H5Dfill((const void*)fillP, (hid_t)fill_type_id, (void*)buffP, (hid_t)buf_type_id, (hid_t)space_id); if (status < 0) { ENVPTR->ReleaseByteArrayElements(ENVPAR buf, buffP, JNI_ABORT); if(fillP) { ENVPTR->ReleaseByteArrayElements(ENVPAR fill, fillP, JNI_ABORT); } h5libraryError(env); return; } if (isCopy2 == JNI_TRUE) { ENVPTR->ReleaseByteArrayElements(ENVPAR buf, buffP, 0); } if(fillP) { ENVPTR->ReleaseByteArrayElements(ENVPAR fill, fillP, JNI_ABORT); } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dset_extent * Signature: (I[J)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dset_1extent (JNIEnv *env, jclass clss, jint loc_id, jlongArray buf) { herr_t status; hsize_t *dims; jlong *buffP; jsize rank; jboolean isCopy; int i = 0; if (buf == NULL) { h5nullArgument(env, "H5Dset_extent: buf is NULL"); return; } rank = ENVPTR->GetArrayLength(ENVPAR buf); if (rank <= 0) { h5JNIFatalError(env, "H5Dset_extent: rank <=0"); return; } buffP = ENVPTR->GetLongArrayElements(ENVPAR buf, &isCopy); if (buffP == NULL) { h5JNIFatalError( env, "H5Dset_extent: buf not pinned"); return; } dims = (hsize_t*) malloc(rank * sizeof(hsize_t)); for (i = 0; i< rank; i++) dims[i] = (hsize_t)buffP[i]; status = H5Dset_extent((hid_t)loc_id, (hsize_t*)dims); free (dims); ENVPTR->ReleaseLongArrayElements(ENVPAR buf, buffP, JNI_ABORT); if (status < 0) { h5libraryError(env); } } herr_t H5D_iterate_cb(void* elem, hid_t elem_id, unsigned ndim, const hsize_t *point, void *op_data) { JNIEnv *cbenv; jint status; jclass cls; jmethodID mid; jbyteArray elemArray; jlongArray pointArray; jsize size; if(JVMPTR->AttachCurrentThread(JVMPAR2 (void**)&cbenv, NULL) != 0) { JVMPTR->DetachCurrentThread(JVMPAR); return -1; } cls = CBENVPTR->GetObjectClass(CBENVPAR visit_callback); if (cls == 0) { JVMPTR->DetachCurrentThread(JVMPAR); return -1; } mid = CBENVPTR->GetMethodID(CBENVPAR cls, "callback", "([BII[JLncsa/hdf/hdf5lib/callbacks/H5D_iterate_t;)I"); if (mid == 0) { JVMPTR->DetachCurrentThread(JVMPAR); return -1; } if (elem == NULL) { JVMPTR->DetachCurrentThread(JVMPAR); return -1; } if (point == NULL) { JVMPTR->DetachCurrentThread(JVMPAR); return -1; } size = H5Tget_size(elem_id); elemArray = CBENVPTR->NewByteArray(CBENVPAR size); if (elemArray == NULL) { JVMPTR->DetachCurrentThread(JVMPAR); return -1; } CBENVPTR->SetByteArrayRegion(CBENVPAR elemArray, 0, size, (jbyte *)elem); pointArray = CBENVPTR->NewLongArray(CBENVPAR 2); if (pointArray == NULL) { JVMPTR->DetachCurrentThread(JVMPAR); return -1; } CBENVPTR->SetLongArrayRegion(CBENVPAR pointArray, 0, 2, (const jlong *)point); status = CBENVPTR->CallIntMethod(CBENVPAR visit_callback, mid, elemArray, elem_id, ndim, pointArray, op_data); CBENVPTR->GetByteArrayRegion(CBENVPAR elemArray, 0, size, (jbyte *)elem); JVMPTR->DetachCurrentThread(JVMPAR); return status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Diterate * Signature: ([BIILjava/lang/Object;Ljava/lang/Object;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Diterate (JNIEnv *env, jclass clss, jbyteArray buf, jint buf_type, jint space, jobject callback_op, jobject op_data) { jboolean isCopy; jbyte *buffP; herr_t status = -1; ENVPTR->GetJavaVM(ENVPAR &jvm); visit_callback = callback_op; if (op_data == NULL) { h5nullArgument(env, "H5Diterate: op_data is NULL"); return -1; } if (callback_op == NULL) { h5nullArgument(env, "H5Diterate: callback_op is NULL"); return -1; } if (buf == NULL) { h5nullArgument(env, "H5Diterate: buf is NULL"); return -1; } buffP = ENVPTR->GetByteArrayElements(ENVPAR buf, &isCopy); if (buffP == NULL) { h5JNIFatalError(env, "H5Diterate: buf not pinned"); return -1; } status = H5Diterate((void*)buffP, (hid_t)buf_type, (hid_t)space, (H5D_operator_t)H5D_iterate_cb, (void*)op_data); if (status < 0) { ENVPTR->ReleaseByteArrayElements(ENVPAR buf, buffP, JNI_ABORT); h5libraryError(env); return status; } if (isCopy == JNI_TRUE) { ENVPTR->ReleaseByteArrayElements(ENVPAR buf, buffP, 0); } return status; } #ifdef __cplusplus } #endif libsis-jhdf5-java-14.12.1/source/c/hdf-java/h5dImp.h000077500000000000000000000221041256564762100216030ustar00rootroot00000000000000/* DO NOT EDIT THIS FILE - it is machine generated */ #include /* Header for class ncsa_hdf_hdf5lib_H5_H5D */ #ifndef _Included_ncsa_hdf_hdf5lib_H5_H5D #define _Included_ncsa_hdf_hdf5lib_H5_H5D #ifdef __cplusplus extern "C" { #endif extern JavaVM *jvm; extern jobject visit_callback; /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Dcreate * Signature: (ILjava/lang/String;III)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Dcreate (JNIEnv*, jclass, jint, jstring, jint, jint, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dchdir_ext * Signature: (Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dchdir_1ext (JNIEnv*, jclass, jstring); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dgetdir_1ext * Signature: ([Ljava/lang/String;I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dgetdir_1ext (JNIEnv*, jclass, jobjectArray, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Dopen * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Dopen (JNIEnv*, jclass, jint, jstring); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Dget_space * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Dget_1space (JNIEnv*, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Dget_type * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Dget_1type (JNIEnv*, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Dget_create_plist * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Dget_1create_1plist (JNIEnv*, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dread * Signature: (IIIII[BZ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dread (JNIEnv*, jclass, jint, jint, jint, jint, jint, jbyteArray, jboolean); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dwrite * Signature: (IIIII[BZ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dwrite (JNIEnv*, jclass, jint, jint, jint, jint, jint, jbyteArray, jboolean); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dextend * Signature: (I[B)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dextend (JNIEnv*, jclass, jint, jbyteArray); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Dclose * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Dclose (JNIEnv*, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dget_storage_size * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dget_1storage_1size (JNIEnv*, jclass, jint); /* * Copies the content of one dataset to another dataset * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dcopy * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dcopy (JNIEnv*, jclass, jint, jint); /* * Copies the content of one dataset to another dataset * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dvlen_get_buf_size * Signature: (III[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dvlen_1get_1buf_1size (JNIEnv*, jclass, jint, jint, jint, jintArray); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dvlen_reclaim * Signature: (III[B)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dvlen_1reclaim (JNIEnv*, jclass, jint, jint, jint, jbyteArray); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Dget_space_status * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Dget_1space_1status (JNIEnv*, jclass, jint, jintArray); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dread_short * Signature: (IIIII[S[Z)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dread_1short (JNIEnv*, jclass, jint, jint, jint, jint, jint, jshortArray, jboolean); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dread_int * Signature: (IIIII[I[Z)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dread_1int (JNIEnv*, jclass, jint, jint, jint, jint, jint, jintArray, jboolean); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dread_long * Signature: (IIIII[J[Z)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dread_1long (JNIEnv*, jclass, jint, jint, jint, jint, jint, jlongArray, jboolean); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dread_float * Signature: (IIIII[F[Z)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dread_1float (JNIEnv*, jclass, jint, jint, jint, jint, jint, jfloatArray, jboolean); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dread_double * Signature: (IIIII[D[Z)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dread_1double (JNIEnv*, jclass, jint, jint, jint, jint, jint, jdoubleArray, jboolean); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dread_string * Signature: (IIIII[Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dread_1string (JNIEnv*, jclass, jint, jint, jint, jint, jint, jobjectArray); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dwrite_short * Signature: (IIIII[S[Z)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dwrite_1short (JNIEnv*, jclass, jint, jint, jint, jint, jint, jshortArray, jboolean); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dwrite_int * Signature: (IIIII[I[Z)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dwrite_1int (JNIEnv*, jclass, jint, jint, jint, jint, jint, jintArray, jboolean); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dwrite_long * Signature: (IIIII[J[Z)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dwrite_1long (JNIEnv*, jclass, jint, jint, jint, jint, jint, jlongArray, jboolean); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dwrite_float * Signature: (IIIII[F[Z)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dwrite_1float (JNIEnv*, jclass, jint, jint, jint, jint, jint, jfloatArray, jboolean); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dwrite_double * Signature: (IIIII[D[Z)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dwrite_1double (JNIEnv*, jclass, jint, jint, jint, jint, jint, jdoubleArray, jboolean); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5DwriteString * Signature: (IIIII[Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5DwriteString (JNIEnv *, jclass, jint, jint, jint, jint, jint, jobjectArray); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5DreadVL * Signature: (IIIII[Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5DreadVL (JNIEnv*, jclass, jint, jint, jint, jint, jint, jobjectArray); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dread_reg_ref * Signature: (IIIII[Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dread_1reg_1ref (JNIEnv*, jclass, jint, jint, jint, jint, jint, jobjectArray); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dread_reg_ref_data * Signature: (IIIII[Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dread_1reg_1ref_1data (JNIEnv*, jclass, jint, jint, jint, jint, jint, jobjectArray); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Dcreate2 * Signature: (ILjava/lang/String;IIIII)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Dcreate2 (JNIEnv *, jclass, jint, jstring, jint, jint, jint, jint, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Dopen2 * Signature: (ILjava/lang/String;I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Dopen2 (JNIEnv *, jclass, jint, jstring, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Dcreate_anon * Signature: (IIIII)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Dcreate_1anon (JNIEnv *, jclass, jint, jint, jint, jint, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dget_space_status * Signature: (I)I; */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dget_1space_1status (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dget_access_plist * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dget_1access_1plist (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dget_offset * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dget_1offset (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dvlen_get_buf_size_long * Signature: (III)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dvlen_1get_1buf_1size_1long (JNIEnv *, jclass, jint, jint, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dfill * Signature: ([BI[BII)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dfill (JNIEnv *, jclass, jbyteArray, jint, jbyteArray, jint, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dset_extent * Signature: (I[J)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Dset_1extent (JNIEnv *, jclass, jint, jlongArray); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Diterate * Signature: ([BIILjava/lang/Object;Ljava/lang/Object;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Diterate (JNIEnv *, jclass, jbyteArray, jint, jint, jobject, jobject); #ifdef __cplusplus } #endif #endif libsis-jhdf5-java-14.12.1/source/c/hdf-java/h5eImp.c000077500000000000000000000340321256564762100216020ustar00rootroot00000000000000/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF Java Products. The full HDF Java copyright * * notice, including terms governing use, modification, and redistribution, * * is contained in the file, COPYING. COPYING can be found at the root of * * the source code distribution tree. You can also access it online at * * http://www.hdfgroup.org/products/licenses.html. If you do not have * * access to the file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #ifdef __cplusplus extern "C" { #endif /* * This code is the C-interface called by Java programs to access the * general library functions of the HDF5 library. * * Each routine wraps a single HDF entry point, generally with the * analogous arguments and return codes. * * For details of the HDF libraries, see the HDF Documentation at: * http://www.hdfgroup.org/HDF5/doc/ * */ #include #include #include "hdf5.h" #include "h5jni.h" #include "h5eImp.h" /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Eauto_is_v2 * Signature: (I)Z */ JNIEXPORT jboolean JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Eauto_1is_1v2 (JNIEnv *env, jclass cls, jint stk_id) { herr_t ret_val = -1; unsigned int is_stack = 0; if (stk_id < 0) { h5badArgument(env, "H5Eauto_is_v2: invalid argument"); return 0; } ret_val = H5Eauto_is_v2(stk_id, &is_stack); if (ret_val < 0) { h5libraryError(env); return 0; } return is_stack; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Eregister_class * Signature: (Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Eregister_1class (JNIEnv *env, jclass cls, jstring cls_name, jstring lib_name, jstring version) { herr_t ret_val = -1; char* the_cls_name; char* the_lib_name; char* the_version; jboolean isCopy; if(cls_name==NULL) { h5nullArgument( env, "H5Eregister_class: error class name is NULL"); return ret_val; } the_cls_name = (char *)ENVPTR->GetStringUTFChars(ENVPAR cls_name,&isCopy); if (the_cls_name == NULL) { h5JNIFatalError( env, "H5Eregister_class: error class name not pinned"); return ret_val; } if(lib_name==NULL) { h5nullArgument( env, "H5Eregister_class: client library or application name is NULL"); return ret_val; } the_lib_name = (char *)ENVPTR->GetStringUTFChars(ENVPAR lib_name,&isCopy); if (the_lib_name == NULL) { h5JNIFatalError( env, "H5Eregister_class: client name not pinned"); return ret_val; } if(version==NULL) { h5nullArgument( env, "H5Eregister_class: version of the client library or application is NULL"); return ret_val; } the_version = (char *)ENVPTR->GetStringUTFChars(ENVPAR version,&isCopy); if (the_version == NULL) { h5JNIFatalError( env, "H5Eregister_class: version not pinned"); return ret_val; } ret_val = H5Eregister_class(the_cls_name, the_lib_name, the_version); ENVPTR->ReleaseStringUTFChars(ENVPAR cls_name, the_cls_name); ENVPTR->ReleaseStringUTFChars(ENVPAR lib_name, the_lib_name); ENVPTR->ReleaseStringUTFChars(ENVPAR version, the_version); if (ret_val < 0) { h5libraryError(env); } return (jint)ret_val; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Eunregister_class * Signature: (I)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Eunregister_1class (JNIEnv *env, jclass cls, jint cls_id) { herr_t ret_val = -1; if (cls_id < 0) { h5badArgument(env, "H5Eunregister_class: invalid argument"); return; } ret_val = H5Eunregister_class((hid_t)cls_id); if (ret_val < 0) { h5libraryError(env); } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Eclose_msg * Signature: (I)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Eclose_1msg (JNIEnv *env, jclass cls, jint err_id) { herr_t ret_val = -1; if (err_id < 0) { h5badArgument(env, "H5Eclose_msg: invalid argument"); return; } ret_val = H5Eclose_msg((hid_t)err_id); if (ret_val < 0) { h5libraryError(env); } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Ecreate_msg * Signature: (IILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Ecreate_1msg (JNIEnv *env, jclass cls, jint err_id, jint msg_type, jstring err_msg) { herr_t ret_val = -1; char* the_err_msg; jboolean isCopy; H5E_type_t error_msg_type = (H5E_type_t)msg_type; if (err_id < 0) { h5badArgument(env, "H5Ecreate_msg: invalid argument"); return ret_val; } if(err_msg==NULL) { h5nullArgument( env, "H5Ecreate_msg: error message is NULL"); return ret_val; } the_err_msg = (char *)ENVPTR->GetStringUTFChars(ENVPAR err_msg,&isCopy); if (the_err_msg == NULL) { h5JNIFatalError( env, "H5Ecreate_msg: error message not pinned"); return ret_val; } ret_val = H5Ecreate_msg((hid_t)err_id, error_msg_type, the_err_msg); ENVPTR->ReleaseStringUTFChars(ENVPAR err_msg, the_err_msg); if (ret_val < 0) { h5libraryError(env); return ret_val; } return (jint)ret_val; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Ecreate_stack * Signature: ()I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Ecreate_1stack (JNIEnv *env, jclass cls) { jint ret_val = -1; ret_val = H5Ecreate_stack(); if (ret_val < 0) { h5libraryError(env); return -1; } return ret_val; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Eget_current_stack * Signature: ()I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Eget_1current_1stack (JNIEnv *env, jclass cls) { hid_t ret_val = H5Eget_current_stack(); if (ret_val < 0) { h5libraryError(env); return -1; } return ret_val; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Eclose_stack * Signature: (I)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Eclose_1stack (JNIEnv *env, jclass cls, jint stk_id) { herr_t ret_val = -1; if (stk_id < 0) { h5badArgument(env, "H5Eclose_stack: invalid argument"); return; } ret_val = H5Eclose_stack((hid_t)stk_id); if (ret_val < 0) { h5libraryError(env); } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Eprint1 * Signature: (Ljava/lang/Object;)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Eprint1 (JNIEnv *env, jclass cls, jobject stream_obj) { herr_t ret_val = -1; if(!stream_obj) ret_val = H5Eprint1(stdout); else ret_val = H5Eprint1((FILE*)stream_obj); if (ret_val < 0) { h5libraryError(env); } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Eprint2 * Signature: (ILjava/lang/Object;)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Eprint2 (JNIEnv *env, jclass cls, jint stk_id, jobject stream_obj) { herr_t ret_val = -1; if (stk_id < 0) { h5badArgument(env, "H5Eprint2: invalid argument"); return; } if(!stream_obj) ret_val = H5Eprint2((hid_t)stk_id, stdout); else ret_val = H5Eprint2((hid_t)stk_id, (FILE*)stream_obj); if (ret_val < 0) { h5libraryError(env); } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Eget_class_name * Signature: (I)Ljava/lang/String; */ JNIEXPORT jstring JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Eget_1class_1name (JNIEnv *env, jclass cls, jint cls_id) { char *namePtr; jstring str; ssize_t buf_size; if (cls_id < 0) { h5badArgument(env, "H5Eget_class_name: invalid argument"); return NULL; } /* get the length of the name */ buf_size = H5Eget_class_name(cls_id, NULL, 0); if (buf_size < 0) { h5badArgument( env, "H5Eget_class_name: buf_size < 0"); return NULL; } if (buf_size == 0) { h5badArgument( env, "H5Eget_class_name: No class name"); return NULL; } buf_size++; /* add extra space for the null terminator */ namePtr = (char*)malloc(sizeof(char)*buf_size); if (namePtr == NULL) { h5outOfMemory( env, "H5Eget_class_name: malloc failed"); return NULL; } buf_size = H5Eget_class_name((hid_t)cls_id, (char *)namePtr, (size_t)buf_size); if (buf_size < 0) { free(namePtr); h5libraryError(env); return NULL; } str = ENVPTR->NewStringUTF(ENVPAR namePtr); free(namePtr); return str; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Eset_current_stack * Signature: (I)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Eset_1current_1stack (JNIEnv *env, jclass cls, jint stk_id) { herr_t ret_val = -1; if (stk_id < 0) { h5badArgument(env, "H5Eset_current_stack: invalid argument"); return; } ret_val = H5Eset_current_stack(stk_id); if (ret_val < 0) { h5libraryError(env); return; } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Epop * Signature: (IJ)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Epop (JNIEnv *env, jclass cls, jint stk_id, jlong count) { herr_t ret_val = -1; if (stk_id < 0) { h5badArgument(env, "H5Epop: invalid argument"); return; } ret_val = H5Epop(stk_id, (size_t)count); if (ret_val < 0) { h5libraryError(env); return; } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Eclear2 * Signature: (I)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Eclear2 (JNIEnv *env, jclass cls, jint stk_id) { herr_t ret_val = -1; if (stk_id < 0) { h5badArgument(env, "H5Eclear2: invalid argument"); return; } ret_val = H5Eclear2(stk_id); if (ret_val < 0) { h5libraryError(env); return; } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Eget_msg * Signature: (I[I)Ljava/lang/String; */ JNIEXPORT jstring JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Eget_1msg (JNIEnv *env, jclass cls, jint msg_id, jintArray error_msg_type_list) { char *namePtr; jstring str; jboolean isCopy; ssize_t buf_size; jint *theArray; H5E_type_t error_msg_type; if (msg_id < 0) { h5badArgument(env, "H5Eget_msg: invalid argument"); return NULL; } /* get the length of the name */ buf_size = H5Eget_msg(msg_id, NULL, NULL, 0); if (buf_size < 0) { h5badArgument( env, "H5Eget_msg: buf_size < 0"); return NULL; } if (buf_size == 0) { h5badArgument( env, "H5Eget_msg: No message"); return NULL; } buf_size++; /* add extra space for the null terminator */ namePtr = (char*)malloc(sizeof(char)*buf_size); if (namePtr == NULL) { h5outOfMemory( env, "H5Eget_msg: malloc failed"); return NULL; } if ( error_msg_type_list == NULL ) { h5nullArgument( env, "H5Eget_msg: error_msg_type_list is NULL"); return NULL; } theArray = (jint *)ENVPTR->GetIntArrayElements(ENVPAR error_msg_type_list,&isCopy); if (theArray == NULL) { h5JNIFatalError( env, "H5Eget_msg: error_msg_type_list not pinned"); return NULL; } buf_size = H5Eget_msg((hid_t)msg_id, &error_msg_type, (char *)namePtr, (size_t)buf_size); if (buf_size < 0) { free(namePtr); ENVPTR->ReleaseIntArrayElements(ENVPAR error_msg_type_list,theArray,JNI_ABORT); h5libraryError(env); return NULL; } theArray[0] = error_msg_type; ENVPTR->ReleaseIntArrayElements(ENVPAR error_msg_type_list,theArray,0); str = ENVPTR->NewStringUTF(ENVPAR namePtr); free(namePtr); return str; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Eget_num * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Eget_1num (JNIEnv *env, jclass cls, jint stk_id) { ssize_t ret_val = -1; if (stk_id < 0) { h5badArgument(env, "H5Eget_num: invalid argument"); return -1; } ret_val = H5Eget_num(stk_id); if (ret_val < 0) { h5libraryError(env); return -1; } return ret_val; } #ifdef __cplusplus } #endif libsis-jhdf5-java-14.12.1/source/c/hdf-java/h5eImp.h000077500000000000000000000064571256564762100216210ustar00rootroot00000000000000/* DO NOT EDIT THIS FILE - it is machine generated */ #include /* Header for class ncsa_hdf_hdf5lib_H5_H5E */ #ifndef _Included_ncsa_hdf_hdf5lib_H5_H5E #define _Included_ncsa_hdf_hdf5lib_H5_H5E #ifdef __cplusplus extern "C" { #endif /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Eauto_is_v2 * Signature: (I)Z */ JNIEXPORT jboolean JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Eauto_1is_1v2 (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Eregister_class * Signature: (Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Eregister_1class (JNIEnv *, jclass, jstring, jstring, jstring); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Eunregister_class * Signature: (I)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Eunregister_1class (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Eclose_msg * Signature: (I)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Eclose_1msg (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Ecreate_msg * Signature: (IILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Ecreate_1msg (JNIEnv *, jclass, jint, jint, jstring); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Ecreate_stack * Signature: ()I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Ecreate_1stack (JNIEnv *, jclass); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Eget_current_stack * Signature: ()I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Eget_1current_1stack (JNIEnv *, jclass); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Eclose_stack * Signature: (I)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Eclose_1stack (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Eprint1 * Signature: (Ljava/lang/Object;)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Eprint1 (JNIEnv *, jclass, jobject); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Eprint2 * Signature: (ILjava/lang/Object;)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Eprint2 (JNIEnv *, jclass, jint, jobject); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Eget_class_name * Signature: (I)Ljava/lang/String; */ JNIEXPORT jstring JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Eget_1class_1name (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Eset_current_stack * Signature: (I)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Eset_1current_1stack (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Epop * Signature: (IJ)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Epop (JNIEnv *, jclass, jint, jlong); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Eclear2 * Signature: (I)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Eclear2 (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Eget_msg * Signature: (I[I)Ljava/lang/String; */ JNIEXPORT jstring JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Eget_1msg (JNIEnv *, jclass, jint, jintArray); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Eget_num * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Eget_1num (JNIEnv *, jclass, jint); #ifdef __cplusplus } #endif #endif libsis-jhdf5-java-14.12.1/source/c/hdf-java/h5fImp.c000077500000000000000000000446001256564762100216050ustar00rootroot00000000000000/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF Java Products. The full HDF Java copyright * * notice, including terms governing use, modification, and redistribution, * * is contained in the file, COPYING. COPYING can be found at the root of * * the source code distribution tree. You can also access it online at * * http://www.hdfgroup.org/products/licenses.html. If you do not have * * access to the file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /* * This code is the C-interface called by Java programs to access the * file interface functions of the HDF5 library. * * Each routine wraps a single HDF entry point, generally with the * analogous arguments and return codes. * * For details of the HDF libraries, see the HDF Documentation at: * http://hdf.ncsa.uiuc.edu/HDF5/doc/ * */ #ifdef __cplusplus extern "C" { #endif #include #include #include #include "hdf5.h" #include "h5jni.h" #include "h5fImp.h" #include "h5util.h" /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fopen * Signature: (Ljava/lang/String;II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Fopen (JNIEnv *env, jclass clss, jstring name, jint flags, jint access_id) { hid_t status; char* file; jboolean isCopy; if (name == NULL) { /* exception -- bad argument? */ h5nullArgument( env, "H5Fopen: name is NULL"); return -1; } file = (char *)ENVPTR->GetStringUTFChars(ENVPAR name,&isCopy); if (file == NULL) { /* exception -- out of memory? */ h5JNIFatalError( env, "H5Fopen: file name not pinned"); return -1; } status = H5Fopen(file, (unsigned) flags, (hid_t) access_id ); ENVPTR->ReleaseStringUTFChars(ENVPAR name,file); if (status < 0) { /* throw exception */ h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fcreate * Signature: (Ljava/lang/String;III)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Fcreate (JNIEnv *env, jclass clss, jstring name, jint flags, jint create_id, jint access_id) { hid_t status; char* file; jboolean isCopy; if (name == NULL) { /* exception -- bad argument? */ h5nullArgument( env, "H5Fcreate: name is NULL"); return -1; } file = (char *)ENVPTR->GetStringUTFChars(ENVPAR name,&isCopy); if (file == NULL) { /* exception -- out of memory? */ h5JNIFatalError( env, "H5Fcreate: file name is not pinned"); return -1; } status = H5Fcreate(file, flags, create_id, access_id); ENVPTR->ReleaseStringUTFChars(ENVPAR name,file); if (status < 0) { /* throw exception */ h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fflush * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fflush (JNIEnv *env, jclass clss, jint object_id, jint scope) { herr_t retVal = -1; retVal = H5Fflush((hid_t) object_id, (H5F_scope_t) scope ); if (retVal < 0) { /* throw exception */ h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fget_name * Signature: (I)Ljava/lang/String; */ JNIEXPORT jstring JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fget_1name (JNIEnv *env, jclass cls, jint file_id) { char *namePtr; jstring str; ssize_t buf_size; /* get the length of the name */ buf_size = H5Fget_name(file_id, NULL, 0); if (buf_size <= 0) { h5badArgument( env, "H5Fget_name: buf_size <= 0"); return NULL; } buf_size++; /* add extra space for the null terminator */ namePtr = (char*)malloc(sizeof(char)*buf_size); if (namePtr == NULL) { h5outOfMemory( env, "H5Fget_name: malloc failed"); return NULL; } buf_size = H5Fget_name ((hid_t) file_id, (char *)namePtr, (size_t)buf_size); if (buf_size < 0) { free(namePtr); h5libraryError(env); return NULL; } str = ENVPTR->NewStringUTF(ENVPAR namePtr); free(namePtr); return str; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fis_hdf5 * Signature: (Ljava/lang/String;)Z */ JNIEXPORT jboolean JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fis_1hdf5 (JNIEnv *env, jclass clss, jstring name) { htri_t retVal = 0; char * file; jboolean isCopy; if (name == NULL) { /* exception -- bad argument? */ h5nullArgument( env, "H5Fis_hdf5: name is NULL"); return JNI_FALSE; } file = (char *)ENVPTR->GetStringUTFChars(ENVPAR name,&isCopy); if (file == NULL) { /* exception -- out of memory? */ h5JNIFatalError( env, "H5Fis_hdf5: file name is not pinned"); return JNI_FALSE; } retVal = H5Fis_hdf5(file); ENVPTR->ReleaseStringUTFChars(ENVPAR name,file); if (retVal > 0) { return JNI_TRUE; } else if (retVal == 0) { return JNI_FALSE; } else { /* raise exception here -- return value is irrelevant */ h5libraryError(env); return JNI_FALSE; } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fget_create_plist * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Fget_1create_1plist (JNIEnv *env, jclass clss, jint file_id) { hid_t retVal = -1; retVal = H5Fget_create_plist((hid_t) file_id ); if (retVal < 0) { /* throw exception */ h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fget_access_plist * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Fget_1access_1plist (JNIEnv *env, jclass clss, jint file_id) { hid_t retVal = -1; retVal = H5Fget_access_plist((hid_t) file_id); if (retVal < 0) { /* throw exception */ h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fget_intent * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fget_1intent (JNIEnv *env, jclass cls, jint file_id) { herr_t ret_val = -1; unsigned intent = 0; ret_val = H5Fget_intent((hid_t) file_id, &intent); if (ret_val < 0) { h5libraryError(env); } return (jint)intent; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fclose * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Fclose (JNIEnv *env, jclass clss, jint file_id) { herr_t status = -1; if (file_id > 0) status = H5Fclose((hid_t) file_id ); if (status < 0) { h5libraryError(env); return -1; } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fmount * Signature: (ILjava/lang/String;II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fmount (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint child_id, jint plist_id) { herr_t status; char* file; jboolean isCopy; if (name == NULL) { /* exception -- bad argument? */ h5nullArgument( env, "H5Fmount: name is NULL"); return -1; } file = (char *)ENVPTR->GetStringUTFChars(ENVPAR name,&isCopy); if (file == NULL) { /* exception -- out of memory? */ h5JNIFatalError( env, "H5Fmount: file name is not pinned"); return -1; } status = H5Fmount((hid_t) loc_id, file, (hid_t) child_id, (hid_t) plist_id ); ENVPTR->ReleaseStringUTFChars(ENVPAR name,file); if (status < 0) { /* throw exception */ h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Funmount * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Funmount (JNIEnv *env, jclass clss, jint loc_id, jstring name) { herr_t status; char* file; jboolean isCopy; if (name == NULL) { /* exception -- bad argument? */ h5nullArgument( env, "H5Funmount: name is NULL"); return -1; } file = (char *)ENVPTR->GetStringUTFChars(ENVPAR name,&isCopy); if (file == NULL) { h5JNIFatalError( env, "H5Funmount: file name is not pinned"); /* exception -- out of memory? */ return -1; } status = H5Funmount((hid_t) loc_id, file ); ENVPTR->ReleaseStringUTFChars(ENVPAR name,file); if (status < 0) { /* throw exception */ h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fget_freespace * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fget_1freespace (JNIEnv *env, jclass cls, jint file_id) { hssize_t ret_val = -1; ret_val = H5Fget_freespace((hid_t)file_id); if (ret_val < 0) { h5libraryError(env); } return (jlong)ret_val; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Freopen * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Freopen (JNIEnv *env, jclass clss, jint file_id) { hid_t retVal = -1; retVal = H5Freopen((hid_t)file_id); if (retVal < 0) { /* throw exception */ h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fget_obj_ids_long * Signature: (IIJ[I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fget_1obj_1ids_1long (JNIEnv *env, jclass cls, jint file_id, jint types, jlong maxObjs, jintArray obj_id_list) { ssize_t ret_val; jint *obj_id_listP; jboolean isCopy; hid_t *id_list; int rank; int i; ret_val = -1; if ( obj_id_list == NULL ) { h5nullArgument( env, "H5Fget_obj_ids_long: obj_id_list is NULL"); return -1; } obj_id_listP = ENVPTR->GetIntArrayElements(ENVPAR obj_id_list,&isCopy); if (obj_id_listP == NULL) { h5JNIFatalError( env, "H5Fget_obj_ids_long: obj_id_list not pinned"); return -1; } rank = (int)ENVPTR->GetArrayLength(ENVPAR obj_id_list); id_list = (hid_t *)malloc( rank * sizeof(hid_t)); if (id_list == NULL) { ENVPTR->ReleaseIntArrayElements(ENVPAR obj_id_list,obj_id_listP,JNI_ABORT); h5JNIFatalError(env, "H5Fget_obj_ids_long: obj_id_list not converted to hid_t"); return -1; } ret_val = H5Fget_obj_ids((hid_t)file_id, (unsigned int)types, (size_t)maxObjs, id_list); if (ret_val < 0) { ENVPTR->ReleaseIntArrayElements(ENVPAR obj_id_list,obj_id_listP,JNI_ABORT); free(id_list); h5libraryError(env); return -1; } for (i = 0; i < rank; i++) { obj_id_listP[i] = id_list[i]; } free(id_list); ENVPTR->ReleaseIntArrayElements(ENVPAR obj_id_list,obj_id_listP,0); return (jlong)ret_val; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fget_obj_ids * Signature: (III[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fget_1obj_1ids (JNIEnv *env, jclass clss, jint file_id, jint types, jint obj_count, jintArray obj_id_list) { ssize_t status=-1; jint *obj_id_listP; jboolean isCopy; if ( obj_id_list == NULL ) { h5nullArgument( env, "H5Fget_obj_ids: obj_id_list is NULL"); return -1; } obj_id_listP = ENVPTR->GetIntArrayElements(ENVPAR obj_id_list,&isCopy); if (obj_id_listP == NULL) { h5JNIFatalError( env, "H5Fget_obj_ids: obj_id_list not pinned"); return -1; } status = H5Fget_obj_ids((hid_t)file_id, (unsigned int)types, (int)obj_count, (hid_t*)obj_id_listP); if (status < 0) { ENVPTR->ReleaseIntArrayElements(ENVPAR obj_id_list,obj_id_listP,JNI_ABORT); h5libraryError(env); } else { ENVPTR->ReleaseIntArrayElements(ENVPAR obj_id_list,obj_id_listP,0); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fget_obj_count(hid_t file_id, unsigned int types ) * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fget_1obj_1count (JNIEnv *env, jclass clss, jint file_id, jint types ) { ssize_t status = -1; status = H5Fget_obj_count((hid_t)file_id, (unsigned int)types ); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fget_obj_count_long * Signature: (II)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fget_1obj_1count_1long (JNIEnv *env, jclass cls, jint file_id, jint types) { ssize_t ret_val = -1; ret_val = H5Fget_obj_count((hid_t)file_id, (unsigned int)types ); if (ret_val < 0) { h5libraryError(env); } return (jlong)ret_val; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fget_name * Signature: (ILjava/lang/String;I)Ljava/lang/String; */ JNIEXPORT jstring JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fget_2name (JNIEnv *env, jclass clss, jint obj_id, jstring name, jint buf_size) { char *aName; jstring str; ssize_t size; if (buf_size <= 0) { h5badArgument( env, "H5Fget_name: buf_size <= 0"); return NULL; } aName = (char*)malloc(sizeof(char)*buf_size); if (aName == NULL) { h5outOfMemory( env, "H5Fget_name: malloc failed"); return NULL; } size = H5Fget_name ((hid_t) obj_id, (char *)aName, (size_t)buf_size); if (size < 0) { free(aName); h5libraryError(env); return NULL; } str = ENVPTR->NewStringUTF(ENVPAR aName); free(aName); return str; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fget_filesize * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fget_1filesize (JNIEnv *env, jclass clss, jint file_id) { herr_t status; hsize_t size = 0; status = H5Fget_filesize ((hid_t) file_id, (hsize_t *) &size); if (status < 0) { h5libraryError(env); } return (jlong) size; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fget_mdc_hit_rate * Signature: (I)D */ JNIEXPORT jdouble JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fget_1mdc_1hit_1rate (JNIEnv *env, jclass cls, jint file_id) { double rate = 0.0; herr_t ret_val = -1; ret_val = H5Fget_mdc_hit_rate((hid_t)file_id, &rate); if (ret_val < 0) { h5libraryError(env); } return (jdouble)rate; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fget_mdc_size * Signature: (I[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fget_1mdc_1size (JNIEnv *env, jclass cls, jint file_id, jlongArray metadata_cache) { herr_t ret_val = -1; jint size = 0; jlong *metadata_cache_ptr; size_t max_size=0, min_clean_size=0, cur_size=0; int cur_num_entries=0; jboolean isCopy; if ( metadata_cache == NULL ) { h5nullArgument( env, "H5Fget_mdc_size: metadata_cache is NULL"); return -1; } size = (int)ENVPTR->GetArrayLength(ENVPAR metadata_cache); if (size < 3) { h5badArgument(env, "H5Fget_mdc_size: length of metadata_cache < 3."); return -1; } ret_val = H5Fget_mdc_size((hid_t)file_id, &max_size, &min_clean_size, &cur_size, &cur_num_entries); if (ret_val < 0) { h5libraryError(env); return -1; } metadata_cache_ptr = ENVPTR->GetLongArrayElements(ENVPAR metadata_cache,&isCopy); metadata_cache_ptr[0] = max_size; metadata_cache_ptr[1] = min_clean_size; metadata_cache_ptr[2] = cur_size; ENVPTR->ReleaseLongArrayElements(ENVPAR metadata_cache, metadata_cache_ptr, 0); return (jint)cur_num_entries; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Freset_mdc_hit_rate_stats * Signature: (I)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Freset_1mdc_1hit_1rate_1stats (JNIEnv *env, jclass cls, jint file_id) { herr_t ret_val = -1; ret_val = H5Freset_mdc_hit_rate_stats((hid_t)file_id); if (ret_val < 0) { h5libraryError(env); } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5export_dataset * Signature: (Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;I)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5export_1dataset (JNIEnv *env, jclass cls, jstring file_export_name, jstring file_name, jstring object_path, jint binary_order) { herr_t status = -1; herr_t ret_val = -1; hid_t file_id = -1; hid_t dataset_id = -1; FILE *stream; char *file_export; char *file; char *object_name; jboolean isCopy; if (file_export_name == NULL) { h5nullArgument(env, "HDF5Library_export_data: file_export_name is NULL"); return; } if (file_name == NULL) { h5nullArgument(env, "HDF5Library_export_data: file_name is NULL"); return; } if (object_path == NULL) { h5nullArgument(env, "HDF5Library_export_data: object_path is NULL"); return; } file = (char *)ENVPTR->GetStringUTFChars(ENVPAR file_name, &isCopy); if (file == NULL) { /* exception -- out of memory? */ h5JNIFatalError( env, "H5Fopen: file name not pinned"); return; } file_id = H5Fopen(file, (unsigned)H5F_ACC_RDWR, (hid_t)H5P_DEFAULT); ENVPTR->ReleaseStringUTFChars(ENVPAR file_name, file); if (file_id < 0) { /* throw exception */ h5libraryError(env); return; } object_name = (char*)ENVPTR->GetStringUTFChars(ENVPAR object_path, &isCopy); if (object_name == NULL) { h5JNIFatalError( env, "H5Dopen: object name not pinned"); return; } dataset_id = H5Dopen2(file_id, (const char*)object_name, (hid_t)H5P_DEFAULT); ENVPTR->ReleaseStringUTFChars(ENVPAR object_path, object_name); if (dataset_id < 0) { H5Fclose(file_id); h5libraryError(env); return; } file_export = (char *)ENVPTR->GetStringUTFChars(ENVPAR file_export_name, 0); stream = fopen(file_export, "w+"); ENVPTR->ReleaseStringUTFChars(ENVPAR file_export_name, file_export); ret_val = h5str_dump_simple_dset(stream, dataset_id, binary_order); if (stream) fclose(stream); H5Dclose(dataset_id); H5Fclose(file_id); if (ret_val < 0) { h5libraryError(env); } } #ifdef __cplusplus } #endif libsis-jhdf5-java-14.12.1/source/c/hdf-java/h5fImp.h000077500000000000000000000114571256564762100216160ustar00rootroot00000000000000/* DO NOT EDIT THIS FILE - it is machine generated */ #include /* Header for class ncsa_hdf_hdf5lib_H5_H5F */ #ifndef _Included_ncsa_hdf_hdf5lib_H5_H5F #define _Included_ncsa_hdf_hdf5lib_H5_H5F #ifdef __cplusplus extern "C" { #endif /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fis_hdf5 * Signature: (Ljava/lang/String;)Z */ JNIEXPORT jboolean JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fis_1hdf5 (JNIEnv *, jclass, jstring); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fcreate * Signature: (Ljava/lang/String;III)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fcreate (JNIEnv *, jclass, jstring, jint, jint, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fopen * Signature: (Ljava/lang/String;II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fopen (JNIEnv *, jclass, jstring, jint, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Freopen * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Freopen (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fflush * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fflush (JNIEnv *, jclass, jint, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fclose * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fclose (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fget_create_plist * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fget_1create_1plist (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fget_access_plist * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fget_1access_1plist (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fget_intent * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fget_1intent (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fget_obj_count * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fget_1obj_1count (JNIEnv *, jclass, jint, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fget_obj_count_long * Signature: (II)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fget_1obj_1count_1long (JNIEnv *, jclass, jint, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fget_obj_count * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fget_1obj_1count (JNIEnv *, jclass, jint, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fget_obj_count_long * Signature: (II)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fget_1obj_1count_1long (JNIEnv *, jclass, jint, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fmount * Signature: (ILjava/lang/String;II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fmount (JNIEnv *, jclass, jint, jstring, jint, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Funmount * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Funmount (JNIEnv *, jclass, jint, jstring); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fget_freespace * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fget_1freespace (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fget_filesize * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fget_1filesize (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fget_mdc_hit_rate * Signature: (I)D */ JNIEXPORT jdouble JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fget_1mdc_1hit_1rate (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fget_mdc_size * Signature: (I[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fget_1mdc_1size (JNIEnv *, jclass, jint, jlongArray); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Freset_mdc_hit_rate_stats * Signature: (I)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Freset_1mdc_1hit_1rate_1stats (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fget_name * Signature: (I)Ljava/lang/String; */ JNIEXPORT jstring JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fget_1name (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fget_name * Signature: (ILjava/lang/String;I)Ljava/lang/String; */ JNIEXPORT jstring JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Fget_2name (JNIEnv *, jclass, jint, jstring, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5export_dataset * Signature: (Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;I)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5export_1dataset (JNIEnv *env, jclass cls, jstring file_export_name, jstring file_name, jstring object_path, jint binary_order); #ifdef __cplusplus } #endif #endif libsis-jhdf5-java-14.12.1/source/c/hdf-java/h5gImp.c000077500000000000000000001156631256564762100216160ustar00rootroot00000000000000/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF Java Products. The full HDF Java copyright * * notice, including terms governing use, modification, and redistribution, * * is contained in the file, COPYING. COPYING can be found at the root of * * the source code distribution tree. You can also access it online at * * http://www.hdfgroup.org/products/licenses.html. If you do not have * * access to the file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /* * This code is the C-interface called by Java programs to access the * Group Object API Functions of the HDF5 library. * * Each routine wraps a single HDF entry point, generally with the * analogous arguments and return codes. * * For details of the HDF libraries, see the HDF Documentation at: * http://hdfdfgroup.org/HDF5/doc/ * */ #ifdef __cplusplus extern "C" { #endif #include #include #include #include #include "hdf5.h" #include "h5jni.h" #include "h5gImp.h" #include "h5util.h" /* missing definitions from hdf5.h */ #ifndef FALSE #define FALSE 0 #endif #ifndef TRUE #define TRUE (!FALSE) #endif #ifdef __cplusplus herr_t obj_info_all(hid_t g_id, const char *name, const H5L_info_t *linfo, void *op_data); herr_t obj_info_max(hid_t g_id, const char *name, const H5L_info_t *linfo, void *op_data); int H5Gget_obj_info_max(hid_t, char **, int *, int *, unsigned long *, int); int H5Gget_obj_info_full( hid_t loc_id, char **objname, int *otype, int *ltype, unsigned long *fno, unsigned long *objno, int indexType, int indexOrder); #else static herr_t obj_info_all(hid_t g_id, const char *name, const H5L_info_t *linfo, void *op_data); static herr_t obj_info_max(hid_t g_id, const char *name, const H5L_info_t *linfo, void *op_data); static int H5Gget_obj_info_max(hid_t, char **, int *, int *, unsigned long *, int); static int H5Gget_obj_info_full( hid_t loc_id, char **objname, int *otype, int *ltype, unsigned long *fno, unsigned long *objno, int indexType, int indexOrder); #endif typedef struct info_all { char **objname; int *otype; int *ltype; unsigned long *objno; unsigned long *fno; unsigned long idxnum; int count; } info_all_t; /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Gcreate * Signature: (ILjava/lang/String;J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Gcreate (JNIEnv *env, jclass clss, jint loc_id, jstring name, jlong size_hint) { hid_t status; char* gName; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Gcreate: name is NULL"); return -1; } gName = (char *)ENVPTR->GetStringUTFChars(ENVPAR name,&isCopy); if (gName == NULL) { h5JNIFatalError( env, "H5Gcreate: file name not pinned"); return -1; } status = H5Gcreate2((hid_t)loc_id, gName, (hid_t)H5P_DEFAULT, (hid_t)H5P_DEFAULT, (hid_t)H5P_DEFAULT ); ENVPTR->ReleaseStringUTFChars(ENVPAR name,gName); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Gopen * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Gopen (JNIEnv *env, jclass clss, jint loc_id, jstring name) { hid_t status; char* gName; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Gopen: name is NULL"); return -1; } gName = (char *)ENVPTR->GetStringUTFChars(ENVPAR name,&isCopy); if (gName == NULL) { h5JNIFatalError( env, "H5Gopen: file name not pinned"); return -1; } status = H5Gopen2((hid_t)loc_id, gName, (hid_t)H5P_DEFAULT ); ENVPTR->ReleaseStringUTFChars(ENVPAR name,gName); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Gclose * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Gclose (JNIEnv *env, jclass clss, jint group_id) { herr_t retVal = H5Gclose((hid_t)group_id) ; if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Glink * Signature: (IILjava/lang/String;Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Glink (JNIEnv *env, jclass clss, jint loc_id, jint link_type, jstring current_name, jstring new_name) { herr_t status; char *cName, *nName; jboolean isCopy; if (current_name == NULL) { h5nullArgument( env, "H5Glink: current_name is NULL"); return -1; } if (new_name == NULL) { h5nullArgument( env, "H5Glink: new_name is NULL"); return -1; } cName = (char *)ENVPTR->GetStringUTFChars(ENVPAR current_name,&isCopy); if (cName == NULL) { h5JNIFatalError( env, "H5Glink: current_name not pinned"); return -1; } nName = (char *)ENVPTR->GetStringUTFChars(ENVPAR new_name,&isCopy); if (nName == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR current_name,cName); h5JNIFatalError( env, "H5Glink: new_name not pinned"); return -1; } status = H5Glink((hid_t)loc_id, (H5G_link_t)link_type, cName, nName); ENVPTR->ReleaseStringUTFChars(ENVPAR new_name,nName); ENVPTR->ReleaseStringUTFChars(ENVPAR current_name,cName); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Glink * Signature: (ILjava/lang/String;IILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Glink2 (JNIEnv *env, jclass clss, jint current_loc_id, jstring current_name, jint link_type, jint new_loc_id, jstring new_name) { herr_t status; char *cName, *nName; jboolean isCopy; if (current_name == NULL) { h5nullArgument( env, "H5Glink2: current_name is NULL"); return -1; } if (new_name == NULL) { h5nullArgument( env, "H5Glink2: new_name is NULL"); return -1; } cName = (char *)ENVPTR->GetStringUTFChars(ENVPAR current_name,&isCopy); if (cName == NULL) { h5JNIFatalError( env, "H5Glink2: current_name not pinned"); return -1; } nName = (char *)ENVPTR->GetStringUTFChars(ENVPAR new_name,&isCopy); if (nName == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR current_name,cName); h5JNIFatalError( env, "H5Glink2: new_name not pinned"); return -1; } status = H5Glink2((hid_t)current_loc_id, cName, (H5G_link_t)link_type, (hid_t)new_loc_id, nName); ENVPTR->ReleaseStringUTFChars(ENVPAR new_name,nName); ENVPTR->ReleaseStringUTFChars(ENVPAR current_name,cName); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gunlink * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Gunlink (JNIEnv *env, jclass clss, jint loc_id, jstring name) { herr_t status; char* gName; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Gunlink: name is NULL"); return -1; } gName = (char *)ENVPTR->GetStringUTFChars(ENVPAR name,&isCopy); if (gName == NULL) { h5JNIFatalError( env, "H5Gunlink: name not pinned"); return -1; } status = H5Gunlink((hid_t)loc_id, gName ); ENVPTR->ReleaseStringUTFChars(ENVPAR name,gName); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gmove * Signature: (ILjava/lang/String;Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Gmove (JNIEnv *env, jclass clss, jint loc_id, jstring src, jstring dst) { herr_t status; char *sName, *dName; jboolean isCopy; if (src == NULL) { h5nullArgument( env, "H5Gmove: src is NULL"); return -1; } if (dst == NULL) { h5nullArgument( env, "H5Gmove: dst is NULL"); return -1; } sName = (char *)ENVPTR->GetStringUTFChars(ENVPAR src,&isCopy); if (sName == NULL) { h5JNIFatalError( env, "H5Gmove: src not pinned"); return -1; } dName = (char *)ENVPTR->GetStringUTFChars(ENVPAR dst,&isCopy); if (dName == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR src,sName); h5JNIFatalError( env, "H5Gmove: dst not pinned"); return -1; } status = H5Gmove((hid_t)loc_id, sName, dName ); ENVPTR->ReleaseStringUTFChars(ENVPAR dst,dName); ENVPTR->ReleaseStringUTFChars(ENVPAR src,sName); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gget_objinfo * Signature: (ILjava/lang/String;Z[J[J[I[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Gget_1objinfo (JNIEnv *env, jclass clss, jint loc_id, jstring name, jboolean follow_link, jlongArray fileno, jlongArray objno, jintArray link_info, jlongArray mtime) { char* gName; jboolean isCopy; herr_t retVal; jint *linkInfo; jlong *fileInfo, *objInfo, *timeInfo; hbool_t follow; H5G_stat_t h5gInfo; if (name == NULL) { h5nullArgument( env, "H5Gget_objinfo: name is NULL"); return -1; } if (follow_link == JNI_TRUE) { follow = TRUE; /* HDF5 'TRUE' */ } else if (follow_link == JNI_FALSE) { follow = FALSE; /* HDF5 'FALSE' */ } else { h5badArgument( env, "H5Gget_objinfo: follow_link is invalid"); return -1; } if (fileno == NULL) { h5nullArgument( env, "H5Gget_objinfo: fileno is NULL"); return -1; } if (ENVPTR->GetArrayLength(ENVPAR fileno) < 2) { h5badArgument( env, "H5Gget_objinfo: fileno input array < 2"); return -1; } if (objno == NULL) { h5nullArgument( env, "H5Gget_objinfo: objno is NULL"); return -1; } if (ENVPTR->GetArrayLength(ENVPAR objno) < 2) { h5badArgument( env, "H5Gget_objinfo: objno input array < 2"); return -1; } if (link_info == NULL) { h5nullArgument( env, "H5Gget_objinfo: link_info is NULL"); return -1; } if (ENVPTR->GetArrayLength(ENVPAR link_info) < 3) { h5badArgument( env, "H5Gget_objinfo: link_info input array < 3"); return -1; } if (mtime == NULL) { h5nullArgument( env, "H5Gget_objinfo: mtime is NULL"); return -1; } gName = (char *)ENVPTR->GetStringUTFChars(ENVPAR name,&isCopy); if (gName == NULL) { h5JNIFatalError( env, "H5Gget_object: name not pinned"); return -1; } fileInfo = (jlong *)ENVPTR->GetLongArrayElements(ENVPAR fileno,&isCopy); if (fileInfo == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR name,gName); h5JNIFatalError( env, "H5Gget_object: fileno not pinned"); return -1; } objInfo = (jlong *)ENVPTR->GetLongArrayElements(ENVPAR objno,&isCopy); if (objInfo == NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR fileno,fileInfo,JNI_ABORT); ENVPTR->ReleaseStringUTFChars(ENVPAR name,gName); h5JNIFatalError( env, "H5Gget_object: objno not pinned"); return -1; } linkInfo = (jint *)ENVPTR->GetIntArrayElements(ENVPAR link_info,&isCopy); if (linkInfo == NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR objno,objInfo,JNI_ABORT); ENVPTR->ReleaseLongArrayElements(ENVPAR fileno,fileInfo,JNI_ABORT); ENVPTR->ReleaseStringUTFChars(ENVPAR name,gName); h5JNIFatalError( env, "H5Gget_object: link_info not pinned"); return -1; } timeInfo = (jlong *)ENVPTR->GetLongArrayElements(ENVPAR mtime,&isCopy); if (timeInfo == NULL) { ENVPTR->ReleaseIntArrayElements(ENVPAR link_info,linkInfo,JNI_ABORT); ENVPTR->ReleaseLongArrayElements(ENVPAR objno,objInfo,JNI_ABORT); ENVPTR->ReleaseLongArrayElements(ENVPAR fileno,fileInfo,JNI_ABORT); ENVPTR->ReleaseStringUTFChars(ENVPAR name,gName); h5JNIFatalError( env, "H5Gget_object: mtime not pinned"); return -1; } retVal = H5Gget_objinfo((hid_t)loc_id, gName, follow, &h5gInfo); if (retVal < 0) { ENVPTR->ReleaseLongArrayElements(ENVPAR mtime,timeInfo,JNI_ABORT); ENVPTR->ReleaseLongArrayElements(ENVPAR objno,objInfo,JNI_ABORT); ENVPTR->ReleaseLongArrayElements(ENVPAR fileno,fileInfo,JNI_ABORT); ENVPTR->ReleaseIntArrayElements(ENVPAR link_info,linkInfo,JNI_ABORT); ENVPTR->ReleaseStringUTFChars(ENVPAR name,gName); h5libraryError(env); return -1; } else { fileInfo[0] = (jlong)h5gInfo.fileno[0]; fileInfo[1] = (jlong)h5gInfo.fileno[1]; objInfo[0] = (jlong)h5gInfo.objno[0]; objInfo[1] = (jlong)h5gInfo.objno[1]; timeInfo[0] = (jlong)h5gInfo.mtime; linkInfo[0] = (jint)h5gInfo.nlink; linkInfo[1] = (jint)h5gInfo.type; linkInfo[2] = (jint)h5gInfo.linklen; ENVPTR->ReleaseLongArrayElements(ENVPAR mtime,timeInfo,0); ENVPTR->ReleaseLongArrayElements(ENVPAR objno,objInfo,0); ENVPTR->ReleaseLongArrayElements(ENVPAR fileno,fileInfo,0); ENVPTR->ReleaseIntArrayElements(ENVPAR link_info,linkInfo,0); ENVPTR->ReleaseStringUTFChars(ENVPAR name,gName); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gget_linkval * Signature: (ILjava/lang/String;I[Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Gget_1linkval (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint size, jobjectArray value) { char* gName; jboolean isCopy; char *lValue; jstring str; herr_t status; if (size < 0) { h5badArgument( env, "H5Gget_linkval: size < 0"); return -1; } if (name == NULL) { h5nullArgument( env, "H5Gget_linkval: name is NULL"); return -1; } lValue = (char *) malloc(sizeof(char)*size); if (lValue == NULL) { h5outOfMemory( env, "H5Gget_linkval: malloc failed "); return -1; } gName = (char *)ENVPTR->GetStringUTFChars(ENVPAR name,&isCopy); if (gName == NULL) { free(lValue); h5JNIFatalError( env, "H5Gget_linkval: name not pinned"); return -1; } status = H5Gget_linkval((hid_t)loc_id, gName, (size_t)size, lValue); ENVPTR->ReleaseStringUTFChars(ENVPAR name,gName); if (status >= 0) { /* may throw OutOfMemoryError */ str = ENVPTR->NewStringUTF(ENVPAR lValue); if (str == NULL) { /* exception -- fatal JNI error */ free(lValue); h5JNIFatalError( env, "H5Gget_linkval: return string not created"); return -1; } /* the SetObjectArrayElement may raise exceptions... */ ENVPTR->SetObjectArrayElement(ENVPAR value,0,(jobject)str); free(lValue); } else { free(lValue); h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gset_comment * Signature: (ILjava/lang/String;Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Gset_1comment (JNIEnv *env, jclass clss, jint loc_id, jstring name, jstring comment) { herr_t status; char *gName, *gComment; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Gset_comment: name is NULL"); return -1; } if (comment == NULL) { h5nullArgument( env, "H5Gset_comment: comment is NULL"); return -1; } gName = (char *)ENVPTR->GetStringUTFChars(ENVPAR name,&isCopy); if (gName == NULL) { h5JNIFatalError( env, "H5Gset_comment: name not pinned"); return -1; } gComment = (char *)ENVPTR->GetStringUTFChars(ENVPAR comment,&isCopy); if (gComment == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR name,gName); h5JNIFatalError( env, "H5Gset_comment: comment not pinned"); return -1; } status = H5Gset_comment((hid_t)loc_id, gName, gComment); ENVPTR->ReleaseStringUTFChars(ENVPAR comment,gComment); ENVPTR->ReleaseStringUTFChars(ENVPAR name,gName); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gget_comment * Signature: (ILjava/lang/String;I[Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Gget_1comment (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint bufsize, jobjectArray comment) { char* gName; jboolean isCopy; char *gComment; jstring str; jint status; if (bufsize <= 0) { h5badArgument( env, "H5Gget_comment: bufsize <= 0"); return -1; } if (name == NULL) { h5nullArgument( env, "H5Gget_comment: name is NULL"); return -1; } if (comment == NULL) { h5nullArgument( env, "H5Gget_comment: comment is NULL"); return -1; } gComment = (char *)malloc(sizeof(char)*bufsize); if (gComment == NULL) { /* exception -- out of memory */ h5outOfMemory( env, "H5Gget_comment: malloc failed"); return -1; } gName = (char *)ENVPTR->GetStringUTFChars(ENVPAR name,&isCopy); if (gName == NULL) { free(gComment); h5JNIFatalError( env, "H5Gget_comment: name not pinned"); return -1; } status = H5Gget_comment((hid_t)loc_id, gName, (size_t)bufsize, gComment); ENVPTR->ReleaseStringUTFChars(ENVPAR name,gName); if (status >= 0) { /* may throw OutOfMemoryError */ str = ENVPTR->NewStringUTF(ENVPAR gComment); if (str == NULL) { free(gComment); h5JNIFatalError( env, "H5Gget_comment: return string not allocated"); return -1; } /* The SetObjectArrayElement may raise exceptions */ ENVPTR->SetObjectArrayElement(ENVPAR comment,0,(jobject)str); free(gComment); } else { free(gComment); h5libraryError(env); } return (jint)status; } /*************************************************************** * New APIs for HDF5.1.8 * ***************************************************************/ /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gget_num_objs * Signature: (I[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Gget_1num_1objs (JNIEnv *env, jclass clss, jint loc_id, jlongArray num_obj) { int status; jlong *num_objP; jboolean isCopy; hsize_t *num_obja; int i; int rank; if (num_obj == NULL) { h5nullArgument( env, "H5Gget_num_objs: num_obj is NULL"); return -1; } num_objP = ENVPTR->GetLongArrayElements(ENVPAR num_obj,&isCopy); if (num_objP == NULL) { h5JNIFatalError(env, "H5Gget_num_objs: num_obj not pinned"); return -1; } rank = (int) ENVPTR->GetArrayLength(ENVPAR num_obj); num_obja = (hsize_t *)malloc( rank * sizeof(hsize_t)); if (num_obja == NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR num_obj,num_objP,JNI_ABORT); h5JNIFatalError(env, "H5Gget_num_objs: num_obj not converted to hsize_t"); return -1; } status = H5Gget_num_objs(loc_id, (hsize_t *)num_obja); if (status < 0) { ENVPTR->ReleaseLongArrayElements(ENVPAR num_obj,num_objP,JNI_ABORT); free(num_obja); h5libraryError(env); return -1; } for (i = 0; i < rank; i++) { num_objP[i] = num_obja[i]; } ENVPTR->ReleaseLongArrayElements(ENVPAR num_obj,num_objP,0); free(num_obja); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gget_objname_by_idx * Signature: (IJ[Ljava/lang/String;J)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Gget_1objname_1by_1idx (JNIEnv *env, jclass clss, jint group_id, jlong idx, jobjectArray name, jlong buf_size) { char *aName; jstring str; hssize_t size; long bs; bs = (long)buf_size; if (bs <= 0) { h5badArgument( env, "H5Gget_objname_by_idx: buf_size <= 0"); return -1; } aName = (char*)malloc(sizeof(char)*bs); if (aName == NULL) { h5outOfMemory(env, "H5Gget_objname_by_idx: malloc failed"); return -1; } size = H5Gget_objname_by_idx((hid_t)group_id, (hsize_t)idx, aName, (size_t)buf_size); if (size < 0) { free(aName); h5libraryError(env); /* exception, returns immediately */ return -1; } /* successful return -- save the string; */ str = ENVPTR->NewStringUTF(ENVPAR aName); if (str == NULL) { free(aName); h5JNIFatalError( env,"H5Gget_objname_by_idx: return string failed"); return -1; } free(aName); /* Note: throws ArrayIndexOutOfBoundsException, ArrayStoreException */ ENVPTR->SetObjectArrayElement(ENVPAR name,0,str); return (jlong)size; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gget_objtype_by_idx * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Gget_1objtype_1by_1idx (JNIEnv *env, jclass clss, jint group_id, jlong idx) { int type; type = H5Gget_objtype_by_idx((hid_t)group_id, (hsize_t)idx ); if (type < 0) { h5libraryError(env); /* exception, returns immediately */ return -1; } return (jint)type; } /* ///////////////////////////////////////////////////////////////////////////////// // // // Add these methods so that we don't need to call H5Gget_objtype_by_idx // in a loop to get information for all the object in a group, which takes // a lot of time to finish if the number of objects is more than 10,000 // ///////////////////////////////////////////////////////////////////////////////// */ /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gget_obj_info_full * Signature: (ILjava/lang/String;[Ljava/lang/String;[I[I[J[JIII)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Gget_1obj_1info_1full (JNIEnv *env, jclass clss, jint loc_id, jstring group_name, jobjectArray objName, jintArray oType, jintArray lType, jlongArray fNo, jlongArray oRef, jint n, jint indx_type, jint indx_order) { herr_t ret_val = -1; char *gName=NULL; char **oName=NULL; jboolean isCopy; jstring str; jint *otarr; jint *ltarr; jlong *refP; jlong *fnoP; unsigned long *refs=NULL; unsigned long *fnos=NULL; int i; int gid = loc_id; int indexType = indx_type; int indexOrder = indx_order; if (group_name != NULL) { gName = (char *)ENVPTR->GetStringUTFChars(ENVPAR group_name,&isCopy); if (gName == NULL) { h5JNIFatalError( env, "H5Gget_obj_info_full: name not pinned"); return -1; } gid = H5Gopen2(loc_id, gName, H5P_DEFAULT); ENVPTR->ReleaseStringUTFChars(ENVPAR group_name,gName); if(gid < 0) { h5JNIFatalError( env, "H5Gget_obj_info_full: could not get group identifier"); return -1; } } if (oType == NULL) { h5nullArgument( env, "H5Gget_obj_info_full: oType is NULL"); return -1; } if (lType == NULL) { h5nullArgument( env, "H5Gget_obj_info_full: lType is NULL"); return -1; } if (oRef == NULL) { h5nullArgument( env, "H5Gget_obj_info_full: oRef is NULL"); return -1; } otarr = ENVPTR->GetIntArrayElements(ENVPAR oType,&isCopy); if (otarr == NULL) { h5JNIFatalError( env, "H5Gget_obj_info_full: otype not pinned"); return -1; } ltarr = ENVPTR->GetIntArrayElements(ENVPAR lType,&isCopy); if (ltarr == NULL) { ENVPTR->ReleaseIntArrayElements(ENVPAR oType,otarr,JNI_ABORT); h5JNIFatalError( env, "H5Gget_obj_info_full: ltype not pinned"); return -1; } refP = ENVPTR->GetLongArrayElements(ENVPAR oRef,&isCopy); fnoP = ENVPTR->GetLongArrayElements(ENVPAR fNo,&isCopy); if (refP == NULL) { ENVPTR->ReleaseIntArrayElements(ENVPAR lType,ltarr,JNI_ABORT); ENVPTR->ReleaseIntArrayElements(ENVPAR oType,otarr,JNI_ABORT); h5JNIFatalError( env, "H5Gget_obj_info_full: type not pinned"); return -1; } oName = (char **)calloc(n, sizeof (*oName)); if (!oName) goto error; refs = (unsigned long *)calloc(n, sizeof (unsigned long)); fnos = (unsigned long *)calloc(n, sizeof (unsigned long)); if (!refs || !fnos) goto error; ret_val = H5Gget_obj_info_full( (hid_t) gid, oName, (int *)otarr, (int *)ltarr, fnos, refs, indexType, indexOrder); if (ret_val < 0) goto error; if (refs) { for (i=0; iNewStringUTF(ENVPAR *(oName+i)); ENVPTR->SetObjectArrayElement(ENVPAR objName,i,(jobject)str); } } /* for (i=0; iReleaseIntArrayElements(ENVPAR lType,ltarr,0); ENVPTR->ReleaseIntArrayElements(ENVPAR oType,otarr,0); ENVPTR->ReleaseLongArrayElements(ENVPAR oRef,refP,0); ENVPTR->ReleaseLongArrayElements(ENVPAR fNo,fnoP,0); if (oName) h5str_array_free(oName, n); if (refs) free(refs); if (fnos) free(fnos); return ret_val; error: if (group_name != NULL) H5Gclose(gid); ENVPTR->ReleaseIntArrayElements(ENVPAR lType,ltarr,JNI_ABORT); ENVPTR->ReleaseIntArrayElements(ENVPAR oType,otarr,JNI_ABORT); ENVPTR->ReleaseLongArrayElements(ENVPAR oRef,refP,JNI_ABORT); ENVPTR->ReleaseLongArrayElements(ENVPAR fNo,fnoP,JNI_ABORT); if (oName) h5str_array_free(oName, n); if (refs) free(refs); if (fnos) free(fnos); h5libraryError(env); return -1; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gget_obj_info_max * Signature: (I[Ljava/lang/String;[I[I[JII)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Gget_1obj_1info_1max (JNIEnv *env, jclass clss, jint loc_id, jobjectArray objName, jintArray oType, jintArray lType, jlongArray oRef, int maxnum, int n) { herr_t ret_val = -1; char **oName=NULL; jboolean isCopy; jstring str; jint *otarr; jint *ltarr; jlong *refP; unsigned long *refs; int i; if (oType == NULL) { h5nullArgument( env, "H5Gget_obj_info_max: oType is NULL"); return -1; } if (lType == NULL) { h5nullArgument( env, "H5Gget_obj_info_max: lType is NULL"); return -1; } if (oRef == NULL) { h5nullArgument( env, "H5Gget_obj_info_all: oRef is NULL"); return -1; } otarr = ENVPTR->GetIntArrayElements(ENVPAR oType,&isCopy); if (otarr == NULL) { h5JNIFatalError( env, "H5Gget_obj_info_max: otype not pinned"); return -1; } ltarr = ENVPTR->GetIntArrayElements(ENVPAR lType,&isCopy); if (ltarr == NULL) { ENVPTR->ReleaseIntArrayElements(ENVPAR oType,otarr,JNI_ABORT); h5JNIFatalError( env, "H5Gget_obj_info_max: ltype not pinned"); return -1; } refP = ENVPTR->GetLongArrayElements(ENVPAR oRef,&isCopy); if (refP == NULL) { ENVPTR->ReleaseIntArrayElements(ENVPAR oType,otarr,JNI_ABORT); ENVPTR->ReleaseIntArrayElements(ENVPAR lType,ltarr,JNI_ABORT); h5JNIFatalError( env, "H5Gget_obj_info_all: type not pinned"); return -1; } oName = (char **)calloc(n, sizeof (*oName)); refs = (unsigned long *)calloc(n, sizeof (unsigned long)); ret_val = H5Gget_obj_info_max( (hid_t) loc_id, oName, (int *)otarr, (int *)ltarr, refs, maxnum ); if (ret_val < 0) { ENVPTR->ReleaseIntArrayElements(ENVPAR lType,ltarr,JNI_ABORT); ENVPTR->ReleaseIntArrayElements(ENVPAR oType,otarr,JNI_ABORT); ENVPTR->ReleaseLongArrayElements(ENVPAR oRef,refP,JNI_ABORT); h5str_array_free(oName, n); free(refs); h5libraryError(env); return -1; } ENVPTR->ReleaseIntArrayElements(ENVPAR lType,ltarr,JNI_ABORT); ENVPTR->ReleaseIntArrayElements(ENVPAR oType,otarr,JNI_ABORT); if (refs) { for (i=0; iReleaseLongArrayElements(ENVPAR oRef,refP,0); if (oName) { for (i=0; iNewStringUTF(ENVPAR *(oName+i)); ENVPTR->SetObjectArrayElement(ENVPAR objName,i,(jobject)str); } } /* for (i=0; iotype+datainfo->count) = -1; *(datainfo->ltype+datainfo->count) = -1; *(datainfo->objname+datainfo->count) = (char *) malloc(strlen(name)+1); strcpy(*(datainfo->objname+datainfo->count), name); *(datainfo->objno+datainfo->count) = -1; } else { *(datainfo->otype+datainfo->count) = object_info.type; *(datainfo->ltype+datainfo->count) = info->type; *(datainfo->objname+datainfo->count) = (char *) malloc(strlen(name)+1); strcpy(*(datainfo->objname+datainfo->count), name); *(datainfo->fno+datainfo->count) = object_info.fileno; *(datainfo->objno+datainfo->count) = (unsigned long)object_info.addr; /* if(info->type==H5L_TYPE_HARD) *(datainfo->objno+datainfo->count) = (unsigned long)info->u.address; else *(datainfo->objno+datainfo->count) = info->u.val_size; */ } datainfo->count++; return 0; } herr_t obj_info_max(hid_t loc_id, const char *name, const H5L_info_t *info, void *op_data) { int type = -1; herr_t retVal = 0; info_all_t* datainfo = (info_all_t*)op_data; H5O_info_t object_info; retVal = H5Oget_info(loc_id, &object_info); if ( retVal < 0) { *(datainfo->otype+datainfo->count) = -1; *(datainfo->ltype+datainfo->count) = -1; *(datainfo->objname+datainfo->count) = NULL; *(datainfo->objno+datainfo->count) = -1; return 1; } else { *(datainfo->otype+datainfo->count) = object_info.type; *(datainfo->ltype+datainfo->count) = info->type; /* this will be freed by h5str_array_free(oName, n)*/ *(datainfo->objname+datainfo->count) = (char *) malloc(strlen(name)+1); strcpy(*(datainfo->objname+datainfo->count), name); if(info->type==H5L_TYPE_HARD) *(datainfo->objno+datainfo->count) = (unsigned long)info->u.address; else *(datainfo->objno+datainfo->count) = info->u.val_size; } datainfo->count++; if(datainfo->count < (int)datainfo->idxnum) return 0; else return 1; } /* * Create a java object of hdf.h5.structs.H5G_info_t * public class H5G_info_t { * public H5G_STORAGE_TYPE storage_type; // Type of storage for links in group * public long nlinks; // Number of links in group * public long max_corder; // Current max. creation order value for group * public int mounted; // Whether group has a file mounted on it * } * */ jobject create_H5G_info_t(JNIEnv *env, H5G_info_t group_info) { jclass cls; jboolean jmounted; jint storage_type; jobject obj; jfieldID fid_storage_type, fid_nlinks, fid_max_corder, fid_mounted; cls = ENVPTR->FindClass(ENVPAR "ncsa/hdf/hdf5lib/structs/H5G_info_t"); if (cls == NULL) return NULL; obj = ENVPTR->AllocObject(ENVPAR cls); if (obj == NULL) return NULL; fid_storage_type = ENVPTR->GetFieldID(ENVPAR cls, "storage_type", "I"); fid_nlinks = ENVPTR->GetFieldID(ENVPAR cls, "nlinks", "J"); fid_max_corder = ENVPTR->GetFieldID(ENVPAR cls, "max_corder", "J"); fid_mounted = ENVPTR->GetFieldID(ENVPAR cls, "mounted", "Z"); if (fid_storage_type==NULL || fid_nlinks==NULL || fid_max_corder==NULL || fid_mounted == NULL) return NULL; jmounted = (group_info.mounted==0) ? JNI_FALSE : JNI_TRUE; storage_type = (jint)group_info.storage_type; ENVPTR->SetIntField(ENVPAR obj, fid_storage_type, (jint)storage_type); ENVPTR->SetLongField(ENVPAR obj, fid_nlinks, (jlong)group_info.nlinks); ENVPTR->SetLongField(ENVPAR obj, fid_max_corder, (jlong)group_info.max_corder); ENVPTR->SetBooleanField(ENVPAR obj, fid_mounted, jmounted); return obj; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Gcreate2 * Signature: (ILjava/lang/String;III)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Gcreate2 (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint link_plist_id, jint create_plist_id, jint access_plist_id) { hid_t status; char* gName; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Gcreate: name is NULL"); return -1; } gName = (char *)ENVPTR->GetStringUTFChars(ENVPAR name,&isCopy); if (gName == NULL) { h5JNIFatalError( env, "H5Gcreate: file name not pinned"); return -1; } status = H5Gcreate2((hid_t)loc_id, gName, link_plist_id, create_plist_id, access_plist_id ); ENVPTR->ReleaseStringUTFChars(ENVPAR name,gName); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Gcreate_anon * Signature: (III)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Gcreate_1anon (JNIEnv *env, jclass cls, jint loc_id, jint gcpl_id, jint gapl_id) { hid_t ret_val; ret_val = H5Gcreate_anon((hid_t)loc_id, (hid_t)gcpl_id, (hid_t)gapl_id); if (ret_val < 0) { h5libraryError(env); } return (jint)ret_val; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Gopen2 * Signature: (ILjava/lang/String;I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Gopen2 (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint access_plist_id) { hid_t status; char* gName; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Gopen: name is NULL"); return -1; } gName = (char *)ENVPTR->GetStringUTFChars(ENVPAR name,&isCopy); if (gName == NULL) { h5JNIFatalError( env, "H5Gopen: file name not pinned"); return -1; } status = H5Gopen2((hid_t)loc_id, gName, (hid_t)access_plist_id ); ENVPTR->ReleaseStringUTFChars(ENVPAR name,gName); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gget_create_plist * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Gget_1create_1plist (JNIEnv *env, jclass cls, jint loc_id) { hid_t ret_val; ret_val = H5Gget_create_plist((hid_t)loc_id); if (ret_val < 0) { h5libraryError(env); } return (jint)ret_val; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gget_info * Signature: (I)Lncsa/hdf/hdf5lib/structs/H5G_info_t; */ JNIEXPORT jobject JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Gget_1info (JNIEnv *env, jclass cls, jint loc_id) { H5G_info_t group_info; herr_t ret_val = -1; ret_val = H5Gget_info( (hid_t) loc_id, &group_info); if (ret_val < 0) { h5libraryError(env); return NULL; } return create_H5G_info_t(env, group_info); } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gget_info_by_name * Signature: (ILjava/lang/String;I)Lncsa/hdf/hdf5lib/structs/H5G_info_t; */ JNIEXPORT jobject JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Gget_1info_1by_1name (JNIEnv *env, jclass cls, jint loc_id, jstring name, jint lapl_id) { H5G_info_t group_info; herr_t ret_val = -1; char* gName; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Gget_info_by_name: name is NULL"); return NULL; } gName = (char *)ENVPTR->GetStringUTFChars(ENVPAR name,&isCopy); if (gName == NULL) { h5JNIFatalError( env, "H5Gget_info_by_name: file name not pinned"); return NULL; } ret_val = H5Gget_info_by_name((hid_t)loc_id, gName, &group_info, (hid_t)lapl_id); ENVPTR->ReleaseStringUTFChars(ENVPAR name,gName); if (ret_val < 0) { h5libraryError(env); return NULL; } return create_H5G_info_t(env, group_info); } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gget_info_by_idx * Signature: (ILjava/lang/String;IIJI)Lncsa/hdf/hdf5lib/structs/H5G_info_t; */ JNIEXPORT jobject JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Gget_1info_1by_1idx (JNIEnv *env, jclass cls, jint loc_id, jstring name, jint index_type, jint order, jlong n, jint lapl_id) { H5G_info_t group_info; herr_t ret_val = -1; char* gName; jboolean isCopy; H5_index_t cindex_type = (H5_index_t)index_type; H5_iter_order_t corder = (H5_iter_order_t)order; if (name == NULL) { h5nullArgument( env, "H5Gget_info_by_idx: name is NULL"); return NULL; } gName = (char *)ENVPTR->GetStringUTFChars(ENVPAR name,&isCopy); if (gName == NULL) { h5JNIFatalError( env, "H5Gget_info_by_idx: file name not pinned"); return NULL; } ret_val = H5Gget_info_by_idx((hid_t)loc_id, gName, cindex_type, corder, (hsize_t)n, &group_info, (hid_t)lapl_id); ENVPTR->ReleaseStringUTFChars(ENVPAR name,gName); if (ret_val < 0) { h5libraryError(env); return NULL; } return create_H5G_info_t(env, group_info); } #ifdef __cplusplus } #endif libsis-jhdf5-java-14.12.1/source/c/hdf-java/h5gImp.h000066400000000000000000000130311256564762100216020ustar00rootroot00000000000000/* DO NOT EDIT THIS FILE - it is machine generated */ #include /* Header for class ncsa_hdf_hdf5lib_H5_H5G */ #ifndef _Included_ncsa_hdf_hdf5lib_H5_H5G #define _Included_ncsa_hdf_hdf5lib_H5_H5G #ifdef __cplusplus extern "C" { #endif /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Gclose * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Gclose (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Gcreate2 * Signature: (ILjava/lang/String;III)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Gcreate2 (JNIEnv *, jclass, jint, jstring, jint, jint, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Gcreate_anon * Signature: (III)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Gcreate_1anon (JNIEnv *, jclass, jint, jint, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Gopen2 * Signature: (ILjava/lang/String;I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Gopen2 (JNIEnv *, jclass, jint, jstring, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Glink * Signature: (ILjava/lang/String;IILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Glink2 (JNIEnv *env, jclass clss, jint current_loc_id, jstring current_name, jint link_type, jint new_loc_id, jstring new_name); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gunlink * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Gunlink (JNIEnv *env, jclass clss, jint loc_id, jstring name); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gget_comment * Signature: (ILjava/lang/String;I[Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Gget_1comment (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint bufsize, jobjectArray comment); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gset_comment * Signature: (ILjava/lang/String;Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Gset_1comment (JNIEnv *env, jclass clss, jint loc_id, jstring name, jstring comment); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gget_linkval * Signature: (ILjava/lang/String;I[Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Gget_1linkval (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint size, jobjectArray value); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gmove * Signature: (ILjava/lang/String;Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Gmove (JNIEnv *env, jclass clss, jint loc_id, jstring src, jstring dst); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gget_objinfo * Signature: (ILjava/lang/String;Z[J[J[I[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Gget_1objinfo (JNIEnv *env, jclass clss, jint loc_id, jstring name, jboolean follow_link, jlongArray fileno, jlongArray objno, jintArray link_info, jlongArray mtime); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gget_num_objs * Signature: (I[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Gget_1num_1objs (JNIEnv *env, jclass clss, jint loc_id, jlongArray num_obj); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gget_create_plist * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Gget_1create_1plist (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gget_info * Signature: (I)Lncsa/hdf/hdf5lib/structs/H5G_info_t; */ JNIEXPORT jobject JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Gget_1info (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gget_info_by_name * Signature: (ILjava/lang/String;I)Lncsa/hdf/hdf5lib/structs/H5G_info_t; */ JNIEXPORT jobject JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Gget_1info_1by_1name (JNIEnv *, jclass, jint, jstring, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gget_info_by_idx * Signature: (ILjava/lang/String;IIJI)Lncsa/hdf/hdf5lib/structs/H5G_info_t; */ JNIEXPORT jobject JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Gget_1info_1by_1idx (JNIEnv *, jclass, jint, jstring, jint, jint, jlong, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Gcreate * Signature: (ILjava/lang/String;J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Gcreate (JNIEnv *, jclass, jint, jstring, jlong); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Gopen * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Gopen (JNIEnv *, jclass, jint, jstring); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Glink * Signature: (IILjava/lang/String;Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Glink (JNIEnv *env, jclass clss, jint loc_id, jint link_type, jstring current_name, jstring new_name); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gget_obj_info_full * Signature: (ILjava/lang/String;[Ljava/lang/String;[I[I[JIII)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Gget_1obj_1info_1full (JNIEnv *env, jclass clss, jint loc_id, jstring group_name, jobjectArray objName, jintArray oType, jintArray lType, jlongArray fNo, jlongArray oRef, jint n, jint indx_type, jint indx_order); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gget_obj_info_max * Signature: (I[Ljava/lang/String;[I[I[JII)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Gget_1obj_1info_1max (JNIEnv *env, jclass clss, jint loc_id, jobjectArray objName, jintArray oType, jintArray lType, jlongArray oRef, int maxnum, int n); #ifdef __cplusplus } #endif #endif libsis-jhdf5-java-14.12.1/source/c/hdf-java/h5iImp.c000077500000000000000000000132571256564762100216140ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ /* * This code is the C-interface called by Java programs to access the * Identifier API Functions of the HDF5 library. * * Each routine wraps a single HDF entry point, generally with the * analogous arguments and return codes. * * For details of the HDF libraries, see the HDF Documentation at: * http://hdf.ncsa.uiuc.edu/HDF5/doc/ * */ #ifdef __cplusplus extern "C" { #endif #include "hdf5.h" #include #include #include "h5jni.h" /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Iget_type * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Iget_1type (JNIEnv *env, jclass clss, jint obj_id) { H5I_type_t retVal = H5I_BADID; retVal = H5Iget_type((hid_t)obj_id); if (retVal == H5I_BADID) { h5libraryError(env); } return (jint)retVal; } /********************************************************************** * * * New functions release 1.6.2 versus release 1.6.1 * * * **********************************************************************/ /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Iget_name * Signature: (ILjava/lang/String;J)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Iget_1name (JNIEnv *env, jclass clss, jint obj_id, jobjectArray name, jlong buf_size) { char *aName; jstring str; hssize_t size; long bs; bs = (long)buf_size; if (bs <= 0) { h5badArgument( env, "H5Iget_name: buf_size <= 0"); return -1; } aName = (char*)malloc(sizeof(char)*bs); if (aName == NULL) { h5outOfMemory( env, "H5Iget_name: malloc failed"); return -1; } size = H5Iget_name((hid_t)obj_id, aName, (size_t)buf_size); if (size < 0) { free(aName); h5libraryError(env); return -1; /* exception, returns immediately */ } /* successful return -- save the string; */ str = ENVPTR->NewStringUTF(ENVPAR aName); ENVPTR->SetObjectArrayElement(ENVPAR name,0,str); free(aName); return (jlong)size; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Iget_ref * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Iget_1ref (JNIEnv *env, jclass clss, jint obj_id) { int retVal = -1; retVal = H5Iget_ref( (hid_t)obj_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Iinc_ref * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Iinc_1ref (JNIEnv *env, jclass clss, jint obj_id) { int retVal = -1; retVal = H5Iinc_ref( (hid_t)obj_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Idec_1ref * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Idec_1ref (JNIEnv *env, jclass clss, jint obj_id) { int retVal = -1; retVal = H5Idec_ref( (hid_t)obj_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /********************************************************************** * * * New functions release 1.6.3 versus release 1.6.2 * * * **********************************************************************/ /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Iget_file_id * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Iget_1file_1id (JNIEnv *env, jclass clss, jint obj_id) { hid_t file_id = 0; file_id = H5Iget_file_id ((hid_t) obj_id); if (file_id < 0) { h5libraryError(env); } return (jint) file_id; } /********************************************************************** * * * New functions release 1.8.0 * * * **********************************************************************/ /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Iget_type_ref * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Iget_1type_1ref (JNIEnv *env, jclass clss, jint type) { int retVal; retVal = H5Iget_type_ref((H5I_type_t)type); if (retVal <0){ h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Inmembers * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Inmembers (JNIEnv *env, jclass clss, jint type) { herr_t retVal; hsize_t num_members; retVal = H5Inmembers((H5I_type_t)type, &num_members); if (retVal <0){ h5libraryError(env); } return (jint)num_members; } #ifdef __cplusplus } #endif libsis-jhdf5-java-14.12.1/source/c/hdf-java/h5jni.h000077500000000000000000000036271256564762100215030ustar00rootroot00000000000000/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF Java Products. The full HDF Java copyright * * notice, including terms governing use, modification, and redistribution, * * is contained in the file, COPYING. COPYING can be found at the root of * * the source code distribution tree. You can also access it online at * * http://www.hdfgroup.org/products/licenses.html. If you do not have * * access to the file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #include "H5version.h" #include #ifndef _Included_h5jni #define _Included_h5jni #ifdef __cplusplus #define ENVPTR (env) #define ENVPAR #define ENVONLY #else #define ENVPTR (*env) #define ENVPAR env, #define ENVONLY env #endif #ifdef __cplusplus extern "C" { #endif extern jboolean h5JNIFatalError(JNIEnv *, char *); extern jboolean h5nullArgument(JNIEnv *, char *); extern jboolean h5badArgument (JNIEnv *, char *); extern jboolean h5outOfMemory (JNIEnv *, char *); extern jboolean h5libraryError(JNIEnv *env ); extern jboolean h5raiseException(JNIEnv *, char *, char *); extern jboolean h5unimplemented( JNIEnv *env, char *functName); /* implemented at H5.c */ extern jint get_enum_value(JNIEnv *env, jobject enum_obj); extern jobject get_enum_object(JNIEnv *env, const char* enum_class_name, jint enum_val, const char* enum_field_desc); /* implemented at H5G.c */ extern jobject create_H5G_info_t(JNIEnv *env, H5G_info_t group_info); #ifdef __cplusplus } #endif #endif libsis-jhdf5-java-14.12.1/source/c/hdf-java/h5lImp.c000077500000000000000000001064051256564762100216150ustar00rootroot00000000000000/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF Java Products. The full HDF Java copyright * * notice, including terms governing use, modification, and redistribution, * * is contained in the file, COPYING. COPYING can be found at the root of * * the source code distribution tree. You can also access it online at * * http://www.hdfgroup.org/products/licenses.html. If you do not have * * access to the file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /* * This code is the C-interface called by Java programs to access the * Link Object API Functions of the HDF5 library. * * Each routine wraps a single HDF entry point, generally with the * analogous arguments and return codes. * * For details of the HDF libraries, see the HDF Documentation at: * http://hdfdfgroup.org/HDF5/doc/ * */ #ifdef __cplusplus extern "C" { #endif #include #include #include "hdf5.h" #include "h5jni.h" #include "h5lImp.h" #ifdef __cplusplus #define CBENVPTR (cbenv) #define CBENVPAR #define JVMPTR (jvm) #define JVMPAR #define JVMPAR2 #else #define CBENVPTR (*cbenv) #define CBENVPAR cbenv, #define JVMPTR (*jvm) #define JVMPAR jvm #define JVMPAR2 jvm, #endif /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lcopy * Signature: (ILjava/lang/String;ILjava/lang/String;II)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Lcopy (JNIEnv *env, jclass clss, jint cur_loc_id, jstring cur_name, jint dst_loc_id, jstring dst_name, jint create_id, jint access_id) { char *lCurName; char *lDstName; jboolean isCopy; herr_t status = -1; if (cur_name == NULL) { h5nullArgument(env, "H5Lcopy: cur_name is NULL"); return; } lCurName = (char*)ENVPTR->GetStringUTFChars(ENVPAR cur_name, &isCopy); if (lCurName == NULL) { h5JNIFatalError(env, "H5Lcopy: cur_name not pinned"); return; } if (dst_name == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR cur_name, lCurName); h5nullArgument(env, "H5Lcopy: dst_name is NULL"); return; } lDstName = (char*)ENVPTR->GetStringUTFChars(ENVPAR dst_name, &isCopy); if (lDstName == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR cur_name, lCurName); h5JNIFatalError(env, "H5Lcopy: dst_name not pinned"); return; } status = H5Lcopy((hid_t)cur_loc_id, (const char*)lCurName, (hid_t)dst_loc_id, (const char*)lDstName, (hid_t)create_id, (hid_t)access_id); ENVPTR->ReleaseStringUTFChars(ENVPAR cur_name, lCurName); ENVPTR->ReleaseStringUTFChars(ENVPAR dst_name, lDstName); if (status < 0) { h5libraryError(env); return; } return; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lcreate_external * Signature: (Ljava/lang/String;Ljava/lang/String;ILjava/lang/String;II)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Lcreate_1external (JNIEnv *env, jclass clss, jstring file_name, jstring cur_name, jint dst_loc_id, jstring dst_name, jint create_id, jint access_id) { char *lFileName; char *lCurName; char *lDstName; jboolean isCopy; herr_t status = -1; if (file_name == NULL) { h5nullArgument(env, "H5Lcreate_external: file_name is NULL"); return; } lFileName = (char*)ENVPTR->GetStringUTFChars(ENVPAR file_name, &isCopy); if (lFileName == NULL) { h5JNIFatalError(env, "H5Lcreate_external: file_name not pinned"); return; } if (cur_name == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR file_name, lFileName); h5nullArgument(env, "H5Lcreate_external: cur_name is NULL"); return; } lCurName = (char*)ENVPTR->GetStringUTFChars(ENVPAR cur_name,&isCopy); if (lCurName == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR file_name, lFileName); h5JNIFatalError(env, "H5Lcreate_external: cur_name not pinned"); return; } if (dst_name == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR file_name, lFileName); ENVPTR->ReleaseStringUTFChars(ENVPAR cur_name, lCurName); h5nullArgument(env, "H5Lcreate_external: dst_name is NULL"); return; } lDstName = (char*)ENVPTR->GetStringUTFChars(ENVPAR dst_name, &isCopy); if (lDstName == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR file_name, lFileName); ENVPTR->ReleaseStringUTFChars(ENVPAR cur_name, lCurName); h5JNIFatalError(env, "H5Lcreate_external: dst_name not pinned"); return; } status = H5Lcreate_external((const char*)lFileName, (const char*)lCurName, (hid_t)dst_loc_id, (const char*)lDstName, (hid_t)create_id, (hid_t)access_id); ENVPTR->ReleaseStringUTFChars(ENVPAR file_name, lFileName); ENVPTR->ReleaseStringUTFChars(ENVPAR cur_name, lCurName); ENVPTR->ReleaseStringUTFChars(ENVPAR dst_name, lDstName); if (status < 0) { h5libraryError(env); return; } return; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lcreate_hard * Signature: (ILjava/lang/String;ILjava/lang/String;II)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Lcreate_1hard (JNIEnv *env, jclass clss, jint cur_loc_id, jstring cur_name, jint dst_loc_id, jstring dst_name, jint create_id, jint access_id) { char *lCurName; char *lDstName; jboolean isCopy; herr_t status = -1; if (cur_name == NULL) { h5nullArgument(env, "H5Lcreate_hard: cur_name is NULL"); return; } lCurName = (char*)ENVPTR->GetStringUTFChars(ENVPAR cur_name, &isCopy); if (lCurName == NULL) { h5JNIFatalError(env, "H5Lcreate_hard: cur_name not pinned"); return; } if (dst_name == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR cur_name, lCurName); h5nullArgument(env, "H5Lcreate_hard: dst_name is NULL"); return; } lDstName = (char*)ENVPTR->GetStringUTFChars(ENVPAR dst_name, &isCopy); if (lDstName == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR cur_name, lCurName); h5JNIFatalError(env, "H5Lcreate_hard: dst_name not pinned"); return; } status = H5Lcreate_hard((hid_t)cur_loc_id, (const char*)lCurName, (hid_t)dst_loc_id, (const char*)lDstName, (hid_t)create_id, (hid_t)access_id); ENVPTR->ReleaseStringUTFChars(ENVPAR cur_name, lCurName); ENVPTR->ReleaseStringUTFChars(ENVPAR dst_name, lDstName); if (status < 0) { h5libraryError(env); return; } return; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lcreate_soft * Signature: (Ljava/lang/String;ILjava/lang/String;II)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Lcreate_1soft (JNIEnv *env, jclass clss, jstring cur_name, jint dst_loc_id, jstring dst_name, jint create_id, jint access_id) { char *lCurName; char *lDstName; jboolean isCopy; herr_t status = -1; if (cur_name == NULL) { h5nullArgument(env, "H5Lcreate_soft: cur_name is NULL"); return; } lCurName = (char*)ENVPTR->GetStringUTFChars(ENVPAR cur_name, &isCopy); if (lCurName == NULL) { h5JNIFatalError(env, "H5Lcreate_soft: cur_name not pinned"); return; } if (dst_name == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR cur_name, lCurName); h5nullArgument(env, "H5Lcreate_soft: dst_name is NULL"); return; } lDstName = (char*)ENVPTR->GetStringUTFChars(ENVPAR dst_name,&isCopy); if (lDstName == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR cur_name, lCurName); h5JNIFatalError(env, "H5Lcreate_soft: dst_name not pinned"); return; } status = H5Lcreate_soft((const char*)lCurName, (hid_t)dst_loc_id, (const char*)lDstName, (hid_t)create_id, (hid_t)access_id); ENVPTR->ReleaseStringUTFChars(ENVPAR cur_name, lCurName); ENVPTR->ReleaseStringUTFChars(ENVPAR dst_name, lDstName); if (status < 0) { h5libraryError(env); return; } return; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Ldelete * Signature: (ILjava/lang/String;I)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Ldelete (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint access_id) { char *lName; jboolean isCopy; herr_t status = -1; if (name == NULL) { h5nullArgument(env, "H5Ldelete: name is NULL"); return; } lName = (char*)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (lName == NULL) { h5JNIFatalError(env, "H5Ldelete: name not pinned"); return; } status = H5Ldelete((hid_t)loc_id, (const char*)lName, (hid_t)access_id); ENVPTR->ReleaseStringUTFChars(ENVPAR name, lName); if (status < 0) { h5libraryError(env); return; } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Ldelete_by_idx * Signature: (ILjava/lang/String;IIJI)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Ldelete_1by_1idx (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint index_field, jint order, jlong link_n, jint access_id) { char *lName; herr_t status; jboolean isCopy; if (name == NULL) { h5nullArgument(env, "H5Ldelete_by_idx: name is NULL"); return; } lName = (char*)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (lName == NULL) { h5JNIFatalError(env, "H5Ldelete_by_idx: name not pinned"); return; } status = H5Ldelete_by_idx((hid_t)loc_id, (const char*)lName, (H5_index_t)index_field, (H5_iter_order_t)order, (hsize_t)link_n, (hid_t)access_id); ENVPTR->ReleaseStringUTFChars(ENVPAR name, lName); if (status < 0) { h5libraryError(env); return; } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lexists * Signature: (ILjava/lang/String;I)Z */ JNIEXPORT jboolean JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Lexists (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint access_id) { char *lName; jboolean isCopy; htri_t bval = 0; if (name == NULL) { h5nullArgument(env, "H5Lexists: name is NULL"); return JNI_FALSE; } lName = (char*)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (lName == NULL) { h5JNIFatalError(env, "H5Lexists: name not pinned"); return JNI_FALSE; } bval = H5Lexists((hid_t)loc_id, (const char*)lName, (hid_t)access_id); ENVPTR->ReleaseStringUTFChars(ENVPAR name, lName); if (bval > 0) { return JNI_TRUE; } else if (bval == 0) { return JNI_FALSE; } else { h5libraryError(env); return JNI_FALSE; } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lget_info * Signature: (ILjava/lang/String;I)Lncsa/hdf/hdf5lib/structs/H5L_info_t; */ JNIEXPORT jobject JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Lget_1info (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint access_id) { char *lName; herr_t status; H5L_info_t infobuf; jboolean isCopy; jclass cls; jmethodID constructor; jvalue args[5]; jobject ret_info_t = NULL; if (name == NULL) { h5nullArgument(env, "H5Lget_info: name is NULL"); return NULL; } lName = (char*)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (lName == NULL) { h5JNIFatalError(env, "H5Lget_info: name not pinned"); return NULL; } status = H5Lget_info((hid_t)loc_id, (const char*)lName, (H5L_info_t*)&infobuf, (hid_t)access_id); ENVPTR->ReleaseStringUTFChars(ENVPAR name, lName); if (status < 0) { h5libraryError(env); return NULL; } // get a reference to your class if you don't have it already cls = ENVPTR->FindClass(ENVPAR "ncsa/hdf/hdf5lib/structs/H5L_info_t"); if (cls == 0) { h5JNIFatalError( env, "JNI error: GetObjectClass failed\n"); return NULL; } // get a reference to the constructor; the name is constructor = ENVPTR->GetMethodID(ENVPAR cls, "", "(IZJIJ)V"); if (constructor == 0) { h5JNIFatalError( env, "JNI error: GetMethodID failed\n"); return NULL; } args[0].i = infobuf.type; args[1].z = infobuf.corder_valid; args[2].j = infobuf.corder; args[3].i = infobuf.cset; if(infobuf.type==0) args[4].j = infobuf.u.address; else args[4].j = infobuf.u.val_size; ret_info_t = ENVPTR->NewObjectA(ENVPAR cls, constructor, args); return ret_info_t; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lget_info_by_idx * Signature: (ILjava/lang/String;IIJI)Lncsa/hdf/hdf5lib/structs/H5L_info_t; */ JNIEXPORT jobject JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Lget_1info_1by_1idx (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint index_field, jint order, jlong link_n, jint access_id) { char *lName; herr_t status; H5L_info_t infobuf; jboolean isCopy; jclass cls; jmethodID constructor; jvalue args[5]; jobject ret_info_t = NULL; if (name == NULL) { h5nullArgument(env, "H5Lget_info_by_idx: name is NULL"); return NULL; } lName = (char*)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (lName == NULL) { h5JNIFatalError(env, "H5Lget_info_by_idx: name not pinned"); return NULL; } status = H5Lget_info_by_idx((hid_t)loc_id, (const char*)lName, (H5_index_t)index_field, (H5_iter_order_t)order, (hsize_t)link_n, (H5L_info_t*)&infobuf, (hid_t)access_id); ENVPTR->ReleaseStringUTFChars(ENVPAR name, lName); if (status < 0) { h5libraryError(env); return NULL; } // get a reference to your class if you don't have it already cls = ENVPTR->FindClass(ENVPAR "ncsa/hdf/hdf5lib/structs/H5L_info_t"); if (cls == 0) { h5JNIFatalError(env, "JNI error: GetObjectClass failed\n"); return NULL; } // get a reference to the constructor; the name is constructor = ENVPTR->GetMethodID(ENVPAR cls, "", "(IZJIJ)V"); if (constructor == 0) { h5JNIFatalError(env, "JNI error: GetMethodID failed\n"); return NULL; } args[0].i = infobuf.type; args[1].z = infobuf.corder_valid; args[2].j = infobuf.corder; args[3].i = infobuf.cset; if(infobuf.type==0) args[4].j = infobuf.u.address; else args[4].j = infobuf.u.val_size; ret_info_t = ENVPTR->NewObjectA(ENVPAR cls, constructor, args); return ret_info_t; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lget_name_by_idx * Signature: (ILjava/lang/String;IIJI)Ljava/lang/String; */ JNIEXPORT jobject JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Lget_1name_1by_1idx (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint index_field, jint order, jlong link_n, jint access_id) { size_t buf_size; char *lName; char *lValue; jboolean isCopy; jlong status_size; jstring str = NULL; if (name == NULL) { h5nullArgument(env, "H5Lget_name_by_idx: name is NULL"); return NULL; } lName = (char*)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (lName == NULL) { h5JNIFatalError(env, "H5Lget_name_by_idx: name not pinned"); return NULL; } /* get the length of the link name */ status_size = H5Lget_name_by_idx((hid_t)loc_id, (const char*)lName, (H5_index_t)index_field, (H5_iter_order_t)order, (hsize_t)link_n, (char*)NULL, (size_t)0, (hid_t)H5P_DEFAULT); if(status_size < 0) { ENVPTR->ReleaseStringUTFChars(ENVPAR name, lName); h5libraryError(env); return NULL; } buf_size = (size_t)status_size + 1;/* add extra space for the null terminator */ lValue = (char*)malloc(sizeof(char) * buf_size); if (lValue == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR name, lName); h5outOfMemory(env, "H5Lget_name_by_idx: malloc failed "); return NULL; } status_size = H5Lget_name_by_idx((hid_t)loc_id, (const char*)lName, (H5_index_t)index_field, (H5_iter_order_t)order, (hsize_t)link_n, (char*)lValue, (size_t)buf_size, (hid_t)access_id); ENVPTR->ReleaseStringUTFChars(ENVPAR name, lName); if (status_size < 0) { free(lValue); h5libraryError(env); return NULL; } /* may throw OutOfMemoryError */ str = ENVPTR->NewStringUTF(ENVPAR lValue); if (str == NULL) { /* exception -- fatal JNI error */ free(lValue); h5JNIFatalError(env, "H5Lget_name_by_idx: return string not created"); return NULL; } free(lValue); return str; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lget_val * Signature: (ILjava/lang/String;[Ljava/lang/String;I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Lget_1val (JNIEnv *env, jclass clss, jint loc_id, jstring name, jobjectArray link_value, jint access_id) { size_t buf_size; herr_t status; H5L_info_t infobuf; char *lName; char *lValue; const char *file_name; const char *obj_name; jboolean isCopy; jstring str; if (name == NULL) { h5nullArgument(env, "H5Lget_val: name is NULL"); return -1; } lName = (char*)ENVPTR->GetStringUTFChars(ENVPAR name,&isCopy); if (lName == NULL) { h5JNIFatalError(env, "H5Lget_val: name not pinned"); return -1; } /* get the length of the link val */ status = H5Lget_info((hid_t)loc_id, (const char*)lName, (H5L_info_t*)&infobuf, (hid_t)H5P_DEFAULT); if(status < 0) { ENVPTR->ReleaseStringUTFChars(ENVPAR name, lName); h5libraryError(env); return -1; } buf_size = infobuf.u.val_size + 1;/* add extra space for the null terminator */ if(infobuf.type == H5L_TYPE_HARD) { ENVPTR->ReleaseStringUTFChars(ENVPAR name, lName); h5JNIFatalError(env, "H5Lget_val: link is hard type"); return -1; } lValue = (char*)malloc(sizeof(char) * buf_size); if (lValue == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR name, lName); h5outOfMemory(env, "H5Lget_val: malloc failed"); return -1; } status = H5Lget_val((hid_t)loc_id, (const char*)lName, (void*)lValue, (size_t)buf_size, (hid_t)access_id); ENVPTR->ReleaseStringUTFChars(ENVPAR name, lName); if (status < 0) { free(lValue); h5libraryError(env); return -1; } /* may throw OutOfMemoryError */ if(infobuf.type == H5L_TYPE_EXTERNAL) { status = H5Lunpack_elink_val((char*)lValue, (size_t)infobuf.u.val_size, (unsigned*)NULL, (const char**)&file_name, (const char**)&obj_name); if (status < 0) { free(lValue); h5libraryError(env); return -1; } str = ENVPTR->NewStringUTF(ENVPAR obj_name); if (str == NULL) { /* exception -- fatal JNI error */ free(lValue); h5JNIFatalError(env, "H5Lget_val: return string not created"); return -1; } ENVPTR->SetObjectArrayElement(ENVPAR link_value, 0, str); str = ENVPTR->NewStringUTF(ENVPAR file_name); if (str == NULL) { /* exception -- fatal JNI error */ free(lValue); h5JNIFatalError(env, "H5Lget_val: return string not created"); return -1; } ENVPTR->SetObjectArrayElement(ENVPAR link_value, 1, str); } else { str = ENVPTR->NewStringUTF(ENVPAR lValue); if (str == NULL) { /* exception -- fatal JNI error */ free(lValue); h5JNIFatalError(env, "H5Lget_val: return string not created"); return -1; } ENVPTR->SetObjectArrayElement(ENVPAR link_value, 0, str); } free(lValue); return infobuf.type; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lget_val_by_idx * Signature: (ILjava/lang/String;IIJ[Ljava/lang/String;I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Lget_1val_1by_1idx (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint index_field, jint order, jlong link_n, jobjectArray link_value, jint access_id) { herr_t status; size_t buf_size; H5L_info_t infobuf; char *lName; void *lValue; const char *file_name; const char *obj_name; jboolean isCopy; jstring str; if (name == NULL) { h5nullArgument(env, "H5Lget_val_by_idx: name is NULL"); return -1; } lName = (char*)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (lName == NULL) { h5JNIFatalError(env, "H5Lget_val_by_idx: name not pinned"); return -1; } /* get the length of the link valuee */ status = H5Lget_info_by_idx((hid_t)loc_id, (const char*)lName, (H5_index_t)index_field, (H5_iter_order_t)order, (hsize_t)link_n, (H5L_info_t*)&infobuf, (hid_t)access_id); if(status < 0) { ENVPTR->ReleaseStringUTFChars(ENVPAR name, lName); h5libraryError(env); return -1; } buf_size = infobuf.u.val_size; if(buf_size < 0) { ENVPTR->ReleaseStringUTFChars(ENVPAR name, lName); h5libraryError(env); return -1; } lValue = (void*)malloc(buf_size); if (lValue == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR name, lName); h5outOfMemory(env, "H5Lget_val_by_idx: malloc failed "); return -1; } status = H5Lget_val_by_idx((hid_t)loc_id, (const char*)lName, (H5_index_t)index_field, (H5_iter_order_t)order, (hsize_t)link_n, (void*)lValue, (size_t)buf_size, (hid_t)access_id); ENVPTR->ReleaseStringUTFChars(ENVPAR name, lName); if (status < 0) { free(lValue); h5libraryError(env); return -1; } /* may throw OutOfMemoryError */ if(infobuf.type == H5L_TYPE_EXTERNAL) { status = H5Lunpack_elink_val((char*)lValue, (size_t)infobuf.u.val_size, (unsigned*)NULL, (const char**)&file_name, (const char**)&obj_name); if (status < 0) { free(lValue); h5libraryError(env); return -1; } str = ENVPTR->NewStringUTF(ENVPAR obj_name); if (str == NULL) { /* exception -- fatal JNI error */ free(lValue); h5JNIFatalError(env, "H5Lget_val_by_idx: return string not created"); return -1; } ENVPTR->SetObjectArrayElement(ENVPAR link_value, 0, str); str = ENVPTR->NewStringUTF(ENVPAR file_name); if (str == NULL) { /* exception -- fatal JNI error */ free(lValue); h5JNIFatalError(env, "H5Lget_val_by_idx: return string not created"); return -1; } ENVPTR->SetObjectArrayElement(ENVPAR link_value, 1, str); } else { str = ENVPTR->NewStringUTF(ENVPAR (char *)lValue); if (str == NULL) { /* exception -- fatal JNI error */ free(lValue); h5JNIFatalError(env, "H5Lget_val_by_idx: return string not created"); return -1; } ENVPTR->SetObjectArrayElement(ENVPAR link_value, 0, str); } free(lValue); return infobuf.type; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lmove * Signature: (ILjava/lang/String;ILjava/lang/String;II)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Lmove (JNIEnv *env, jclass clss, jint cur_loc_id, jstring cur_name, jint dst_loc_id, jstring dst_name, jint create_id, jint access_id) { char *lCurName; char *lDstName; jboolean isCopy; herr_t status = -1; if (cur_name == NULL) { h5nullArgument(env, "H5Lcreate_hard: cur_name is NULL"); return; } lCurName = (char*)ENVPTR->GetStringUTFChars(ENVPAR cur_name, &isCopy); if (lCurName == NULL) { h5JNIFatalError(env, "H5Lcreate_hard: cur_name not pinned"); return; } if (dst_name == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR cur_name, lCurName); h5nullArgument(env, "H5Lcreate_hard: dst_name is NULL"); return; } lDstName = (char*)ENVPTR->GetStringUTFChars(ENVPAR dst_name, &isCopy); if (lDstName == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR cur_name, lCurName); h5JNIFatalError( env, "H5Lcreate_hard: dst_name not pinned"); return; } status = H5Lmove((hid_t)cur_loc_id, (const char*)lCurName, (hid_t)dst_loc_id, (const char*)lDstName, (hid_t)create_id, (hid_t)access_id); ENVPTR->ReleaseStringUTFChars(ENVPAR cur_name, lCurName); ENVPTR->ReleaseStringUTFChars(ENVPAR dst_name, lDstName); if (status < 0) { h5libraryError(env); return; } return; } herr_t H5L_iterate_cb(hid_t g_id, const char *name, const H5L_info_t *info, void *op_data) { JNIEnv *cbenv; jint status; jclass cls; jmethodID mid; jstring str; jmethodID constructor; jvalue args[5]; jobject cb_info_t = NULL; if(JVMPTR->AttachCurrentThread(JVMPAR2 (void**)&cbenv, NULL) != 0) { /* printf("JNI H5L_iterate_cb error: AttachCurrentThread failed\n"); */ JVMPTR->DetachCurrentThread(JVMPAR); return -1; } cls = CBENVPTR->GetObjectClass(CBENVPAR visit_callback); if (cls == 0) { /* printf("JNI H5L_iterate_cb error: GetObjectClass failed\n"); */ JVMPTR->DetachCurrentThread(JVMPAR); return -1; } mid = CBENVPTR->GetMethodID(CBENVPAR cls, "callback", "(ILjava/lang/String;Lncsa/hdf/hdf5lib/structs/H5L_info_t;Lncsa/hdf/hdf5lib/callbacks/H5L_iterate_t;)I"); if (mid == 0) { /* printf("JNI H5L_iterate_cb error: GetMethodID failed\n"); */ JVMPTR->DetachCurrentThread(JVMPAR); return -1; } str = CBENVPTR->NewStringUTF(CBENVPAR name); // get a reference to your class if you don't have it already cls = CBENVPTR->FindClass(CBENVPAR "ncsa/hdf/hdf5lib/structs/H5L_info_t"); if (cls == 0) { /* printf("JNI H5L_iterate_cb error: GetObjectClass info failed\n"); */ JVMPTR->DetachCurrentThread(JVMPAR); return -1; } // get a reference to the constructor; the name is constructor = CBENVPTR->GetMethodID(CBENVPAR cls, "", "(IZJIJ)V"); if (constructor == 0) { /* printf("JNI H5L_iterate_cb error: GetMethodID constructor failed\n"); */ JVMPTR->DetachCurrentThread(JVMPAR); return -1; } args[0].i = info->type; args[1].z = info->corder_valid; args[2].j = info->corder; args[3].i = info->cset; if(info->type==0) args[4].j = info->u.address; else args[4].j = info->u.val_size; cb_info_t = CBENVPTR->NewObjectA(CBENVPAR cls, constructor, args); status = CBENVPTR->CallIntMethod(CBENVPAR visit_callback, mid, g_id, str, cb_info_t, op_data); JVMPTR->DetachCurrentThread(JVMPAR); return status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lvisit * Signature: (IIILjava/lang/Object;Ljava/lang/Object;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Lvisit (JNIEnv *env, jclass clss, jint grp_id, jint idx_type, jint order, jobject callback_op, jobject op_data) { herr_t status = -1; ENVPTR->GetJavaVM(ENVPAR &jvm); visit_callback = callback_op; if (op_data == NULL) { h5nullArgument(env, "H5Lvisit: op_data is NULL"); return -1; } if (callback_op == NULL) { h5nullArgument(env, "H5Lvisit: callback_op is NULL"); return -1; } status = H5Lvisit((hid_t)grp_id, (H5_index_t)idx_type, (H5_iter_order_t)order, (H5L_iterate_t)H5L_iterate_cb, (void*)op_data); if (status < 0) { h5libraryError(env); return status; } return status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lvisit_by_name * Signature: (ILjava/lang/String;IILjava/lang/Object;Ljava/lang/Object;I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Lvisit_1by_1name (JNIEnv *env, jclass clss, jint grp_id, jstring name, jint idx_type, jint order, jobject callback_op, jobject op_data, jint access_id) { jboolean isCopy; char *lName; herr_t status = -1; ENVPTR->GetJavaVM(ENVPAR &jvm); visit_callback = callback_op; if (name == NULL) { h5nullArgument(env, "H5Lvisit_by_name: name is NULL"); return -1; } lName = (char*)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (lName == NULL) { h5JNIFatalError(env, "H5Lvisit_by_name: name not pinned"); return -1; } if (op_data == NULL) { h5nullArgument(env, "H5Lvisit_by_name: op_data is NULL"); return -1; } if (callback_op == NULL) { h5nullArgument(env, "H5Lvisit_by_name: callback_op is NULL"); return -1; } status = H5Lvisit_by_name((hid_t)grp_id, (const char*)lName, (H5_index_t)idx_type, (H5_iter_order_t)order, (H5L_iterate_t)H5L_iterate_cb, (void*)op_data, (hid_t)access_id); ENVPTR->ReleaseStringUTFChars(ENVPAR name, lName); if (status < 0) { h5libraryError(env); return status; } return status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Literate * Signature: (IIIJLjava/lang/Object;Ljava/lang/Object;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Literate (JNIEnv *env, jclass clss, jint grp_id, jint idx_type, jint order, jlong idx, jobject callback_op, jobject op_data) { hsize_t start_idx = (hsize_t)idx; herr_t status = -1; ENVPTR->GetJavaVM(ENVPAR &jvm); visit_callback = callback_op; if (op_data == NULL) { h5nullArgument(env, "H5Literate: op_data is NULL"); return -1; } if (callback_op == NULL) { h5nullArgument(env, "H5Literate: callback_op is NULL"); return -1; } status = H5Literate((hid_t)grp_id, (H5_index_t)idx_type, (H5_iter_order_t)order, (hsize_t*)&start_idx, (H5L_iterate_t)H5L_iterate_cb, (void*)op_data); if (status < 0) { h5libraryError(env); return status; } return status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Literate_by_name * Signature: (ILjava/lang/String;IIJLjava/lang/Object;Ljava/lang/Object;I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Literate_1by_1name (JNIEnv *env, jclass clss, jint grp_id, jstring name, jint idx_type, jint order, jlong idx, jobject callback_op, jobject op_data, jint access_id) { jboolean isCopy; char *lName; hsize_t start_idx = (hsize_t)idx; herr_t status = -1; ENVPTR->GetJavaVM(ENVPAR &jvm); visit_callback = callback_op; if (name == NULL) { h5nullArgument(env, "H5Literate_by_name: name is NULL"); return -1; } lName = (char*)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (lName == NULL) { h5JNIFatalError(env, "H5Literate_by_name: name not pinned"); return -1; } if (op_data == NULL) { h5nullArgument(env, "H5Literate_by_name: op_data is NULL"); return -1; } if (callback_op == NULL) { h5nullArgument(env, "H5Literate_by_name: callback_op is NULL"); return -1; } status = H5Literate_by_name((hid_t)grp_id, (const char*)lName, (H5_index_t)idx_type, (H5_iter_order_t)order, (hsize_t*)&start_idx, (H5L_iterate_t)H5L_iterate_cb, (void*)op_data, (hid_t)access_id); ENVPTR->ReleaseStringUTFChars(ENVPAR name, lName); if (status < 0) { h5libraryError(env); return status; } return status; } #ifdef __cplusplus } #endif libsis-jhdf5-java-14.12.1/source/c/hdf-java/h5lImp.h000066400000000000000000000121461256564762100216150ustar00rootroot00000000000000/* DO NOT EDIT THIS FILE - it is machine generated */ #include /* Header for class ncsa_hdf_hdf5lib_H5_H5_H5L */ #ifndef _Included_ncsa_hdf_hdf5lib_H5_H5L #define _Included_ncsa_hdf_hdf5lib_H5_H5L #ifdef __cplusplus extern "C" { #endif extern JavaVM *jvm; extern jobject visit_callback; /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lcopy * Signature: (ILjava/lang/String;ILjava/lang/String;II)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Lcopy (JNIEnv *, jclass, jint, jstring, jint, jstring, jint, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lcreate_external * Signature: (Ljava/lang/String;Ljava/lang/String;ILjava/lang/String;II)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Lcreate_1external (JNIEnv *, jclass, jstring, jstring, jint, jstring, jint, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lcreate_hard * Signature: (ILjava/lang/String;ILjava/lang/String;II)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Lcreate_1hard (JNIEnv *, jclass, jint, jstring, jint, jstring, jint, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lcreate_soft * Signature: (Ljava/lang/String;ILjava/lang/String;II)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Lcreate_1soft (JNIEnv *, jclass, jstring, jint, jstring, jint, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Ldelete * Signature: (ILjava/lang/String;I)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Ldelete (JNIEnv *, jclass, jint, jstring, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Ldelete_by_idx * Signature: (ILjava/lang/String;IIJI)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Ldelete_1by_1idx (JNIEnv *, jclass, jint, jstring, jint, jint, jlong, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lexists * Signature: (ILjava/lang/String;I)Z */ JNIEXPORT jboolean JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Lexists (JNIEnv *, jclass, jint, jstring, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lget_info * Signature: (ILjava/lang/String;I)Lncsa/hdf/hdf5lib/structs/H5L_info_t; */ JNIEXPORT jobject JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Lget_1info (JNIEnv *, jclass, jint, jstring, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lget_info_by_idx * Signature: (ILjava/lang/String;IIJI)Lncsa/hdf/hdf5lib/structs/H5L_info_t; */ JNIEXPORT jobject JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Lget_1info_1by_1idx (JNIEnv *, jclass, jint, jstring, jint, jint, jlong, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lget_name_by_idx * Signature: (ILjava/lang/String;IIJI)Ljava/lang/String; */ JNIEXPORT jobject JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Lget_1name_1by_1idx (JNIEnv *, jclass, jint, jstring, jint, jint, jlong, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lget_val * Signature: (ILjava/lang/String;[Ljava/lang/String;I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Lget_1val (JNIEnv *, jclass, jint, jstring, jobjectArray, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lget_val_by_idx * Signature: (ILjava/lang/String;IIJ[Ljava/lang/String;I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Lget_1val_1by_1idx (JNIEnv *, jclass, jint, jstring, jint, jint, jlong, jobjectArray, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lmove * Signature: (ILjava/lang/String;ILjava/lang/String;II)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Lmove (JNIEnv *, jclass, jint, jstring, jint, jstring, jint, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lvisit * Signature: (IIILjava/lang/Object;Ljava/lang/Object;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Lvisit (JNIEnv *, jclass, jint, jint, jint, jobject, jobject); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lvisit_by_name * Signature: (ILjava/lang/String;IILjava/lang/Object;Ljava/lang/Object;I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Lvisit_1by_1name (JNIEnv *, jclass, jint, jstring, jint, jint, jobject, jobject, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Literate * Signature: (IIIJLjava/lang/Object;Ljava/lang/Object;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Literate (JNIEnv *, jclass, jint, jint, jint, jlong, jobject, jobject); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Literate_by_name * Signature: (ILjava/lang/String;IILjava/lang/Object;Ljava/lang/Object;I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Literate_1by_1name (JNIEnv *, jclass, jint, jstring, jint, jint, jlong, jobject, jobject, jint); #ifdef __cplusplus } #endif #endif libsis-jhdf5-java-14.12.1/source/c/hdf-java/h5oImp.c000077500000000000000000000765371256564762100216340ustar00rootroot00000000000000/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF Java Products. The full HDF Java copyright * * notice, including terms governing use, modification, and redistribution, * * is contained in the file, COPYING. COPYING can be found at the root of * * the source code distribution tree. You can also access it online at * * http://www.hdfgroup.org/products/licenses.html. If you do not have * * access to the file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /* * This code is the C-interface called by Java programs to access the * Link Object API Functions of the HDF5 library. * * Each routine wraps a single HDF entry point, generally with the * analogous arguments and return codes. * * For details of the HDF libraries, see the HDF Documentation at: * http://hdfdfgroup.org/HDF5/doc/ * */ #ifdef __cplusplus extern "C" { #endif #include #include #include "hdf5.h" #include "h5jni.h" #include "h5oImp.h" #ifdef __cplusplus #define CBENVPTR (cbenv) #define CBENVPAR #define JVMPTR (jvm) #define JVMPAR #define JVMPAR2 #else #define CBENVPTR (*cbenv) #define CBENVPAR cbenv, #define JVMPTR (*jvm) #define JVMPAR jvm #define JVMPAR2 jvm, #endif /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Oopen * Signature: (ILjava/lang/String;I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Oopen (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint access_plist_id) { hid_t status; char* oName; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Oopen: name is NULL"); return -1; } oName = (char *)ENVPTR->GetStringUTFChars(ENVPAR name,&isCopy); if (oName == NULL) { h5JNIFatalError( env, "H5Oopen: object name not pinned"); return -1; } status = H5Oopen((hid_t)loc_id, oName, (hid_t)access_plist_id ); ENVPTR->ReleaseStringUTFChars(ENVPAR name, oName); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Oclose * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Oclose (JNIEnv *env, jclass clss, jint object_id) { herr_t retVal = H5Oclose((hid_t)object_id) ; if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Ocopy * Signature: (ILjava/lang/String;ILjava/lang/String;II)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Ocopy (JNIEnv *env, jclass clss, jint cur_loc_id, jstring cur_name, jint dst_loc_id, jstring dst_name, jint create_id, jint access_id) { char *lCurName; char *lDstName; jboolean isCopy; herr_t status = -1; if (cur_name == NULL) { h5nullArgument(env, "H5Ocopy: cur_name is NULL"); return; } lCurName = (char*)ENVPTR->GetStringUTFChars(ENVPAR cur_name, &isCopy); if (lCurName == NULL) { h5JNIFatalError(env, "H5Ocopy: cur_name not pinned"); return; } if (dst_name == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR cur_name, lCurName); h5nullArgument(env, "H5Ocopy: dst_name is NULL"); return; } lDstName = (char*)ENVPTR->GetStringUTFChars(ENVPAR dst_name, &isCopy); if (lDstName == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR cur_name, lCurName); h5JNIFatalError(env, "H5Ocopy: dst_name not pinned"); return; } status = H5Ocopy((hid_t)cur_loc_id, (const char*)lCurName, (hid_t)dst_loc_id, (const char*)lDstName, (hid_t)create_id, (hid_t)access_id); ENVPTR->ReleaseStringUTFChars(ENVPAR cur_name, lCurName); ENVPTR->ReleaseStringUTFChars(ENVPAR dst_name, lDstName); if (status < 0) { h5libraryError(env); return; } return; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Oget_info * Signature: (I)Lncsa/hdf/hdf5lib/structs/H5O_info_t; */ JNIEXPORT jobject JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Oget_1info (JNIEnv *env, jclass clss, jint loc_id) { herr_t status; H5O_info_t infobuf; jclass cls; jmethodID constructor; jvalue args[12]; jobject hdrinfobuf; jobject ihinfobuf1; jobject ihinfobuf2; jobject ret_info_t = NULL; status = H5Oget_info((hid_t)loc_id, (H5O_info_t*)&infobuf); if (status < 0) { h5libraryError(env); return NULL; } // get a reference to the H5_hdr_info_t class cls = ENVPTR->FindClass(ENVPAR "ncsa/hdf/hdf5lib/structs/H5O_hdr_info_t"); if (cls == 0) { h5JNIFatalError( env, "JNI error: GetObjectClass H5O_hdr_info_t failed\n"); return NULL; } // get a reference to the constructor; the name is constructor = ENVPTR->GetMethodID(ENVPAR cls, "", "(IIIIJJJJJJ)V"); if (constructor == 0) { h5JNIFatalError( env, "JNI error: GetMethodID H5O_hdr_info_t failed\n"); return NULL; } args[0].i = infobuf.hdr.version; args[1].i = infobuf.hdr.nmesgs; args[2].i = infobuf.hdr.nchunks; args[3].i = infobuf.hdr.flags; args[4].j = infobuf.hdr.space.total; args[5].j = infobuf.hdr.space.meta; args[6].j = infobuf.hdr.space.mesg; args[7].j = infobuf.hdr.space.free; args[8].j = infobuf.hdr.mesg.present; args[9].j = infobuf.hdr.mesg.shared; hdrinfobuf = ENVPTR->NewObjectA(ENVPAR cls, constructor, args); // get a reference to the H5_ih_info_t class cls = ENVPTR->FindClass(ENVPAR "ncsa/hdf/hdf5lib/structs/H5_ih_info_t"); if (cls == 0) { h5JNIFatalError( env, "JNI error: GetObjectClass H5_ih_info_t failed\n"); return NULL; } // get a reference to the constructor; the name is constructor = ENVPTR->GetMethodID(ENVPAR cls, "", "(JJ)V"); if (constructor == 0) { h5JNIFatalError( env, "JNI error: GetMethodID H5_ih_info_t failed\n"); return NULL; } args[0].j = infobuf.meta_size.obj.index_size; args[1].j = infobuf.meta_size.obj.heap_size; ihinfobuf1 = ENVPTR->NewObjectA(ENVPAR cls, constructor, args); args[0].j = infobuf.meta_size.attr.index_size; args[1].j = infobuf.meta_size.attr.heap_size; ihinfobuf2 = ENVPTR->NewObjectA(ENVPAR cls, constructor, args); // get a reference to the H5O_info_t class cls = ENVPTR->FindClass(ENVPAR "ncsa/hdf/hdf5lib/structs/H5O_info_t"); if (cls == 0) { h5JNIFatalError( env, "JNI error: GetObjectClass H5O_info_t failed\n"); return NULL; } // get a reference to the constructor; the name is constructor = ENVPTR->GetMethodID(ENVPAR cls, "", "(JJIIJJJJJLncsa/hdf/hdf5lib/structs/H5O_hdr_info_t;Lncsa/hdf/hdf5lib/structs/H5_ih_info_t;Lncsa/hdf/hdf5lib/structs/H5_ih_info_t;)V"); if (constructor == 0) { h5JNIFatalError( env, "JNI error: GetMethodID H5O_info_t failed\n"); return NULL; } args[0].j = infobuf.fileno; args[1].j = infobuf.addr; args[2].i = infobuf.type; args[3].i = infobuf.rc; args[4].j = infobuf.num_attrs; args[5].j = infobuf.atime; args[6].j = infobuf.mtime; args[7].j = infobuf.ctime; args[8].j = infobuf.btime; args[9].l = hdrinfobuf; args[10].l = ihinfobuf1; args[11].l = ihinfobuf2; ret_info_t = ENVPTR->NewObjectA(ENVPAR cls, constructor, args); return ret_info_t; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Oget_info_by_name * Signature: (ILjava/lang/String;IIJI)Lncsa/hdf/hdf5lib/structs/H5O_info_t; */ JNIEXPORT jobject JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Oget_1info_1by_1name (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint access_id) { char *lName; herr_t status; H5O_info_t infobuf; jboolean isCopy; jclass cls; jmethodID constructor; jvalue args[12]; jobject hdrinfobuf; jobject ihinfobuf1; jobject ihinfobuf2; jobject ret_info_t = NULL; if (name == NULL) { h5nullArgument(env, "H5Oget_info_by_name: name is NULL"); return NULL; } lName = (char*)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (lName == NULL) { h5JNIFatalError(env, "H5Oget_info_by_name: name not pinned"); return NULL; } status = H5Oget_info_by_name((hid_t)loc_id, (const char*)lName, (H5O_info_t*)&infobuf, (hid_t)access_id); ENVPTR->ReleaseStringUTFChars(ENVPAR name, lName); if (status < 0) { h5libraryError(env); return NULL; } // get a reference to the H5_hdr_info_t class cls = ENVPTR->FindClass(ENVPAR "ncsa/hdf/hdf5lib/structs/H5O_hdr_info_t"); if (cls == 0) { h5JNIFatalError( env, "JNI error: GetObjectClass H5O_hdr_info_t failed\n"); return NULL; } // get a reference to the constructor; the name is constructor = ENVPTR->GetMethodID(ENVPAR cls, "", "(IIIIJJJJJJ)V"); if (constructor == 0) { h5JNIFatalError( env, "JNI error: GetMethodID H5O_hdr_info_t failed\n"); return NULL; } args[0].i = infobuf.hdr.version; args[1].i = infobuf.hdr.nmesgs; args[2].i = infobuf.hdr.nchunks; args[3].i = infobuf.hdr.flags; args[4].j = infobuf.hdr.space.total; args[5].j = infobuf.hdr.space.meta; args[6].j = infobuf.hdr.space.mesg; args[7].j = infobuf.hdr.space.free; args[8].j = infobuf.hdr.mesg.present; args[9].j = infobuf.hdr.mesg.shared; hdrinfobuf = ENVPTR->NewObjectA(ENVPAR cls, constructor, args); // get a reference to the H5_ih_info_t class cls = ENVPTR->FindClass(ENVPAR "ncsa/hdf/hdf5lib/structs/H5_ih_info_t"); if (cls == 0) { h5JNIFatalError( env, "JNI error: GetObjectClass H5_ih_info_t failed\n"); return NULL; } // get a reference to the constructor; the name is constructor = ENVPTR->GetMethodID(ENVPAR cls, "", "(JJ)V"); if (constructor == 0) { h5JNIFatalError( env, "JNI error: GetMethodID H5_ih_info_t failed\n"); return NULL; } args[0].j = infobuf.meta_size.obj.index_size; args[1].j = infobuf.meta_size.obj.heap_size; ihinfobuf1 = ENVPTR->NewObjectA(ENVPAR cls, constructor, args); args[0].j = infobuf.meta_size.attr.index_size; args[1].j = infobuf.meta_size.attr.heap_size; ihinfobuf2 = ENVPTR->NewObjectA(ENVPAR cls, constructor, args); // get a reference to the H5O_info_t class cls = ENVPTR->FindClass(ENVPAR "ncsa/hdf/hdf5lib/structs/H5O_info_t"); if (cls == 0) { h5JNIFatalError( env, "JNI error: GetObjectClass H5O_info_t failed\n"); return NULL; } // get a reference to the constructor; the name is constructor = ENVPTR->GetMethodID(ENVPAR cls, "", "(JJIIJJJJJLncsa/hdf/hdf5lib/structs/H5O_hdr_info_t;Lncsa/hdf/hdf5lib/structs/H5_ih_info_t;Lncsa/hdf/hdf5lib/structs/H5_ih_info_t;)V"); if (constructor == 0) { h5JNIFatalError( env, "JNI error: GetMethodID H5O_info_t failed\n"); return NULL; } args[0].j = infobuf.fileno; args[1].j = infobuf.addr; args[2].i = infobuf.type; args[3].i = infobuf.rc; args[4].j = infobuf.num_attrs; args[5].j = infobuf.atime; args[6].j = infobuf.mtime; args[7].j = infobuf.ctime; args[8].j = infobuf.btime; args[9].l = hdrinfobuf; args[10].l = ihinfobuf1; args[11].l = ihinfobuf2; ret_info_t = ENVPTR->NewObjectA(ENVPAR cls, constructor, args); return ret_info_t; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Oget_info_by_idx * Signature: (ILjava/lang/String;IIJI)Lncsa/hdf/hdf5lib/structs/H5O_info_t; */ JNIEXPORT jobject JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Oget_1info_1by_1idx (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint index_field, jint order, jlong link_n, jint access_id) { char *lName; herr_t status; H5O_info_t infobuf; jboolean isCopy; jclass cls; jmethodID constructor; jvalue args[12]; jobject hdrinfobuf; jobject ihinfobuf1; jobject ihinfobuf2; jobject ret_info_t = NULL; if (name == NULL) { h5nullArgument(env, "H5Oget_info_by_idx: name is NULL"); return NULL; } lName = (char*)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (lName == NULL) { h5JNIFatalError(env, "H5Oget_info_by_idx: name not pinned"); return NULL; } status = H5Oget_info_by_idx((hid_t)loc_id, (const char*)lName, (H5_index_t)index_field, (H5_iter_order_t)order, (hsize_t)link_n, (H5O_info_t*)&infobuf, (hid_t)access_id); ENVPTR->ReleaseStringUTFChars(ENVPAR name, lName); if (status < 0) { h5libraryError(env); return NULL; } // get a reference to the H5_hdr_info_t class cls = ENVPTR->FindClass(ENVPAR "ncsa/hdf/hdf5lib/structs/H5O_hdr_info_t"); if (cls == 0) { h5JNIFatalError( env, "JNI error: GetObjectClass H5O_hdr_info_t failed\n"); return NULL; } // get a reference to the constructor; the name is constructor = ENVPTR->GetMethodID(ENVPAR cls, "", "(IIIIJJJJJJ)V"); if (constructor == 0) { h5JNIFatalError( env, "JNI error: GetMethodID H5O_hdr_info_t failed\n"); return NULL; } args[0].i = infobuf.hdr.version; args[1].i = infobuf.hdr.nmesgs; args[2].i = infobuf.hdr.nchunks; args[3].i = infobuf.hdr.flags; args[4].j = infobuf.hdr.space.total; args[5].j = infobuf.hdr.space.meta; args[6].j = infobuf.hdr.space.mesg; args[7].j = infobuf.hdr.space.free; args[8].j = infobuf.hdr.mesg.present; args[9].j = infobuf.hdr.mesg.shared; hdrinfobuf = ENVPTR->NewObjectA(ENVPAR cls, constructor, args); // get a reference to the H5_ih_info_t class cls = ENVPTR->FindClass(ENVPAR "ncsa/hdf/hdf5lib/structs/H5_ih_info_t"); if (cls == 0) { h5JNIFatalError( env, "JNI error: GetObjectClass H5_ih_info_t failed\n"); return NULL; } // get a reference to the constructor; the name is constructor = ENVPTR->GetMethodID(ENVPAR cls, "", "(JJ)V"); if (constructor == 0) { h5JNIFatalError( env, "JNI error: GetMethodID H5_ih_info_t failed\n"); return NULL; } args[0].j = infobuf.meta_size.obj.index_size; args[1].j = infobuf.meta_size.obj.heap_size; ihinfobuf1 = ENVPTR->NewObjectA(ENVPAR cls, constructor, args); args[0].j = infobuf.meta_size.attr.index_size; args[1].j = infobuf.meta_size.attr.heap_size; ihinfobuf2 = ENVPTR->NewObjectA(ENVPAR cls, constructor, args); // get a reference to the H5O_info_t class cls = ENVPTR->FindClass(ENVPAR "ncsa/hdf/hdf5lib/structs/H5O_info_t"); if (cls == 0) { h5JNIFatalError( env, "JNI error: GetObjectClass H5O_info_t failed\n"); return NULL; } // get a reference to the constructor; the name is constructor = ENVPTR->GetMethodID(ENVPAR cls, "", "(JJIIJJJJJLncsa/hdf/hdf5lib/structs/H5O_hdr_info_t;Lncsa/hdf/hdf5lib/structs/H5_ih_info_t;Lncsa/hdf/hdf5lib/structs/H5_ih_info_t;)V"); if (constructor == 0) { h5JNIFatalError( env, "JNI error: GetMethodID H5O_info_t failed\n"); return NULL; } args[0].j = infobuf.fileno; args[1].j = infobuf.addr; args[2].i = infobuf.type; args[3].i = infobuf.rc; args[4].j = infobuf.num_attrs; args[5].j = infobuf.atime; args[6].j = infobuf.mtime; args[7].j = infobuf.ctime; args[8].j = infobuf.btime; args[9].l = hdrinfobuf; args[10].l = ihinfobuf1; args[11].l = ihinfobuf2; ret_info_t = ENVPTR->NewObjectA(ENVPAR cls, constructor, args); return ret_info_t; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Olink * Signature: (IILjava/lang/String;II)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Olink (JNIEnv *env, jclass clss, jint cur_loc_id, jint dst_loc_id, jstring dst_name, jint create_id, jint access_id) { char *lDstName; jboolean isCopy; herr_t status = -1; if (dst_name == NULL) { h5nullArgument(env, "H5Ocreate_hard: dst_name is NULL"); return; } lDstName = (char*)ENVPTR->GetStringUTFChars(ENVPAR dst_name, &isCopy); if (lDstName == NULL) { h5JNIFatalError( env, "H5Ocreate_hard: dst_name not pinned"); return; } status = H5Olink((hid_t)cur_loc_id, (hid_t)dst_loc_id, (const char*)lDstName, (hid_t)create_id, (hid_t)access_id); ENVPTR->ReleaseStringUTFChars(ENVPAR dst_name, lDstName); if (status < 0) { h5libraryError(env); return; } return; } herr_t H5O_iterate_cb(hid_t g_id, const char *name, const H5O_info_t *info, void *op_data) { JNIEnv *cbenv; jint status; jclass cls; jmethodID mid; jstring str; jmethodID constructor; jvalue args[12]; jobject hdrinfobuf; jobject ihinfobuf1; jobject ihinfobuf2; jobject cb_info_t = NULL; if(JVMPTR->AttachCurrentThread(JVMPAR2 (void**)&cbenv, NULL) != 0) { /* printf("JNI H5O_iterate_cb error: AttachCurrentThread failed\n"); */ JVMPTR->DetachCurrentThread(JVMPAR); return -1; } cls = CBENVPTR->GetObjectClass(CBENVPAR visit_callback); if (cls == 0) { /* printf("JNI H5O_iterate_cb error: GetObjectClass failed\n"); */ JVMPTR->DetachCurrentThread(JVMPAR); return -1; } mid = CBENVPTR->GetMethodID(CBENVPAR cls, "callback", "(ILjava/lang/String;Lncsa/hdf/hdf5lib/structs/H5O_info_t;Lncsa/hdf/hdf5lib/callbacks/H5O_iterate_t;)I"); if (mid == 0) { /* printf("JNI H5O_iterate_cb error: GetMethodID failed\n"); */ JVMPTR->DetachCurrentThread(JVMPAR); return -1; } str = CBENVPTR->NewStringUTF(CBENVPAR name); // get a reference to the H5_hdr_info_t class cls = CBENVPTR->FindClass(CBENVPAR "ncsa/hdf/hdf5lib/structs/H5O_hdr_info_t"); if (cls == 0) { JVMPTR->DetachCurrentThread(JVMPAR); return -1; } // get a reference to the constructor; the name is constructor = CBENVPTR->GetMethodID(CBENVPAR cls, "", "(IIIIJJJJJJ)V"); if (constructor == 0) { JVMPTR->DetachCurrentThread(JVMPAR); return -1; } args[0].i = info->hdr.version; args[1].i = info->hdr.nmesgs; args[2].i = info->hdr.nchunks; args[3].i = info->hdr.flags; args[4].j = info->hdr.space.total; args[5].j = info->hdr.space.meta; args[6].j = info->hdr.space.mesg; args[7].j = info->hdr.space.free; args[8].j = info->hdr.mesg.present; args[9].j = info->hdr.mesg.shared; hdrinfobuf = CBENVPTR->NewObjectA(CBENVPAR cls, constructor, args); // get a reference to the H5_ih_info_t class cls = CBENVPTR->FindClass(CBENVPAR "ncsa/hdf/hdf5lib/structs/H5_ih_info_t"); if (cls == 0) { JVMPTR->DetachCurrentThread(JVMPAR); return -1; } // get a reference to the constructor; the name is constructor = CBENVPTR->GetMethodID(CBENVPAR cls, "", "(JJ)V"); if (constructor == 0) { JVMPTR->DetachCurrentThread(JVMPAR); return -1; } args[0].j = info->meta_size.obj.index_size; args[1].j = info->meta_size.obj.heap_size; ihinfobuf1 = CBENVPTR->NewObjectA(CBENVPAR cls, constructor, args); args[0].j = info->meta_size.attr.index_size; args[1].j = info->meta_size.attr.heap_size; ihinfobuf2 = CBENVPTR->NewObjectA(CBENVPAR cls, constructor, args); // get a reference to the H5O_info_t class cls = CBENVPTR->FindClass(CBENVPAR "ncsa/hdf/hdf5lib/structs/H5O_info_t"); if (cls == 0) { JVMPTR->DetachCurrentThread(JVMPAR); return -1; } // get a reference to the constructor; the name is constructor = CBENVPTR->GetMethodID(CBENVPAR cls, "", "(JJIIJJJJJLncsa/hdf/hdf5lib/structs/H5O_hdr_info_t;Lncsa/hdf/hdf5lib/structs/H5_ih_info_t;Lncsa/hdf/hdf5lib/structs/H5_ih_info_t;)V"); if (constructor == 0) { JVMPTR->DetachCurrentThread(JVMPAR); return -1; } args[0].j = info->fileno; args[1].j = info->addr; args[2].i = info->type; args[3].i = info->rc; args[4].j = info->num_attrs; args[5].j = info->atime; args[6].j = info->mtime; args[7].j = info->ctime; args[8].j = info->btime; args[9].l = hdrinfobuf; args[10].l = ihinfobuf1; args[11].l = ihinfobuf2; cb_info_t = CBENVPTR->NewObjectA(CBENVPAR cls, constructor, args); status = CBENVPTR->CallIntMethod(CBENVPAR visit_callback, mid, g_id, str, cb_info_t, op_data); JVMPTR->DetachCurrentThread(JVMPAR); return status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Ovisit * Signature: (IIILjava/lang/Object;Ljava/lang/Object;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Ovisit (JNIEnv *env, jclass clss, jint grp_id, jint idx_type, jint order, jobject callback_op, jobject op_data) { herr_t status = -1; ENVPTR->GetJavaVM(ENVPAR &jvm); visit_callback = callback_op; if (op_data == NULL) { h5nullArgument(env, "H5Ovisit: op_data is NULL"); return -1; } if (callback_op == NULL) { h5nullArgument(env, "H5Ovisit: callback_op is NULL"); return -1; } status = H5Ovisit((hid_t)grp_id, (H5_index_t)idx_type, (H5_iter_order_t)order, (H5O_iterate_t)H5O_iterate_cb, (void*)op_data); if (status < 0) { h5libraryError(env); return status; } return status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Ovisit_by_name * Signature: (ILjava/lang/String;IILjava/lang/Object;Ljava/lang/Object;I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Ovisit_1by_1name (JNIEnv *env, jclass clss, jint grp_id, jstring name, jint idx_type, jint order, jobject callback_op, jobject op_data, jint access_id) { jboolean isCopy; char *lName; herr_t status = -1; ENVPTR->GetJavaVM(ENVPAR &jvm); visit_callback = callback_op; if (name == NULL) { h5nullArgument(env, "H5Ovisit_by_name: name is NULL"); return -1; } lName = (char*)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (lName == NULL) { h5JNIFatalError(env, "H5Ovisit_by_name: name not pinned"); return -1; } if (op_data == NULL) { h5nullArgument(env, "H5Ovisit_by_name: op_data is NULL"); return -1; } if (callback_op == NULL) { h5nullArgument(env, "H5Ovisit_by_name: callback_op is NULL"); return -1; } status = H5Ovisit_by_name((hid_t)grp_id, (const char*)lName, (H5_index_t)idx_type, (H5_iter_order_t)order, (H5O_iterate_t)H5O_iterate_cb, (void*)op_data, (hid_t)access_id); ENVPTR->ReleaseStringUTFChars(ENVPAR name, lName); if (status < 0) { h5libraryError(env); return status; } return status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Oset_comment * Signature: (ILjava/lang/String;)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Oset_1comment (JNIEnv *env, jclass clss, jint loc_id, jstring comment) { herr_t status; char *oComment; jboolean isCopy; if (comment == NULL) { oComment = NULL; } else { oComment = (char *)ENVPTR->GetStringUTFChars(ENVPAR comment, &isCopy); if (oComment == NULL) { h5JNIFatalError( env, "H5Oset_comment: comment not pinned"); return; } } status = H5Oset_comment((hid_t)loc_id, (const char*)oComment); ENVPTR->ReleaseStringUTFChars(ENVPAR comment, oComment); if (status < 0) { h5libraryError(env); } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Oset_comment_by_name * Signature: (ILjava/lang/String;Ljava/lang/String;I)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Oset_1comment_1by_1name (JNIEnv *env, jclass clss, jint loc_id, jstring name, jstring comment, jint access_id) { herr_t status; char *oName; char *oComment; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Oset_comment_by_name: name is NULL"); return; } oName = (char *)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (oName == NULL) { h5JNIFatalError( env, "H5Oset_comment_by_name: name not pinned"); return; } if (comment == NULL) { oComment = NULL; } else { oComment = (char *)ENVPTR->GetStringUTFChars(ENVPAR comment,&isCopy); if (oComment == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR name, oName); h5JNIFatalError( env, "H5Oset_comment_by_name: comment not pinned"); return; } } status = H5Oset_comment_by_name((hid_t)loc_id, (const char*)oName, (const char*)oComment, (hid_t)access_id); ENVPTR->ReleaseStringUTFChars(ENVPAR comment, oComment); ENVPTR->ReleaseStringUTFChars(ENVPAR name, oName); if (status < 0) { h5libraryError(env); } return; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Oget_comment * Signature: (I)Ljava/lang/String; */ JNIEXPORT jstring JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Oget_1comment (JNIEnv *env, jclass clss, jint loc_id) { char *oComment; size_t buf_size; ssize_t status; jstring str; /* get the length of the comment */ buf_size = H5Oget_comment((hid_t)loc_id, NULL, 0); if (buf_size < 0) { h5badArgument( env, "H5Oget_comment: buf_size < 0"); return NULL; } if (buf_size == 0) { return NULL; } buf_size++; /* add extra space for the null terminator */ oComment = (char *)malloc(sizeof(char)*buf_size); if (oComment == NULL) { /* exception -- out of memory */ h5outOfMemory( env, "H5Oget_comment: malloc failed"); return NULL; } status = H5Oget_comment((hid_t)loc_id, (char*)oComment, (size_t)buf_size); if (status >= 0) { /* may throw OutOfMemoryError */ str = ENVPTR->NewStringUTF(ENVPAR oComment); free(oComment); if (str == NULL) { h5JNIFatalError( env, "H5Oget_comment: return string not allocated"); return NULL; } } else { free(oComment); h5libraryError(env); return NULL; } return (jstring)str; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Oget_comment_by_name * Signature: (ILjava/lang/String;I)Ljava/lang/String; */ JNIEXPORT jstring JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Oget_1comment_1by_1name (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint access_id) { char *oComment; char *oName; size_t buf_size; ssize_t status; jstring str; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Oget_comment_by_name: name is NULL"); return NULL; } oName = (char *)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (oName == NULL) { h5JNIFatalError( env, "H5Oget_comment_by_name: name not pinned"); return NULL; } /* get the length of the comment */ buf_size = H5Oget_comment_by_name((hid_t)loc_id, (const char*)oName, NULL, 0, (hid_t)access_id); if (buf_size < 0) { ENVPTR->ReleaseStringUTFChars(ENVPAR name, oName); h5badArgument( env, "H5Oget_comment_by_name: buf_size < 0"); return NULL; } if (buf_size == 0) { ENVPTR->ReleaseStringUTFChars(ENVPAR name, oName); return NULL; } buf_size++; /* add extra space for the null terminator */ oComment = (char *)malloc(sizeof(char)*buf_size); if (oComment == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR name, oName); h5outOfMemory( env, "H5Oget_comment_by_name: malloc failed"); return NULL; } status = H5Oget_comment_by_name((hid_t)loc_id, (const char*)oName, (char*)oComment, (size_t)buf_size, (hid_t)access_id); ENVPTR->ReleaseStringUTFChars(ENVPAR name, oName); if (status >= 0) { /* may throw OutOfMemoryError */ str = ENVPTR->NewStringUTF(ENVPAR oComment); free(oComment); if (str == NULL) { h5JNIFatalError( env, "H5Oget_comment_by_name: return string not allocated"); return NULL; } } else { free(oComment); h5libraryError(env); return NULL; } return (jstring)str; } #ifdef __cplusplus } #endif libsis-jhdf5-java-14.12.1/source/c/hdf-java/h5oImp.h000066400000000000000000000074671256564762100216320ustar00rootroot00000000000000/* DO NOT EDIT THIS FILE - it is machine generated */ #include /* Header for class ncsa_hdf_hdf5lib_H5_H5_H5O */ #ifndef _Included_ncsa_hdf_hdf5lib_H5_H5O #define _Included_ncsa_hdf_hdf5lib_H5_H5O #ifdef __cplusplus extern "C" { #endif extern JavaVM *jvm; extern jobject visit_callback; /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Oopen * Signature: (ILjava/lang/String;I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Oopen (JNIEnv *, jclass, jint, jstring, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Oclose * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Oclose (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Ocopy * Signature: (ILjava/lang/String;ILjava/lang/String;II)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Ocopy (JNIEnv *, jclass, jint, jstring, jint, jstring, jint, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Oget_info * Signature: (I)Lncsa/hdf/hdf5lib/structs/H5O_info_t; */ JNIEXPORT jobject JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Oget_1info (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Oget_info_by_name * Signature: (ILjava/lang/String;I)Lncsa/hdf/hdf5lib/structs/H5O_info_t; */ JNIEXPORT jobject JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Oget_1info_1by_1name (JNIEnv *, jclass, jint, jstring, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Oget_info_by_idx * Signature: (ILjava/lang/String;IIJI)Lncsa/hdf/hdf5lib/structs/H5O_info_t; */ JNIEXPORT jobject JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Oget_1info_1by_1idx (JNIEnv *, jclass, jint, jstring, jint, jint, jlong, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Olink * Signature: (IILjava/lang/String;II)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Olink (JNIEnv *, jclass, jint, jint, jstring, jint, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Ovisit * Signature: (IIILjava/lang/Object;Ljava/lang/Object;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Ovisit (JNIEnv *, jclass, jint, jint, jint, jobject, jobject); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Ovisit_by_name * Signature: (ILjava/lang/String;IILjava/lang/Object;Ljava/lang/Object;I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Ovisit_1by_1name (JNIEnv *, jclass, jint, jstring, jint, jint, jobject, jobject, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Oset_comment * Signature: (ILjava/lang/String;)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Oset_1comment (JNIEnv *env, jclass clss, jint loc_id, jstring comment); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Oset_comment_by_name * Signature: (ILjava/lang/String;Ljava/lang/String;I)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Oset_1comment_1by_1name (JNIEnv *env, jclass clss, jint loc_id, jstring name, jstring comment, jint access_id); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Oget_comment * Signature: (I)Ljava/lang/String; */ JNIEXPORT jstring JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Oget_1comment (JNIEnv *env, jclass clss, jint loc_id); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Oget_comment_by_name * Signature: (ILjava/lang/String;I)Ljava/lang/String; */ JNIEXPORT jstring JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Oget_1comment_1by_1name (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint access_id); #ifdef __cplusplus } #endif #endif libsis-jhdf5-java-14.12.1/source/c/hdf-java/h5pImp.c000077500000000000000000004237531256564762100216310ustar00rootroot00000000000000/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF Java Products. The full HDF Java copyright * * notice, including terms governing use, modification, and redistribution, * * is contained in the file, COPYING. COPYING can be found at the root of * * the source code distribution tree. You can also access it online at * * http://www.hdfgroup.org/products/licenses.html. If you do not have * * access to the file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /* * This code is the C-interface called by Java programs to access the * Property List API Functions of the HDF5 library. * * Each routine wraps a single HDF entry point, generally with the * analogous arguments and return codes. * * For details of the HDF libraries, see the HDF Documentation at: * http://hdf.ncsa.uiuc.edu/HDF5/doc/ * */ #ifdef __cplusplus extern "C" { #endif #include #include #include "hdf5.h" #include "h5jni.h" #include "h5pImp.h" #include "h5util.h" #ifndef FALSE #define FALSE 0 #endif #ifndef TRUE #define TRUE (!FALSE) #endif /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pcreate * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Pcreate (JNIEnv *env, jclass clss, jint type) { hid_t retVal = -1; retVal = H5Pcreate((hid_t)type); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pclose * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Pclose (JNIEnv *env, jclass clss, jint plist) { herr_t retVal = 0; if (plist > 0) retVal = H5Pclose((hid_t)plist); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_class * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1class (JNIEnv *env, jclass clss, jint plist) { hid_t retVal = H5P_NO_CLASS; retVal = H5Pget_class((hid_t) plist); if (retVal == H5P_NO_CLASS) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pcopy * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Pcopy (JNIEnv *env, jclass clss, jint plist) { hid_t retVal = -1; retVal = H5Pcopy((hid_t)plist); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_version * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1version (JNIEnv *env, jclass clss, jint plist, jintArray version_info) { herr_t status; jint *theArray; jboolean isCopy; if (version_info == NULL) { h5nullArgument(env, "H5Pget_version: version_info input array is NULL"); return -1; } if (ENVPTR->GetArrayLength(ENVPAR version_info) < 4) { h5badArgument(env, "H5Pget_version: version_info input array < 4"); return -1; } theArray = (jint *)ENVPTR->GetIntArrayElements(ENVPAR version_info,&isCopy); if (theArray == NULL) { h5JNIFatalError(env, "H5Pget_version: version_info not pinned"); return -1; } status = H5Pget_version((hid_t)plist, (unsigned *)&(theArray[0]), (unsigned *)&(theArray[1]), (unsigned *)&(theArray[2]), (unsigned *)&(theArray[3])); if (status < 0) { ENVPTR->ReleaseIntArrayElements(ENVPAR version_info, theArray, JNI_ABORT); h5libraryError(env); return -1; } ENVPTR->ReleaseIntArrayElements(ENVPAR version_info, theArray, 0); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_userblock * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1userblock (JNIEnv *env, jclass clss, jint plist, jlong size) { long sz; herr_t retVal = -1; sz = (long)size; retVal = H5Pset_userblock((hid_t)plist, (hsize_t)sz); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_userblock * Signature: (I[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1userblock (JNIEnv *env, jclass clss, jint plist, jlongArray size) { herr_t status; jlong *theArray; jboolean isCopy; hsize_t s; if (size == NULL) { /* exception ? */ h5nullArgument(env, "H5Pget_userblock: size is NULL"); return -1; } theArray = (jlong *)ENVPTR->GetLongArrayElements(ENVPAR size, &isCopy); if (theArray == NULL) { h5JNIFatalError(env, "H5Pget_userblock: size not pinned"); return -1; } status = H5Pget_userblock((hid_t)plist, &s); if (status < 0) { ENVPTR->ReleaseLongArrayElements(ENVPAR size, theArray, JNI_ABORT); h5libraryError(env); return -1; } theArray[0] = s; ENVPTR->ReleaseLongArrayElements(ENVPAR size, theArray, 0); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_sizes * Signature: (III)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1sizes (JNIEnv *env, jclass clss, jint plist, jint sizeof_addr, jint sizeof_size) { herr_t retVal = -1; retVal = H5Pset_sizes((hid_t)plist, (size_t)sizeof_addr, (size_t)sizeof_size); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_sizes * Signature: (I[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1sizes (JNIEnv *env, jclass clss, jint plist, jlongArray size) { herr_t status; jlong *theArray; jboolean isCopy; size_t ss; size_t sa; if (size == NULL) { h5nullArgument(env, "H5Pget_sizes: size is NULL"); return -1; } if (ENVPTR->GetArrayLength(ENVPAR size) < 2) { h5badArgument(env, "H5Pget_sizes: size input array < 2 elements"); return -1; } theArray = (jlong *)ENVPTR->GetLongArrayElements(ENVPAR size, &isCopy); if (theArray == NULL) { h5JNIFatalError(env, "H5Pget_sizes: size not pinned"); return -1; } status = H5Pget_sizes((hid_t)plist, &sa, &ss); if (status < 0) { ENVPTR->ReleaseLongArrayElements(ENVPAR size, theArray, JNI_ABORT); h5libraryError(env); return -1; } theArray[0] = sa; theArray[1] = ss; ENVPTR->ReleaseLongArrayElements(ENVPAR size, theArray, 0); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_sym_k * Signature: (III)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1sym_1k (JNIEnv *env, jclass clss, jint plist, jint ik, jint lk) { herr_t retVal = -1; retVal = H5Pset_sym_k((hid_t)plist, (int)ik, (int)lk); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_sym_k * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1sym_1k (JNIEnv *env, jclass clss, jint plist, jintArray size) { herr_t status; jint *theArray; jboolean isCopy; if (size == NULL) { h5nullArgument(env, "H5Pget_sym_k: size is NULL"); return -1; } if (ENVPTR->GetArrayLength(ENVPAR size) < 2) { h5badArgument(env, "H5Pget_sym_k: size < 2 elements"); return -1; } theArray = (jint *)ENVPTR->GetIntArrayElements(ENVPAR size, &isCopy); if (theArray == NULL) { h5JNIFatalError(env, "H5Pget_sym_k: size not pinned"); return -1; } status = H5Pget_sym_k((hid_t)plist, (unsigned *)&(theArray[0]), (unsigned *)&(theArray[1])); if (status < 0) { ENVPTR->ReleaseIntArrayElements(ENVPAR size, theArray, JNI_ABORT); h5libraryError(env); return -1; } ENVPTR->ReleaseIntArrayElements(ENVPAR size, theArray, 0); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_istore_k * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1istore_1k (JNIEnv *env, jclass clss, jint plist, jint ik) { herr_t retVal = -1; retVal = H5Pset_istore_k((hid_t)plist, (int)ik); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_istore_k * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1istore_1k (JNIEnv *env, jclass clss, jint plist, jintArray ik) { herr_t status; jint *theArray; jboolean isCopy; if (ik == NULL) { h5nullArgument(env, "H5Pget_store_k: ik is NULL"); return -1; } theArray = (jint *)ENVPTR->GetIntArrayElements(ENVPAR ik, &isCopy); if (theArray == NULL) { h5JNIFatalError(env, "H5Pget_store_k: size not pinned"); return -1; } status = H5Pget_istore_k((hid_t)plist, (unsigned *)&(theArray[0])); if (status < 0) { ENVPTR->ReleaseIntArrayElements(ENVPAR ik, theArray, JNI_ABORT); h5libraryError(env); return -1; } ENVPTR->ReleaseIntArrayElements(ENVPAR ik, theArray, 0); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_layout * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1layout (JNIEnv *env, jclass clss, jint plist, jint layout) { herr_t retVal = -1; retVal = H5Pset_layout((hid_t)plist, (H5D_layout_t)layout); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_layout * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1layout (JNIEnv *env, jclass clss, jint plist) { H5D_layout_t retVal = H5D_LAYOUT_ERROR; retVal = H5Pget_layout((hid_t)plist); if (retVal == H5D_LAYOUT_ERROR) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_chunk * Signature: (II[B)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1chunk (JNIEnv *env, jclass clss, jint plist, jint ndims, jbyteArray dim) { herr_t status; jbyte *theArray; jboolean isCopy; hsize_t *da; hsize_t *lp; jlong *jlp; int i; int rank; if (dim == NULL) { h5nullArgument(env, "H5Pset_chunk: dim array is NULL"); return -1; } i = ENVPTR->GetArrayLength(ENVPAR dim); rank = i / sizeof(jlong); if (rank < ndims) { h5badArgument(env, "H5Pset_chunk: dims array < ndims"); return -1; } theArray = (jbyte *)ENVPTR->GetByteArrayElements(ENVPAR dim, &isCopy); if (theArray == NULL) { h5JNIFatalError(env, "H5Pset_chunk: dim array not pinned"); return -1; } da = lp = (hsize_t *)malloc(rank * sizeof(hsize_t)); if (da == NULL) { ENVPTR->ReleaseByteArrayElements(ENVPAR dim, theArray, JNI_ABORT); h5JNIFatalError(env, "H5Pset_chunk: dims not converted to hsize_t"); return -1; } jlp = (jlong *)theArray; for (i = 0; i < rank; i++) { *lp = (hsize_t)*jlp; lp++; jlp++; } status = H5Pset_chunk((hid_t)plist, (int)ndims, da); ENVPTR->ReleaseByteArrayElements(ENVPAR dim, theArray, JNI_ABORT); free(da); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_chunk * Signature: (II[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1chunk (JNIEnv *env, jclass clss, jint plist, jint max_ndims, jlongArray dims) { herr_t status; jlong *theArray; jboolean isCopy; hsize_t *da; int i; if (dims == NULL) { h5nullArgument(env, "H5Pget_chunk: dims is NULL"); return -1; } if (ENVPTR->GetArrayLength(ENVPAR dims) < max_ndims) { h5badArgument(env, "H5Pget_chunk: dims array < max_ndims"); return -1; } theArray = (jlong *)ENVPTR->GetLongArrayElements(ENVPAR dims, &isCopy); if (theArray == NULL) { h5JNIFatalError(env, "H5Pget_chunk: input dims not pinned"); return -1; } da = (hsize_t *)malloc(max_ndims * sizeof(hsize_t)); if (da == NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR dims, theArray, JNI_ABORT); h5JNIFatalError(env, "H5Pget_chunk: dims not converted to hsize_t"); return -1; } status = H5Pget_chunk((hid_t)plist, (int)max_ndims, da); if (status < 0) { ENVPTR->ReleaseLongArrayElements(ENVPAR dims, theArray, JNI_ABORT); free (da); h5libraryError(env); return -1; } for (i = 0; i < max_ndims; i++) { theArray[i] = da[i]; } free (da); ENVPTR->ReleaseLongArrayElements(ENVPAR dims, theArray, 0); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_alignment * Signature: (IJJ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1alignment (JNIEnv *env, jclass clss, jint plist, jlong threshold, jlong alignment) { long thr; long align; herr_t retVal = -1; thr = (long)threshold; align = (long)alignment; retVal = H5Pset_alignment((hid_t)plist, (hsize_t)thr, (hsize_t)align); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_alignment * Signature: (I[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1alignment (JNIEnv *env, jclass clss, jint plist, jlongArray alignment) { herr_t status; jlong *theArray; jboolean isCopy; hsize_t t; hsize_t a; if (alignment == NULL) { h5nullArgument(env, "H5Pget_alignment: input alignment is NULL"); return -1; } if (ENVPTR->GetArrayLength(ENVPAR alignment) < 2) { h5badArgument(env, "H5Pget_alignment: allingment input array < 2"); return -1; } theArray = (jlong *)ENVPTR->GetLongArrayElements(ENVPAR alignment, &isCopy); if (theArray == NULL) { h5JNIFatalError(env, "H5Pget_alignment: input array not pinned"); return -1; } status = H5Pget_alignment((hid_t)plist, &t, &a); if (status < 0) { ENVPTR->ReleaseLongArrayElements(ENVPAR alignment, theArray, JNI_ABORT); h5libraryError(env); return -1; } theArray[0] = t; theArray[1] = a; ENVPTR->ReleaseLongArrayElements(ENVPAR alignment, theArray, 0); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_external * Signature: (ILjava/lang/String;JJ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1external (JNIEnv *env, jclass clss, jint plist, jstring name, jlong offset, jlong size) { herr_t status; char *file; jboolean isCopy; long off; long sz; off = (long)offset; sz = (long)size; if (name == NULL) { h5nullArgument(env, "H5Pset_external: name is NULL"); return -1; } file = (char *)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (file == NULL) { h5JNIFatalError(env, "H5Pset_external: name not pinned"); return -1; } status = H5Pset_external((hid_t)plist, file, (off_t)off, (hsize_t)sz); ENVPTR->ReleaseStringUTFChars(ENVPAR name, file); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_external_count * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1external_1count (JNIEnv *env, jclass clss, jint plist) { int retVal = -1; retVal = H5Pget_external_count((hid_t)plist); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_external * Signature: (IIJ[Ljava/lang/String;[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1external (JNIEnv *env, jclass clss, jint plist, jint idx, jlong name_size, jobjectArray name, jlongArray size) { herr_t status; jlong *theArray; jboolean isCopy; char *file; jstring str; off_t o; hsize_t s; if (name_size < 0) { h5badArgument(env, "H5Pget_external: name_size < 0"); return -1; } else if (name_size == 0) { file = NULL; } else { file = (char *)malloc(sizeof(char)*(size_t)name_size); } if (size != NULL) { if (ENVPTR->GetArrayLength(ENVPAR size) < 2) { free(file); h5badArgument(env, "H5Pget_external: size input array < 2"); return -1; } theArray = (jlong *)ENVPTR->GetLongArrayElements(ENVPAR size, &isCopy); if (theArray == NULL) { free(file); h5JNIFatalError( env, "H5Pget_external: size array not pinned"); return -1; } } status = H5Pget_external((hid_t) plist, (int)idx, (size_t)name_size, file, (off_t *)&o, (hsize_t *)&s); if (status < 0) { if (size != NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR size, theArray, JNI_ABORT); } free(file); h5libraryError(env); return -1; } if (size != NULL) { theArray[0] = o; theArray[1] = s; ENVPTR->ReleaseLongArrayElements(ENVPAR size, theArray, 0); } if (file != NULL) { /* NewStringUTF may throw OutOfMemoryError */ str = ENVPTR->NewStringUTF(ENVPAR file); if (str == NULL) { free(file); h5JNIFatalError(env, "H5Pget_external: return array not created"); return -1; } /* SetObjectArrayElement may raise exceptions */ ENVPTR->SetObjectArrayElement(ENVPAR name, 0, (jobject)str); free(file); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_fill_value * Signature: (II[B)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1fill_1value (JNIEnv *env, jclass clss, jint plist_id, jint type_id, jbyteArray value) { jint status = -1; jbyte *byteP; jboolean isCopy; if (value != NULL) { byteP = ENVPTR->GetByteArrayElements(ENVPAR value, &isCopy); if (byteP == NULL) { h5JNIFatalError(env, "H5Pget_fill_value: value array not pinned"); return -1; } } status = H5Pset_fill_value((hid_t)plist_id, (hid_t)type_id, byteP); if (status < 0) { if (value != NULL) { ENVPTR->ReleaseByteArrayElements(ENVPAR value, byteP, JNI_ABORT); } h5libraryError(env); return -1; } if (value != NULL) { ENVPTR->ReleaseByteArrayElements(ENVPAR value, byteP, JNI_ABORT); } return status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_fill_value * Signature: (II[B)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1fill_1value (JNIEnv *env, jclass clss, jint plist_id, jint type_id, jbyteArray value) { jint status; jbyte *byteP; jboolean isCopy; if (value == NULL) { h5badArgument(env, "H5Pget_fill_value: value is NULL"); return -1; } byteP = ENVPTR->GetByteArrayElements(ENVPAR value, &isCopy); if (byteP == NULL) { h5JNIFatalError(env, "H5Pget_fill_value: value array not pinned"); return -1; } status = H5Pget_fill_value((hid_t)plist_id, (hid_t)type_id, byteP); if (status < 0) { ENVPTR->ReleaseByteArrayElements(ENVPAR value, byteP, JNI_ABORT); h5libraryError(env); return -1; } ENVPTR->ReleaseByteArrayElements(ENVPAR value, byteP, 0); return status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_filter * Signature: (IIIJ[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1filter (JNIEnv *env, jclass clss, jint plist, jint filter, jint flags, jlong cd_nelmts, jintArray cd_values) { herr_t status; jint *theArray; jboolean isCopy; if (cd_values == NULL) status = H5Pset_filter((hid_t)plist, (H5Z_filter_t)filter, (unsigned int)flags, (size_t)cd_nelmts, NULL); else { theArray = (jint *)ENVPTR->GetIntArrayElements(ENVPAR cd_values, &isCopy); if (theArray == NULL) { h5JNIFatalError(env, "H5Pset_filter: input array not pinned"); return -1; } status = H5Pset_filter((hid_t)plist, (H5Z_filter_t)filter, (unsigned int)flags, (size_t)cd_nelmts, (const unsigned int *)theArray); ENVPTR->ReleaseIntArrayElements(ENVPAR cd_values, theArray, JNI_ABORT); } if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_nfilters * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1nfilters (JNIEnv *env, jclass clss, jint plist) { int retVal = -1; retVal = H5Pget_nfilters((hid_t)plist); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_filter * Signature: (II[I[J[IJ[Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1filter (JNIEnv *env, jclass clss, jint plist, jint filter_number, jintArray flags, jlongArray cd_nelmts, jintArray cd_values, jlong namelen, jobjectArray name) { herr_t status; jint *flagsArray; jlong *cd_nelmtsArray; jint *cd_valuesArray; jboolean isCopy; jstring str; char *filter; if (namelen <= 0) { h5badArgument(env, "H5Pget_filter: namelen <= 0"); return -1; } if (flags == NULL) { h5badArgument(env, "H5Pget_filter: flags is NULL"); return -1; } if (cd_nelmts == NULL) { h5badArgument(env, "H5Pget_filter: cd_nelmts is NULL"); return -1; } if (cd_values == NULL) { h5badArgument(env, "H5Pget_filter: cd_values is NULL"); return -1; } filter = (char *)malloc(sizeof(char)*(size_t)namelen); if (filter == NULL) { h5outOfMemory(env, "H5Pget_filter: namelent malloc failed"); return -1; } flagsArray = (jint *)ENVPTR->GetIntArrayElements(ENVPAR flags, &isCopy); if (flagsArray == NULL) { free(filter); h5JNIFatalError(env, "H5Pget_filter: flags array not pinned"); return -1; } cd_nelmtsArray = (jlong *)ENVPTR->GetLongArrayElements(ENVPAR cd_nelmts, &isCopy); if (cd_nelmtsArray == NULL) { ENVPTR->ReleaseIntArrayElements(ENVPAR flags, flagsArray, JNI_ABORT); free(filter); h5JNIFatalError(env, "H5Pget_filter: nelmts array not pinned"); return -1; } cd_valuesArray = (jint *)ENVPTR->GetIntArrayElements(ENVPAR cd_values, &isCopy); if (cd_valuesArray == NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR cd_nelmts, cd_nelmtsArray, JNI_ABORT); ENVPTR->ReleaseIntArrayElements(ENVPAR flags, flagsArray, JNI_ABORT); free(filter); h5JNIFatalError(env, "H5Pget_filter: elmts array not pinned"); return -1; } { /* direct cast (size_t *)variable fails on 32-bit environment */ long long cd_nelmts_temp = *(cd_nelmtsArray); size_t cd_nelmts_t = (size_t)cd_nelmts_temp; unsigned int filter_config; status = H5Pget_filter2((hid_t)plist, (int)filter_number, (unsigned int *)flagsArray, &cd_nelmts_t, (unsigned int *)cd_valuesArray, (size_t)namelen, filter, &filter_config); *cd_nelmtsArray = cd_nelmts_t; } if (status < 0) { ENVPTR->ReleaseIntArrayElements(ENVPAR cd_values, cd_valuesArray, JNI_ABORT); ENVPTR->ReleaseLongArrayElements(ENVPAR cd_nelmts, cd_nelmtsArray, JNI_ABORT); ENVPTR->ReleaseIntArrayElements(ENVPAR flags, flagsArray, JNI_ABORT); free(filter); h5libraryError(env); return -1; } ENVPTR->ReleaseIntArrayElements(ENVPAR cd_values, cd_valuesArray, 0); ENVPTR->ReleaseLongArrayElements(ENVPAR cd_nelmts, cd_nelmtsArray, 0); ENVPTR->ReleaseIntArrayElements(ENVPAR flags, flagsArray, 0); /* NewStringUTF may throw OutOfMemoryError */ str = ENVPTR->NewStringUTF(ENVPAR filter); if (str == NULL) { free(filter); h5JNIFatalError(env, "H5Pget_filter: return string not pinned"); return -1; } /* SetObjectArrayElement may throw exceptiosn */ ENVPTR->SetObjectArrayElement(ENVPAR name, 0, (jobject)str); free(filter); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_driver * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1driver (JNIEnv *env, jclass clss, jint plist) { hid_t retVal = -1; retVal = H5Pget_driver((hid_t) plist); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_cache * Signature: (IIJJD)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1cache (JNIEnv *env, jclass clss, jint plist, jint mdc_nelmts, jlong rdcc_nelmts, jlong rdcc_nbytes, jdouble rdcc_w0) { herr_t retVal = -1; retVal = H5Pset_cache((hid_t)plist, (int)mdc_nelmts, (size_t)rdcc_nelmts, (size_t)rdcc_nbytes, (double) rdcc_w0); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_cache * Signature: (I[I[J[J[D)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1cache (JNIEnv *env, jclass clss, jint plist, jintArray mdc_nelmts, jlongArray rdcc_nelmts, jlongArray rdcc_nbytes, jdoubleArray rdcc_w0) { herr_t status; jint mode; jdouble *w0Array; jlong *rdcc_nelmtsArray; jlong *nbytesArray; jboolean isCopy; if (rdcc_w0 == NULL) { w0Array = (jdouble *)NULL; } else { w0Array = (jdouble *)ENVPTR->GetDoubleArrayElements(ENVPAR rdcc_w0, &isCopy); if (w0Array == NULL) { h5JNIFatalError(env, "H5Pget_cache: w0_array array not pinned"); return -1; } } if (rdcc_nelmts == NULL) { rdcc_nelmtsArray = (jlong *) NULL; } else { rdcc_nelmtsArray = (jlong *)ENVPTR->GetLongArrayElements(ENVPAR rdcc_nelmts, &isCopy); if (rdcc_nelmtsArray == NULL) { /* exception -- out of memory */ if (w0Array != NULL) { ENVPTR->ReleaseDoubleArrayElements(ENVPAR rdcc_w0, w0Array, JNI_ABORT); } h5JNIFatalError(env, "H5Pget_cache: rdcc_nelmts array not pinned"); return -1; } } if (rdcc_nbytes == NULL) { nbytesArray = (jlong *) NULL; } else { nbytesArray = (jlong *)ENVPTR->GetLongArrayElements(ENVPAR rdcc_nbytes, &isCopy); if (nbytesArray == NULL) { if (w0Array != NULL) { ENVPTR->ReleaseDoubleArrayElements(ENVPAR rdcc_w0, w0Array, JNI_ABORT); } if (rdcc_nelmtsArray != NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR rdcc_nelmts, rdcc_nelmtsArray, JNI_ABORT); } h5JNIFatalError(env, "H5Pget_cache: nbytesArray array not pinned"); return -1; } } { /* direct cast (size_t *)variable fails on 32-bit environment */ long long rdcc_nelmts_temp = *(rdcc_nelmtsArray); size_t rdcc_nelmts_t = (size_t)rdcc_nelmts_temp; long long nbytes_temp = *(nbytesArray); size_t nbytes_t = (size_t)nbytes_temp; status = H5Pget_cache((hid_t)plist, (int *)NULL, &rdcc_nelmts_t, &nbytes_t, (double *)w0Array); *rdcc_nelmtsArray = rdcc_nelmts_t; *nbytesArray = nbytes_t; } if (status < 0) { mode = JNI_ABORT; } else { mode = 0; /* commit and free */ } if (rdcc_nelmtsArray != NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR rdcc_nelmts, rdcc_nelmtsArray, mode); } if (nbytesArray != NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR rdcc_nbytes, nbytesArray, mode); } if (w0Array != NULL) { ENVPTR->ReleaseDoubleArrayElements(ENVPAR rdcc_w0, w0Array, mode); } if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_buffer * Signature: (IJ[B[B)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1buffer (JNIEnv *env, jclass clss, jint plist, jlong size, jbyteArray tconv, jbyteArray bkg) { h5unimplemented(env, "H5Pset_buffer: not implemented"); return -1; #ifdef notdef /* DON'T IMPLEMENT THIS!!! */ jint status = -1; jbyte *tconvP; jbyte *bkgP; jboolean isCopy; if (tconv == NULL) tconvP = (jbyte *)NULL; else { tconvP = ENVPTR->GetByteArrayElements(ENVPAR tconv, &isCopy); if (tconvP == NULL) { h5JNIFatalError(env, "H5Pset_buffer: tconv not pinned"); return -1; } } if (bkg == NULL) bkgP = (jbyte *)NULL; else { bkgP = ENVPTR->GetByteArrayElements(ENVPAR bkg, &isCopy); if (bkgP == NULL) { h5JNIFatalError(env, "H5Pset_buffer: bkg not pinned"); return -1; } } status = H5Pset_buffer((hid_t)plist, (size_t)size, tconvP, bkgP); if (status < 0) { if (tconv != NULL) ENVPTR->ReleaseByteArrayElements(ENVPAR tconv, tconvP, JNI_ABORT); if (bkg != NULL) ENVPTR->ReleaseByteArrayElements(ENVPAR bkg, bkgP, JNI_ABORT); h5libraryError(env); return -1; } if (tconv != NULL) ENVPTR->ReleaseByteArrayElements(ENVPAR tconv, tconvP, 0); if (bkg != NULL) ENVPTR->ReleaseByteArrayElements(ENVPAR bkg, bkgP, 0); return status; #endif } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_buffer * Signature: (I[B[B)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1buffer (JNIEnv *env, jclass clss, jint plist, jbyteArray tconv, jbyteArray bkg) { h5unimplemented(env, "H5Pset_buffer: not implemented"); return -1; #ifdef notdef /* DON'T IMPLEMENT THIS!!! */ jlong status = -1; jbyte *tconvP; jbyte *bkgP; jboolean isCopy; if (tconv == NULL) { h5nullArgument(env, "H5Pget_buffer: tconv input array is NULL"); return -1; } tconvP = ENVPTR->GetByteArrayElements(ENVPAR tconv, &isCopy); if (tconvP == NULL) { h5JNIFatalError(env, "H5Pget_buffer: tconv not pinned"); return -1; } if (bkg == NULL) { h5nullArgument(env, "H5Pget_buffer: bkg array is NULL"); return -1; } bkgP = ENVPTR->GetByteArrayElements(ENVPAR bkg, &isCopy); if (bkgP == NULL) { h5JNIFatalError(env, "H5Pget_buffer: bkg not pinned"); return -1; } status = H5Pget_buffer((hid_t)plist, tconvP, bkgP); if (status < 0) { ENVPTR->ReleaseByteArrayElements(ENVPAR tconv, tconvP, JNI_ABORT); ENVPTR->ReleaseByteArrayElements(ENVPAR bkg, bkgP, JNI_ABORT); h5libraryError(env); return -1; } ENVPTR->ReleaseByteArrayElements(ENVPAR tconv, tconvP, 0); ENVPTR->ReleaseByteArrayElements(ENVPAR bkg, bkgP, 0); return status; #endif } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_buffer_size * Signature: (IJ)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1buffer_1size (JNIEnv *env, jclass clss, jint plist, jlong size) { herr_t status = -1; status = H5Pset_buffer((hid_t)plist, (size_t)size, NULL, NULL); if (status < 0) { h5libraryError(env); return; } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_buffer_size * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1buffer_1size (JNIEnv *env, jclass clss, jint plist) { size_t size = -1; size = H5Pget_buffer((hid_t)plist, NULL, NULL); if (size < 0) { h5libraryError(env); return -1; } return (jlong)size; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_preserve * Signature: (IZ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1preserve (JNIEnv *env, jclass clss, jint plist, jboolean status) { hbool_t st; herr_t retVal = -1; if (status == JNI_TRUE) { st = TRUE; } else if (status == JNI_FALSE) { st = FALSE; } else { /* exception -- bad argument */ h5badArgument(env, "H5Pset_preserve: status not TRUE or FALSE"); return -1; } retVal = H5Pset_preserve((hid_t)plist, (hbool_t)st); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_preserve * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1preserve (JNIEnv *env, jclass clss, jint plist) { herr_t retValue = -1; retValue = H5Pget_preserve((hid_t)plist); if (retValue < 0) { h5libraryError(env); } return (jint)retValue; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_deflate * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1deflate (JNIEnv *env, jclass clss, jint plist, jint level) { herr_t retValue = -1; retValue = H5Pset_deflate((hid_t)plist, (int)level); if (retValue < 0) { h5libraryError(env); } return (jint)retValue; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_gc_references * Signature: (IZ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1gc_1references (JNIEnv *env, jclass clss, jint fapl_id, jboolean gc_ref) { herr_t retVal = -1; unsigned gc_ref_val; if (gc_ref == JNI_TRUE) { gc_ref_val = 1; } else { gc_ref_val = 0; } retVal = H5Pset_gc_references((hid_t)fapl_id, gc_ref_val); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_gc_references * Signature: (I[Z)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1gc_1references (JNIEnv *env, jclass clss, jint fapl_id, jbooleanArray gc_ref) { herr_t status; jboolean *theArray; jboolean isCopy; unsigned gc_ref_val = 0; if (gc_ref == NULL) { h5nullArgument(env, "H5Pget_gc_references: gc_ref input array is NULL"); return -1; } theArray = (jboolean *)ENVPTR->GetBooleanArrayElements(ENVPAR gc_ref, &isCopy); if (theArray == NULL) { h5JNIFatalError(env, "H5Pget_gc_references: gc_ref not pinned"); return -1; } status = H5Pget_gc_references((hid_t)fapl_id, (unsigned *)&gc_ref_val); if (status < 0) { ENVPTR->ReleaseBooleanArrayElements(ENVPAR gc_ref, theArray, JNI_ABORT); h5libraryError(env); return -1; } if (gc_ref_val == 1) { theArray[0] = JNI_TRUE; } else { theArray[0] = JNI_FALSE; } ENVPTR->ReleaseBooleanArrayElements(ENVPAR gc_ref, theArray, 0); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_gcreferences * Signature: (I)Z */ JNIEXPORT jboolean JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1gcreferences (JNIEnv *env, jclass clss, jint fapl_id) { herr_t status; unsigned gc_ref_val = 0; status = H5Pget_gc_references((hid_t)fapl_id, (unsigned *)&gc_ref_val); if (status < 0) { h5libraryError(env); return JNI_FALSE; } if (gc_ref_val == 1) { return JNI_TRUE; } return JNI_FALSE; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_btree_ratios * Signature: (IDDD)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1btree_1ratios (JNIEnv *env, jclass clss, jint plist_id, jdouble left, jdouble middle, jdouble right) { herr_t status; status = H5Pset_btree_ratios((hid_t)plist_id, (double)left,(double)middle, (double)right); if (status < 0) { h5libraryError(env); return -1; } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_btree_ratios * Signature: (I[D[D[D)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1btree_1ratios (JNIEnv *env, jclass clss, jint plist_id, jdoubleArray left, jdoubleArray middle, jdoubleArray right) { herr_t status; jdouble *leftP; jdouble *middleP; jdouble *rightP; jboolean isCopy; if (left == NULL) { h5nullArgument(env, "H5Pget_btree_ratios: left input array is NULL"); return -1; } if (middle == NULL) { h5nullArgument(env, "H5Pget_btree_ratios: middle input array is NULL"); return -1; } if (right == NULL) { h5nullArgument(env, "H5Pget_btree_ratios: right input array is NULL"); return -1; } leftP = (jdouble *)ENVPTR->GetDoubleArrayElements(ENVPAR left, &isCopy); if (leftP == NULL) { h5JNIFatalError(env, "H5Pget_btree_ratios: left not pinned"); return -1; } middleP = (jdouble *)ENVPTR->GetDoubleArrayElements(ENVPAR middle, &isCopy); if (middleP == NULL) { ENVPTR->ReleaseDoubleArrayElements(ENVPAR left, leftP, JNI_ABORT); h5JNIFatalError(env, "H5Pget_btree_ratios: middle not pinned"); return -1; } rightP = (jdouble *)ENVPTR->GetDoubleArrayElements(ENVPAR right, &isCopy); if (rightP == NULL) { ENVPTR->ReleaseDoubleArrayElements(ENVPAR left, leftP, JNI_ABORT); ENVPTR->ReleaseDoubleArrayElements(ENVPAR middle, middleP, JNI_ABORT); h5JNIFatalError(env, "H5Pget_btree_ratios: middle not pinned"); return -1; } status = H5Pget_btree_ratios((hid_t)plist_id, (double *)leftP, (double *)middleP, (double *)rightP); if (status < 0) { ENVPTR->ReleaseDoubleArrayElements(ENVPAR left, leftP, JNI_ABORT); ENVPTR->ReleaseDoubleArrayElements(ENVPAR middle, middleP, JNI_ABORT); ENVPTR->ReleaseDoubleArrayElements(ENVPAR right, rightP, JNI_ABORT); h5libraryError(env); return -1; } ENVPTR->ReleaseDoubleArrayElements(ENVPAR left, leftP, 0); ENVPTR->ReleaseDoubleArrayElements(ENVPAR middle, middleP, 0); ENVPTR->ReleaseDoubleArrayElements(ENVPAR right, rightP, 0); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_small_data_block_size * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1small_1data_1block_1size (JNIEnv *env, jclass clss, jint plist, jlong size) { long sz; herr_t retVal = -1; sz = (long)size; retVal = H5Pset_small_data_block_size((hid_t)plist, (hsize_t)sz); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_small_data_block_size * Signature: (I[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1small_1data_1block_1size (JNIEnv *env, jclass clss, jint plist, jlongArray size) { herr_t status; jlong *theArray; jboolean isCopy; hsize_t s; if (size == NULL) { /* exception ? */ h5nullArgument(env, "H5Pget_small_user_block_size: size is NULL"); return -1; } theArray = (jlong *)ENVPTR->GetLongArrayElements(ENVPAR size, &isCopy); if (theArray == NULL) { h5JNIFatalError(env, "H5Pget_userblock: size not pinned"); return -1; } status = H5Pget_small_data_block_size((hid_t)plist, &s); if (status < 0) { ENVPTR->ReleaseLongArrayElements(ENVPAR size, theArray, JNI_ABORT); h5libraryError(env); return -1; } theArray[0] = s; ENVPTR->ReleaseLongArrayElements(ENVPAR size, theArray, 0); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_small_data_block_size_long * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1small_1data_1block_1size_1long (JNIEnv *env, jclass clss, jint plist) { herr_t status; hsize_t s; status = H5Pget_small_data_block_size((hid_t)plist, &s); if (status < 0) { h5libraryError(env); return -1; } return (jlong)s; } /*************************************************************** * New APIs for HDF5.1.6 * ***************************************************************/ /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_alloc_time * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1alloc_1time (JNIEnv *env, jclass clss, jint plist, jint alloc_time) { herr_t retVal = -1; retVal = H5Pset_alloc_time((hid_t)plist, (H5D_alloc_time_t)alloc_time); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_alloc_time * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1alloc_1time (JNIEnv *env, jclass clss, jint plist, jintArray alloc_time) { herr_t retVal = -1; jint *theArray; jboolean isCopy; H5D_alloc_time_t time; if (alloc_time == NULL) { /* exception ? */ h5nullArgument(env, "H5Pget_alloc_time: alloc_time is NULL"); return -1; } theArray = (jint *)ENVPTR->GetIntArrayElements(ENVPAR alloc_time, &isCopy); if (theArray == NULL) { h5JNIFatalError(env, "H5Pget_alloc_time: alloc_time not pinned"); return -1; } retVal = H5Pget_alloc_time((hid_t)plist, &time ); if (retVal < 0) { ENVPTR->ReleaseIntArrayElements(ENVPAR alloc_time, theArray, JNI_ABORT); h5libraryError(env); return -1; } theArray[0] = time; ENVPTR->ReleaseIntArrayElements(ENVPAR alloc_time, theArray, 0); return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_fill_time * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1fill_1time (JNIEnv *env, jclass clss, jint plist, jint fill_time) { herr_t retVal = -1; retVal = H5Pset_fill_time((hid_t)plist, (H5D_fill_time_t)fill_time); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_fill_time * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1fill_1time (JNIEnv *env, jclass clss, jint plist, jintArray fill_time) { herr_t retVal = -1; jint *theArray; jboolean isCopy; H5D_fill_time_t time; if (fill_time == NULL) { /* exception ? */ h5nullArgument(env, "H5Pget_fill_time: fill_time is NULL"); return -1; } theArray = (jint *)ENVPTR->GetIntArrayElements(ENVPAR fill_time, &isCopy); if (theArray == NULL) { h5JNIFatalError(env, "H5Pget_fill_time: fill_time not pinned"); return -1; } retVal = H5Pget_fill_time((hid_t)plist, &time); if (retVal < 0) { ENVPTR->ReleaseIntArrayElements(ENVPAR fill_time, theArray, JNI_ABORT); h5libraryError(env); return -1; } theArray[0] = time; ENVPTR->ReleaseIntArrayElements(ENVPAR fill_time, theArray, 0); return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pfill_value_defined * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pfill_1value_1defined (JNIEnv *env, jclass clss, jint plist, jintArray status) { herr_t retVal = -1; jint *theArray; jboolean isCopy; H5D_fill_value_t value; if (status == NULL) { /* exception ? */ h5nullArgument(env, "H5Pfill_value_defined: status is NULL"); return -1; } theArray = (jint *)ENVPTR->GetIntArrayElements(ENVPAR status, &isCopy); if (theArray == NULL) { h5JNIFatalError(env, "H5Pfill_value_defined: status not pinned"); return -1; } retVal = H5Pfill_value_defined((hid_t)plist, &value ); if (retVal < 0) { ENVPTR->ReleaseIntArrayElements(ENVPAR status, theArray, JNI_ABORT); h5libraryError(env); return -1; } theArray[0] = value; ENVPTR->ReleaseIntArrayElements(ENVPAR status, theArray, 0); return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_fletcher32 * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1fletcher32 (JNIEnv *env, jclass clss, jint plist) { herr_t retVal = -1; retVal = H5Pset_fletcher32((hid_t)plist); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_edc_check * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1edc_1check (JNIEnv *env, jclass clss, jint plist, jint check) { herr_t retVal = -1; retVal = H5Pset_edc_check((hid_t)plist, (H5Z_EDC_t)check); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_edc_check * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1edc_1check (JNIEnv *env, jclass clss, jint plist) { H5Z_EDC_t retVal = (H5Z_EDC_t)-1; retVal = H5Pget_edc_check((hid_t)plist); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_shuffle * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1shuffle (JNIEnv *env, jclass clss, jint plist) { herr_t retVal = -1; retVal = H5Pset_shuffle((hid_t)plist); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_szip * Signature: (III)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1szip (JNIEnv *env, jclass clss, jint plist, jint options_mask, jint pixels_per_block) { herr_t retVal = -1; retVal = H5Pset_szip((hid_t)plist, (unsigned int)options_mask, (unsigned int)pixels_per_block); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_hyper_vector_size * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1hyper_1vector_1size (JNIEnv *env, jclass clss, jint plist, jlong vector_size) { herr_t retVal = -1; retVal = H5Pset_hyper_vector_size((hid_t)plist, (size_t)vector_size); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_hyper_vector_size * Signature: (I[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1hyper_1vector_1size (JNIEnv *env, jclass clss, jint plist, jlongArray vector_size) { herr_t retVal = -1; jlong *theArray; size_t size; jboolean isCopy; if (vector_size == NULL) { /* exception ? */ h5nullArgument(env, "H5Pget_hyper_vector_size: vector_size is NULL"); return -1; } theArray = (jlong *)ENVPTR->GetLongArrayElements(ENVPAR vector_size, &isCopy); if (theArray == NULL) { h5JNIFatalError(env, "H5Pget_hyper_vector_size: vector_size not pinned"); return -1; } retVal = H5Pget_hyper_vector_size((hid_t)plist, &size); if (retVal < 0) { ENVPTR->ReleaseLongArrayElements(ENVPAR vector_size, theArray, JNI_ABORT); h5libraryError(env); return -1; } theArray[0] = size; ENVPTR->ReleaseLongArrayElements(ENVPAR vector_size, theArray, 0); return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pall_filters_avail * Signature: (I)Z */ JNIEXPORT jboolean JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pall_1filters_1avail (JNIEnv *env, jclass clss, jint dcpl_id) { htri_t bval; bval = H5Pall_filters_avail((hid_t)dcpl_id); if (bval > 0) { return JNI_TRUE; } else if (bval == 0) { return JNI_FALSE; } else { h5libraryError(env); return JNI_FALSE; } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pmodify_filter * Signature: (IIIJ[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pmodify_1filter (JNIEnv *env, jclass clss, jint plist, jint filter, jint flags, jlong cd_nelmts, jintArray cd_values) { herr_t status; jint *cd_valuesP; jboolean isCopy; if (cd_values == NULL) { h5nullArgument(env, "H5Pmodify_filter: cd_values is NULL"); return -1; } cd_valuesP = ENVPTR->GetIntArrayElements(ENVPAR cd_values,&isCopy); if (cd_valuesP == NULL) { h5JNIFatalError(env, "H5Pmodify_filter: cd_values not pinned"); return -1; } status = H5Pmodify_filter((hid_t)plist, (H5Z_filter_t)filter,(const unsigned int)flags, (size_t)cd_nelmts, (unsigned int *)cd_valuesP); ENVPTR->ReleaseIntArrayElements(ENVPAR cd_values, cd_valuesP, JNI_ABORT); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_filter_by_id * Signature: (II[I[J[IJ[Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1filter_1by_1id (JNIEnv *env, jclass clss, jint plist, jint filter, jintArray flags, jlongArray cd_nelmts, jintArray cd_values, jlong namelen, jobjectArray name) { herr_t status; jint *cd_valuesArray; jint *flagsArray; jlong *cd_nelmtsArray; jboolean isCopy; jstring str; char *aName; int i = 0; int rank; long bs; bs = (long)namelen; if (bs <= 0) { h5badArgument(env, "H5Pget_filter_by_id: namelen <= 0"); return -1; } if (flags == NULL) { h5nullArgument(env, "H5Pget_filter_by_id: flags is NULL"); return -1; } if (cd_nelmts == NULL) { h5nullArgument(env, "H5Pget_filter_by_id: cd_nelms is NULL"); return -1; } if (cd_values == NULL) { h5nullArgument(env, "H5Pget_filter_by_id: cd_values is NULL"); return -1; } if (name == NULL) { h5nullArgument(env, "H5Pget_filter_by_id: name is NULL"); return -1; } aName = (char*)malloc(sizeof(char)*bs); if (aName == NULL) { h5outOfMemory(env, "H5Pget_filter_by_id: malloc failed"); return -1; } flagsArray = ENVPTR->GetIntArrayElements(ENVPAR flags, &isCopy); if (flagsArray == NULL) { free(aName); h5JNIFatalError(env, "H5Pget_filter_by_id: flags not pinned"); return -1; } cd_nelmtsArray = ENVPTR->GetLongArrayElements(ENVPAR cd_nelmts, &isCopy); if (cd_nelmtsArray == NULL) { ENVPTR->ReleaseIntArrayElements(ENVPAR flags, flagsArray, JNI_ABORT); free(aName); h5JNIFatalError(env, "H5Pget_filter_by_id: cd_nelms not pinned"); return -1; } cd_valuesArray = ENVPTR->GetIntArrayElements(ENVPAR cd_values, &isCopy); rank = ENVPTR->GetArrayLength(ENVPAR cd_values); if (cd_valuesArray == NULL) { ENVPTR->ReleaseIntArrayElements(ENVPAR flags, flagsArray, JNI_ABORT); ENVPTR->ReleaseLongArrayElements(ENVPAR cd_nelmts, cd_nelmtsArray, JNI_ABORT); ENVPTR->ReleaseIntArrayElements(ENVPAR cd_values, cd_valuesArray, JNI_ABORT); free(aName); h5JNIFatalError(env, "H5Pget_filter_by_id: cd_values array not converted to unsigned int."); return -1; } { /* direct cast (size_t *)variable fails on 32-bit environment */ long long cd_nelmts_temp = *(cd_nelmtsArray); size_t cd_nelmts_t = (size_t)cd_nelmts_temp; unsigned int filter_config; status = H5Pget_filter_by_id2( (hid_t)plist, (H5Z_filter_t)filter, (unsigned int *)flagsArray, &cd_nelmts_t, (unsigned int *)cd_valuesArray, (size_t)namelen, (char *)aName, &filter_config); *cd_nelmtsArray = cd_nelmts_t; } if (status < 0) { ENVPTR->ReleaseIntArrayElements(ENVPAR flags, flagsArray, JNI_ABORT); ENVPTR->ReleaseLongArrayElements(ENVPAR cd_nelmts, cd_nelmtsArray, JNI_ABORT); ENVPTR->ReleaseIntArrayElements(ENVPAR cd_values, cd_valuesArray, JNI_ABORT); free(aName); h5libraryError(env); return -1; } str = ENVPTR->NewStringUTF(ENVPAR aName); ENVPTR->ReleaseIntArrayElements(ENVPAR flags, flagsArray, 0); ENVPTR->ReleaseLongArrayElements(ENVPAR cd_nelmts, cd_nelmtsArray, 0); ENVPTR->ReleaseIntArrayElements(ENVPAR cd_values, cd_valuesArray, 0); free(aName); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_fclose_degree * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1fclose_1degree (JNIEnv *env, jclass clss, jint plist, jint fc_degree) { herr_t retVal = -1; retVal = H5Pset_fclose_degree((hid_t)plist, (H5F_close_degree_t)fc_degree); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_fclose_degree * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1fclose_1degree (JNIEnv *env, jclass clss, jint plist) { H5F_close_degree_t degree; herr_t retVal = -1; retVal = H5Pget_fclose_degree((hid_t)plist, °ree); if (retVal < 0) { h5libraryError(env); } return (jint)degree; } /********************************************************************** * * * File access properties * * * **********************************************************************/ /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_fapl_family * Signature: (IJI)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1fapl_1family (JNIEnv *env, jclass clss, jint plist, jlong memb_size, jint memb_plist) { long ms; herr_t retVal = -1; ms = (long)memb_size; retVal = H5Pset_fapl_family((hid_t)plist, (hsize_t)ms, (hid_t)memb_plist); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_fapl_family * Signature: (I[J[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1fapl_1family (JNIEnv *env, jclass clss, jint tid, jlongArray memb_size, jintArray memb_plist) { herr_t status; jlong *sizeArray; jint *plistArray; jboolean isCopy; hsize_t *sa; int i; int rank; if (memb_size == NULL) { h5nullArgument(env, "H5Pget_family: memb_size is NULL"); return -1; } if (memb_plist == NULL) { h5nullArgument(env, "H5Pget_family: memb_plist is NULL"); return -1; } sizeArray = (jlong *)ENVPTR->GetLongArrayElements(ENVPAR memb_size, &isCopy); if (sizeArray == NULL) { h5JNIFatalError(env, "H5Pget_family: sizeArray not pinned"); return -1; } rank = ENVPTR->GetArrayLength(ENVPAR memb_size); sa = (hsize_t *)malloc( rank * sizeof(hsize_t)); if (sa == NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR memb_size, sizeArray, JNI_ABORT); h5JNIFatalError(env, "H5Screate-simple: dims not converted to hsize_t"); return -1; } plistArray = (jint *)ENVPTR->GetIntArrayElements(ENVPAR memb_plist, &isCopy); if (plistArray == NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR memb_size, sizeArray, JNI_ABORT); h5JNIFatalError(env, "H5Pget_family: plistArray not pinned"); return -1; } status = H5Pget_fapl_family ((hid_t)tid, sa, (hid_t *)plistArray); if (status < 0) { free(sa); ENVPTR->ReleaseLongArrayElements(ENVPAR memb_size, sizeArray, JNI_ABORT); ENVPTR->ReleaseIntArrayElements(ENVPAR memb_plist, plistArray, JNI_ABORT); h5libraryError(env); return -1; } for (i = 0; i < rank; i++) { sizeArray[i] = sa[i]; } free(sa); ENVPTR->ReleaseLongArrayElements(ENVPAR memb_size, sizeArray, 0); ENVPTR->ReleaseIntArrayElements(ENVPAR memb_plist, plistArray, 0); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_fapl_core * Signature: (IJZ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1fapl_1core (JNIEnv *env, jclass clss, jint fapl_id, jlong increment, jboolean backing_store) { herr_t retVal = -1; retVal = H5Pset_fapl_core((hid_t)fapl_id, (size_t)increment, (hbool_t)backing_store); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_fapl_core * Signature: (I[J[Z)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1fapl_1core (JNIEnv *env, jclass clss, jint fapl_id, jlongArray increment, jbooleanArray backing_store) { herr_t status; jlong *incArray; jboolean *backArray; jboolean isCopy; if (increment == NULL) { h5nullArgument(env, "H5Pget_fapl_core: increment is NULL"); return -1; } if (backing_store == NULL) { h5nullArgument(env, "H5Pget_fapl_core: backing_store is NULL"); return -1; } incArray = (jlong *)ENVPTR->GetLongArrayElements(ENVPAR increment, &isCopy); if (incArray == NULL) { h5JNIFatalError(env, "H5Pget_fapl_core: incArray not pinned"); return -1; } backArray = (jboolean *)ENVPTR->GetBooleanArrayElements(ENVPAR backing_store, &isCopy); if (backArray == NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR increment, incArray, JNI_ABORT); h5JNIFatalError(env, "H5Pget_fapl_core: backArray not pinned"); return -1; } { /* direct cast (size_t *)variable fails on 32-bit environment */ long long inc_temp = *(incArray); size_t inc_t = (size_t)inc_temp; status = H5Pget_fapl_core((hid_t)fapl_id, &inc_t, (hbool_t *)backArray); *incArray = inc_t; } if (status < 0) { ENVPTR->ReleaseLongArrayElements(ENVPAR increment, incArray, JNI_ABORT); ENVPTR->ReleaseBooleanArrayElements(ENVPAR backing_store, backArray, JNI_ABORT); h5libraryError(env); return -1; } ENVPTR->ReleaseLongArrayElements(ENVPAR increment, incArray, 0); ENVPTR->ReleaseBooleanArrayElements(ENVPAR backing_store, backArray, 0); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_family_offset * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1family_1offset (JNIEnv *env, jclass clss, jint fapl_id, jlong offset) { herr_t retVal = -1; retVal = H5Pset_family_offset ((hid_t)fapl_id, (hsize_t)offset); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_family_offset * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1family_1offset (JNIEnv *env, jclass clss, jint fapl_id) { hsize_t offset = -1; herr_t retVal = -1; retVal = H5Pget_family_offset ((hid_t)fapl_id, &offset); if (retVal < 0) { h5libraryError(env); } return (jlong)offset; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_fapl_log * Signature: (ILjava/lang/String;JJ)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1fapl_1log (JNIEnv *env, jclass clss, jint fapl_id, jstring logfile, jlong flags, jlong buf_size) { herr_t retVal = -1; char *pLogfile; jboolean isCopy; if (logfile == NULL) { h5nullArgument(env, "H5Pset_fapl_log: logfile is NULL"); return; } pLogfile = (char *)ENVPTR->GetStringUTFChars(ENVPAR logfile, &isCopy); if (pLogfile == NULL) { h5JNIFatalError(env, "H5Pset_fapl_log: logfile not pinned"); return; } #if (H5_VERS_RELEASE > 6) /* H5_VERSION_GE(1,8,7) */ retVal = H5Pset_fapl_log( (hid_t)fapl_id, (const char *)pLogfile, (unsigned long long)flags, (size_t)buf_size ); #else retVal = H5Pset_fapl_log( (hid_t)fapl_id, (const char *)pLogfile, (unsigned int)flags, (size_t)buf_size ); #endif if (retVal < 0) { h5libraryError(env); } ENVPTR->ReleaseStringUTFChars(ENVPAR logfile, pLogfile); if (retVal < 0) { h5libraryError(env); } return; } /********************************************************************** * * * New functions release 1.6.3 versus release 1.6.2 * * * **********************************************************************/ /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Premove_filter * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5P1remove_1filter (JNIEnv *env, jclass clss, jint obj_id, jint filter) { herr_t status; status = H5Premove_filter ((hid_t)obj_id, (H5Z_filter_t)filter); if (status < 0) { h5libraryError(env); } return status; } /********************************************************************** * * Modified by Peter Cao on July 26, 2006: Some of the Generic Property APIs have callback function pointers, which Java does not support. Only the Generic Property APIs without function pointers are implemented * * **********************************************************************/ /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset * Signature: (ILjava/lang/String;I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset (JNIEnv *env, jclass clss, jint plid, jstring name, jint val) { char *cstr; jboolean isCopy; hid_t retVal = -1; if (name == NULL) { h5nullArgument(env, "H5Pset: name is NULL"); return -1; } cstr = (char *)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (cstr == NULL) { h5JNIFatalError(env, "H5Pset: name not pinned"); return -1; } retVal = H5Pset((hid_t)plid, cstr, &val); ENVPTR->ReleaseStringUTFChars(ENVPAR name, cstr); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pexist * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pexist (JNIEnv *env, jclass clss, jint plid, jstring name) { char *cstr; jboolean isCopy; hid_t retVal = -1; if (name == NULL) { h5nullArgument(env, "H5Pexist: name is NULL"); return -1; } cstr = (char *)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (cstr == NULL) { h5JNIFatalError(env, "H5Pexist: name not pinned"); return -1; } retVal = H5Pexist((hid_t)plid, cstr); ENVPTR->ReleaseStringUTFChars(ENVPAR name, cstr); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_size * Signature: (ILjava/lang/String;)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1size (JNIEnv *env, jclass clss, jint plid, jstring name) { char *cstr; jboolean isCopy; hid_t retVal = -1; size_t size; if (name == NULL) { h5nullArgument( env, "H5Pget_size: name is NULL"); return -1; } cstr = (char *)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (cstr == NULL) { h5JNIFatalError( env, "H5Pget_size: name not pinned"); return -1; } retVal = H5Pget_size((hid_t)plid, cstr, &size); ENVPTR->ReleaseStringUTFChars(ENVPAR name, cstr); if (retVal < 0) { h5libraryError(env); } return (jlong) size; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_nprops * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1nprops (JNIEnv *env, jclass clss, jint plid) { hid_t retVal = -1; size_t nprops; retVal = H5Pget_nprops((hid_t)plid, &nprops); if (retVal < 0) { h5libraryError(env); } return (jlong)nprops; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_class_name * Signature: (I)Ljava/lang/String; */ JNIEXPORT jstring JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1class_1name (JNIEnv *env, jclass clss, jint plid) { char *c_str; jstring j_str; c_str = H5Pget_class_name((hid_t)plid); if (c_str == NULL) { h5libraryError(env); return NULL; } j_str = ENVPTR->NewStringUTF(ENVPAR c_str); H5free_memory(c_str); if (j_str == NULL) { h5JNIFatalError(env,"H5Pget_class_name: return string failed"); } return j_str; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_class_parent * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1class_1parent (JNIEnv *env, jclass clss, jint plid) { hid_t retVal = -1; retVal = H5Pget_class_parent((hid_t)plid); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pisa_class * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pisa_1class (JNIEnv *env, jclass clss, jint plid, jint pcls) { htri_t retVal = -1; retVal = H5Pisa_class((hid_t)plid, (hid_t)pcls); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget (JNIEnv *env, jclass clss, jint plid, jstring name) { char *cstr; jboolean isCopy; jint val; jint retVal = -1; if (name == NULL) { h5nullArgument(env, "H5Pget: name is NULL"); return -1; } cstr = (char *)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (cstr == NULL) { h5JNIFatalError(env, "H5Pget: name not pinned"); return -1; } retVal = H5Pget((hid_t)plid, cstr, &val); ENVPTR->ReleaseStringUTFChars(ENVPAR name, cstr); if (retVal < 0) { h5libraryError(env); } return (jint)val; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pequal * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pequal (JNIEnv *env, jclass clss, jint plid1, jint plid2) { htri_t retVal = -1; retVal = H5Pequal((hid_t)plid1, (hid_t)plid2); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pcopy_prop * Signature: (IILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pcopy_1prop (JNIEnv *env, jclass clss, jint dst_plid, jint src_plid, jstring name) { char *cstr; jboolean isCopy; jint retVal = -1; if (name == NULL) { h5nullArgument(env, "H5Pcopy_prop: name is NULL"); return -1; } cstr = (char *)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (cstr == NULL) { h5JNIFatalError(env, "H5Pcopy_prop: name not pinned"); return -1; } retVal = H5Pcopy_prop((hid_t)dst_plid, (hid_t)src_plid, cstr); ENVPTR->ReleaseStringUTFChars(ENVPAR name, cstr); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Premove * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Premove (JNIEnv *env, jclass clss, jint plid, jstring name) { char *cstr; jboolean isCopy; jint retVal = -1; if (name == NULL) { h5nullArgument(env, "H5Premove: name is NULL"); return -1; } cstr = (char *)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (cstr == NULL) { h5JNIFatalError(env, "H5Premove: name not pinned"); return -1; } retVal = H5Premove((hid_t)plid, cstr); ENVPTR->ReleaseStringUTFChars(ENVPAR name, cstr); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Punregister * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Punregister (JNIEnv *env, jclass clss, jint plid, jstring name) { char *cstr; jboolean isCopy; jint retVal = -1; if (name == NULL) { h5nullArgument(env, "H5Punregister: name is NULL"); return -1; } cstr = (char *)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (cstr == NULL) { h5JNIFatalError(env, "H5Punregister: name not pinned"); return -1; } retVal = H5Punregister((hid_t)plid, cstr); ENVPTR->ReleaseStringUTFChars(ENVPAR name, cstr); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pclose_list * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pclose_1class (JNIEnv *env, jclass clss, jint plid) { hid_t retVal = -1; retVal = H5Pclose_class((hid_t)plid); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_filter2 * Signature: (II[I[J[IJ[Ljava/lang/String;[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1filter2 (JNIEnv *env, jclass clss, jint plist, jint filter_number, jintArray flags, jlongArray cd_nelmts, jintArray cd_values, jlong namelen, jobjectArray name, jintArray filter_config) { herr_t status; jint *flagsArray; jlong *cd_nelmtsArray; jint *cd_valuesArray; jint *filter_configArray; jboolean isCopy; char *filter; jstring str; if (namelen <= 0) { h5badArgument(env, "H5Pget_filter: namelen <= 0"); return -1; } if (flags == NULL) { h5badArgument(env, "H5Pget_filter: flags is NULL"); return -1; } if (cd_nelmts == NULL) { h5badArgument(env, "H5Pget_filter: cd_nelmts is NULL"); return -1; } if (filter_config == NULL) { h5badArgument(env, "H5Pget_filter: filter_config is NULL"); return -1; } filter = (char *)malloc(sizeof(char)*(size_t)namelen); if (filter == NULL) { h5outOfMemory(env, "H5Pget_filter: namelent malloc failed"); return -1; } flagsArray = (jint *)ENVPTR->GetIntArrayElements(ENVPAR flags, &isCopy); if (flagsArray == NULL) { free(filter); h5JNIFatalError(env, "H5Pget_filter: flags array not pinned"); return -1; } cd_nelmtsArray = (jlong *)ENVPTR->GetLongArrayElements(ENVPAR cd_nelmts, &isCopy); if (cd_nelmtsArray == NULL) { ENVPTR->ReleaseIntArrayElements(ENVPAR flags, flagsArray, JNI_ABORT); free(filter); h5JNIFatalError(env, "H5Pget_filter: nelmts array not pinned"); return -1; } filter_configArray = (jint *)ENVPTR->GetIntArrayElements(ENVPAR filter_config, &isCopy); if (filter_configArray == NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR cd_nelmts, cd_nelmtsArray, JNI_ABORT); ENVPTR->ReleaseIntArrayElements(ENVPAR flags, flagsArray, JNI_ABORT); free(filter); h5JNIFatalError(env, "H5Pget_filter: filter_config array not pinned"); return -1; } if (*cd_nelmtsArray == 0 && cd_values == NULL) { /* direct cast (size_t *)variable fails on 32-bit environment */ long long cd_nelmts_temp = 0; size_t cd_nelmts_t = (size_t)cd_nelmts_temp; status = H5Pget_filter2((hid_t)plist, (int)filter_number, (unsigned int *)flagsArray, &cd_nelmts_t, NULL, (size_t)namelen, filter, (unsigned int *)filter_configArray); *cd_nelmtsArray = cd_nelmts_t; } else { if (cd_values == NULL) { h5badArgument(env, "H5Pget_filter: cd_values is NULL"); return -1; } cd_valuesArray = (jint *)ENVPTR->GetIntArrayElements(ENVPAR cd_values, &isCopy); if (cd_valuesArray == NULL) { ENVPTR->ReleaseIntArrayElements(ENVPAR filter_config, filter_configArray, JNI_ABORT); ENVPTR->ReleaseLongArrayElements(ENVPAR cd_nelmts, cd_nelmtsArray, JNI_ABORT); ENVPTR->ReleaseIntArrayElements(ENVPAR flags, flagsArray, JNI_ABORT); free(filter); h5JNIFatalError(env, "H5Pget_filter: elmts array not pinned"); return -1; } { /* direct cast (size_t *)variable fails on 32-bit environment */ long long cd_nelmts_temp = *(cd_nelmtsArray); size_t cd_nelmts_t = (size_t)cd_nelmts_temp; status = H5Pget_filter2((hid_t)plist, (int)filter_number, (unsigned int *)flagsArray, &cd_nelmts_t, (unsigned int *)cd_valuesArray, (size_t)namelen, filter, (unsigned int *)filter_configArray); *cd_nelmtsArray = cd_nelmts_t; } } if (status < 0) { if (cd_values) ENVPTR->ReleaseIntArrayElements(ENVPAR cd_values, cd_valuesArray, JNI_ABORT); ENVPTR->ReleaseIntArrayElements(ENVPAR filter_config, filter_configArray, JNI_ABORT); ENVPTR->ReleaseLongArrayElements(ENVPAR cd_nelmts, cd_nelmtsArray, JNI_ABORT); ENVPTR->ReleaseIntArrayElements(ENVPAR flags, flagsArray, JNI_ABORT); free(filter); h5libraryError(env); return -1; } if (cd_values) ENVPTR->ReleaseIntArrayElements(ENVPAR cd_values, cd_valuesArray, 0); ENVPTR->ReleaseIntArrayElements(ENVPAR filter_config, filter_configArray, 0); ENVPTR->ReleaseLongArrayElements(ENVPAR cd_nelmts, cd_nelmtsArray, 0); ENVPTR->ReleaseIntArrayElements(ENVPAR flags, flagsArray, 0); /* NewStringUTF may throw OutOfMemoryError */ str = ENVPTR->NewStringUTF(ENVPAR filter); if (str == NULL) { free(filter); h5JNIFatalError(env, "H5Pget_filter: return string not pinned"); return -1; } /* SetObjectArrayElement may throw exceptiosn */ ENVPTR->SetObjectArrayElement(ENVPAR name, 0, (jobject)str); free(filter); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_filter_by_id2 * Signature: (II[I[J[IJ[Ljava/lang/String;[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1filter_1by_1id2 (JNIEnv *env, jclass clss, jint plist, jint filter, jintArray flags, jlongArray cd_nelmts, jintArray cd_values, jlong namelen, jobjectArray name, jintArray filter_config) { herr_t status; int i = 0; jint *cd_valuesArray; jint *flagsArray; jint *filter_configArray; jlong *cd_nelmtsArray; jboolean isCopy; long bs; char *aName; jstring str; bs = (long)namelen; if (bs <= 0) { h5badArgument(env, "H5Pget_filter_by_id: namelen <= 0"); return -1; } if (flags == NULL) { h5nullArgument(env, "H5Pget_filter_by_id: flags is NULL"); return -1; } if (cd_nelmts == NULL) { h5nullArgument(env, "H5Pget_filter_by_id: cd_nelms is NULL"); return -1; } if (cd_values == NULL) { h5nullArgument(env, "H5Pget_filter_by_id: cd_values is NULL"); return -1; } if (name == NULL) { h5nullArgument(env, "H5Pget_filter_by_id: name is NULL"); return -1; } if (filter_config == NULL) { h5badArgument(env, "H5Pget_filter_by_id: filter_config is NULL"); return -1; } aName = (char*)malloc(sizeof(char)*bs); if (aName == NULL) { h5outOfMemory(env, "H5Pget_filter_by_id: malloc failed"); return -1; } flagsArray = ENVPTR->GetIntArrayElements(ENVPAR flags,&isCopy); if (flagsArray == NULL) { free(aName); h5JNIFatalError(env, "H5Pget_filter_by_id: flags not pinned"); return -1; } cd_nelmtsArray = ENVPTR->GetLongArrayElements(ENVPAR cd_nelmts, &isCopy); if (cd_nelmtsArray == NULL) { ENVPTR->ReleaseIntArrayElements(ENVPAR flags, flagsArray, JNI_ABORT); free(aName); h5JNIFatalError(env, "H5Pget_filter_by_id: cd_nelms not pinned"); return -1; } cd_valuesArray = ENVPTR->GetIntArrayElements(ENVPAR cd_values, &isCopy); if (cd_valuesArray == NULL) { ENVPTR->ReleaseIntArrayElements(ENVPAR flags, flagsArray, JNI_ABORT); ENVPTR->ReleaseLongArrayElements(ENVPAR cd_nelmts, cd_nelmtsArray, JNI_ABORT); free(aName); h5JNIFatalError(env, "H5Pget_filter_by_id: cd_values array not converted to unsigned int."); return -1; } filter_configArray = ENVPTR->GetIntArrayElements(ENVPAR filter_config, &isCopy); if (filter_configArray == NULL) { ENVPTR->ReleaseIntArrayElements(ENVPAR flags, flagsArray, JNI_ABORT); ENVPTR->ReleaseLongArrayElements(ENVPAR cd_nelmts, cd_nelmtsArray, JNI_ABORT); ENVPTR->ReleaseIntArrayElements(ENVPAR cd_values, cd_valuesArray, JNI_ABORT); free(aName); h5JNIFatalError(env, "H5Pget_filter_by_id: flags not pinned"); return -1; } { /* direct cast (size_t *)variable fails on 32-bit environment */ long long cd_nelmts_temp = *(cd_nelmtsArray); size_t cd_nelmts_t = (size_t)cd_nelmts_temp; status = H5Pget_filter_by_id2((hid_t)plist, (H5Z_filter_t)filter, (unsigned int *)flagsArray, &cd_nelmts_t, (unsigned int *)cd_valuesArray, (size_t)namelen, (char *)aName, (unsigned int *)filter_configArray); *cd_nelmtsArray = cd_nelmts_t; } if (status < 0) { ENVPTR->ReleaseIntArrayElements(ENVPAR flags, flagsArray, JNI_ABORT); ENVPTR->ReleaseLongArrayElements(ENVPAR cd_nelmts, cd_nelmtsArray, JNI_ABORT); ENVPTR->ReleaseIntArrayElements(ENVPAR cd_values, cd_valuesArray, JNI_ABORT); ENVPTR->ReleaseIntArrayElements(ENVPAR filter_config, filter_configArray, JNI_ABORT); free(aName); h5libraryError(env); return -1; } str = ENVPTR->NewStringUTF(ENVPAR aName); ENVPTR->ReleaseIntArrayElements(ENVPAR flags, flagsArray, 0); ENVPTR->ReleaseLongArrayElements(ENVPAR cd_nelmts, cd_nelmtsArray, 0); ENVPTR->ReleaseIntArrayElements(ENVPAR cd_values, cd_valuesArray, 0); ENVPTR->ReleaseIntArrayElements(ENVPAR filter_config, filter_configArray, 0); free(aName); return (jint)status; } /********************************************************************** * * * New functions release 1.8.0 * * * **********************************************************************/ /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_nlinks * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1nlinks (JNIEnv *env, jclass clss, jint lapl_id) { herr_t retVal = -1; size_t nlinks; retVal = H5Pget_nlinks((hid_t)lapl_id, &nlinks); if (retVal < 0) { h5libraryError(env); } return (jlong) nlinks; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_nlinks * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1nlinks (JNIEnv *env, jclass clss, jint lapl_id, jlong nlinks) { herr_t retVal = -1; if (nlinks <= 0) { h5badArgument(env, "H5Pset_1nlinks: nlinks_l <= 0"); return -1; } retVal = H5Pset_nlinks((hid_t)lapl_id, (size_t)nlinks); if(retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_libver_bounds * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1libver_1bounds (JNIEnv *env, jclass clss, jint fapl_id, jintArray libver) { herr_t retVal = -1; H5F_libver_t *theArray = NULL; jboolean isCopy; if (libver == NULL) { h5nullArgument(env, "H5Pget_libver_bounds: libversion bounds is NULL"); return -1; } theArray = (H5F_libver_t *)ENVPTR->GetIntArrayElements(ENVPAR libver, &isCopy); if (theArray == NULL) { h5JNIFatalError(env, "H5Pget_libver_bounds: input not pinned"); return -1; } retVal = H5Pget_libver_bounds((hid_t)fapl_id, &(theArray[0]), &(theArray[1])); if(retVal < 0) { ENVPTR->ReleaseIntArrayElements(ENVPAR libver, (jint *)theArray, JNI_ABORT); h5libraryError(env); return -1; } ENVPTR->ReleaseIntArrayElements(ENVPAR libver, (jint *)theArray, 0); return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_libver_bounds * Signature: (III)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1libver_1bounds (JNIEnv *env, jclass clss, jint fapl_id, jint low, jint high) { herr_t retVal = -1; if ((H5F_libver_t)high != H5F_LIBVER_LATEST) { h5badArgument(env, "H5Pset_libver_bounds: invalid high library version bound"); return -1; } if(((H5F_libver_t)low !=H5F_LIBVER_EARLIEST) && ((H5F_libver_t)low != H5F_LIBVER_LATEST)) { h5badArgument(env, "H5Pset_libver_bounds: invalid low library version bound"); return -1; } retVal = H5Pset_libver_bounds((hid_t)fapl_id, (H5F_libver_t)low, (H5F_libver_t)high); if(retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_link_creation_order * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1link_1creation_1order (JNIEnv *env, jclass clss, jint gcpl_id) { herr_t retVal = -1; unsigned crt_order_flags; retVal = H5Pget_link_creation_order((hid_t)gcpl_id, &crt_order_flags); if(retVal < 0) { h5libraryError(env); } return (jint)crt_order_flags; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_link_creation_order * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1link_1creation_1order (JNIEnv *env, jclass clss, jint gcpl_id, jint crt_order_flags) { herr_t retVal = -1; retVal = H5Pset_link_creation_order((hid_t)gcpl_id, crt_order_flags); if(retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_attr_creation_order * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1attr_1creation_1order (JNIEnv *env, jclass clss, jint ocpl_id) { herr_t retVal = -1; unsigned crt_order_flags; retVal = H5Pget_attr_creation_order((hid_t)ocpl_id, &crt_order_flags); if(retVal < 0) { h5libraryError(env); } return (jint)crt_order_flags; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_attr_creation_order * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1attr_1creation_1order (JNIEnv *env, jclass clss, jint ocpl_id, jint crt_order_flags) { herr_t retVal = -1; retVal = H5Pset_attr_creation_order((hid_t)ocpl_id, crt_order_flags); if(retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_copy_object * Signature: (II)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1copy_1object (JNIEnv *env, jclass clss, jint ocp_plist_id, jint copy_options) { herr_t retVal = -1; retVal = H5Pset_copy_object((hid_t)ocp_plist_id, (unsigned)copy_options); if(retVal < 0) { h5libraryError(env); } return; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_copy_object * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1copy_1object (JNIEnv *env, jclass clss, jint ocp_plist_id) { herr_t retVal = -1; unsigned copy_options; retVal = H5Pget_copy_object((hid_t)ocp_plist_id, ©_options); if(retVal < 0) { h5libraryError(env); } return (jint)copy_options; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_create_intermediate_group * Signature: (IZ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1create_1intermediate_1group (JNIEnv *env, jclass clss, jint lcpl_id, jboolean crt_intermed_group) { herr_t retVal = -1; retVal = H5Pset_create_intermediate_group((hid_t)lcpl_id, (unsigned)crt_intermed_group); if(retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_create_intermediate_group * Signature: (I)Z */ JNIEXPORT jboolean JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1create_1intermediate_1group (JNIEnv *env, jclass clss, jint lcpl_id) { herr_t retVal = -1; unsigned crt_intermed_group; retVal = H5Pget_create_intermediate_group((hid_t)lcpl_id, &crt_intermed_group); if(retVal < 0) { h5libraryError(env); } return (jboolean)crt_intermed_group; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_data_transform * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1data_1transform (JNIEnv *env, jclass clss, jint plist_id, jstring expression) { herr_t retVal = -1; char *express; jboolean isCopy; if (expression == NULL) { h5nullArgument(env, "H5Pset_data_transform: expression is NULL"); return -1; } express = (char *)ENVPTR->GetStringUTFChars(ENVPAR expression, &isCopy); if (express == NULL) { h5JNIFatalError(env, "H5Pset_data_transform: expression is not pinned"); return -1; } retVal = H5Pset_data_transform((hid_t)plist_id, (const char*)express); ENVPTR->ReleaseStringUTFChars(ENVPAR expression, express); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_data_transform * Signature: (I[Ljava/lang/String;J)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1data_1transform (JNIEnv *env, jclass clss, jint plist_id, jobjectArray expression, jlong size) { ssize_t buf_size; char *express; jlong express_size; jstring str = NULL; if (size <= 0) { h5badArgument(env, "H5Pget_data_transform: size <= 0"); return -1; } express_size = (jlong)H5Pget_data_transform((hid_t)plist_id, (char*)NULL, (size_t)size); if(express_size < 0) { h5libraryError(env); return -1; } buf_size = (ssize_t)express_size + 1;/* add extra space for the null terminator */ express = (char*)malloc(sizeof(char)*buf_size); if (express == NULL) { h5outOfMemory(env, "H5Pget_data_transform: malloc failed "); return -1; } express_size = (jlong)H5Pget_data_transform((hid_t)plist_id, (char*)express, (size_t)size); if (express_size < 0) { free(express); h5libraryError(env); return -1; } str = ENVPTR->NewStringUTF(ENVPAR express); if (str == NULL) { /* exception -- fatal JNI error */ free(express); h5JNIFatalError(env, "H5Pget_data_transform: return string not created"); return -1; } ENVPTR->SetObjectArrayElement(ENVPAR expression, 0, str); free(express); return express_size; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_elink_acc_flags * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1elink_1acc_1flags (JNIEnv *env, jclass clss, jint lapl_id) { herr_t status; unsigned flags; status = H5Pget_elink_acc_flags((hid_t)lapl_id, &flags); if(status < 0) { h5libraryError(env); } return (jint)flags; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_elink_acc_flags * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1elink_1acc_1flags (JNIEnv *env, jclass clss, jint lapl_id, jint flags) { herr_t retVal; if (((unsigned) flags != H5F_ACC_RDWR) && ((unsigned) flags != H5F_ACC_RDONLY) && ((unsigned) flags != H5F_ACC_DEFAULT)) { h5badArgument(env, "H5Pset_elink_acc_flags: invalid flags value"); return -1; } retVal = H5Pset_elink_acc_flags((hid_t)lapl_id, (unsigned)flags); if (retVal < 0) { h5libraryError(env); } return (jint) retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_link_phase_change * Signature: (III)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1link_1phase_1change (JNIEnv *env, jclass clss, jint gcpl_id, jint max_compact, jint min_dense) { herr_t retVal; if(max_compact < min_dense) { h5badArgument(env, "H5Pset_link_phase_change: max compact value must be >= min dense value"); return -1; } if(max_compact > 65535) { h5badArgument(env, "H5Pset_link_phase_change: max compact value must be < 65536"); return -1; } if(min_dense > 65535) { h5badArgument(env, "H5Pset_link_phase_change: min dense value must be < 65536"); return -1; } retVal = H5Pset_link_phase_change((hid_t)gcpl_id, (unsigned)max_compact, (unsigned)min_dense); if(retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_link_phase_change * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1link_1phase_1change (JNIEnv *env, jclass clss, jint gcpl_id, jintArray links) { herr_t retVal = -1; unsigned *theArray = NULL; jboolean isCopy; if (links == NULL) { h5nullArgument( env, "H5Pget_link_phase_change: links is NULL"); return -1; } theArray = (unsigned *)ENVPTR->GetIntArrayElements(ENVPAR links, &isCopy); if (theArray == NULL) { h5JNIFatalError( env, "H5Pget_link_phase_change: input not pinned"); return -1; } retVal = H5Pget_link_phase_change((hid_t)gcpl_id, &(theArray[0]), &(theArray[1])); if(retVal < 0) { ENVPTR->ReleaseIntArrayElements(ENVPAR links, (jint *)theArray, JNI_ABORT); h5libraryError(env); return -1; } ENVPTR->ReleaseIntArrayElements(ENVPAR links, (jint *)theArray, 0); return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_attr_phase_change * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1attr_1phase_1change (JNIEnv *env, jclass clss, jint ocpl_id, jintArray attributes) { herr_t retVal = -1; unsigned *theArray = NULL; jboolean isCopy; if (attributes == NULL) { h5nullArgument(env, "H5Pget_attr_phase_change: attributes is NULL"); return -1; } theArray = (unsigned *)ENVPTR->GetIntArrayElements(ENVPAR attributes, &isCopy); if (theArray == NULL) { h5JNIFatalError(env, "H5Pget_attr_phase_change: input not pinned"); return -1; } retVal = H5Pget_attr_phase_change((hid_t)ocpl_id, &(theArray[0]), &(theArray[1])); if(retVal < 0) { ENVPTR->ReleaseIntArrayElements(ENVPAR attributes, (jint *)theArray, JNI_ABORT); h5libraryError(env); return -1; } ENVPTR->ReleaseIntArrayElements(ENVPAR attributes, (jint *)theArray, 0); return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_shared_mesg_phase_change * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1shared_1mesg_1phase_1change (JNIEnv *env, jclass clss, jint fcpl_id, jintArray size) { herr_t retVal = -1; unsigned *theArray = NULL; jboolean isCopy; if (size == NULL) { h5nullArgument(env, "H5Pget_shared_mesg_phase_change: size is NULL"); return -1; } theArray = (unsigned *)ENVPTR->GetIntArrayElements(ENVPAR size, &isCopy); if (theArray == NULL) { h5JNIFatalError(env, "H5Pget_shared_mesg_phase_change: input not pinned"); return -1; } retVal = H5Pget_shared_mesg_phase_change((hid_t)fcpl_id, &(theArray[0]), &(theArray[1])); if(retVal < 0) { ENVPTR->ReleaseIntArrayElements(ENVPAR size, (jint *)theArray, JNI_ABORT); h5libraryError(env); return -1; } ENVPTR->ReleaseIntArrayElements(ENVPAR size, (jint *)theArray, 0); return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_shared_mesg_phase_change * Signature: (III)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1shared_1mesg_1phase_1change (JNIEnv *env, jclass clss, jint fcpl_id, jint max_list, jint min_btree) { herr_t retVal; /* Check that values are sensible. The min_btree value must be no greater * than the max list plus one. * * Range check to make certain they will fit into encoded form. */ if(max_list + 1 < min_btree) { h5badArgument(env, "H5Pset_shared_mesg_phase_change: minimum B-tree value is greater than maximum list value"); return -1; } if(max_list > H5O_SHMESG_MAX_LIST_SIZE) { h5badArgument(env, "H5Pset_shared_mesg_phase_change: max list value is larger than H5O_SHMESG_MAX_LIST_SIZE"); return -1; } if(min_btree > H5O_SHMESG_MAX_LIST_SIZE) { h5badArgument(env, "H5Pset_shared_mesg_phase_change: min btree value is larger than H5O_SHMESG_MAX_LIST_SIZE"); return -1; } retVal = H5Pset_shared_mesg_phase_change((hid_t)fcpl_id, (unsigned)max_list, (unsigned)min_btree); if(retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_shared_mesg_nindexes * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1shared_1mesg_1nindexes (JNIEnv *env, jclass clss, jint fcpl_id) { herr_t status; unsigned nindexes; status = H5Pget_shared_mesg_nindexes((hid_t)fcpl_id, &nindexes); if(status < 0) { h5libraryError(env); } return (jint)nindexes; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_shared_mesg_nindexes * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1shared_1mesg_1nindexes (JNIEnv *env, jclass clss, jint plist_id, jint nindexes) { herr_t retVal; if (nindexes > H5O_SHMESG_MAX_NINDEXES) { h5badArgument(env, "H5Pset_shared_mesg_nindexes: number of indexes is greater than H5O_SHMESG_MAX_NINDEXES"); return -1; } retVal = H5Pset_shared_mesg_nindexes((hid_t)plist_id, (unsigned)nindexes); if(retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_shared_mesg_index * Signature: (IIII)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1shared_1mesg_1index (JNIEnv *env, jclass clss, jint fcpl_id, jint index_num, jint mesg_type_flags, jint min_mesg_size) { herr_t retVal; unsigned nindexes;/* Number of SOHM indexes */ /* Check arguments */ if(mesg_type_flags > H5O_SHMESG_ALL_FLAG) { h5badArgument(env, "H5Pset_shared_mesg_index: unrecognized flags in mesg_type_flags"); return -1; } /* Read the current number of indexes */ if(H5Pget_shared_mesg_nindexes((hid_t)fcpl_id, &nindexes) < 0) { h5libraryError(env); } /* Range check */ if((unsigned)index_num >= nindexes) { h5badArgument(env, "H5Pset_shared_mesg_index: index_num is too large; no such index"); return -1; } retVal = H5Pset_shared_mesg_index((hid_t)fcpl_id, (unsigned)index_num, (unsigned) mesg_type_flags, (unsigned) min_mesg_size); if(retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_shared_mesg_index * Signature: (II[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1shared_1mesg_1index (JNIEnv *env, jclass clss, jint fcpl_id, jint index_num, jintArray mesg_info) { herr_t retVal = -1; unsigned nindexes;/* Number of SOHM indexes */ unsigned *theArray = NULL; jboolean isCopy; /* Read the current number of indexes */ if(H5Pget_shared_mesg_nindexes((hid_t)fcpl_id, &nindexes)<0) { h5libraryError(env); } /* Range check */ if((unsigned)index_num >= nindexes) { h5badArgument(env, "H5Pget_shared_mesg_index: index_num is too large; no such index"); return -1; } if (mesg_info == NULL) { h5nullArgument(env, "H5Pget_shared_mesg_index: mesg_info is NULL"); return -1; } theArray = (unsigned *)ENVPTR->GetIntArrayElements(ENVPAR mesg_info, &isCopy); if (theArray == NULL) { h5JNIFatalError(env, "H5Pget_shared_mesg_index: input not pinned"); return -1; } retVal = H5Pget_shared_mesg_index((hid_t)fcpl_id, (unsigned)index_num, &(theArray[0]), &(theArray[1])); if(retVal < 0) { ENVPTR->ReleaseIntArrayElements(ENVPAR mesg_info, (jint *)theArray, JNI_ABORT); h5libraryError(env); return -1; } ENVPTR->ReleaseIntArrayElements(ENVPAR mesg_info, (jint *)theArray, 0); return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_local_heap_size_hint * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1local_1heap_1size_1hint (JNIEnv *env, jclass clss, jint gcpl_id, jlong size_hint) { herr_t retVal = -1; retVal = H5Pset_local_heap_size_hint((hid_t)gcpl_id, (size_t)size_hint); if(retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_local_heap_size_hint * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1local_1heap_1size_1hint (JNIEnv *env, jclass clss, jint gcpl_id) { herr_t status; size_t size_hint; status = H5Pget_local_heap_size_hint((hid_t)gcpl_id, &size_hint); if(status < 0) { h5libraryError(env); } return (jlong)size_hint; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_nbit * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1nbit (JNIEnv *env, jclass clss, jint plist_id) { herr_t retVal = -1; retVal = H5Pset_nbit((hid_t)plist_id); if(retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_scaleoffset * Signature: (III)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1scaleoffset (JNIEnv *env, jclass clss, jint plist_id, jint scale_type, jint scale_factor) { herr_t retVal = -1; /* Check arguments */ if(scale_factor < 0) { h5badArgument(env, "H5Pset_scaleoffset: scale factor must be > 0"); return -1; } if(scale_type != H5Z_SO_FLOAT_DSCALE && scale_type != H5Z_SO_FLOAT_ESCALE && scale_type != H5Z_SO_INT){ h5badArgument(env, "H5Pset_scaleoffset: invalid scale type"); return -1; } retVal = H5Pset_scaleoffset((hid_t)plist_id, (H5Z_SO_scale_type_t)scale_type, scale_factor); if(retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_est_link_info * Signature: (III)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1est_1link_1info (JNIEnv *env, jclass clss, jint gcpl_id, jint est_num_entries, jint est_name_len) { herr_t retVal = -1; /* Range check values */ if(est_num_entries > 65535) { h5badArgument(env, "H5Pset_est_link_info: est. number of entries must be < 65536"); return -1; } if(est_name_len > 65535) { h5badArgument(env, "H5Pset_est_link_info: est. name length must be < 65536"); return -1; } retVal = H5Pset_est_link_info((hid_t)gcpl_id, (unsigned)est_num_entries, (unsigned)est_name_len); if(retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_est_link_info * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1est_1link_1info (JNIEnv *env, jclass clss, jint gcpl_id, jintArray link_info) { herr_t retVal = -1; unsigned *theArray = NULL; jboolean isCopy; if (link_info == NULL) { h5nullArgument(env, "H5Pget_est_link_info: link_info is NULL"); return -1; } theArray = (unsigned *)ENVPTR->GetIntArrayElements(ENVPAR link_info,&isCopy); if (theArray == NULL) { h5JNIFatalError(env, "H5Pget_est_link_info: input not pinned"); return -1; } retVal= H5Pget_est_link_info((hid_t)gcpl_id, &(theArray[0]), &(theArray[1])); if(retVal < 0) { ENVPTR->ReleaseIntArrayElements(ENVPAR link_info, (jint *)theArray, JNI_ABORT); h5libraryError(env); return -1; } ENVPTR->ReleaseIntArrayElements(ENVPAR link_info, (jint *)theArray, 0); return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_elink_fapl * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1elink_1fapl (JNIEnv *env, jclass clss, jint lapl_id, jint fapl_id) { herr_t retVal = -1; retVal = H5Pset_elink_fapl((hid_t)lapl_id, (hid_t)fapl_id); if(retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Pget_elink_fapl * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Pget_1elink_1fapl (JNIEnv *env, jclass clss, jint lapl_id) { hid_t retVal = -1; retVal = H5Pget_elink_fapl((hid_t)lapl_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_elink_prefix * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1elink_1prefix (JNIEnv *env, jclass clss, jint lapl_id, jstring prefix) { herr_t retVal = -1; const char *aName; jboolean isCopy; if (prefix == NULL) { h5nullArgument(env, "H5Pset_elink_prefix: prefix is NULL"); return -1; } aName = (const char*)ENVPTR->GetStringUTFChars(ENVPAR prefix, &isCopy); if (aName == NULL) { h5JNIFatalError(env, "H5Pset_elink_prefix: prefix not pinned"); return -1; } retVal = H5Pset_elink_prefix((hid_t)lapl_id, aName); if(retVal < 0) { ENVPTR->ReleaseStringUTFChars(ENVPAR prefix, aName); h5libraryError(env); return -1; } ENVPTR->ReleaseStringUTFChars(ENVPAR prefix, aName); return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_elink_prefix * Signature: (I[Ljava/lang/String;)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1elink_1prefix (JNIEnv *env, jclass clss, jint lapl_id, jobjectArray prefix) { size_t size = -1; char *pre; jlong prefix_size; jstring str = NULL; if (prefix == NULL) { h5nullArgument(env, "H5Pget_elink_prefix: prefix is NULL"); return -1; } prefix_size = (jlong)H5Pget_elink_prefix((hid_t)lapl_id, (char*)NULL, size); if(prefix_size < 0) { h5libraryError(env); return -1; } size = (size_t)prefix_size + 1;/* add extra space for the null terminator */ pre = (char*)malloc(sizeof(char)*size); if (pre == NULL) { h5outOfMemory(env, "H5Pget_elink_prefix: malloc failed "); return -1; } prefix_size = (jlong)H5Pget_elink_prefix((hid_t)lapl_id, (char*)pre, size); if (prefix_size < 0) { free(pre); h5libraryError(env); return -1; } str = ENVPTR->NewStringUTF(ENVPAR pre); if (str == NULL) { /* exception -- fatal JNI error */ free(pre); h5JNIFatalError(env, "H5Pget_elink_prefix: return string not created"); return -1; } ENVPTR->SetObjectArrayElement(ENVPAR prefix, 0, str); free(pre); return prefix_size; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_fapl_direct * Signature: (IJJJ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1fapl_1direct (JNIEnv *env, jclass clss, jint fapl_id, jlong alignment, jlong block_size, jlong cbuf_size) { herr_t retVal = -1; #ifdef H5_HAVE_DIRECT retVal = H5Pset_fapl_direct((hid_t)fapl_id, (size_t)alignment, (size_t)block_size, (size_t)cbuf_size); #endif if(retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_fapl_direct * Signature: (I[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1fapl_1direct (JNIEnv *env, jclass clss, jint fapl_id, jlongArray info) { herr_t retVal = -1; #ifdef H5_HAVE_DIRECT size_t alignment = 0; size_t block_size = 0; size_t cbuf_size = 0; jlong *theArray; jboolean isCopy; if (info == NULL) { h5nullArgument(env, "H5Pget_fapl_direct: info input array is NULL"); return -1; } if (ENVPTR->GetArrayLength(ENVPAR info) < 3) { h5badArgument( env, "H5Pget_fapl_direct: info input array < 4"); return -1; } theArray = (jlong *)ENVPTR->GetLongArrayElements(ENVPAR info, &isCopy); if (theArray == NULL) { h5JNIFatalError(env, "H5Pget_fapl_direct: info not pinned"); return -1; } retVal = H5Pget_fapl_direct((hid_t)fapl_id, &alignment, &block_size, &cbuf_size); if(retVal <0) { ENVPTR->ReleaseLongArrayElements(ENVPAR info, theArray, JNI_ABORT); h5libraryError(env); } else { theArray[0] = alignment; theArray[1] = block_size; theArray[2] = cbuf_size; ENVPTR->ReleaseLongArrayElements(ENVPAR info, theArray, 0); } #else if (retVal < 0) { h5libraryError(env); } #endif return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_fapl_sec2 * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1fapl_1sec2 (JNIEnv *env, jclass clss, jint fapl_id) { herr_t retVal = -1; retVal = H5Pset_fapl_sec2((hid_t) fapl_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_fapl_stdio * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1fapl_1stdio (JNIEnv *env, jclass clss, jint fapl_id) { herr_t retVal = -1; retVal = H5Pset_fapl_stdio((hid_t) fapl_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_fapl_windows * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1fapl_1windows (JNIEnv *env, jclass clss, jint fapl_id) { herr_t retVal = -1; #ifdef H5_HAVE_WINDOWS retVal = H5Pset_fapl_windows((hid_t) fapl_id); #endif if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_fapl_muti * Signature: (I[I[I[Ljava/lang/String;[J)Z */ JNIEXPORT jboolean JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1fapl_1multi (JNIEnv *env, jclass clss, jint tid, jintArray memb_map, jintArray memb_fapl, jobjectArray memb_name, jlongArray memb_addr) { herr_t status; int i; jint *themapArray = NULL; jint *thefaplArray = NULL; jlong *theaddrArray = NULL; char **mName = NULL; jstring str; jboolean isCopy; int relax = 0; if (memb_map) { themapArray = (jint *)ENVPTR->GetIntArrayElements(ENVPAR memb_map, &isCopy); if (themapArray == NULL) { h5JNIFatalError(env, "H5Pget_fapl_muti: memb_map not pinned"); return -1; } } if (memb_fapl) { thefaplArray = (jint *)ENVPTR->GetIntArrayElements(ENVPAR memb_fapl, &isCopy); if (thefaplArray == NULL) { if (memb_map) ENVPTR->ReleaseIntArrayElements(ENVPAR memb_map, themapArray, JNI_ABORT); h5JNIFatalError(env, "H5Pget_fapl_muti: memb_fapl not pinned"); return -1; } } if (memb_addr) { theaddrArray = (jlong *)ENVPTR->GetLongArrayElements(ENVPAR memb_addr, &isCopy); if (theaddrArray == NULL) { if (memb_map) ENVPTR->ReleaseIntArrayElements(ENVPAR memb_map, themapArray, JNI_ABORT); if (memb_fapl) ENVPTR->ReleaseIntArrayElements(ENVPAR memb_fapl, thefaplArray, JNI_ABORT); h5JNIFatalError(env, "H5Pget_fapl_muti: memb_addr not pinned"); return -1; } } if (memb_name) mName = (char **)calloc(H5FD_MEM_NTYPES, sizeof (*mName)); status = H5Pget_fapl_multi((hid_t)tid, (H5FD_mem_t *)themapArray, (hid_t *)thefaplArray, mName, (haddr_t *)theaddrArray, (hbool_t *)&relax); if (status < 0) { if (memb_map) ENVPTR->ReleaseIntArrayElements(ENVPAR memb_map, themapArray, JNI_ABORT); if (memb_fapl) ENVPTR->ReleaseIntArrayElements(ENVPAR memb_fapl, thefaplArray, JNI_ABORT); if (memb_addr) ENVPTR->ReleaseLongArrayElements(ENVPAR memb_addr, theaddrArray, JNI_ABORT); if (memb_name) h5str_array_free(mName, H5FD_MEM_NTYPES); h5libraryError(env); return -1; } if (memb_map) { ENVPTR->ReleaseIntArrayElements(ENVPAR memb_map, themapArray, 0); } if (memb_fapl) { ENVPTR->ReleaseIntArrayElements(ENVPAR memb_fapl, thefaplArray, 0); } if (memb_addr) { ENVPTR->ReleaseLongArrayElements(ENVPAR memb_addr, theaddrArray, 0); } if (memb_name) { if (mName) { for (i = 0; i < H5FD_MEM_NTYPES; i++) { if (*(mName + i)) { str = ENVPTR->NewStringUTF(ENVPAR *(mName+i)); ENVPTR->SetObjectArrayElement(ENVPAR memb_name, i, (jobject)str); } } /* for (i=0; iGetIntArrayElements(ENVPAR memb_map, &isCopy); if (themapArray == NULL) { h5JNIFatalError(env, "H5Pget_fapl_muti: memb_map not pinned"); return; } } if (memb_fapl) { thefaplArray = (jint *)ENVPTR->GetIntArrayElements(ENVPAR memb_fapl, &isCopy); if (thefaplArray == NULL) { if (memb_map) ENVPTR->ReleaseIntArrayElements(ENVPAR memb_map, themapArray, JNI_ABORT); h5JNIFatalError(env, "H5Pget_fapl_muti: memb_fapl not pinned"); return; } } if (memb_addr) { theaddrArray = (jlong *)ENVPTR->GetLongArrayElements(ENVPAR memb_addr, &isCopy); if (theaddrArray == NULL) { if (memb_map) ENVPTR->ReleaseIntArrayElements(ENVPAR memb_map, themapArray, JNI_ABORT); if (memb_fapl) ENVPTR->ReleaseIntArrayElements(ENVPAR memb_fapl, thefaplArray, JNI_ABORT); h5JNIFatalError(env, "H5Pget_fapl_muti: memb_addr not pinned"); return; } } memset(member_name, 0, H5FD_MEM_NTYPES * sizeof(char*)); if (memb_name) { int i; for (i = 0; i < H5FD_MEM_NTYPES; i++) { jstring obj = (jstring) ENVPTR->GetObjectArrayElement(ENVPAR (jobjectArray) memb_name, i); if (obj != 0) { jsize length = ENVPTR->GetStringUTFLength(ENVPAR obj); const char *utf8 = ENVPTR->GetStringUTFChars(ENVPAR obj, 0); if (utf8) { member_name[i] = (char*)malloc(strlen(utf8) + 1); if (member_name[i]) { strcpy(member_name[i], utf8); } } ENVPTR->ReleaseStringUTFChars(ENVPAR obj, utf8); ENVPTR->DeleteLocalRef(ENVPAR obj); } } mName = (const char **)member_name; } status = H5Pset_fapl_multi((hid_t)tid, (const H5FD_mem_t *)themapArray, (const hid_t *)thefaplArray, mName, (const haddr_t *)theaddrArray, (hbool_t)relax); if (status < 0) { if (memb_map) ENVPTR->ReleaseIntArrayElements(ENVPAR memb_map, themapArray, JNI_ABORT); if (memb_fapl) ENVPTR->ReleaseIntArrayElements(ENVPAR memb_fapl, thefaplArray, JNI_ABORT); if (memb_addr) ENVPTR->ReleaseLongArrayElements(ENVPAR memb_addr, theaddrArray, JNI_ABORT); h5libraryError(env); return; } if (memb_map) ENVPTR->ReleaseIntArrayElements(ENVPAR memb_map, themapArray, 0); if (memb_fapl) ENVPTR->ReleaseIntArrayElements(ENVPAR memb_fapl, thefaplArray, 0); if (memb_addr) ENVPTR->ReleaseLongArrayElements(ENVPAR memb_addr, theaddrArray, 0); if (memb_name) { if (mName != NULL) { int i; Sjc = ENVPTR->FindClass(ENVPAR "java/lang/String"); if (Sjc == NULL) { return; } for (i = 0; i < H5FD_MEM_NTYPES; i++) { rstring = ENVPTR->NewStringUTF(ENVPAR member_name[i]); o = ENVPTR->GetObjectArrayElement(ENVPAR memb_name, i); if (o == NULL) { return; } bb = ENVPTR->IsInstanceOf(ENVPAR o, Sjc); if (bb == JNI_FALSE) { return; } ENVPTR->SetObjectArrayElement(ENVPAR memb_name, i, (jobject)rstring); ENVPTR->DeleteLocalRef(ENVPAR o); free(member_name[i]); } } } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_fapl_split * Signature: (ILjava/lang/String;ILjava/lang/String;I)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1fapl_1split (JNIEnv *env, jclass clss, jint fapl_id, jstring metaext, jint meta_pl_id, jstring rawext, jint raw_pl_id) { herr_t retVal = -1; const char *mstr; const char *rstr; jboolean isCopy; if (metaext == NULL) { h5nullArgument( env, "H5Pset_fapl_split: metaext is NULL"); return; } mstr = (const char *)ENVPTR->GetStringUTFChars(ENVPAR metaext, &isCopy); if (mstr == NULL) { h5JNIFatalError( env, "H5Pset_fapl_split: metaext not pinned"); return; } if (rawext == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR metaext, mstr); h5nullArgument( env, "H5Pset_fapl_split: rawext is NULL"); return; } rstr = (const char *)ENVPTR->GetStringUTFChars(ENVPAR rawext, &isCopy); if (rstr == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR metaext, mstr); h5JNIFatalError( env, "H5Pset_fapl_split: rawext not pinned"); return; } retVal = H5Pset_fapl_split((hid_t)fapl_id, mstr, (hid_t)meta_pl_id, rstr, (hid_t)raw_pl_id); ENVPTR->ReleaseStringUTFChars(ENVPAR metaext, mstr); ENVPTR->ReleaseStringUTFChars(ENVPAR rawext, rstr); if (retVal < 0) { h5libraryError(env); } return; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_meta_block_size * Signature: (IJ)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1meta_1block_1size (JNIEnv *env, jclass clss, jint plist, jlong size) { long sz; herr_t status = -1; sz = (long)size; status = H5Pset_meta_block_size((hid_t)plist, (hsize_t)sz); if (status < 0) { h5libraryError(env); } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_meta_block_size * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1meta_1block_1size (JNIEnv *env, jclass clss, jint plist) { herr_t status; hsize_t s; status = H5Pget_meta_block_size((hid_t)plist, &s); if (status < 0) { h5libraryError(env); return -1; } return (jlong)s; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_sieve_buf_size * Signature: (IJ)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1sieve_1buf_1size (JNIEnv *env, jclass clss, jint plist, jlong size) { size_t sz; herr_t status = -1; sz = (size_t)size; status = H5Pset_sieve_buf_size((hid_t)plist, (size_t)sz); if (status < 0) { h5libraryError(env); } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_sieve_buf_size * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1sieve_1buf_1size (JNIEnv *env, jclass clss, jint plist) { herr_t status; size_t s; status = H5Pget_sieve_buf_size((hid_t)plist, &s); if (status < 0) { h5libraryError(env); return -1; } return (jlong)s; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_elink_file_cache_size * Signature: (II)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1elink_1file_1cache_1size (JNIEnv *env, jclass clss, jint plist, jint size) { #if (H5_VERS_RELEASE > 6) /* H5_VERSION_GE(1,8,7) */ unsigned sz; herr_t status = -1; sz = (unsigned)size; status = H5Pset_elink_file_cache_size((hid_t)plist, (unsigned)sz); if (status < 0) { h5libraryError(env); } #else h5unimplemented(env, "H5Pset_elink_file_cache_size: only available > 1.8.6"); #endif } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_elink_file_cache_size * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1elink_1file_1cache_1size (JNIEnv *env, jclass clss, jint plist) { #if (H5_VERS_RELEASE > 6) /* H5_VERSION_GE(1,8,7) */ herr_t status; unsigned s; status = H5Pget_elink_file_cache_size((hid_t)plist, &s); if (status < 0) { h5libraryError(env); return -1; } return (jint)s; #else h5unimplemented(env, "H5Pget_elink_file_cache_size: only available > 1.8.6"); return -1; #endif } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_mdc_config * Signature: (I)Lncsa/hdf/hdf5lib/structs/H5AC_cache_config_t; */ JNIEXPORT jobject JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1mdc_1config (JNIEnv *env, jclass clss, jint plist) { herr_t status = -1; H5AC_cache_config_t cacheinfo; jclass cls; jmethodID constructor; jvalue args[30]; jstring j_str = NULL; jobject ret_info_t = NULL; memset(&cacheinfo, 0, sizeof(H5AC_cache_config_t)); cacheinfo.version = H5AC__CURR_CACHE_CONFIG_VERSION; status = H5Pget_mdc_config((hid_t)plist, (H5AC_cache_config_t*)&cacheinfo); if (status < 0) { h5libraryError(env); return NULL; } // get a reference to your class if you don't have it already cls = ENVPTR->FindClass(ENVPAR "ncsa/hdf/hdf5lib/structs/H5AC_cache_config_t"); // get a reference to the constructor; the name is constructor = ENVPTR->GetMethodID(ENVPAR cls, "", "(IZZZLjava/lang/String;ZZJDJJJIDDZJIDDIDDZJIZDII)V"); args[0].i = cacheinfo.version; args[1].z = cacheinfo.rpt_fcn_enabled; args[2].z = cacheinfo.open_trace_file; args[3].z = cacheinfo.close_trace_file; if (cacheinfo.trace_file_name != NULL) { j_str = ENVPTR->NewStringUTF(ENVPAR cacheinfo.trace_file_name); } args[4].l = j_str; args[5].z = cacheinfo.evictions_enabled; args[6].z = cacheinfo.set_initial_size; args[7].j = (jlong)cacheinfo.initial_size; args[8].d = cacheinfo.min_clean_fraction; args[9].j = (jlong)cacheinfo.max_size; args[10].j = (jlong)cacheinfo.min_size; args[11].j = cacheinfo.epoch_length; args[12].i = cacheinfo.incr_mode; args[13].d = cacheinfo.lower_hr_threshold; args[14].d = cacheinfo.increment; args[15].z = cacheinfo.apply_max_increment; args[16].j = (jlong)cacheinfo.max_increment; args[17].i = cacheinfo.flash_incr_mode; args[18].d = cacheinfo.flash_multiple; args[19].d = cacheinfo.flash_threshold; args[20].i = cacheinfo.decr_mode; args[21].d = cacheinfo.upper_hr_threshold; args[22].d = cacheinfo.decrement; args[23].z = cacheinfo.apply_max_decrement; args[24].j = (jlong)cacheinfo.max_decrement; args[25].i = cacheinfo.epochs_before_eviction; args[26].z = cacheinfo.apply_empty_reserve; args[27].d = cacheinfo.empty_reserve; args[28].i = cacheinfo.dirty_bytes_threshold; #if (H5_VERS_RELEASE >= 6) args[29].i = cacheinfo.metadata_write_strategy; #endif ret_info_t = ENVPTR->NewObjectA(ENVPAR cls, constructor, args); return ret_info_t; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_mdc_config * Signature: (ILncsa/hdf/hdf5lib/structs/H5AC_cache_config_t;)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1mdc_1config (JNIEnv *env, jclass clss, jint plist, jobject cache_config) { herr_t status; jclass cls; jfieldID fid; jstring j_str; const char *str; H5AC_cache_config_t cacheinfo; cls = ENVPTR->GetObjectClass(ENVPAR cache_config); fid = ENVPTR->GetFieldID(ENVPAR cls, "version", "I"); if(fid == 0) { h5badArgument(env, "H5Pset_mdc_config: version"); return; } cacheinfo.version = ENVPTR->GetIntField(ENVPAR cache_config, fid); if(ENVPTR->ExceptionOccurred(ENVONLY)) { h5JNIFatalError(env, "H5Pset_mdc_config: loading version failed"); return; } fid = ENVPTR->GetFieldID(ENVPAR cls, "rpt_fcn_enabled", "Z"); if(fid == 0) { h5badArgument(env, "H5Pset_mdc_config: rpt_fcn_enabled"); return; } cacheinfo.rpt_fcn_enabled = ENVPTR->GetBooleanField(ENVPAR cache_config, fid); if(ENVPTR->ExceptionOccurred(ENVONLY)) { h5JNIFatalError(env, "H5Pset_mdc_config: loading rpt_fcn_enabled failed"); return; } fid = ENVPTR->GetFieldID(ENVPAR cls, "open_trace_file", "Z"); if(fid == 0) { h5badArgument(env, "H5Pset_mdc_config: open_trace_file"); return; } cacheinfo.open_trace_file = ENVPTR->GetBooleanField(ENVPAR cache_config, fid); if(ENVPTR->ExceptionOccurred(ENVONLY)) { h5JNIFatalError(env, "H5Pset_mdc_config: loading open_trace_file failed"); return; } fid = ENVPTR->GetFieldID(ENVPAR cls, "close_trace_file", "Z"); if(fid == 0) { h5badArgument(env, "H5Pset_mdc_config: close_trace_file"); return; } cacheinfo.close_trace_file = ENVPTR->GetBooleanField(ENVPAR cache_config, fid); if(ENVPTR->ExceptionOccurred(ENVONLY)) { h5JNIFatalError(env, "H5Pset_mdc_config: loading close_trace_file failed"); return; } fid = ENVPTR->GetFieldID(ENVPAR cls, "trace_file_name", "Ljava/lang/String;"); if(fid == 0) { h5badArgument(env, "H5Pset_mdc_config: trace_file_name"); return; } j_str = (jstring)ENVPTR->GetObjectField(ENVPAR cache_config, fid); str = ENVPTR->GetStringUTFChars(ENVPAR j_str, NULL); if (str == NULL) { h5JNIFatalError(env, "H5Pset_mdc_config: out of memory trace_file_name"); return; } strncpy(cacheinfo.trace_file_name, str, 1025); ENVPTR->ReleaseStringUTFChars(ENVPAR j_str, str); if(ENVPTR->ExceptionOccurred(ENVONLY)) { h5JNIFatalError(env, "H5Pset_mdc_config: loading trace_file_name failed"); return; } fid = ENVPTR->GetFieldID(ENVPAR cls, "evictions_enabled", "Z"); if(fid == 0) { h5badArgument(env, "H5Pset_mdc_config: evictions_enabled"); return; } cacheinfo.evictions_enabled = ENVPTR->GetBooleanField(ENVPAR cache_config, fid); if(ENVPTR->ExceptionOccurred(ENVONLY)) { h5JNIFatalError(env, "H5Pset_mdc_config: loading evictions_enabled failed"); return; } fid = ENVPTR->GetFieldID(ENVPAR cls, "set_initial_size", "Z"); if(fid == 0) { h5badArgument(env, "H5Pset_mdc_config: set_initial_size"); return; } cacheinfo.set_initial_size = ENVPTR->GetBooleanField(ENVPAR cache_config, fid); if(ENVPTR->ExceptionOccurred(ENVONLY)) { h5JNIFatalError(env, "H5Pset_mdc_config: loading set_initial_size failed"); return; } fid = ENVPTR->GetFieldID(ENVPAR cls, "initial_size", "J"); if(fid == 0) { h5badArgument(env, "H5Pset_mdc_config: initial_size"); return; } cacheinfo.initial_size = (size_t)ENVPTR->GetLongField(ENVPAR cache_config, fid); if(ENVPTR->ExceptionOccurred(ENVONLY)) { h5JNIFatalError(env, "H5Pset_mdc_config: loading initial_size failed"); return; } fid = ENVPTR->GetFieldID(ENVPAR cls, "min_clean_fraction", "D"); if(fid == 0) { h5badArgument(env, "H5Pset_mdc_config: min_clean_fraction"); return; } cacheinfo.min_clean_fraction = ENVPTR->GetDoubleField(ENVPAR cache_config, fid); if(ENVPTR->ExceptionOccurred(ENVONLY)) { h5JNIFatalError(env, "H5Pset_mdc_config: loading min_clean_fraction failed"); return; } fid = ENVPTR->GetFieldID(ENVPAR cls, "max_size", "J"); if(fid == 0) { h5badArgument(env, "H5Pset_mdc_config: max_size"); return; } cacheinfo.max_size = (size_t)ENVPTR->GetLongField(ENVPAR cache_config, fid); if(ENVPTR->ExceptionOccurred(ENVONLY)) { h5JNIFatalError(env, "H5Pset_mdc_config: loading max_size failed"); return; } fid = ENVPTR->GetFieldID(ENVPAR cls, "min_size", "J"); if(fid == 0) { h5badArgument(env, "H5Pset_mdc_config: min_size"); return; } cacheinfo.min_size = (size_t)ENVPTR->GetLongField(ENVPAR cache_config, fid); if(ENVPTR->ExceptionOccurred(ENVONLY)) { h5JNIFatalError(env, "H5Pset_mdc_config: loading min_size failed"); return; } fid = ENVPTR->GetFieldID(ENVPAR cls, "epoch_length", "J"); if(fid == 0) { h5badArgument(env, "H5Pset_mdc_config: epoch_length"); return; } cacheinfo.epoch_length = (long int)ENVPTR->GetLongField(ENVPAR cache_config, fid); if(ENVPTR->ExceptionOccurred(ENVONLY)) { h5JNIFatalError(env, "H5Pset_mdc_config: loading epoch_length failed"); return; } fid = ENVPTR->GetFieldID(ENVPAR cls, "incr_mode", "I"); if(fid == 0) { h5badArgument(env, "H5Pset_mdc_config: incr_mode"); return; } cacheinfo.incr_mode = (enum H5C_cache_incr_mode)ENVPTR->GetIntField(ENVPAR cache_config, fid); if(ENVPTR->ExceptionOccurred(ENVONLY)) { h5JNIFatalError(env, "H5Pset_mdc_config: loading incr_mode failed"); return; } fid = ENVPTR->GetFieldID(ENVPAR cls, "lower_hr_threshold", "D"); if(fid == 0) { h5badArgument(env, "H5Pset_mdc_config: lower_hr_threshold"); return; } cacheinfo.lower_hr_threshold = ENVPTR->GetDoubleField(ENVPAR cache_config, fid); if(ENVPTR->ExceptionOccurred(ENVONLY)) { h5JNIFatalError(env, "H5Pset_mdc_config: loading lower_hr_threshold failed"); return; } fid = ENVPTR->GetFieldID(ENVPAR cls, "increment", "D"); if(fid == 0) { h5badArgument(env, "H5Pset_mdc_config: increment"); return; } cacheinfo.increment = ENVPTR->GetDoubleField(ENVPAR cache_config, fid); if(ENVPTR->ExceptionOccurred(ENVONLY)) { h5JNIFatalError(env, "H5Pset_mdc_config: loading increment failed"); return; } fid = ENVPTR->GetFieldID(ENVPAR cls, "apply_max_increment", "Z"); if(fid == 0) { h5badArgument(env, "H5Pset_mdc_config: apply_max_increment"); return; } cacheinfo.apply_max_increment = ENVPTR->GetBooleanField(ENVPAR cache_config, fid); if(ENVPTR->ExceptionOccurred(ENVONLY)) { h5JNIFatalError(env, "H5Pset_mdc_config: loading apply_max_increment failed"); return; } fid = ENVPTR->GetFieldID(ENVPAR cls, "max_increment", "J"); if(fid == 0) { h5badArgument(env, "H5Pset_mdc_config: max_increment"); return; } cacheinfo.max_increment = (size_t)ENVPTR->GetLongField(ENVPAR cache_config, fid); if(ENVPTR->ExceptionOccurred(ENVONLY)) { h5JNIFatalError(env, "H5Pset_mdc_config: loading max_increment failed"); return; } fid = ENVPTR->GetFieldID(ENVPAR cls, "flash_incr_mode", "I"); if(fid == 0) { h5badArgument(env, "H5Pset_mdc_config: flash_incr_mode"); return; } cacheinfo.flash_incr_mode = (enum H5C_cache_flash_incr_mode)ENVPTR->GetIntField(ENVPAR cache_config, fid); if(ENVPTR->ExceptionOccurred(ENVONLY)) { h5JNIFatalError(env, "H5Pset_mdc_config: loading flash_incr_mode failed"); return; } fid = ENVPTR->GetFieldID(ENVPAR cls, "flash_multiple", "D"); if(fid == 0) { h5badArgument(env, "H5Pset_mdc_config: flash_multiple"); return; } cacheinfo.flash_multiple = ENVPTR->GetDoubleField(ENVPAR cache_config, fid); if(ENVPTR->ExceptionOccurred(ENVONLY)) { h5JNIFatalError(env, "H5Pset_mdc_config: loading flash_multiple failed"); return; } fid = ENVPTR->GetFieldID(ENVPAR cls, "flash_threshold", "D"); if(fid == 0) { h5badArgument(env, "H5Pset_mdc_config: flash_threshold"); return; } cacheinfo.flash_threshold = ENVPTR->GetDoubleField(ENVPAR cache_config, fid); if(ENVPTR->ExceptionOccurred(ENVONLY)) { h5JNIFatalError(env, "H5Pset_mdc_config: loading flash_threshold failed"); return; } fid = ENVPTR->GetFieldID(ENVPAR cls, "decr_mode", "I"); if(fid == 0) { h5badArgument(env, "H5Pset_mdc_config: decr_mode"); return; } cacheinfo.decr_mode = (enum H5C_cache_decr_mode)ENVPTR->GetIntField(ENVPAR cache_config, fid); if(ENVPTR->ExceptionOccurred(ENVONLY)) { h5JNIFatalError(env, "H5Pset_mdc_config: loading decr_mode failed"); return; } fid = ENVPTR->GetFieldID(ENVPAR cls, "upper_hr_threshold", "D"); if(fid == 0) { h5badArgument(env, "H5Pset_mdc_config: upper_hr_threshold"); return; } cacheinfo.upper_hr_threshold = ENVPTR->GetDoubleField(ENVPAR cache_config, fid); if(ENVPTR->ExceptionOccurred(ENVONLY)) { h5JNIFatalError(env, "H5Pset_mdc_config: loading upper_hr_threshold failed"); return; } fid = ENVPTR->GetFieldID(ENVPAR cls, "decrement", "D"); if(fid == 0) { h5badArgument(env, "H5Pset_mdc_config: decrement"); return; } cacheinfo.decrement = ENVPTR->GetDoubleField(ENVPAR cache_config, fid); if(ENVPTR->ExceptionOccurred(ENVONLY)) { h5JNIFatalError(env, "H5Pset_mdc_config: loading decrement failed"); return; } fid = ENVPTR->GetFieldID(ENVPAR cls, "apply_max_decrement", "Z"); if(fid == 0) { h5badArgument(env, "H5Pset_mdc_config: apply_max_decrement"); return; } cacheinfo.apply_max_decrement = ENVPTR->GetBooleanField(ENVPAR cache_config, fid); if(ENVPTR->ExceptionOccurred(ENVONLY)) { h5JNIFatalError(env, "H5Pset_mdc_config: loading apply_max_decrement failed"); return; } fid = ENVPTR->GetFieldID(ENVPAR cls, "max_decrement", "J"); if(fid == 0) { h5badArgument(env, "H5Pset_mdc_config: max_decrement"); return; } cacheinfo.max_decrement = (size_t)ENVPTR->GetLongField(ENVPAR cache_config, fid); if(ENVPTR->ExceptionOccurred(ENVONLY)) { h5JNIFatalError(env, "H5Pset_mdc_config: loading max_decrement failed"); return; } fid = ENVPTR->GetFieldID(ENVPAR cls, "epochs_before_eviction", "I"); if(fid == 0) { h5badArgument(env, "H5Pset_mdc_config: epochs_before_eviction"); return; } cacheinfo.epochs_before_eviction = ENVPTR->GetIntField(ENVPAR cache_config, fid); if(ENVPTR->ExceptionOccurred(ENVONLY)) { h5JNIFatalError(env, "H5Pset_mdc_config: loading epochs_before_eviction failed"); return; } fid = ENVPTR->GetFieldID(ENVPAR cls, "apply_empty_reserve", "Z"); if(fid == 0) { h5badArgument(env, "H5Pset_mdc_config: apply_empty_reserve"); return; } cacheinfo.apply_empty_reserve = ENVPTR->GetBooleanField(ENVPAR cache_config, fid); if(ENVPTR->ExceptionOccurred(ENVONLY)) { h5JNIFatalError(env, "H5Pset_mdc_config: loading apply_empty_reserve failed"); return; } fid = ENVPTR->GetFieldID(ENVPAR cls, "empty_reserve", "D"); if(fid == 0) { h5badArgument(env, "H5Pset_mdc_config: empty_reserve"); return; } cacheinfo.empty_reserve = ENVPTR->GetDoubleField(ENVPAR cache_config, fid); if(ENVPTR->ExceptionOccurred(ENVONLY)) { h5JNIFatalError(env, "H5Pset_mdc_config: loading empty_reserve failed"); return; } fid = ENVPTR->GetFieldID(ENVPAR cls, "dirty_bytes_threshold", "I"); if(fid == 0) { h5badArgument(env, "H5Pset_mdc_config: dirty_bytes_threshold"); return; } cacheinfo.dirty_bytes_threshold = ENVPTR->GetIntField(ENVPAR cache_config, fid); if(ENVPTR->ExceptionOccurred(ENVONLY)) { h5JNIFatalError(env, "H5Pset_mdc_config: loading dirty_bytes_threshold failed"); return; } fid = ENVPTR->GetFieldID(ENVPAR cls, "metadata_write_strategy", "I"); if(fid == 0) { h5badArgument(env, "H5Pset_mdc_config: metadata_write_strategy"); return; } #if (H5_VERS_RELEASE >= 6) cacheinfo.metadata_write_strategy = ENVPTR->GetIntField(ENVPAR cache_config, fid); #endif if(ENVPTR->ExceptionOccurred(ENVONLY)) { h5JNIFatalError(env, "H5Pset_mdc_config: loading metadata_write_strategy failed"); return; } status = H5Pset_mdc_config((hid_t)plist, (H5AC_cache_config_t*)&cacheinfo); if (status < 0) { h5libraryError(env); return; } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_chunk_cache * Signature: (IJJD)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1chunk_1cache (JNIEnv *env, jclass clss, jint dapl, jlong rdcc_nslots, jlong rdcc_nbytes, jdouble rdcc_w0) { herr_t retVal = -1; retVal = H5Pset_chunk_cache((hid_t)dapl, (size_t)rdcc_nslots, (size_t)rdcc_nbytes, (double) rdcc_w0); if (retVal < 0) { h5libraryError(env); } return; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_chunk_cache * Signature: (I[J[J[D)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1chunk_1cache (JNIEnv *env, jclass clss, jint dapl, jlongArray rdcc_nslots, jlongArray rdcc_nbytes, jdoubleArray rdcc_w0) { herr_t status; jint mode; jdouble *w0Array; jlong *rdcc_nslotsArray; jlong *nbytesArray; jboolean isCopy; if (rdcc_w0 == NULL) { w0Array = (jdouble *)NULL; } else { w0Array = (jdouble *)ENVPTR->GetDoubleArrayElements(ENVPAR rdcc_w0, &isCopy); if (w0Array == NULL) { h5JNIFatalError(env, "H5Pget_chunk_cache: w0_array array not pinned"); return; } } if (rdcc_nslots == NULL) { rdcc_nslotsArray = (jlong *)NULL; } else { rdcc_nslotsArray = (jlong *)ENVPTR->GetLongArrayElements(ENVPAR rdcc_nslots, &isCopy); if (rdcc_nslotsArray == NULL) { /* exception -- out of memory */ if (w0Array != NULL) { ENVPTR->ReleaseDoubleArrayElements(ENVPAR rdcc_w0, w0Array, JNI_ABORT); } h5JNIFatalError(env, "H5Pget_chunk_cache: rdcc_nslots array not pinned"); return; } } if (rdcc_nbytes == NULL) { nbytesArray = (jlong *)NULL; } else { nbytesArray = (jlong *)ENVPTR->GetLongArrayElements(ENVPAR rdcc_nbytes, &isCopy); if (nbytesArray == NULL) { if (w0Array != NULL) { ENVPTR->ReleaseDoubleArrayElements(ENVPAR rdcc_w0, w0Array, JNI_ABORT); } if (rdcc_nslotsArray != NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR rdcc_nslots, rdcc_nslotsArray, JNI_ABORT); } h5JNIFatalError(env, "H5Pget_chunk_cache: nbytesArray array not pinned"); return; } } { /* direct cast (size_t *)variable fails on 32-bit environment */ long long rdcc_nslots_temp = *(rdcc_nslotsArray); size_t rdcc_nslots_t = (size_t)rdcc_nslots_temp; long long nbytes_temp = *(nbytesArray); size_t nbytes_t = (size_t)nbytes_temp; status = H5Pget_chunk_cache((hid_t)dapl, &rdcc_nslots_t, &nbytes_t, (double *)w0Array); *rdcc_nslotsArray = rdcc_nslots_t; *nbytesArray = nbytes_t; } if (status < 0) { mode = JNI_ABORT; } else { mode = 0; /* commit and free */ } if (rdcc_nslotsArray != NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR rdcc_nslots, rdcc_nslotsArray, mode); } if (nbytesArray != NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR rdcc_nbytes, nbytesArray, mode); } if (w0Array != NULL) { ENVPTR->ReleaseDoubleArrayElements(ENVPAR rdcc_w0, w0Array, mode); } if (status < 0) { h5libraryError(env); } return; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_obj_track_times * Signature: (I)Z */ JNIEXPORT jboolean JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1obj_1track_1times (JNIEnv *env, jclass clss, jint objplid) { herr_t status; hbool_t track_times; status = H5Pget_obj_track_times((hid_t)objplid, &track_times); if (status < 0) { h5libraryError(env); return JNI_FALSE; } if (track_times == 1) { return JNI_TRUE; } return JNI_FALSE; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_obj_track_times * Signature: (IZ)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1obj_1track_1times (JNIEnv *env, jclass clss, jint objplid, jboolean track_times) { herr_t status; hbool_t track; if (track_times == JNI_TRUE) { track = 1; } else { track = 0; } status = H5Pset_obj_track_times((hid_t)objplid, track); if (status < 0) { h5libraryError(env); } return; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_char_encoding * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1char_1encoding (JNIEnv *env, jclass clss, jint acpl) { herr_t status; H5T_cset_t encoding; status = H5Pget_char_encoding((hid_t)acpl, &encoding); if (status < 0) { h5libraryError(env); } return encoding; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_char_encoding * Signature: (II)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1char_1encoding (JNIEnv *env, jclass clss, jint acpl, jint encoding) { herr_t status; status = H5Pset_char_encoding((hid_t)acpl, (H5T_cset_t)encoding); if (status < 0) { h5libraryError(env); } return; } #ifdef __cplusplus } #endif libsis-jhdf5-java-14.12.1/source/c/hdf-java/h5pImp.h000066400000000000000000001114721256564762100216230ustar00rootroot00000000000000/* DO NOT EDIT THIS FILE - it is machine generated */ #include /* Header for class ncsa_hdf_hdf5lib_H5_H5_H5P */ #ifndef _Included_ncsa_hdf_hdf5lib_H5_H5P #define _Included_ncsa_hdf_hdf5lib_H5_H5P #ifdef __cplusplus extern "C" { #endif extern JavaVM *jvm; extern jobject visit_callback; /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pall_filters_avail * Signature: (I)Z */ JNIEXPORT jboolean JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pall_1filters_1avail (JNIEnv *env, jclass clss, jint dcpl_id); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pclose * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Pclose (JNIEnv *env, jclass clss, jint plist); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pclose_list * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pclose_1class (JNIEnv *env, jclass clss, jint plid); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pcopy * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Pcopy (JNIEnv *env, jclass clss, jint plist); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pcopy_prop * Signature: (IILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pcopy_1prop (JNIEnv *env, jclass clss, jint dst_plid, jint src_plid, jstring name); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pcreate * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Pcreate (JNIEnv *env, jclass clss, jint type); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pequal * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pequal (JNIEnv *env, jclass clss, jint plid1, jint plid2); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pexist * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pexist (JNIEnv *env, jclass clss, jint plid, jstring name); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pfill_value_defined * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pfill_1value_1defined (JNIEnv *env, jclass clss, jint plist, jintArray status); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget (JNIEnv *env, jclass clss, jint plid, jstring name); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_alignment * Signature: (I[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1alignment (JNIEnv *env, jclass clss, jint plist, jlongArray alignment); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_alloc_time * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1alloc_1time (JNIEnv *env, jclass clss, jint plist, jintArray alloc_time); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_attr_creation_order * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1attr_1creation_1order (JNIEnv *env, jclass clss, jint ocpl_id); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_attr_phase_change * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1attr_1phase_1change (JNIEnv *env, jclass clss, jint ocpl_id, jintArray attributes); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_btree_ratios * Signature: (I[D[D[D)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1btree_1ratios (JNIEnv *env, jclass clss, jint plist_id, jdoubleArray left, jdoubleArray middle, jdoubleArray right); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_buffer * Signature: (I[B[B)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1buffer (JNIEnv *env, jclass clss, jint plist, jbyteArray tconv, jbyteArray bkg); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_buffer_size * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1buffer_1size (JNIEnv *env, jclass clss, jint plist); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_cache * Signature: (I[I[J[J[D)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1cache (JNIEnv *env, jclass clss, jint plist, jintArray mdc_nelmts, jlongArray rdcc_nelmts, jlongArray rdcc_nbytes, jdoubleArray rdcc_w0); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_char_encoding * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1char_1encoding (JNIEnv *env, jclass clss, jint acpl); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_chunk * Signature: (II[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1chunk (JNIEnv *env, jclass clss, jint plist, jint max_ndims, jlongArray dims); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_chunk_cache * Signature: (I[J[J[D)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1chunk_1cache (JNIEnv *env, jclass clss, jint dapl, jlongArray rdcc_nslots, jlongArray rdcc_nbytes, jdoubleArray rdcc_w0); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_class * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1class (JNIEnv *env, jclass clss, jint plist); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_class_name * Signature: (I)Ljava/lang/String; */ JNIEXPORT jstring JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1class_1name (JNIEnv *env, jclass clss, jint plid); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_class_parent * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1class_1parent (JNIEnv *env, jclass clss, jint plid); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_copy_object * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1copy_1object (JNIEnv *env, jclass clss, jint ocp_plist_id); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_create_intermediate_group * Signature: (I)Z */ JNIEXPORT jboolean JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1create_1intermediate_1group (JNIEnv *env, jclass clss, jint lcpl_id); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_data_transform * Signature: (I[Ljava/lang/String;J)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1data_1transform (JNIEnv *env, jclass clss, jint plist_id, jobjectArray expression, jlong size); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_driver * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1driver (JNIEnv *env, jclass clss, jint plist); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_edc_check * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1edc_1check (JNIEnv *env, jclass clss, jint plist); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_elink_acc_flags * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1elink_1acc_1flags (JNIEnv *env, jclass clss, jint lapl_id); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Pget_elink_fapl * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Pget_1elink_1fapl (JNIEnv *env, jclass clss, jint lapl_id); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_elink_file_cache_size * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1elink_1file_1cache_1size (JNIEnv *env, jclass clss, jint plist); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_elink_prefix * Signature: (I[Ljava/lang/String;)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1elink_1prefix (JNIEnv *env, jclass clss, jint lapl_id, jobjectArray prefix); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_est_link_info * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1est_1link_1info (JNIEnv *env, jclass clss, jint gcpl_id, jintArray link_info); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_external * Signature: (IIJ[Ljava/lang/String;[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1external (JNIEnv *env, jclass clss, jint plist, jint idx, jlong name_size, jobjectArray name, jlongArray size); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_external_count * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1external_1count (JNIEnv *env, jclass clss, jint plist); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_family_offset * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1family_1offset (JNIEnv *env, jclass clss, jint fapl_id); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_fapl_core * Signature: (I[J[Z)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1fapl_1core (JNIEnv *env, jclass clss, jint fapl_id, jlongArray increment, jbooleanArray backing_store); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_fapl_direct * Signature: (I[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1fapl_1direct (JNIEnv *env, jclass clss, jint fapl_id, jlongArray info); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_fapl_family * Signature: (I[J[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1fapl_1family (JNIEnv *env, jclass clss, jint tid, jlongArray memb_size, jintArray memb_plist); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_fapl_muti * Signature: (I[I[I[Ljava/lang/String;[J)Z */ JNIEXPORT jboolean JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1fapl_1multi (JNIEnv *env, jclass clss, jint tid, jintArray memb_map, jintArray memb_fapl, jobjectArray memb_name, jlongArray memb_addr); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_fclose_degree * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1fclose_1degree (JNIEnv *env, jclass clss, jint plist); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_fill_time * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1fill_1time (JNIEnv *env, jclass clss, jint plist, jintArray fill_time); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_fill_value * Signature: (II[B)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1fill_1value (JNIEnv *env, jclass clss, jint plist_id, jint type_id, jbyteArray value); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_filter * Signature: (II[I[J[IJ[Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1filter (JNIEnv *env, jclass clss, jint plist, jint filter_number, jintArray flags, jlongArray cd_nelmts, jintArray cd_values, jlong namelen, jobjectArray name); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_filter2 * Signature: (II[I[J[IJ[Ljava/lang/String;[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1filter2 (JNIEnv *env, jclass clss, jint plist, jint filter_number, jintArray flags, jlongArray cd_nelmts, jintArray cd_values, jlong namelen, jobjectArray name, jintArray filter_config); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_filter_by_id * Signature: (II[I[J[IJ[Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1filter_1by_1id (JNIEnv *env, jclass clss, jint plist, jint filter, jintArray flags, jlongArray cd_nelmts, jintArray cd_values, jlong namelen, jobjectArray name); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_filter_by_id2 * Signature: (II[I[J[IJ[Ljava/lang/String;[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1filter_1by_1id2 (JNIEnv *env, jclass clss, jint plist, jint filter, jintArray flags, jlongArray cd_nelmts, jintArray cd_values, jlong namelen, jobjectArray name, jintArray filter_config); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_gc_references * Signature: (I[Z)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1gc_1references (JNIEnv *env, jclass clss, jint fapl_id, jbooleanArray gc_ref); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_gcreferences * Signature: (I)Z */ JNIEXPORT jboolean JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1gcreferences (JNIEnv *env, jclass clss, jint fapl_id); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_hyper_vector_size * Signature: (I[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1hyper_1vector_1size (JNIEnv *env, jclass clss, jint plist, jlongArray vector_size); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_istore_k * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1istore_1k (JNIEnv *env, jclass clss, jint plist, jintArray ik); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_layout * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1layout (JNIEnv *env, jclass clss, jint plist); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_libver_bounds * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1libver_1bounds (JNIEnv *env, jclass clss, jint fapl_id, jintArray libver); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_link_creation_order * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1link_1creation_1order (JNIEnv *env, jclass clss, jint gcpl_id); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_link_phase_change * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1link_1phase_1change (JNIEnv *env, jclass clss, jint gcpl_id, jintArray links); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_local_heap_size_hint * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1local_1heap_1size_1hint (JNIEnv *env, jclass clss, jint gcpl_id); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_mdc_config * Signature: (I)Lncsa/hdf/hdf5lib/structs/H5AC_cache_config_t; */ JNIEXPORT jobject JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1mdc_1config (JNIEnv *env, jclass clss, jint plist); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_meta_block_size * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1meta_1block_1size (JNIEnv *env, jclass clss, jint plist); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_nfilters * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1nfilters (JNIEnv *env, jclass clss, jint plist); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_nlinks * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1nlinks (JNIEnv *env, jclass clss, jint lapl_id); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_nprops * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1nprops (JNIEnv *env, jclass clss, jint plid); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_obj_track_times * Signature: (I)Z */ JNIEXPORT jboolean JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1obj_1track_1times (JNIEnv *env, jclass clss, jint objplid); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_preserve * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1preserve (JNIEnv *env, jclass clss, jint plist); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_sieve_buf_size * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1sieve_1buf_1size (JNIEnv *env, jclass clss, jint plist); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_shared_mesg_index * Signature: (II[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1shared_1mesg_1index (JNIEnv *env, jclass clss, jint fcpl_id, jint index_num, jintArray mesg_info); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_shared_mesg_nindexes * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1shared_1mesg_1nindexes (JNIEnv *env, jclass clss, jint fcpl_id); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_shared_mesg_phase_change * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1shared_1mesg_1phase_1change (JNIEnv *env, jclass clss, jint fcpl_id, jintArray size); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_size * Signature: (ILjava/lang/String;)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1size (JNIEnv *env, jclass clss, jint plid, jstring name); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_sizes * Signature: (I[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1sizes (JNIEnv *env, jclass clss, jint plist, jlongArray size); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_small_data_block_size * Signature: (I[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1small_1data_1block_1size (JNIEnv *env, jclass clss, jint plist, jlongArray size); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_small_data_block_size_long * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1small_1data_1block_1size_1long (JNIEnv *env, jclass clss, jint plist); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_sym_k * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1sym_1k (JNIEnv *env, jclass clss, jint plist, jintArray size); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_userblock * Signature: (I[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1userblock (JNIEnv *env, jclass clss, jint plist, jlongArray size); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_version * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pget_1version (JNIEnv *env, jclass clss, jint plist, jintArray version_info); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pisa_class * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pisa_1class (JNIEnv *env, jclass clss, jint plid, jint pcls); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pmodify_filter * Signature: (IIIJ[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pmodify_1filter (JNIEnv *env, jclass clss, jint plist, jint filter, jint flags, jlong cd_nelmts, jintArray cd_values); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Premove * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Premove (JNIEnv *env, jclass clss, jint plid, jstring name); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Premove_filter * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5P1remove_1filter (JNIEnv *env, jclass clss, jint obj_id, jint filter); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset * Signature: (ILjava/lang/String;I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset (JNIEnv *env, jclass clss, jint plid, jstring name, jint val); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_alignment * Signature: (IJJ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1alignment (JNIEnv *env, jclass clss, jint plist, jlong threshold, jlong alignment); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_alloc_time * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1alloc_1time (JNIEnv *env, jclass clss, jint plist, jint alloc_time); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_attr_creation_order * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1attr_1creation_1order (JNIEnv *env, jclass clss, jint ocpl_id, jint crt_order_flags); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_btree_ratios * Signature: (IDDD)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1btree_1ratios (JNIEnv *env, jclass clss, jint plist_id, jdouble left, jdouble middle, jdouble right); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_buffer * Signature: (IJ[B[B)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1buffer (JNIEnv *env, jclass clss, jint plist, jlong size, jbyteArray tconv, jbyteArray bkg); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_buffer_size * Signature: (IJ)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1buffer_1size (JNIEnv *env, jclass clss, jint plist, jlong size); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_cache * Signature: (IIJJD)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1cache (JNIEnv *env, jclass clss, jint plist, jint mdc_nelmts, jlong rdcc_nelmts, jlong rdcc_nbytes, jdouble rdcc_w0); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_char_encoding * Signature: (II)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1char_1encoding (JNIEnv *env, jclass clss, jint acpl, jint encoding); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_chunk * Signature: (II[B)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1chunk (JNIEnv *env, jclass clss, jint plist, jint ndims, jbyteArray dim); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_chunk_cache * Signature: (IJJD)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1chunk_1cache (JNIEnv *env, jclass clss, jint dapl, jlong rdcc_nslots, jlong rdcc_nbytes, jdouble rdcc_w0); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_copy_object * Signature: (II)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1copy_1object (JNIEnv *env, jclass clss, jint ocp_plist_id, jint copy_options); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_create_intermediate_group * Signature: (IZ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1create_1intermediate_1group (JNIEnv *env, jclass clss, jint lcpl_id, jboolean crt_intermed_group); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_data_transform * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1data_1transform (JNIEnv *env, jclass clss, jint plist_id, jstring expression); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_deflate * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1deflate (JNIEnv *env, jclass clss, jint plist, jint level); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_edc_check * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1edc_1check (JNIEnv *env, jclass clss, jint plist, jint check); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_elink_acc_flags * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1elink_1acc_1flags (JNIEnv *env, jclass clss, jint lapl_id, jint flags); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_elink_fapl * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1elink_1fapl (JNIEnv *env, jclass clss, jint lapl_id, jint fapl_id); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_elink_file_cache_size * Signature: (II)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1elink_1file_1cache_1size (JNIEnv *env, jclass clss, jint plist, jint size); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_elink_prefix * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1elink_1prefix (JNIEnv *env, jclass clss, jint lapl_id, jstring prefix); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_est_link_info * Signature: (III)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1est_1link_1info (JNIEnv *env, jclass clss, jint gcpl_id, jint est_num_entries, jint est_name_len); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_external * Signature: (ILjava/lang/String;JJ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1external (JNIEnv *env, jclass clss, jint plist, jstring name, jlong offset, jlong size); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_family_offset * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1family_1offset (JNIEnv *env, jclass clss, jint fapl_id, jlong offset); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_fapl_core * Signature: (IJZ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1fapl_1core (JNIEnv *env, jclass clss, jint fapl_id, jlong increment, jboolean backing_store); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_fapl_direct * Signature: (IJJJ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1fapl_1direct (JNIEnv *env, jclass clss, jint fapl_id, jlong alignment, jlong block_size, jlong cbuf_size); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_fapl_family * Signature: (IJI)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1fapl_1family (JNIEnv *env, jclass clss, jint plist, jlong memb_size, jint memb_plist); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_fapl_log * Signature: (ILjava/lang/String;JJ)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1fapl_1log (JNIEnv *env, jclass clss, jint fapl_id, jstring logfile, jlong flags, jlong buf_size); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_fapl_muti * Signature: (I[I[I[Ljava/lang/String;[JZ)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1fapl_1multi (JNIEnv *env, jclass clss, jint tid, jintArray memb_map, jintArray memb_fapl, jobjectArray memb_name, jlongArray memb_addr, jboolean relax); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_fapl_sec2 * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1fapl_1sec2 (JNIEnv *env, jclass clss, jint fapl_id); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_fapl_split * Signature: (ILjava/lang/String;ILjava/lang/String;I)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1fapl_1split (JNIEnv *env, jclass clss, jint fapl_id, jstring metaext, jint meta_pl_id, jstring rawext, jint raw_pl_id); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_fapl_stdio * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1fapl_1stdio (JNIEnv *env, jclass clss, jint fapl_id); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_fapl_windows * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1fapl_1windows (JNIEnv *env, jclass clss, jint fapl_id); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_fclose_degree * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1fclose_1degree (JNIEnv *env, jclass clss, jint plist, jint fc_degree); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_fill_time * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1fill_1time (JNIEnv *env, jclass clss, jint plist, jint fill_time); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_fill_value * Signature: (II[B)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1fill_1value (JNIEnv *env, jclass clss, jint plist_id, jint type_id, jbyteArray value); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_filter * Signature: (IIIJ[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1filter (JNIEnv *env, jclass clss, jint plist, jint filter, jint flags, jlong cd_nelmts, jintArray cd_values); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_fletcher32 * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1fletcher32 (JNIEnv *env, jclass clss, jint plist); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_gc_references * Signature: (IZ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1gc_1references (JNIEnv *env, jclass clss, jint fapl_id, jboolean gc_ref); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_hyper_vector_size * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1hyper_1vector_1size (JNIEnv *env, jclass clss, jint plist, jlong vector_size); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_istore_k * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1istore_1k (JNIEnv *env, jclass clss, jint plist, jint ik); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_layout * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1layout (JNIEnv *env, jclass clss, jint plist, jint layout); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_libver_bounds * Signature: (III)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1libver_1bounds (JNIEnv *env, jclass clss, jint fapl_id, jint low, jint high); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_link_creation_order * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1link_1creation_1order (JNIEnv *env, jclass clss, jint gcpl_id, jint crt_order_flags); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_link_phase_change * Signature: (III)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1link_1phase_1change (JNIEnv *env, jclass clss, jint gcpl_id, jint max_compact, jint min_dense); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_local_heap_size_hint * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1local_1heap_1size_1hint (JNIEnv *env, jclass clss, jint gcpl_id, jlong size_hint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_mdc_config * Signature: (ILncsa/hdf/hdf5lib/structs/H5AC_cache_config_t;)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1mdc_1config (JNIEnv *env, jclass clss, jint plist, jobject cache_config); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_meta_block_size * Signature: (IJ)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1meta_1block_1size (JNIEnv *env, jclass clss, jint fapl_id, jlong size); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_nbit * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1nbit (JNIEnv *env, jclass clss, jint plist_id); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_nlinks * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1nlinks (JNIEnv *env, jclass clss, jint lapl_id, jlong nlinks); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_obj_track_times * Signature: (IZ)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1obj_1track_1times (JNIEnv *env, jclass clss, jint objplid, jboolean track_times); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_preserve * Signature: (IZ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1preserve (JNIEnv *env, jclass clss, jint plist, jboolean status); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_scaleoffset * Signature: (III)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1scaleoffset (JNIEnv *env, jclass clss, jint plist_id, jint scale_type, jint scale_factor); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_sieve_buf_size * Signature: (IJ)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1sieve_1buf_1size (JNIEnv *env, jclass clss, jint fapl_id, jlong size); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_shared_mesg_index * Signature: (IIII)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1shared_1mesg_1index (JNIEnv *env, jclass clss, jint fcpl_id, jint index_num, jint mesg_type_flags, jint min_mesg_size); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_shared_mesg_nindexes * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1shared_1mesg_1nindexes (JNIEnv *env, jclass clss, jint plist_id, jint nindexes); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_shared_mesg_phase_change * Signature: (III)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1shared_1mesg_1phase_1change (JNIEnv *env, jclass clss, jint fcpl_id, jint max_list, jint min_btree); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_shuffle * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1shuffle (JNIEnv *env, jclass clss, jint plist); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_sizes * Signature: (III)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1sizes (JNIEnv *env, jclass clss, jint plist, jint sizeof_addr, jint sizeof_size); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_small_data_block_size * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1small_1data_1block_1size (JNIEnv *env, jclass clss, jint plist, jlong size); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_sym_k * Signature: (III)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1sym_1k (JNIEnv *env, jclass clss, jint plist, jint ik, jint lk); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_szip * Signature: (III)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1szip (JNIEnv *env, jclass clss, jint plist, jint options_mask, jint pixels_per_block); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_userblock * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Pset_1userblock (JNIEnv *env, jclass clss, jint plist, jlong size); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Punregister * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Punregister (JNIEnv *env, jclass clss, jint plid, jstring name); #ifdef __cplusplus } #endif #endif libsis-jhdf5-java-14.12.1/source/c/hdf-java/h5rImp.c000077500000000000000000000234261256564762100216240ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ /* * This code is the C-interface called by Java programs to access the * Reference API Functions of the HDF5 library. * * Each routine wraps a single HDF entry point, generally with the * analogous arguments and return codes. * * For details of the HDF libraries, see the HDF Documentation at: * http://hdf.ncsa.uiuc.edu/HDF5/doc/ * */ #ifdef __cplusplus extern "C" { #endif #include "hdf5.h" #include #include #include "h5jni.h" /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Rcreate * Signature: ([BILjava/lang/String;II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Rcreate (JNIEnv *env, jclass clss, jbyteArray ref, jint loc_id, jstring name, jint ref_type, jint space_id) { char* rName; jboolean isCopy; herr_t status; jbyte *refP; if (ref == NULL) { h5nullArgument( env, "H5Rcreate: ref is NULL"); return -1; } if (name == NULL) { h5nullArgument( env, "H5Rcreate: name is NULL"); return -1; } if (ref_type == H5R_OBJECT) { if (ENVPTR->GetArrayLength(ENVPAR ref) != H5R_OBJ_REF_BUF_SIZE) { h5badArgument( env, "H5Rcreate: ref input array != H5R_OBJ_REF_BUF_SIZE"); return -1; } } else if (ref_type == H5R_DATASET_REGION) { if (ENVPTR->GetArrayLength(ENVPAR ref) != H5R_DSET_REG_REF_BUF_SIZE) { h5badArgument( env, "H5Rcreate: region ref input array != H5R_DSET_REG_REF_BUF_SIZE"); return -1; } } else { h5badArgument( env, "H5Rcreate: ref_type unknown type "); return -1; } refP = (jbyte *)ENVPTR->GetByteArrayElements(ENVPAR ref, &isCopy); if (refP == NULL) { h5JNIFatalError(env, "H5Rcreate: ref not pinned"); return -1; } rName = (char *)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (rName == NULL) { ENVPTR->ReleaseByteArrayElements(ENVPAR ref,refP,JNI_ABORT); h5JNIFatalError(env, "H5Rcreate: name not pinned"); return -1; } status = H5Rcreate(refP, loc_id, rName, (H5R_type_t)ref_type, space_id); ENVPTR->ReleaseStringUTFChars(ENVPAR name, rName); if (status < 0) { ENVPTR->ReleaseByteArrayElements(ENVPAR ref, refP, JNI_ABORT); h5libraryError(env); } else { ENVPTR->ReleaseByteArrayElements(ENVPAR ref, refP, 0); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Rdereference * Signature: (II[B)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Rdereference (JNIEnv *env, jclass clss, jint dataset, jint ref_type, jbyteArray ref ) { jboolean isCopy; jbyte *refP; hid_t status; if (ref == NULL) { h5nullArgument( env, "H5Rdereference: ref is NULL"); return -1; } if ((ref_type == H5R_OBJECT) && ENVPTR->GetArrayLength(ENVPAR ref) != H5R_OBJ_REF_BUF_SIZE) { h5badArgument( env, "H5Rdereference: obj ref input array != H5R_OBJ_REF_BUF_SIZE"); return -1; } else if ((ref_type == H5R_DATASET_REGION) && ENVPTR->GetArrayLength(ENVPAR ref) != H5R_DSET_REG_REF_BUF_SIZE) { h5badArgument( env, "H5Rdereference: region ref input array != H5R_DSET_REG_REF_BUF_SIZE"); return -1; } refP = (jbyte *)ENVPTR->GetByteArrayElements(ENVPAR ref, &isCopy); if (refP == NULL) { h5JNIFatalError(env, "H5Rderefernce: ref not pinned"); return -1; } status = H5Rdereference((hid_t)dataset, (H5R_type_t)ref_type, refP); ENVPTR->ReleaseByteArrayElements(ENVPAR ref, refP, JNI_ABORT); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Rget_region * Signature: (II[B)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Rget_1region (JNIEnv *env, jclass clss, jint dataset, jint ref_type, jbyteArray ref ) { hid_t status; jboolean isCopy; jbyte *refP; if (ref_type != H5R_DATASET_REGION) { h5badArgument( env, "H5Rget_region: bad ref_type "); return -1; } if (ref == NULL) { h5nullArgument( env, "H5Rget_region: ref is NULL"); return -1; } if ( ENVPTR->GetArrayLength(ENVPAR ref) != H5R_DSET_REG_REF_BUF_SIZE) { h5badArgument( env, "H5Rget_region: region ref input array != H5R_DSET_REG_REF_BUF_SIZE"); return -1; } refP = (jbyte *)ENVPTR->GetByteArrayElements(ENVPAR ref, &isCopy); if (refP == NULL) { h5JNIFatalError(env, "H5Rget_region: ref not pinned"); return -1; } status = H5Rget_region((hid_t)dataset, (H5R_type_t)ref_type, refP); ENVPTR->ReleaseByteArrayElements(ENVPAR ref, refP, JNI_ABORT); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5G_obj_t H5Rget_obj_type * Signature: (II[B)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Rget_1obj_1type (JNIEnv *env, jclass clss, jint loc_id, jint ref_type, jbyteArray ref) { int retVal =-1; jboolean isCopy; jbyte *refP; H5O_type_t object_info; if (ref == NULL) { h5nullArgument( env, "H5Rget_object_type: ref is NULL"); return -1; } refP = (jbyte *)ENVPTR->GetByteArrayElements(ENVPAR ref, &isCopy); if (refP == NULL) { h5JNIFatalError(env, "H5Rget_object_type: ref not pinned"); return -1; } retVal = H5Rget_obj_type2((hid_t)loc_id, (H5R_type_t)ref_type, refP, &object_info); if(retVal >= 0) retVal = object_info; ENVPTR->ReleaseByteArrayElements(ENVPAR ref, refP, JNI_ABORT); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: int H5Rget_obj_type2 * Signature: (II[B[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Rget_1obj_1type2 (JNIEnv *env, jclass clss, jint loc_id, jint ref_type, jbyteArray ref, jintArray ref_obj) { jint status; jboolean isCopy; jbyte *refP; jint *ref_objP; int retVal; if (ref == NULL) { h5nullArgument( env, "H5Rget_object_type: ref is NULL"); return -1; } if (ref_obj == NULL) { h5nullArgument( env, "H5Rget_object_type: ref_obj is NULL"); return -1; } refP = (jbyte *)ENVPTR->GetByteArrayElements(ENVPAR ref, &isCopy); if (refP == NULL) { h5JNIFatalError(env, "H5Rget_object_type: ref not pinned"); return -1; } ref_objP = (jint *)ENVPTR->GetIntArrayElements(ENVPAR ref_obj, &isCopy); if (ref_objP == NULL) { ENVPTR->ReleaseByteArrayElements(ENVPAR ref,refP,0); h5JNIFatalError(env, "H5Rget_object_type: ref_obj not pinned"); return -1; } status = H5Rget_obj_type2((hid_t)loc_id, (H5R_type_t)ref_type, refP, (H5O_type_t*)ref_objP); retVal = ref_objP[0]; ENVPTR->ReleaseByteArrayElements(ENVPAR ref, refP, JNI_ABORT); if (status < 0) { ENVPTR->ReleaseIntArrayElements(ENVPAR ref_obj,ref_objP, JNI_ABORT); h5libraryError(env); } else { ENVPTR->ReleaseIntArrayElements(ENVPAR ref_obj, ref_objP, 0); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Rget_name * Signature: (II[B[Ljava/lang/String;J)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Rget_1name (JNIEnv *env, jclass clss, jint loc_id, jint ref_type, jbyteArray ref, jobjectArray name, jlong size) { jlong ret_val = -1; jbyte *refP; jboolean isCopy; char *aName=NULL; jstring str; size_t bs; bs = (long)size; if (bs <= 0) { h5badArgument( env, "H5Rget_name: size <= 0"); return -1; } if (ref == NULL) { h5nullArgument( env, "H5Rget_name: ref is NULL"); return -1; } if ((ref_type == H5R_OBJECT) && ENVPTR->GetArrayLength(ENVPAR ref) != H5R_OBJ_REF_BUF_SIZE) { h5badArgument( env, "H5Rdereference: obj ref input array != H5R_OBJ_REF_BUF_SIZE"); return -1; } else if ((ref_type == H5R_DATASET_REGION) && ENVPTR->GetArrayLength(ENVPAR ref) != H5R_DSET_REG_REF_BUF_SIZE) { h5badArgument( env, "H5Rdereference: region ref input array != H5R_DSET_REG_REF_BUF_SIZE"); return -1; } refP = (jbyte *)ENVPTR->GetByteArrayElements(ENVPAR ref, &isCopy); if (refP == NULL) { h5JNIFatalError(env, "H5Rcreate: ref not pinned"); return -1; } aName = (char*)malloc(sizeof(char)*bs); if (aName == NULL) { ENVPTR->ReleaseByteArrayElements(ENVPAR ref, refP, JNI_ABORT); h5outOfMemory( env, "H5Aget_name: malloc failed"); return -1; } ret_val = (jlong) H5Rget_name( (hid_t)loc_id, (H5R_type_t) ref_type, refP, aName, bs) ; ENVPTR->ReleaseByteArrayElements(ENVPAR ref, refP, JNI_ABORT); if (ret_val < 0) { free(aName); h5libraryError(env); return -1; } str = ENVPTR->NewStringUTF(ENVPAR aName); ENVPTR->SetObjectArrayElement(ENVPAR name, 0, str); if (aName) free (aName); return ret_val; } #ifdef __cplusplus } #endif libsis-jhdf5-java-14.12.1/source/c/hdf-java/h5sImp.c000077500000000000000000001146161256564762100216270ustar00rootroot00000000000000/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF Java Products. The full HDF Java copyright * * notice, including terms governing use, modification, and redistribution, * * is contained in the file, COPYING. COPYING can be found at the root of * * the source code distribution tree. You can also access it online at * * http://www.hdfgroup.org/products/licenses.html. If you do not have * * access to the file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /* * This code is the C-interface called by Java programs to access the * Dataspace Object API Functions of the HDF5 library. * * Each routine wraps a single HDF entry point, generally with the * analogous arguments and return codes. * * For details of the HDF libraries, see the HDF Documentation at: * http://hdfdfgroup.org/HDF5/doc/ * */ #ifdef __cplusplus extern "C" { #endif #include #include #include "hdf5.h" #include "h5jni.h" #include "h5sImp.h" /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Screate * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Screate(JNIEnv *env, jclass clss, jint type) { hid_t retVal = -1; retVal = H5Screate((H5S_class_t) type); if (retVal < 0) h5libraryError(env); return (jint) retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Screate_simple * Signature: (I[J[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Screate_1simple( JNIEnv *env, jclass clss, jint rank, jlongArray dims, jlongArray maxdims) { hid_t status; jlong *dimsP, *maxdimsP; jboolean isCopy; hsize_t *sa = NULL; hsize_t *msa = NULL; int i; int drank, mrank; hsize_t *lp; jlong *jlp; if (rank < 0) { h5badArgument(env, "H5Screate_simple: rank is invalid"); return -1; } if (dims == NULL) { h5nullArgument(env, "H5Screate_simple: dims is NULL"); return -1; } drank = (int) ENVPTR->GetArrayLength(ENVPAR dims); if (drank != rank) { h5badArgument(env, "H5Screate_simple: dims rank is invalid"); return -1; } if(maxdims != NULL) { mrank = (int) ENVPTR->GetArrayLength(ENVPAR maxdims); if (mrank != rank) { h5badArgument(env, "H5Screate_simple: maxdims rank is invalid"); return -1; } } dimsP = ENVPTR->GetLongArrayElements(ENVPAR dims, &isCopy); if (dimsP == NULL) { h5JNIFatalError(env, "H5Screate_simple: dims not pinned"); return -1; } sa = lp = (hsize_t *)malloc(rank * sizeof(hsize_t)); if (sa == NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR dims, dimsP, JNI_ABORT); h5JNIFatalError(env, "H5Screate_simple: dims not converted to hsize_t"); return -1; } jlp = (jlong *)dimsP; for (i = 0; i < rank; i++) { *lp = (hsize_t)*jlp; lp++; jlp++; } if (maxdims == NULL) { maxdimsP = NULL; msa = (hsize_t *)maxdimsP; } else { maxdimsP = ENVPTR->GetLongArrayElements(ENVPAR maxdims, &isCopy); if (maxdimsP == NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR dims, dimsP, JNI_ABORT); free (sa); h5JNIFatalError(env, "H5Screate_simple: maxdims not pinned"); return -1; } msa = lp = (hsize_t *)malloc(rank * sizeof(hsize_t)); if (msa == NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR dims, dimsP, JNI_ABORT); ENVPTR->ReleaseLongArrayElements(ENVPAR maxdims, maxdimsP, JNI_ABORT); free (sa); h5JNIFatalError(env, "H5Screate_simple: dims not converted to hsize_t"); return -1; } jlp = (jlong *)maxdimsP; for (i = 0; i < mrank; i++) { *lp = (hsize_t)*jlp; lp++; jlp++; } } status = H5Screate_simple(rank, (const hsize_t *)sa, (const hsize_t *)msa); if (maxdimsP != NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR maxdims, maxdimsP, JNI_ABORT); if (msa) free (msa); } ENVPTR->ReleaseLongArrayElements(ENVPAR dims, dimsP, JNI_ABORT); if (sa) free (sa); if (status < 0) h5libraryError(env); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Scopy * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Scopy(JNIEnv *env, jclass clss, jint space_id) { hid_t retVal = -1; retVal = H5Scopy(space_id); if (retVal < 0) h5libraryError(env); return (jint) retVal; } #ifdef notdef // 10/28/99 -- added code to copy the array -- this is not used, // but serves as a reminder in case we try to implement this in // the future.... /* * Note: the argument coord is actually long coord[][], which has been * flattened by the caller. */ /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sselect_elements * Signature: (III[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sselect_1elements (JNIEnv *env, jclass clss, jint space_id, jint op, jint num_elemn, jlongArray coord) { herr_t status; jint i; jlong *P; jboolean isCopy; hssize_t *sa; int rank; if (coord == NULL) { h5nullArgument( env, "H5Sselect_elements: coord is NULL"); return -1; } P = ENVPTR->GetLongArrayElements(ENVPAR env,coord,&isCopy); if (P == NULL) { h5JNIFatalError(env, "H5Sselect_elements: coord not pinned"); return -1; } sa = (hssize_t *)malloc( num_elems * 2 * sizeof(hssize_t)); if (sa == NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR env,coord,P,JNI_ABORT); h5JNIFatalError(env, "H5Sselect_elements: coord array not converted to hssize_t"); return -1; } for (i= 0; i < (num_elsms * 2); i++) { sa[i] = P[i]; } status = H5Sselect_elements (space_id, (H5S_seloper_t)op, num_elemn, (const hssize_t **)&sa); ENVPTR->ReleaseLongArrayElements(ENVPAR env, coord, P, JNI_ABORT); free(sa); if (status < 0) h5libraryError(env); return (jint)status; } #endif /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sselect_elements * Signature: (III[B)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sselect_1elements( JNIEnv *env, jclass clss, jint space_id, jint op, jint num_elemn, jbyteArray coord) { int ii; hsize_t *lp = NULL; hsize_t *llp; jlong *jlp; herr_t status; jbyte *P; jboolean isCopy; jsize size; int nlongs; if (coord == NULL) { h5nullArgument(env, "H5Sselect_elements: coord is NULL"); return -1; } P = ENVPTR->GetByteArrayElements(ENVPAR coord, &isCopy); if (P == NULL) { h5JNIFatalError(env, "H5Sselect_elements: coord not pinned"); return -1; } size = (int) ENVPTR->GetArrayLength(ENVPAR coord); nlongs = size / sizeof(jlong); lp = (hsize_t *)malloc(nlongs * sizeof(hsize_t)); jlp = (jlong *)P; llp = lp; for (ii = 0; ii < nlongs; ii++) { *lp = (hsize_t)*jlp; lp++; jlp++; } status = H5Sselect_elements (space_id, (H5S_seloper_t)op, num_elemn, (const hsize_t *)llp); ENVPTR->ReleaseByteArrayElements(ENVPAR coord, P, JNI_ABORT); if (llp) free (llp); if (status < 0) h5libraryError(env); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sselect_all * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sselect_1all(JNIEnv *env, jclass clss, jint space_id) { herr_t retVal = -1; retVal = H5Sselect_all(space_id); if (retVal < 0) h5libraryError(env); return (jint) retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sselect_none * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sselect_1none(JNIEnv *env, jclass clss, jint space_id) { herr_t retVal = -1; retVal = H5Sselect_none(space_id); if (retVal < 0) h5libraryError(env); return (jint) retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sselect_valid * Signature: (I)Z */ JNIEXPORT jboolean JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sselect_1valid( JNIEnv *env, jclass clss, jint space_id) { htri_t bval; bval = H5Sselect_valid(space_id); if (bval > 0) { return JNI_TRUE; } else if (bval == 0) { return JNI_FALSE; } else { h5libraryError(env); return JNI_FALSE; } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sget_simple_extent_npoints * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sget_1simple_1extent_1npoints( JNIEnv *env, jclass clss, jint space_id) { hssize_t retVal = -1; retVal = H5Sget_simple_extent_npoints(space_id); if (retVal < 0) h5libraryError(env); return (jlong) retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sget_select_npoints * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sget_1select_1npoints( JNIEnv *env, jclass clss, jint space_id) { hssize_t retVal = -1; retVal = H5Sget_select_npoints(space_id); if (retVal < 0) h5libraryError(env); return (jlong) retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sget_select_type * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sget_1select_1type( JNIEnv *env, jclass clss, jint space_id) { int retVal = -1; retVal = H5Sget_select_type(space_id); if (retVal < 0) h5libraryError(env); return (jint) retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sget_simple_extent_ndims * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sget_1simple_1extent_1ndims( JNIEnv *env, jclass clss, jint space_id) { int retVal = -1; retVal = H5Sget_simple_extent_ndims(space_id); if (retVal < 0) h5libraryError(env); return (jint) retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sget_simple_extent_dims * Signature: (I[J[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sget_1simple_1extent_1dims( JNIEnv *env, jclass clss, jint space_id, jlongArray dims, jlongArray maxdims) { int status; jlong *dimsP, *maxdimsP; jboolean isCopy; hsize_t *sa; hsize_t *msa; int i; int rank = -1; int mrank; if (dims == NULL) { dimsP = NULL; sa = (hsize_t *)dimsP; } else { dimsP = ENVPTR->GetLongArrayElements(ENVPAR dims, &isCopy); if (dimsP == NULL) { h5JNIFatalError(env, "H5Pget_simple_extent_dims: dims not pinned"); return -1; } rank = (int) ENVPTR->GetArrayLength(ENVPAR dims); sa = (hsize_t *)malloc( rank * sizeof(hsize_t)); if (sa == NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR dims,dimsP,JNI_ABORT); h5JNIFatalError(env,"H5Sget_simple_extent_dims: dims not converted to hsize_t"); return -1; } } if (maxdims == NULL) { maxdimsP = NULL; msa = (hsize_t *)maxdimsP; } else { maxdimsP = ENVPTR->GetLongArrayElements(ENVPAR maxdims,&isCopy); if (maxdimsP == NULL) { if (dimsP != NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR dims,dimsP,JNI_ABORT); free(sa); } h5JNIFatalError(env, "H5Pget_simple_extent_dims: maxdims not pinned"); return -1; } mrank = (int) ENVPTR->GetArrayLength(ENVPAR maxdims); if(rank < 0) rank = mrank; else if(mrank != rank) { if (dimsP != NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR dims,dimsP,JNI_ABORT); free(sa); } ENVPTR->ReleaseLongArrayElements(ENVPAR maxdims,maxdimsP,JNI_ABORT); h5JNIFatalError(env, "H5Sget_simple_extent_dims: maxdims rank not same as dims"); return -1; } msa = (hsize_t *)malloc( rank * sizeof(hsize_t)); if (msa == NULL) { if (dimsP != NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR dims,dimsP,JNI_ABORT); free(sa); } ENVPTR->ReleaseLongArrayElements(ENVPAR maxdims,maxdimsP,JNI_ABORT); h5JNIFatalError(env, "H5Sget_simple_extent_dims: maxdims not converted to hsize_t"); return -1; } } status = H5Sget_simple_extent_dims(space_id, (hsize_t *)sa, (hsize_t *)msa); if (status < 0) { if (dimsP != NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR dims,dimsP,JNI_ABORT); free(sa); } if (maxdimsP != NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR maxdims,maxdimsP,JNI_ABORT); free(msa); } h5libraryError(env); return -1; } if (dimsP != NULL) { for (i = 0; i < rank; i++) { dimsP[i] = sa[i]; } free(sa); ENVPTR->ReleaseLongArrayElements(ENVPAR dims,dimsP,0); } if (maxdimsP != NULL) { for (i = 0; i < rank; i++) { maxdimsP[i] = msa[i]; } free(msa); ENVPTR->ReleaseLongArrayElements(ENVPAR maxdims,maxdimsP,0); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sget_simple_extent_type * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sget_1simple_1extent_1type( JNIEnv *env, jclass clss, jint space_id) { H5S_class_t retVal = H5S_NO_CLASS; if (space_id < 0) h5libraryError(env); retVal = H5Sget_simple_extent_type(space_id); return (jint) retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sset_extent_simple * Signature: (II[J[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sset_1extent_1simple( JNIEnv *env, jclass clss, jint space_id, jint rank, jlongArray dims, jlongArray maxdims) { herr_t status; jlong *dimsP, *maxdimsP; jboolean isCopy; hsize_t *sa; hsize_t *msa; int i; int drank, mrank; hsize_t *lp; jlong *jlp; if (dims == NULL) { h5nullArgument(env, "H5Sset_simple_extent: dims is NULL"); return -1; } drank = (int) ENVPTR->GetArrayLength(ENVPAR dims); if (drank != rank) { h5badArgument(env, "H5Screate_simple: dims rank is invalid"); return -1; } if(maxdims != NULL) { mrank = (int) ENVPTR->GetArrayLength(ENVPAR maxdims); if (mrank != rank) { h5badArgument(env, "H5Screate_simple: maxdims rank is invalid"); return -1; } } dimsP = ENVPTR->GetLongArrayElements(ENVPAR dims, &isCopy); if (dimsP == NULL) { h5JNIFatalError(env, "H5Pset_simple_extent: dims not pinned"); return -1; } sa = lp = (hsize_t *)malloc(rank * sizeof(hsize_t)); if (sa == NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR dims,dimsP,JNI_ABORT); h5JNIFatalError(env,"H5Sset_simple_extent: dims not converted to hsize_t"); return -1; } jlp = (jlong *)dimsP; for (i = 0; i < rank; i++) { *lp = (hsize_t)*jlp; lp++; jlp++; } if (maxdims == NULL) { maxdimsP = NULL; msa = (hsize_t *)maxdimsP; } else { maxdimsP = ENVPTR->GetLongArrayElements(ENVPAR maxdims,&isCopy); if (maxdimsP == NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR dims,dimsP,JNI_ABORT); h5JNIFatalError(env, "H5Pset_simple_extent: maxdims not pinned"); return -1; } msa = lp = (hsize_t *)malloc(rank * sizeof(hsize_t)); if (msa == NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR dims,dimsP,JNI_ABORT); ENVPTR->ReleaseLongArrayElements(ENVPAR maxdims,maxdimsP,JNI_ABORT); free (sa); h5JNIFatalError(env, "H5Sset_simple_extent: maxdims not converted to hsize_t"); return -1; } jlp = (jlong *)maxdimsP; for (i = 0; i < rank; i++) { *lp = (hsize_t)*jlp; lp++; jlp++; } } status = H5Sset_extent_simple(space_id, rank, (hsize_t *)sa, (hsize_t *)msa); ENVPTR->ReleaseLongArrayElements(ENVPAR dims,dimsP,JNI_ABORT); free (sa); if (maxdimsP != NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR maxdims,maxdimsP,JNI_ABORT); free (msa); } if (status < 0) h5libraryError(env); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sis_simple * Signature: (I)Z */ JNIEXPORT jboolean JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sis_1simple(JNIEnv *env, jclass clss, jint space_id) { htri_t bval; bval = H5Sis_simple(space_id); if (bval > 0) { return JNI_TRUE; } else if (bval == 0) { return JNI_FALSE; } else { h5libraryError(env); return JNI_FALSE; } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Soffset_simple * Signature: (I[B)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Soffset_1simple(JNIEnv *env, jclass clss, jint space_id, jbyteArray offset) { herr_t status; jbyte *P = NULL; jboolean isCopy; hssize_t *sa; int rank; int i; hssize_t *lp; jlong *jlp; if (offset != NULL) { P = ENVPTR->GetByteArrayElements(ENVPAR offset, &isCopy); if (P == NULL) { h5JNIFatalError(env, "H5Soffset_simple: offset not pinned"); return -1; } i = (int) ENVPTR->GetArrayLength(ENVPAR offset); rank = i / sizeof(jlong); sa = lp = (hssize_t *)malloc(rank * sizeof(hssize_t)); if (sa == NULL) { ENVPTR->ReleaseByteArrayElements(ENVPAR offset,P,JNI_ABORT); h5JNIFatalError(env,"H5Soffset_simple: offset not converted to hssize_t"); return -1; } jlp = (jlong *)P; for (i = 0; i < rank; i++) { *lp = (hssize_t)*jlp; lp++; jlp++; } } else { P = NULL; sa = (hssize_t *)P; } status = H5Soffset_simple(space_id, sa); if (P != NULL) { ENVPTR->ReleaseByteArrayElements(ENVPAR offset,P,JNI_ABORT); free(sa); } if (status < 0) h5libraryError(env); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sextent_copy * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sextent_1copy(JNIEnv *env, jclass clss, jint space_id, jint src_id) { herr_t retVal = -1; retVal = H5Sextent_copy(space_id, src_id); if (retVal < 0) h5libraryError(env); return (jint) retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sextent_equal * Signature: (II)Z */ JNIEXPORT jboolean JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sextent_1equal (JNIEnv *env, jclass clss, jint space_id, jint src_id) { htri_t bval; bval = H5Sextent_equal(space_id, src_id); if (bval > 0) { return JNI_TRUE; } else if (bval == 0) { return JNI_FALSE; } else { h5libraryError(env); return JNI_FALSE; } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sset_extent_none * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sset_1extent_1none( JNIEnv *env, jclass clss, jint space_id) { herr_t retVal = -1; retVal = H5Sset_extent_none(space_id); if (retVal < 0) h5libraryError(env); return (jint) retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sselect_hyperslab * Signature: (II[J[J[J[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sselect_1hyperslab( JNIEnv *env, jclass clss, jint space_id, jint op, jlongArray start, jlongArray stride, jlongArray count, jlongArray block) { herr_t status; jlong *startP, *strideP, *countP, *blockP; jboolean isCopy; hsize_t *strt; hsize_t *strd; hsize_t *cnt; hsize_t *blk; int rank; int i; hsize_t *lp; jlong *jlp; if (start == NULL) { h5nullArgument(env, "H5Sselect_hyperslab: start is NULL"); return -1; } if (count == NULL) { h5nullArgument(env, "H5Sselect_hyperslab: count is NULL"); return -1; } rank = (int) ENVPTR->GetArrayLength(ENVPAR start); if (rank != ENVPTR->GetArrayLength(ENVPAR count)) { h5badArgument(env, "H5Sselect_hyperslab: count and start have different rank!"); return -1; } startP = ENVPTR->GetLongArrayElements(ENVPAR start, &isCopy); if (startP == NULL) { h5JNIFatalError(env, "H5Sselect_hyperslab: start not pinned"); return -1; } strt = lp = (hsize_t *)malloc(rank * sizeof(hsize_t)); if (strt == NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR start,startP,JNI_ABORT); h5JNIFatalError(env,"H5Sselect_hyperslab: start not converted to hsize_t"); return -1; } jlp = (jlong *)startP; for (i = 0; i < rank; i++) { *lp = (hsize_t)*jlp; lp++; jlp++; } countP = ENVPTR->GetLongArrayElements(ENVPAR count,&isCopy); if (countP == NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR start, startP,JNI_ABORT); free(strt); h5JNIFatalError(env, "H5Sselect_hyperslab: count not pinned"); return -1; } cnt = lp = (hsize_t *)malloc(rank * sizeof(hsize_t)); if (cnt == NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR start, startP,JNI_ABORT); ENVPTR->ReleaseLongArrayElements(ENVPAR count, countP,JNI_ABORT); free(strt); h5JNIFatalError(env, "H5Sselect_hyperslab: count not converted to hsize_t"); return -1; } jlp = (jlong *)countP; for (i = 0; i < rank; i++) { *lp = (hsize_t)*jlp; lp++; jlp++; } if (stride == NULL) { strideP = NULL; strd = (hsize_t *)strideP; } else { strideP = ENVPTR->GetLongArrayElements(ENVPAR stride,&isCopy); if (strideP == NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR count, countP,JNI_ABORT); ENVPTR->ReleaseLongArrayElements(ENVPAR start, startP,JNI_ABORT); free(cnt); free(strt); h5badArgument( env, "H5Sselect_hyperslab: stride not pinned"); return -1; } strd = lp = (hsize_t *)malloc(rank * sizeof(hsize_t)); if (strd == NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR count, countP,JNI_ABORT); ENVPTR->ReleaseLongArrayElements(ENVPAR start, startP,JNI_ABORT); ENVPTR->ReleaseLongArrayElements(ENVPAR stride, strideP,JNI_ABORT); free(cnt); free(strt); h5JNIFatalError(env, "H5Sselect_hyperslab: stride not converted to hsize_t"); return -1; } jlp = (jlong *)strideP; for (i = 0; i < rank; i++) { *lp = (hsize_t)*jlp; lp++; jlp++; } } if (block == NULL) { blockP = NULL; blk = (hsize_t *)blockP; } else { blockP = ENVPTR->GetLongArrayElements(ENVPAR block,&isCopy); if (blockP == NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR stride, strideP,JNI_ABORT); ENVPTR->ReleaseLongArrayElements(ENVPAR count, countP,JNI_ABORT); ENVPTR->ReleaseLongArrayElements(ENVPAR start, startP,JNI_ABORT); free(cnt); free(strt); if (strd != NULL) { free(strd); } h5JNIFatalError(env, "H5Sselect_hyperslab: block not pinned"); return -1; } blk = lp = (hsize_t *)malloc(rank * sizeof(hsize_t)); if (blk == NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR stride, strideP,JNI_ABORT); ENVPTR->ReleaseLongArrayElements(ENVPAR count, countP,JNI_ABORT); ENVPTR->ReleaseLongArrayElements(ENVPAR start, startP,JNI_ABORT); ENVPTR->ReleaseLongArrayElements(ENVPAR block, blockP,JNI_ABORT); free(cnt); free(strt); if (strd != NULL) { free(strd); } h5JNIFatalError(env, "H5Sget_simple_extent: block not converted to hsize_t"); return -1; } jlp = (jlong *)blockP; for (i = 0; i < rank; i++) { *lp = (hsize_t)*jlp; lp++; jlp++; } } status = H5Sselect_hyperslab (space_id, (H5S_seloper_t)op, (const hsize_t *)strt, (const hsize_t *)strd, (const hsize_t *)cnt, (const hsize_t *)blk); ENVPTR->ReleaseLongArrayElements(ENVPAR start, startP, JNI_ABORT); ENVPTR->ReleaseLongArrayElements(ENVPAR count, countP, JNI_ABORT); free(strt); free(cnt); if (strideP != NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR stride, strideP, JNI_ABORT); free(strd); } if (blockP != NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR block, blockP, JNI_ABORT); free(blk); } if (status < 0) h5libraryError(env); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sclose * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Sclose(JNIEnv *env, jclass clss, jint space_id) { herr_t retVal = -1; retVal = H5Sclose(space_id); if (retVal < 0) { h5libraryError(env); } return (jint) retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sget_select_hyper_nblocks * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sget_1select_1hyper_1nblocks( JNIEnv *env, jclass clss, jint spaceid) { hssize_t status; status = H5Sget_select_hyper_nblocks((hid_t) spaceid); if (status < 0) h5libraryError(env); return (jlong) status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sget_select_elem_npoints * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sget_1select_1elem_1npoints( JNIEnv *env, jclass clss, jint spaceid) { hssize_t status; status = H5Sget_select_elem_npoints((hid_t) spaceid); if (status < 0) h5libraryError(env); return (jlong) status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sget_select_hyper_blocklist * Signature: (IJJ[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sget_1select_1hyper_1blocklist( JNIEnv *env, jclass clss, jint spaceid, jlong startblock, jlong numblocks, jlongArray buf) { herr_t status; jlong *bufP; jboolean isCopy; hsize_t *ba; int i; int rank; long st; long nb; st = (long) startblock; nb = (long) numblocks; if (buf == NULL) { h5nullArgument(env, "H5Sget_select_hyper_blocklist: buf is NULL"); return -1; } rank = H5Sget_simple_extent_ndims(spaceid); if(rank <= 0) rank = 1; if (ENVPTR->GetArrayLength(ENVPAR buf) < (numblocks * rank)) { h5badArgument(env, "H5Sget_select_hyper_blocklist: buf input array too small"); return -1; } bufP = ENVPTR->GetLongArrayElements(ENVPAR buf, &isCopy); if (bufP == NULL) { h5JNIFatalError( env, "H5Sget_select_hyper_blocklist: buf not pinned"); return -1; } ba = (hsize_t *)malloc( nb * 2 * (long)rank * sizeof(hsize_t)); if (ba == NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR buf, bufP,JNI_ABORT); h5JNIFatalError(env, "H5Screate-simple: buffer not converted to hsize_t"); return -1; } status = H5Sget_select_hyper_blocklist((hid_t)spaceid, (hsize_t)st, (hsize_t)nb, (hsize_t *)ba); if (status < 0) { ENVPTR->ReleaseLongArrayElements(ENVPAR buf, bufP, JNI_ABORT); free (ba); h5libraryError(env); return -1; } for (i = 0; i < (numblocks*2*rank); i++) { bufP[i] = ba[i]; } free (ba); ENVPTR->ReleaseLongArrayElements(ENVPAR buf, bufP, 0); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sget_select_elem_pointlist * Signature: (IJJ[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sget_1select_1elem_1pointlist( JNIEnv *env, jclass clss, jint spaceid, jlong startpoint, jlong numpoints, jlongArray buf) { herr_t status; jlong *bufP; jboolean isCopy; hsize_t *ba; int i; int rank; if (buf == NULL) { h5nullArgument(env, "H5Sget_select_elem_pointlist: buf is NULL"); return -1; } rank = H5Sget_simple_extent_ndims(spaceid); if(rank <= 0) rank = 1; if (ENVPTR->GetArrayLength(ENVPAR buf) < (numpoints * rank)) { h5badArgument(env, "H5Sget_select_elem_pointlist: buf input array too small"); return -1; } bufP = ENVPTR->GetLongArrayElements(ENVPAR buf, &isCopy); if (bufP == NULL) { h5JNIFatalError( env, "H5Sget_select_elem_pointlist: buf not pinned"); return -1; } ba = (hsize_t *)malloc( ((long)numpoints * (long)rank) * sizeof(hsize_t)); if (ba == NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR buf,bufP,JNI_ABORT); h5JNIFatalError(env,"H5Sget_select_elem_pointlist: buf not converted to hsize_t"); return -1; } status = H5Sget_select_elem_pointlist((hid_t)spaceid, (hsize_t)startpoint, (hsize_t)numpoints, (hsize_t *)ba); if (status < 0) { free (ba); ENVPTR->ReleaseLongArrayElements(ENVPAR buf,bufP,JNI_ABORT); h5libraryError(env); return -1; } for (i = 0; i < (numpoints*rank); i++) { bufP[i] = ba[i]; } free (ba) ; ENVPTR->ReleaseLongArrayElements(ENVPAR buf,bufP,0); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sget_select_bounds * Signature: (I[J[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sget_1select_1bounds( JNIEnv *env, jclass clss, jint spaceid, jlongArray start, jlongArray end) { herr_t status; jlong *startP, *endP; jboolean isCopy; hsize_t *strt; hsize_t *en; int rank; int i; if (start == NULL) { h5nullArgument(env, "H5Sget_select_bounds: start is NULL"); return -1; } if (end == NULL) { h5nullArgument(env, "H5Sget_select_bounds: end is NULL"); return -1; } startP = ENVPTR->GetLongArrayElements(ENVPAR start, &isCopy); if (startP == NULL) { h5JNIFatalError( env, "H5Sget_select_bounds: start not pinned"); return -1; } rank = (int)ENVPTR->GetArrayLength(ENVPAR start); strt = (hsize_t *)malloc( rank * sizeof(hsize_t)); if (strt == NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR start,startP,JNI_ABORT); h5JNIFatalError(env,"H5Sget_select_bounds: start not converted to hsize_t"); return -1; } endP = ENVPTR->GetLongArrayElements(ENVPAR end,&isCopy); if (endP == NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR start,startP,JNI_ABORT); free(strt); h5JNIFatalError( env, "H5Sget_select_bounds: end not pinned"); return -1; } en = (hsize_t *)malloc( rank * sizeof(hsize_t)); if (en == NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR end,endP,JNI_ABORT); ENVPTR->ReleaseLongArrayElements(ENVPAR start,startP,JNI_ABORT); free(strt); h5JNIFatalError(env, "H5Sget_simple_extent: dims not converted to hsize_t"); return -1; } status = H5Sget_select_bounds((hid_t) spaceid, (hsize_t *)strt, (hsize_t *)en); if (status < 0) { ENVPTR->ReleaseLongArrayElements(ENVPAR start,startP,JNI_ABORT); ENVPTR->ReleaseLongArrayElements(ENVPAR end,endP,JNI_ABORT); free(strt); free(en); h5libraryError(env); return -1; } for (i = 0; i < rank; i++) { startP[i] = strt[i]; endP[i] = en[i]; } ENVPTR->ReleaseLongArrayElements(ENVPAR start,startP,0); ENVPTR->ReleaseLongArrayElements(ENVPAR end,endP,0); free(strt); free(en); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sencode * Signature: (I)[B */ JNIEXPORT jbyteArray JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sencode (JNIEnv *env, jclass cls, jint obj_id) { herr_t status = -1; unsigned char *bufPtr; size_t buf_size = 0; jbyteArray returnedArray = NULL; if (obj_id < 0) { h5badArgument(env, "H5Sencode: invalid argument"); return NULL; } status = H5Sencode(obj_id, NULL, &buf_size); if (status < 0) { h5libraryError(env); return NULL; } if (buf_size < 0) { h5badArgument( env, "H5Sencode: buf_size < 0"); return NULL; } bufPtr = (unsigned char*)calloc((size_t)1, buf_size); if (bufPtr == NULL) { h5outOfMemory( env, "H5Sencode: calloc failed"); return NULL; } status = H5Sencode((hid_t)obj_id, bufPtr, &buf_size); if (status < 0) { free(bufPtr); h5libraryError(env); return NULL; } returnedArray = ENVPTR->NewByteArray(ENVPAR buf_size); ENVPTR->SetByteArrayRegion(ENVPAR returnedArray, 0, buf_size, (jbyte *)bufPtr); free(bufPtr); return returnedArray; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sdecode * Signature: ([B)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sdecode (JNIEnv *env, jclass cls, jbyteArray buf) { hid_t sid = -1; jbyte *bufP; jboolean isCopy; if (buf == NULL) { h5nullArgument(env, "H5Sdecode: buf is NULL"); return -1; } bufP = ENVPTR->GetByteArrayElements(ENVPAR buf, &isCopy); if (bufP == NULL) { h5JNIFatalError( env, "H5Sdecode: buf not pinned"); return -1; } sid = H5Sdecode(bufP); if (sid < 0) { ENVPTR->ReleaseByteArrayElements(ENVPAR buf, bufP, JNI_ABORT); h5libraryError(env); return -1; } ENVPTR->ReleaseByteArrayElements(ENVPAR buf, bufP, JNI_ABORT); return (jint)sid; } #ifdef __cplusplus } #endif libsis-jhdf5-java-14.12.1/source/c/hdf-java/h5sImp.h000077500000000000000000000135321256564762100216270ustar00rootroot00000000000000/* DO NOT EDIT THIS FILE - it is machine generated */ #include /* Header for class ncsa_hdf_hdf5lib_H5_H5S */ #ifndef _Included_ncsa_hdf_hdf5lib_H5_H5S #define _Included_ncsa_hdf_hdf5lib_H5_H5S #ifdef __cplusplus extern "C" { #endif /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sclose * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Sclose (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Scopy * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Scopy (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Screate * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Screate (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Screate_simple * Signature: (I[J[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Screate_1simple (JNIEnv *, jclass, jint, jlongArray, jlongArray); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sdecode * Signature: ([B)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sdecode (JNIEnv *env, jclass cls, jbyteArray buf); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sencode * Signature: (I)[B */ JNIEXPORT jbyteArray JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sencode (JNIEnv *env, jclass cls, jint obj_id); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sextent_copy * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sextent_1copy (JNIEnv *, jclass, jint, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sextent_equal * Signature: (II)Z */ JNIEXPORT jboolean JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sextent_1equal (JNIEnv *, jclass, jint, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sget_select_bounds * Signature: (I[J[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sget_1select_1bounds (JNIEnv *, jclass, jint, jlongArray, jlongArray); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sget_select_elem_npoints * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sget_1select_1elem_1npoints (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sget_select_elem_pointlist * Signature: (IJJ[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sget_1select_1elem_1pointlist (JNIEnv *, jclass, jint, jlong, jlong, jlongArray); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sget_select_hyper_blocklist * Signature: (IJJ[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sget_1select_1hyper_1blocklist (JNIEnv *, jclass, jint, jlong, jlong, jlongArray); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sget_select_hyper_nblocks * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sget_1select_1hyper_1nblocks (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sget_select_npoints * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sget_1select_1npoints (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sget_select_type * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sget_1select_1type (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sget_simple_extent_dims * Signature: (I[J[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sget_1simple_1extent_1dims (JNIEnv *, jclass, jint, jlongArray, jlongArray); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sget_simple_extent_ndims * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sget_1simple_1extent_1ndims (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sget_simple_extent_npoints * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sget_1simple_1extent_1npoints (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sget_simple_extent_type * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sget_1simple_1extent_1type (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sis_simple * Signature: (I)Z */ JNIEXPORT jboolean JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sis_1simple (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Soffset_simple * Signature: (I[B)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Soffset_1simple (JNIEnv *, jclass, jint, jbyteArray); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sselect_all * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sselect_1all (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sselect_elements * Signature: (III[B)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sselect_1elements (JNIEnv *, jclass, jint, jint, jint, jbyteArray); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sselect_hyperslab * Signature: (II[J[J[J[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sselect_1hyperslab (JNIEnv *, jclass, jint, jint, jlongArray, jlongArray, jlongArray, jlongArray); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sselect_none * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sselect_1none (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sselect_valid * Signature: (I)Z */ JNIEXPORT jboolean JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sselect_1valid (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sset_extent_none * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sset_1extent_1none (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sset_extent_simple * Signature: (II[J[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Sset_1extent_1simple (JNIEnv *, jclass, jint, jint, jlongArray, jlongArray); #ifdef __cplusplus } #endif #endif libsis-jhdf5-java-14.12.1/source/c/hdf-java/h5tImp.c000077500000000000000000001310621256564762100216220ustar00rootroot00000000000000/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF Java Products. The full HDF Java copyright * * notice, including terms governing use, modification, and redistribution, * * is contained in the file, COPYING. COPYING can be found at the root of * * the source code distribution tree. You can also access it online at * * http://www.hdfgroup.org/products/licenses.html. If you do not have * * access to the file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /* * This code is the C-interface called by Java programs to access the * Group Object API Functions of the HDF5 library. * * Each routine wraps a single HDF entry point, generally with the * analogous arguments and return codes. * * For details of the HDF libraries, see the HDF Documentation at: * http://hdfdfgroup.org/HDF5/doc/ * */ #ifdef __cplusplus extern "C" { #endif #include #include #include #include #include "hdf5.h" #include "h5jni.h" #include "h5tImp.h" //#include "h5util.h" /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Topen * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Topen (JNIEnv *env, jclass clss, jint loc_id, jstring name) { hid_t status; char* tname; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Topen: name is NULL"); return -1; } tname = (char *)ENVPTR->GetStringUTFChars(ENVPAR name,&isCopy); if (tname == NULL) { h5JNIFatalError(env, "H5Topen: name not pinned"); return -1; } status = H5Topen2(loc_id, tname, (hid_t)H5P_DEFAULT); ENVPTR->ReleaseStringUTFChars(ENVPAR name,tname); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tcommit1 * Signature: (ILjava/lang/String;I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tcommit1 (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint type) { herr_t status; char* tname; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Tcommit: name is NULL"); return -1; } tname = (char *)ENVPTR->GetStringUTFChars(ENVPAR name,&isCopy); if (tname == NULL) { h5JNIFatalError(env, "H5Tcommit: name not pinned"); return -1; } status = H5Tcommit2(loc_id, tname, type, (hid_t)H5P_DEFAULT, (hid_t)H5P_DEFAULT, (hid_t)H5P_DEFAULT); ENVPTR->ReleaseStringUTFChars(ENVPAR name,tname); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tcommitted * Signature: (I)Z */ JNIEXPORT jboolean JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tcommitted (JNIEnv *env, jclass clss, jint type) { htri_t bval; bval = H5Tcommitted(type); if (bval > 0) { return JNI_TRUE; } else if (bval == 0) { return JNI_FALSE; } else { /* raise exception -- return value is irrelevant */ h5libraryError(env); return JNI_FALSE; } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tcreate * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Tcreate (JNIEnv *env, jclass clss, jint dclass, jlong size) { hid_t retVal = -1; retVal = H5Tcreate((H5T_class_t )dclass, (size_t)size ); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tcopy * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Tcopy (JNIEnv *env, jclass clss, jint type_id) { hid_t retVal = -1; retVal = H5Tcopy(type_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tequal * Signature: (II)Z */ JNIEXPORT jboolean JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tequal (JNIEnv *env, jclass clss, jint type_id1, jint type_id2) { htri_t bval; bval = H5Tequal(type_id1, type_id2 ); if (bval > 0) { return JNI_TRUE; } else if (bval == 0) { return JNI_FALSE; } else { /* raise exception -- return value is irrelevant */ h5libraryError(env); return JNI_FALSE; } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tlock * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tlock (JNIEnv *env, jclass clss, jint type_id) { herr_t retVal = -1; retVal = H5Tlock(type_id ); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_class * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1class (JNIEnv *env, jclass clss, jint type_id) { H5T_class_t retVal = H5T_NO_CLASS; retVal = H5Tget_class(type_id ); if (retVal == H5T_NO_CLASS) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_size * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1size (JNIEnv *env, jclass clss, jint type_id) { size_t retVal = 0; retVal = H5Tget_size(type_id ); if (retVal == 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_size_long * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1size_1long (JNIEnv *env, jclass clss, jint type_id) { size_t retVal = 0; retVal = H5Tget_size(type_id ); if (retVal == 0) { h5libraryError(env); } return (jlong)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_size * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tset_1size (JNIEnv *env, jclass clss, jint type_id, jlong size) { herr_t retVal = -1; retVal = H5Tset_size(type_id, (size_t)size ); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_order * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1order (JNIEnv *env, jclass clss, jint type_id) { H5T_order_t retVal = H5T_ORDER_ERROR; retVal = H5Tget_order(type_id ); if (retVal == H5T_ORDER_ERROR) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_order * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tset_1order (JNIEnv *env, jclass clss, jint type_id, jint order) { herr_t retVal = -1; retVal = H5Tset_order(type_id, (H5T_order_t)order); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_precision * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1precision (JNIEnv *env, jclass clss, jint type_id) { size_t retVal = 0; retVal = H5Tget_precision(type_id); if (retVal == 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_precision_long * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1precision_1long (JNIEnv *env, jclass clss, jint type_id) { size_t retVal = 0; retVal = H5Tget_precision(type_id); if (retVal == 0) { h5libraryError(env); } return (jlong)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_precision * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tset_1precision (JNIEnv *env, jclass clss, jint type_id, jlong precision) { herr_t retVal = -1; retVal = H5Tset_precision(type_id, (size_t)precision); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_offset * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1offset (JNIEnv *env, jclass clss, jint type_id) { int retVal = 0; retVal = H5Tget_offset(type_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_offset * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tset_1offset (JNIEnv *env, jclass clss, jint type_id, jlong offset) { herr_t retVal = -1; retVal = H5Tset_offset(type_id, (size_t)offset); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_pad * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1pad (JNIEnv *env, jclass clss, jint type_id, jintArray pad) { herr_t status; jboolean isCopy; jint *P; if (pad == NULL) { h5nullArgument( env, "H5Tget_pad: pad is NULL"); return -1; } P = ENVPTR->GetIntArrayElements(ENVPAR pad,&isCopy); if (P == NULL) { h5JNIFatalError(env, "H5Tget_pad: pad not pinned"); return -1; } status = H5Tget_pad(type_id, (H5T_pad_t *)&(P[0]), (H5T_pad_t *)&(P[1])); if (status < 0) { ENVPTR->ReleaseIntArrayElements(ENVPAR pad,P,JNI_ABORT); h5libraryError(env); return -1; } ENVPTR->ReleaseIntArrayElements(ENVPAR pad,P,0); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_pad * Signature: (III)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tset_1pad (JNIEnv *env, jclass clss, jint type_id, jint lsb, jint msb) { herr_t retVal = -1; retVal = H5Tset_pad(type_id, (H5T_pad_t)lsb, (H5T_pad_t)msb); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_sign * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1sign (JNIEnv *env, jclass clss, jint type_id) { H5T_sign_t retVal = H5T_SGN_ERROR; retVal = H5Tget_sign(type_id); if (retVal == H5T_SGN_ERROR) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_sign * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tset_1sign (JNIEnv *env, jclass clss, jint type_id, jint sign) { herr_t retVal = -1; retVal = H5Tset_sign(type_id, (H5T_sign_t)sign); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_fields_int * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1fields_1int (JNIEnv *env, jclass clss, jint type_id, jintArray fields) { herr_t status; jboolean isCopy; jint *P; if (fields == NULL) { h5nullArgument( env, "H5Tget_fields: fields is NULL"); return -1; } if (ENVPTR->GetArrayLength(ENVPAR fields) < 5) { h5badArgument( env, "H5Tget_fields: fields input array < order 5"); return -1; } P = ENVPTR->GetIntArrayElements(ENVPAR fields,&isCopy); if (P == NULL) { h5JNIFatalError(env, "H5Tget_fields: fields not pinned"); return -1; } status = H5Tget_fields(type_id, (size_t *)&(P[0]), (size_t *)&(P[1]), (size_t *)&(P[2]), (size_t *)&(P[3]), (size_t *)&(P[4])); if (status < 0) { ENVPTR->ReleaseIntArrayElements(ENVPAR fields,P,JNI_ABORT); h5libraryError(env); return -1; } ENVPTR->ReleaseIntArrayElements(ENVPAR fields,P,0); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_fields * Signature: (I[J)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1fields (JNIEnv *env, jclass clss, jint type_id, jlongArray fields) { herr_t status; jboolean isCopy; jlong *fieldsArray; if (fields == NULL) { h5nullArgument( env, "H5Tget_fields: fields is NULL"); return; } if (ENVPTR->GetArrayLength(ENVPAR fields) < 5) { h5badArgument( env, "H5Tget_fields: fields input array < order 5"); return; } fieldsArray = ENVPTR->GetLongArrayElements(ENVPAR fields, &isCopy); if (fieldsArray == NULL) { h5JNIFatalError(env, "H5Tget_fields: fields not pinned"); return; } { /* direct cast (size_t *)variable fails on 32-bit environment */ size_t spos_t = 0; size_t epos_t = 0; size_t esize_t = 0; size_t mpos_t = 0; size_t msize_t = 0; long long fields_temp = *(&fieldsArray[0]); spos_t = (size_t)fields_temp; fields_temp = *(&fieldsArray[1]); epos_t = (size_t)fields_temp; fields_temp = *(&fieldsArray[2]); esize_t = (size_t)fields_temp; fields_temp = *(&fieldsArray[3]); mpos_t = (size_t)fields_temp; fields_temp = *(&fieldsArray[4]); msize_t = (size_t)fields_temp; status = H5Tget_fields(type_id, &spos_t, &epos_t, &esize_t, &mpos_t, &msize_t); *(&fieldsArray[0]) = spos_t; *(&fieldsArray[1]) = epos_t; *(&fieldsArray[2]) = esize_t; *(&fieldsArray[3]) = mpos_t; *(&fieldsArray[4]) = msize_t; } if (status < 0) { ENVPTR->ReleaseLongArrayElements(ENVPAR fields, fieldsArray, JNI_ABORT); h5libraryError(env); return; } ENVPTR->ReleaseLongArrayElements(ENVPAR fields, fieldsArray, 0); } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_fields * Signature: (IJJJJJ)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tset_1fields (JNIEnv *env, jclass clss, jint type_id, jlong spos, jlong epos, jlong esize, jlong mpos, jlong msize) { herr_t retVal = -1; retVal = H5Tset_fields(type_id, (size_t)spos, (size_t)epos, (size_t)esize, (size_t)mpos, (size_t)msize); if (retVal < 0) { h5libraryError(env); } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_ebias * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1ebias (JNIEnv *env, jclass clss, jint type_id) { size_t retVal = 0; retVal = H5Tget_ebias(type_id); if (retVal == 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_ebias_long * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1ebias_1long (JNIEnv *env, jclass clss, jint type_id) { size_t retVal = 0; retVal = H5Tget_ebias(type_id); if (retVal == 0) { h5libraryError(env); } return (jlong)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_ebias * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tset_1ebias (JNIEnv *env, jclass clss, jint type_id, jlong ebias) { herr_t retVal = -1; retVal = H5Tset_ebias(type_id, (size_t)ebias); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_norm * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1norm (JNIEnv *env, jclass clss, jint type_id) { H5T_norm_t retVal = H5T_NORM_ERROR; retVal = H5Tget_norm(type_id); if (retVal == H5T_NORM_ERROR) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_norm * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tset_1norm (JNIEnv *env, jclass clss, jint type_id, jint norm) { herr_t retVal = -1; retVal = H5Tset_norm(type_id, (H5T_norm_t )norm); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_inpad * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1inpad (JNIEnv *env, jclass clss, jint type_id) { H5T_pad_t retVal = H5T_PAD_ERROR; retVal = H5Tget_inpad(type_id ); if (retVal == H5T_PAD_ERROR) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_inpad * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tset_1inpad (JNIEnv *env, jclass clss, jint type_id, jint inpad) { herr_t retVal = -1; retVal = H5Tset_inpad(type_id, (H5T_pad_t) inpad); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_cset * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1cset (JNIEnv *env, jclass clss, jint type_id) { H5T_cset_t retVal = H5T_CSET_ERROR; retVal = H5Tget_cset(type_id); if (retVal == H5T_CSET_ERROR) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_cset * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tset_1cset (JNIEnv *env, jclass clss, jint type_id, jint cset) { herr_t retVal = -1; retVal = H5Tset_cset(type_id, (H5T_cset_t)cset); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_strpad * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1strpad (JNIEnv *env, jclass clss, jint type_id) { H5T_str_t retVal = H5T_STR_ERROR; retVal = H5Tget_strpad(type_id); if (retVal == H5T_STR_ERROR) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_strpad * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tset_1strpad (JNIEnv *env, jclass clss, jint type_id, jint strpad) { herr_t retVal = -1; retVal = H5Tset_strpad(type_id, (H5T_str_t)strpad); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_nmembers * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1nmembers (JNIEnv *env, jclass clss, jint type_id) { int retVal = -1; retVal = H5Tget_nmembers(type_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_member_name * Signature: (II)Ljava/lang/String; */ JNIEXPORT jstring JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1member_1name (JNIEnv *env, jclass clss, jint type_id, jint field_idx) { char *name; jstring str; name = H5Tget_member_name(type_id, field_idx); if (name == NULL) { return NULL; } /* may throw OutOfMemoryError */ str = ENVPTR->NewStringUTF(ENVPAR name); H5free_memory(name); if (str == NULL) { h5JNIFatalError(env, "H5Tget_member_name: returned string not created"); return NULL; } return str; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_member_index * Signature: (ILjava/lang/String)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1member_1index (JNIEnv *env, jclass clss, jint type_id, jstring field_name) { char *tname; int index; jboolean isCopy; if (field_name == NULL) { h5nullArgument( env, "H5Tget_member_index: field_name is NULL"); return -1; } tname = (char *)ENVPTR->GetStringUTFChars(ENVPAR field_name,&isCopy); if (tname == NULL) { h5JNIFatalError(env, "H5Tget_member_index: field_name not pinned"); return -1; } index = H5Tget_member_index(type_id, tname); ENVPTR->ReleaseStringUTFChars(ENVPAR field_name,tname); if (index < 0) { h5libraryError(env); } return index; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_member_type * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Tget_1member_1type (JNIEnv *env, jclass clss, jint type_id, jint field_idx) { hid_t retVal = -1; retVal = H5Tget_member_type(type_id, field_idx); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_member_offset * Signature: (II)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1member_1offset (JNIEnv *env, jclass clss, jint type_id, jint memno) { size_t retVal = 0; retVal = H5Tget_member_offset((hid_t)type_id, memno); return (jlong)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_member_class * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1member_1class (JNIEnv *env, jclass clss, jint type_id, jint memno) { int retVal = 0; retVal = H5Tget_member_class((hid_t)type_id, memno); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tinsert * Signature: (ILjava/lang/String;JI)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tinsert (JNIEnv *env, jclass clss, jint type_id, jstring name, jlong offset, jint field_id) { herr_t status; char* tname; jboolean isCopy; long off; off = (long)offset; if (name == NULL) { h5nullArgument( env, "H5Tinsert: name is NULL"); return -1; } tname =(char *)ENVPTR->GetStringUTFChars(ENVPAR name,&isCopy); if (tname == NULL) { h5JNIFatalError(env, "H5Tinsert: name not pinned"); return -1; } status = H5Tinsert(type_id, tname, (size_t)off, field_id); ENVPTR->ReleaseStringUTFChars(ENVPAR name,tname); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tpack * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tpack (JNIEnv *env, jclass clss, jint type_id) { herr_t retVal = -1; retVal = H5Tpack(type_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Tclose * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Tclose (JNIEnv *env, jclass clss, jint type_id) { herr_t retVal = 0; retVal = H5Tclose(type_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Tvlen_create * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Tvlen_1create (JNIEnv *env, jclass clss, jint base_id) { hid_t status; status = H5Tvlen_create((hid_t)base_id); if (status < 0) h5libraryError(env); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_tag * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tset_1tag (JNIEnv *env, jclass clss, jint type, jstring tag) { herr_t status; char *tagP; jboolean isCopy; if (tag == NULL) { h5nullArgument( env, "H5Tset_tag: tag is NULL"); return -1; } tagP = (char *)ENVPTR->GetStringUTFChars(ENVPAR tag,&isCopy); if (tagP == NULL) { h5JNIFatalError( env, "H5Tset_tag: tag not pinned"); return -1; } status = H5Tset_tag((hid_t)type, tagP); ENVPTR->ReleaseStringUTFChars(ENVPAR tag,tagP); if (status < 0) h5libraryError(env); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_tag * Signature: (I)Ljava/lang/String; */ JNIEXPORT jstring JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1tag (JNIEnv *env, jclass clss, jint type) { jstring str; char *tag; tag = H5Tget_tag((hid_t)type); if (tag == NULL) return NULL; /* may throw OutOfMemoryError */ str = ENVPTR->NewStringUTF(ENVPAR tag); H5free_memory(tag); if (str == NULL) { h5JNIFatalError(env, "H5Tget_tag: returned string not created"); return NULL; } return str; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_super * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Tget_1super (JNIEnv *env, jclass clss, jint type) { hid_t status; status = H5Tget_super((hid_t)type); if (status < 0) h5libraryError(env); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Tenum_create * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Tenum_1create (JNIEnv *env, jclass clss, jint base_id) { hid_t status; status = H5Tenum_create((hid_t)base_id); if (status < 0) h5libraryError(env); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tenum_insert_int * Signature: (ILjava/lang/String;[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tenum_1insert_1int (JNIEnv *env, jclass clss, jint type, jstring name, jintArray value) { herr_t status; jint *intP; char *nameP; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Tenum_insert: name is NULL"); return -1; } nameP = (char *)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (nameP == NULL) { h5JNIFatalError( env, "H5Tenum_insert: name not pinned"); return -1; } if ( value == NULL ) { ENVPTR->ReleaseStringUTFChars(ENVPAR name, nameP); h5nullArgument( env, "H5Tenum_insert: value is NULL"); return -1; } intP = ENVPTR->GetIntArrayElements(ENVPAR value, &isCopy); if (intP == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR name, nameP); h5JNIFatalError( env, "H5Tenum_insert: value not pinned"); return -1; } status = H5Tenum_insert((hid_t)type, nameP, intP); ENVPTR->ReleaseStringUTFChars(ENVPAR name, nameP); if (status < 0) { ENVPTR->ReleaseIntArrayElements(ENVPAR value, intP, JNI_ABORT); h5libraryError(env); return -1; } ENVPTR->ReleaseIntArrayElements(ENVPAR value, intP, JNI_ABORT); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tenum_insert * Signature: (ILjava/lang/String;[B)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tenum_1insert (JNIEnv *env, jclass clss, jint type, jstring name, jbyteArray value) { herr_t status; jbyte *byteP; char *nameP; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Tenum_insert: name is NULL"); return; } nameP = (char *)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (nameP == NULL) { h5JNIFatalError( env, "H5Tenum_insert: name not pinned"); return; } if ( value == NULL ) { ENVPTR->ReleaseStringUTFChars(ENVPAR name, nameP); h5nullArgument( env, "H5Tenum_insert: value is NULL"); return; } byteP = ENVPTR->GetByteArrayElements(ENVPAR value, &isCopy); if (byteP == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR name, nameP); h5JNIFatalError( env, "H5Tenum_insert: value not pinned"); return; } status = H5Tenum_insert((hid_t)type, nameP, byteP); ENVPTR->ReleaseStringUTFChars(ENVPAR name, nameP); ENVPTR->ReleaseByteArrayElements(ENVPAR value, byteP, JNI_ABORT); if (status < 0) { h5libraryError(env); } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tenum_nameof_int * Signature: (I[I[Ljava/lang/String;I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tenum_1nameof_1int (JNIEnv *env, jclass clss, jint type, jintArray value, jobjectArray name, jint size) { hid_t status; jint *intP; char *nameP; jboolean isCopy; jstring str; if (size <= 0) { h5badArgument( env, "H5Tenum_nameof: name size < 0"); return -1; } nameP = (char *)malloc(sizeof(char)*size); if (nameP == NULL) { /* exception -- out of memory */ h5outOfMemory( env, "H5Tenum_nameof: malloc name size"); return -1; } if ( value == NULL ) { free(nameP); h5nullArgument( env, "H5Tenum_nameof: value is NULL"); return -1; } intP = ENVPTR->GetIntArrayElements(ENVPAR value, &isCopy); if (intP == NULL) { free(nameP); h5JNIFatalError( env, "H5Tenum_nameof: value not pinned"); return -1; } status = H5Tenum_nameof((hid_t)type, intP, nameP, (size_t)size); ENVPTR->ReleaseIntArrayElements(ENVPAR value, intP, JNI_ABORT); if (status < 0) { free(nameP); h5libraryError(env); return -1; } str = ENVPTR->NewStringUTF(ENVPAR nameP); if (str == NULL) { free(nameP); h5JNIFatalError( env, "H5Tenum_nameof: return array not created"); return -1; } /* SetObjectArrayElement may raise exceptions */ ENVPTR->SetObjectArrayElement(ENVPAR name, 0, (jobject)str); free(nameP); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tenum_nameof * Signature: (I[BJ)Ljava/lang/String; */ JNIEXPORT jstring JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tenum_1nameof (JNIEnv *env, jclass clss, jint type, jbyteArray value, jlong size) { hid_t status; jbyte *byteP; char *nameP; jboolean isCopy; jstring str; if (size <= 0) { h5badArgument( env, "H5Tenum_nameof: name size < 0"); return NULL; } nameP = (char *)malloc(sizeof(char)*(size_t)size); if (nameP == NULL) { /* exception -- out of memory */ h5outOfMemory( env, "H5Tenum_nameof: malloc name size"); return NULL; } if ( value == NULL ) { free(nameP); h5nullArgument( env, "H5Tenum_nameof: value is NULL"); return NULL; } byteP = ENVPTR->GetByteArrayElements(ENVPAR value, &isCopy); if (byteP == NULL) { free(nameP); h5JNIFatalError( env, "H5Tenum_nameof: value not pinned"); return NULL; } status = H5Tenum_nameof((hid_t)type, byteP, nameP, (size_t)size); ENVPTR->ReleaseByteArrayElements(ENVPAR value, byteP, JNI_ABORT); if (status < 0) { free(nameP); h5libraryError(env); return NULL; } str = ENVPTR->NewStringUTF(ENVPAR nameP); if (str == NULL) { free(nameP); h5JNIFatalError( env, "H5Tenum_nameof: return array not created"); return NULL; } free(nameP); return str; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tenum_valueof_int * Signature: (ILjava/lang/String;[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tenum_1valueof_1int (JNIEnv *env, jclass clss, jint type, jstring name, jintArray value) { hid_t status; jint *intP; char *nameP; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Tenum_valueof: name is NULL"); return -1; } nameP = (char *)ENVPTR->GetStringUTFChars(ENVPAR name, &isCopy); if (nameP == NULL) { h5JNIFatalError( env, "H5Tenum_valueof: name not pinned"); return -1; } if ( value == NULL ) { ENVPTR->ReleaseStringUTFChars(ENVPAR name, nameP); h5nullArgument( env, "H5Tenum_valueof: value is NULL"); return -1; } intP = ENVPTR->GetIntArrayElements(ENVPAR value, &isCopy); if (intP == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR name, nameP); h5JNIFatalError( env, "H5Tenum_valueof: value not pinned"); return -1; } status = H5Tenum_valueof((hid_t)type, nameP, intP); ENVPTR->ReleaseStringUTFChars(ENVPAR name, nameP); if (status < 0) { ENVPTR->ReleaseIntArrayElements(ENVPAR value, intP, JNI_ABORT); h5libraryError(env); } ENVPTR->ReleaseIntArrayElements(ENVPAR value, intP, 0); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tenum_valueof * Signature: (ILjava/lang/String;[B)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tenum_1valueof (JNIEnv *env, jclass clss, jint type, jstring name, jbyteArray value) { hid_t status; jbyte *byteP; char *nameP; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Tenum_valueof: name is NULL"); return; } nameP = (char *)ENVPTR->GetStringUTFChars(ENVPAR name,&isCopy); if (nameP == NULL) { h5JNIFatalError( env, "H5Tenum_valueof: name not pinned"); return; } if (value == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR name, nameP); h5nullArgument( env, "H5Tenum_valueof: value is NULL"); return; } byteP = ENVPTR->GetByteArrayElements(ENVPAR value, &isCopy); if (byteP == NULL) { ENVPTR->ReleaseStringUTFChars(ENVPAR name,nameP); h5JNIFatalError( env, "H5Tenum_valueof: value not pinned"); return; } status = H5Tenum_valueof((hid_t)type, nameP, byteP); ENVPTR->ReleaseStringUTFChars(ENVPAR name, nameP); if (status < 0) { ENVPTR->ReleaseByteArrayElements(ENVPAR value, byteP, JNI_ABORT); h5libraryError(env); return; } ENVPTR->ReleaseByteArrayElements(ENVPAR value, byteP, 0); } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_member_value_int * Signature: (II[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1member_1value_1int (JNIEnv *env, jclass clss, jint type, jint membno, jintArray value) { hid_t status; jint *intP; jboolean isCopy; if ( value == NULL ) { h5nullArgument( env, "H5Tget_member_value: value is NULL"); return -1; } intP = ENVPTR->GetIntArrayElements(ENVPAR value,&isCopy); if (intP == NULL) { h5JNIFatalError( env, "H5Tget_member_value: value not pinned"); return -1; } status = H5Tget_member_value((hid_t)type, (int)membno, intP); if (status < 0) { ENVPTR->ReleaseIntArrayElements(ENVPAR value,intP,JNI_ABORT); h5libraryError(env); } ENVPTR->ReleaseIntArrayElements(ENVPAR value,intP,0); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_member_value * Signature: (II[B)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1member_1value (JNIEnv *env, jclass clss, jint type, jint membno, jbyteArray value) { hid_t status; jbyte *byteP; jboolean isCopy; if ( value == NULL ) { h5nullArgument( env, "H5Tget_member_value: value is NULL"); return; } byteP = ENVPTR->GetByteArrayElements(ENVPAR value,&isCopy); if (byteP == NULL) { h5JNIFatalError( env, "H5Tget_member_value: value not pinned"); return; } status = H5Tget_member_value((hid_t)type, (int)membno, byteP); if (status < 0) { ENVPTR->ReleaseByteArrayElements(ENVPAR value,byteP,JNI_ABORT); h5libraryError(env); return; } ENVPTR->ReleaseByteArrayElements(ENVPAR value,byteP,0); } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Tarray_create * Signature: (II[I[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Tarray_1create (JNIEnv *env, jclass clss, jint base, jint rank, jintArray dims, jintArray perms) { hid_t status; jint *dimsP; jint *permP; int dlen; hsize_t *cdims=NULL; jboolean isCopy; int i; if (rank <= 0) { h5badArgument( env, "H5Tarray_create: rank is < 1"); return -1; } if ( dims == NULL ) { h5nullArgument( env, "H5Tarray_create: dims is NULL"); return -1; } dimsP = ENVPTR->GetIntArrayElements(ENVPAR dims,&isCopy); if (dimsP == NULL) { h5JNIFatalError( env, "H5Tarray_create: dimsP not pinned"); return -1; } dlen = ENVPTR->GetArrayLength(ENVPAR dims); if (dlen != rank) { h5JNIFatalError( env, "H5Tarray_create: dims len != rank"); ENVPTR->ReleaseIntArrayElements(ENVPAR dims,dimsP,JNI_ABORT); return -1; } if (perms == NULL) { permP = NULL; } else { permP = ENVPTR->GetIntArrayElements(ENVPAR perms,&isCopy); if (permP == NULL) { h5JNIFatalError( env, "H5Tarray_create: permP not pinned"); ENVPTR->ReleaseIntArrayElements(ENVPAR dims,dimsP,JNI_ABORT); return -1; } } cdims = (hsize_t *)malloc(dlen * sizeof(hsize_t)); for (i = 0; i < dlen; i++) { cdims[i] = (hsize_t)dimsP[i]; } status = H5Tarray_create2((hid_t)base, (int)rank, (const hsize_t *)cdims); ENVPTR->ReleaseIntArrayElements(ENVPAR dims,dimsP,JNI_ABORT); if (permP != NULL) { ENVPTR->ReleaseIntArrayElements(ENVPAR perms,permP,JNI_ABORT); } free (cdims); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_array_dims * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1array_1ndims (JNIEnv *env, jclass clss, jint dt) { hid_t status; status = H5Tget_array_ndims((hid_t)dt); if (status < 0) h5libraryError(env); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tarray_get_dims * Signature: (I[I[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1array_1dims (JNIEnv *env, jclass clss, jint dt, jintArray dims, jintArray perms) { hid_t status; jint *dimsP; jint *permP = NULL; //parameter perm is never used int dlen; int i; hsize_t *cdims=NULL; jboolean isCopy; if ( dims == NULL ) { h5nullArgument( env, "H5Tget_array_dims: value is NULL"); return -1; } dimsP = ENVPTR->GetIntArrayElements(ENVPAR dims,&isCopy); if (dimsP == NULL) { h5JNIFatalError( env, "H5Tget_array_dims: dimsP not pinned"); return -1; } dlen = ENVPTR->GetArrayLength(ENVPAR dims); cdims = (hsize_t *)malloc(dlen * sizeof(hsize_t)); status = H5Tget_array_dims2((hid_t)dt, (hsize_t *)cdims); if (status < 0) { ENVPTR->ReleaseIntArrayElements(ENVPAR dims,dimsP,JNI_ABORT); h5libraryError(env); return -1; } for (i = 0; i < dlen; i++) { dimsP[i] = (jint) cdims[i]; } ENVPTR->ReleaseIntArrayElements(ENVPAR dims,dimsP,0); if (cdims) free(cdims); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tis_variable_str * Signature: (I)Z */ JNIEXPORT jboolean JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tis_1variable_1str (JNIEnv *env, jclass clss, jint dtype_id) { htri_t bval; bval = H5Tis_variable_str((hid_t)dtype_id); if (bval > 0) { return JNI_TRUE; } else if (bval == 0) { return JNI_FALSE; } else { h5libraryError(env); return JNI_FALSE; } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_native_type * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Tget_1native_1type (JNIEnv *env, jclass clss, jint dtype_id, jint direction) { hid_t native_tid; native_tid = H5Tget_native_type((hid_t)dtype_id, (H5T_direction_t)direction); if (native_tid < 0){ h5libraryError(env); return -1; } return (jint)native_tid; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tdetect_class * Signature: (II)Z */ JNIEXPORT jboolean JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tdetect_1class (JNIEnv *env, jclass clss, jint dtype_id, jint dtype_class) { htri_t bval; bval = H5Tdetect_class((hid_t)dtype_id, (H5T_class_t)dtype_class); if (bval > 0) { return JNI_TRUE; } else if (bval == 0) { return JNI_FALSE; } else { h5libraryError(env); return JNI_FALSE; } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Topen2 * Signature: (ILjava/lang/String;I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Topen2 (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint access_plist) { hid_t status; char* tname; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Topen2: name is NULL"); return -1; } tname = (char *)ENVPTR->GetStringUTFChars(ENVPAR name,&isCopy); if (tname == NULL) { h5JNIFatalError(env, "H5Topen2: name not pinned"); return -1; } status = H5Topen2(loc_id, tname, (hid_t)access_plist); ENVPTR->ReleaseStringUTFChars(ENVPAR name,tname); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tcommit * Signature: (ILjava/lang/String;IIII)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tcommit (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint type, jint link_plist_id, jint create_plist_id, jint access_plist_id) { herr_t status; char* tname; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Tcommit2: name is NULL"); return; } tname = (char *)ENVPTR->GetStringUTFChars(ENVPAR name,&isCopy); if (tname == NULL) { h5JNIFatalError(env, "H5Tcommit2: name not pinned"); return; } status = H5Tcommit2(loc_id, tname, type, (hid_t)link_plist_id, (hid_t)create_plist_id, (hid_t)access_plist_id); ENVPTR->ReleaseStringUTFChars(ENVPAR name,tname); if (status < 0) { h5libraryError(env); } return; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Tarray_create2 * Signature: (II[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Tarray_1create2 (JNIEnv *env, jclass clss, jint base, jint rank, jlongArray dims) { hid_t status; jlong *dimsP; int dlen; hsize_t *cdims=NULL; jboolean isCopy; int i; if (rank <= 0) { h5badArgument( env, "H5Tarray_create: rank is < 1"); return -1; } if ( dims == NULL ) { h5nullArgument( env, "H5Tarray_create: dims is NULL"); return -1; } dimsP = ENVPTR->GetLongArrayElements(ENVPAR dims,&isCopy); if (dimsP == NULL) { h5JNIFatalError( env, "H5Tarray_create: dimsP not pinned"); return -1; } dlen = ENVPTR->GetArrayLength(ENVPAR dims); if (dlen != rank) { ENVPTR->ReleaseLongArrayElements(ENVPAR dims,dimsP,JNI_ABORT); return -1; } cdims = (hsize_t *)malloc(dlen * sizeof(hsize_t)); for (i = 0; i < dlen; i++) { cdims[i] = (hsize_t)dimsP[i]; } status = H5Tarray_create2((hid_t)base, (int)rank, (const hsize_t *)cdims); ENVPTR->ReleaseLongArrayElements(ENVPAR dims,dimsP,JNI_ABORT); free (cdims); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tarray_get_dims2 * Signature: (I[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1array_1dims2 (JNIEnv *env, jclass clss, jint dt, jlongArray dims) { hid_t status; jlong *dimsP; int dlen; int i; hsize_t *cdims=NULL; jboolean isCopy; if ( dims == NULL ) { h5nullArgument( env, "H5Tget_array_dims: value is NULL"); return -1; } dimsP = ENVPTR->GetLongArrayElements(ENVPAR dims,&isCopy); if (dimsP == NULL) { h5JNIFatalError( env, "H5Tget_array_dims: dimsP not pinned"); return -1; } dlen = ENVPTR->GetArrayLength(ENVPAR dims); cdims = (hsize_t *)malloc(dlen * sizeof(hsize_t)); status = H5Tget_array_dims2((hid_t)dt, (hsize_t *)cdims); if (status < 0) { if (cdims) free(cdims); ENVPTR->ReleaseLongArrayElements(ENVPAR dims,dimsP,JNI_ABORT); h5libraryError(env); return -1; } for (i = 0; i < dlen; i++) { dimsP[i] = (jlong) cdims[i]; } ENVPTR->ReleaseLongArrayElements(ENVPAR dims,dimsP,0); if (cdims) free(cdims); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tcovert * Signature: (I[BJ)Ljava/lang/String; * H5Tconvert(int src_id, int dst_id, long nelmts, byte[] buf, byte[] background, int plist_id) */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tconvert (JNIEnv *env, jclass clss, jint src_id, jint dst_id, jlong nelmts, jbyteArray buf, jbyteArray background, jint plist_id) { hid_t status; jbyte *bufP, *bgP=NULL; jboolean isCopy; if (nelmts <= 0) { h5badArgument( env, "H5Tconvert: name nelmts < 0"); return; } bufP = ENVPTR->GetByteArrayElements(ENVPAR buf, &isCopy); if (bufP == NULL) { h5JNIFatalError( env, "H5Tconvert: value not pinned"); return; } if (background) bgP = ENVPTR->GetByteArrayElements(ENVPAR background, &isCopy); status = H5Tconvert( (hid_t) src_id, (hid_t) dst_id, (size_t) nelmts, (void *)bufP, (void *)bgP, (hid_t) plist_id ) ; ENVPTR->ReleaseByteArrayElements(ENVPAR buf, bufP, 0); if (bgP) ENVPTR->ReleaseByteArrayElements(ENVPAR background, bgP, JNI_ABORT); } #ifdef __cplusplus } #endif libsis-jhdf5-java-14.12.1/source/c/hdf-java/h5tImp.h000077500000000000000000000333571256564762100216370ustar00rootroot00000000000000/* DO NOT EDIT THIS FILE - it is machine generated */ #include /* Header for class ncsa_hdf_hdf5lib_H5_H5T */ #ifndef _Included_ncsa_hdf_hdf5lib_H5_H5T #define _Included_ncsa_hdf_hdf5lib_H5_H5T #ifdef __cplusplus extern "C" { #endif /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Topen * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Topen (JNIEnv *, jclass, jint, jstring); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tcommit1 * Signature: (ILjava/lang/String;I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tcommit1 (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint type); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tcommitted * Signature: (I)Z */ JNIEXPORT jboolean JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tcommitted (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tcreate * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tcreate (JNIEnv *, jclass, jint, jlong); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tcopy * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tcopy (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tequal * Signature: (II)Z */ JNIEXPORT jboolean JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tequal (JNIEnv *, jclass, jint, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tlock * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tlock (JNIEnv *env, jclass clss, jint type_id); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_class * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1class (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_size * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1size (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_size_long * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1size_1long (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_size * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tset_1size (JNIEnv *env, jclass clss, jint type_id, jlong size); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_order * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1order (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_order * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tset_1order (JNIEnv *env, jclass clss, jint type_id, jint order); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_precision * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1precision (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_precision * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1precision_1long (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_precision * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tset_1precision (JNIEnv *env, jclass clss, jint type_id, jlong precision); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_offset * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1offset (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_offset * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tset_1offset (JNIEnv *env, jclass clss, jint type_id, jlong offset); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_pad * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1pad (JNIEnv *, jclass, jint, jintArray); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_pad * Signature: (III)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tset_1pad (JNIEnv *env, jclass clss, jint type_id, jint lsb, jint msb); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_sign * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1sign (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_sign * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tset_1sign (JNIEnv *env, jclass clss, jint type_id, jint sign); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_fields_int * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1fields_1int (JNIEnv *env, jclass clss, jint type_id, jintArray fields); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_fields * Signature: (I[J)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1fields (JNIEnv *env, jclass clss, jint type_id, jlongArray fields); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_fields * Signature: (IJJJJJ)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tset_1fields (JNIEnv *env, jclass clss, jint type_id, jlong spos, jlong epos, jlong esize, jlong mpos, jlong msize); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_ebias * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1ebias (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_ebias_long * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1ebias_1long (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_ebias * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tset_1ebias (JNIEnv *env, jclass clss, jint type_id, jlong ebias); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_norm * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1norm (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_norm * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tset_1norm (JNIEnv *env, jclass clss, jint type_id, jint norm); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_inpad * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1inpad (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_inpad * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tset_1inpad (JNIEnv *env, jclass clss, jint type_id, jint inpad); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_cset * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1cset (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_cset * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tset_1cset (JNIEnv *env, jclass clss, jint type_id, jint cset); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_strpad * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1strpad (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_strpad * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tset_1strpad (JNIEnv *env, jclass clss, jint type_id, jint strpad); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_nmembers * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1nmembers (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_member_name * Signature: (II)Ljava/lang/String; */ JNIEXPORT jstring JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1member_1name (JNIEnv *, jclass, jint, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_member_index * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1member_1index (JNIEnv *, jclass, jint, jstring); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Tget_member_type * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Tget_1member_1type (JNIEnv *, jclass, jint, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_member_offset * Signature: (II)J */ JNIEXPORT jlong JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1member_1offset (JNIEnv *, jclass, jint, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_member_class * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1member_1class (JNIEnv *, jclass, jint, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tinsert * Signature: (ILjava/lang/String;JI)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tinsert (JNIEnv *env, jclass clss, jint type_id, jstring name, jlong offset, jint field_id); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tpack * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tpack (JNIEnv *env, jclass clss, jint type_id); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Tclose * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Tclose (JNIEnv *env, jclass clss, jint type_id); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Tvlen_create * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Tvlen_1create (JNIEnv *env, jclass clss, jint base_id); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_tag * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tset_1tag (JNIEnv *env, jclass clss, jint type, jstring tag); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_tag * Signature: (I)Ljava/lang/String; */ JNIEXPORT jstring JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1tag (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_super * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1super (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Tenum_create * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Tenum_1create (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tenum_insert_int * Signature: (ILjava/lang/String;[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tenum_1insert_1int (JNIEnv *, jclass, jint, jstring, jintArray); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tenum_insert * Signature: (ILjava/lang/String;[B)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tenum_1insert (JNIEnv *, jclass, jint, jstring, jbyteArray); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tenum_nameof_int * Signature: (I[I[Ljava/lang/String;I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tenum_1nameof_1int (JNIEnv *env, jclass clss, jint type, jintArray value, jobjectArray name, jint size); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tenum_nameof * Signature: (I[BJ)Ljava/lang/String; */ JNIEXPORT jstring JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tenum_1nameof (JNIEnv *, jclass, jint, jbyteArray, jlong size); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tenum_valueof_int * Signature: (ILjava/lang/String;[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tenum_1valueof_1int (JNIEnv *, jclass, jint, jstring, jintArray); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tenum_valueof * Signature: (ILjava/lang/String;[B)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tenum_1valueof (JNIEnv *, jclass, jint, jstring, jbyteArray); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_member_value_int * Signature: (II[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1member_1value_1int (JNIEnv *, jclass, jint, jint, jintArray); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_member_value * Signature: (II[B)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1member_1value (JNIEnv *, jclass, jint, jint, jbyteArray); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Tarray_create * Signature: (II[I[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Tarray_1create (JNIEnv *, jclass, jint, jint, jintArray, jintArray); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_array_ndims * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1array_1ndims (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_array_dims * Signature: (I[I[I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1array_1dims (JNIEnv *, jclass, jint, jintArray, jintArray); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tis_variable_str * Signature: (I)Z */ JNIEXPORT jboolean JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tis_1variable_1str (JNIEnv *, jclass, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_native_type * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1native_1type (JNIEnv *, jclass, jint, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tdetect_class * Signature: (II)Z */ JNIEXPORT jboolean JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tdetect_1class (JNIEnv *, jclass, jint, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Topen2 * Signature: (ILjava/lang/String;I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Topen2 (JNIEnv *, jclass, jint, jstring, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tcommit * Signature: (ILjava/lang/String;IIII)V */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tcommit (JNIEnv *, jclass, jint, jstring, jint, jint, jint, jint); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: _H5Tarray_create2 * Signature: (II[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5__1H5Tarray_1create2 (JNIEnv *, jclass, jint, jint, jlongArray); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_array_dims2 * Signature: (I[J)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Tget_1array_1dims2 (JNIEnv *, jclass, jint, jlongArray); #ifdef __cplusplus } #endif #endif libsis-jhdf5-java-14.12.1/source/c/hdf-java/h5util.c000077500000000000000000002027551256564762100216760ustar00rootroot00000000000000/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the files COPYING and Copyright.html. COPYING can be found at the root * * of the source code distribution tree; Copyright.html can be found at the * * root level of an installed copy of the electronic HDF5 document set and * * is linked from the top-level documents page. It can also be found at * * http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have * * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #ifdef __cplusplus extern "C" { #endif #include #include #include #include "hdf5.h" #include "h5util.h" #include "jni.h" /* size of hyperslab buffer when a dataset is bigger than H5TOOLS_MALLOCSIZE */ hsize_t H5TOOLS_BUFSIZE = (32 * 1024 * 1024); /* 32 MB */ int H5TOOLS_TEXT_BLOCK = 16; /* Number of elements on a line in a text export file */ JavaVM *jvm; jobject visit_callback; int h5str_dump_region_blocks(h5str_t *str, hid_t region, hid_t region_obj); int h5str_dump_region_points(h5str_t *str, hid_t region, hid_t region_obj); int h5str_is_zero(const void *_mem, size_t size); hid_t h5str_get_native_type(hid_t type); hid_t h5str_get_little_endian_type(hid_t type); hid_t h5str_get_big_endian_type(hid_t type); htri_t h5str_detect_vlen(hid_t tid); htri_t h5str_detect_vlen_str(hid_t tid); int h5tools_dump_simple_data(FILE *stream, hid_t container, hid_t type, void *_mem, hsize_t nelmts); int h5str_render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t block_nelmts); int render_bin_output_region_data_blocks(FILE *stream, hid_t region_id, hid_t container, int ndims, hid_t type_id, hssize_t nblocks, hsize_t *ptdata); int render_bin_output_region_blocks(FILE *stream, hid_t region_space, hid_t region_id, hid_t container); int render_bin_output_region_data_points(FILE *stream, hid_t region_space, hid_t region_id, hid_t container, int ndims, hid_t type_id, hssize_t npoints, hsize_t *ptdata); int render_bin_output_region_points(FILE *stream, hid_t region_space, hid_t region_id, hid_t container); /** frees memory held by array of strings */ void h5str_array_free(char **strs, size_t len) { size_t i; if (!strs || len <= 0) return; for (i = 0; i < len; i++) { if (*(strs + i)) free(*(strs + i)); } /* for (i=0; i 0) { str->s = (char *) malloc(len); str->max = len; str->s[0] = '\0'; } } /** free string memory */ void h5str_free(h5str_t *str) { if (str && str->max > 0) { free(str->s); memset(str, 0, sizeof(h5str_t)); } } /** reset the max size of the string */ void h5str_resize(h5str_t *str, size_t new_len) { char *new_str; if (!str || new_len <= 0 || str->max == new_len) return; new_str = (char *) malloc(new_len); if (new_len > str->max) /* increase memory */ strcpy(new_str, str->s); else strncpy(new_str, str->s, new_len - 1); free(str->s); str->s = new_str; str->max = new_len; } /* appends a copy of the string pointed to by cstr to the h5str. Return Value: the char string point to str->s */ char* h5str_append(h5str_t *str, const char* cstr) { size_t len; if (!str) return NULL; else if (!cstr) return str->s; len = strlen(str->s) + strlen(cstr); while (len >= str->max) /* not enough to hold the new string, double the space */ { h5str_resize(str, str->max * 2); } return strcat(str->s, cstr); } /** print value of a data point into string. Return Value: On success, the total number of characters printed is returned. On error, a negative number is returned. */ int h5str_sprintf(h5str_t *str, hid_t container, hid_t tid, void *ptr, int expand_data) { unsigned char tmp_uchar = 0; char tmp_char = 0; unsigned short tmp_ushort = 0; short tmp_short = 0; unsigned int tmp_uint = 0; int tmp_int = 0; unsigned long tmp_ulong = 0; long tmp_long = 0; unsigned long long tmp_ullong = 0; long long tmp_llong = 0; float tmp_float = 0.0; double tmp_double = 0.0; long double tmp_ldouble = 0.0; static char fmt_llong[8], fmt_ullong[8]; hid_t mtid = -1; size_t offset; size_t nll; char *this_str; int this_strlen; int i; int n; int len; hvl_t *vlptr; char *cptr = (char*) ptr; unsigned char *ucptr = (unsigned char*) ptr; H5T_class_t tclass = H5Tget_class(tid); size_t size = H5Tget_size(tid); H5T_sign_t nsign = H5Tget_sign(tid); int bdata_print = 0; if (!str || !ptr) return -1; /* Build default formats for long long types */ if (!fmt_llong[0]) { sprintf(fmt_llong, "%%%sd", H5_PRINTF_LL_WIDTH); sprintf(fmt_ullong, "%%%su", H5_PRINTF_LL_WIDTH); } this_str = NULL; this_strlen = 0; switch (tclass) { case H5T_FLOAT: if (sizeof(float) == size) { /* if (H5Tequal(tid, H5T_NATIVE_FLOAT)) */ memcpy(&tmp_float, ptr, sizeof(float)); this_str = (char*) malloc(25); sprintf(this_str, "%g", tmp_float); } else if (sizeof(double) == size) { /* if (H5Tequal(tid, H5T_NATIVE_DOUBLE)) */ memcpy(&tmp_double, ptr, sizeof(double)); this_str = (char*) malloc(25); sprintf(this_str, "%g", tmp_double); } #if H5_SIZEOF_LONG_DOUBLE !=0 else if (sizeof(long double) == size) { /* if (H5Tequal(tid, H5T_NATIVE_LDOUBLE)) */ memcpy(&tmp_ldouble, ptr, sizeof(long double)); this_str = (char*) malloc(27); sprintf(this_str, "%Lf", tmp_ldouble); } #endif break; case H5T_STRING: { char *tmp_str; size = 0; if (H5Tis_variable_str(tid)) { tmp_str = *(char**) ptr; if (tmp_str != NULL) size = strlen(tmp_str); } else { tmp_str = cptr; } /* Check for NULL pointer for string */ if (tmp_str == NULL) { this_str = (char *) malloc(5); strncpy(this_str, "NULL", 4); } else { if (size > 0) { this_str = (char *) malloc(size+1); strncpy(this_str, tmp_str, size); } } } break; case H5T_INTEGER: if (sizeof(char) == size) { if(H5T_SGN_NONE == nsign) { /* if (H5Tequal(tid, H5T_NATIVE_UCHAR)) */ memcpy(&tmp_uchar, ptr, sizeof(unsigned char)); this_str = (char*) malloc(7); sprintf(this_str, "%u", tmp_uchar); } else { /* if (H5Tequal(tid, H5T_NATIVE_SCHAR)) */ memcpy(&tmp_char, ptr, sizeof(char)); this_str = (char*) malloc(7); sprintf(this_str, "%hhd", tmp_char); } } else if (sizeof(int) == size) { if(H5T_SGN_NONE == nsign) { /* if (H5Tequal(tid, H5T_NATIVE_UINT)) */ memcpy(&tmp_uint, ptr, sizeof(unsigned int)); this_str = (char*) malloc(14); sprintf(this_str, "%u", tmp_uint); } else { /* if (H5Tequal(tid, H5T_NATIVE_INT)) */ memcpy(&tmp_int, ptr, sizeof(int)); this_str = (char*) malloc(14); sprintf(this_str, "%d", tmp_int); } } else if (sizeof(short) == size) { if(H5T_SGN_NONE == nsign) { /* if (H5Tequal(tid, H5T_NATIVE_USHORT)) */ memcpy(&tmp_ushort, ptr, sizeof(unsigned short)); this_str = (char*) malloc(9); sprintf(this_str, "%u", tmp_ushort); } else { /* if (H5Tequal(tid, H5T_NATIVE_SHORT)) */ memcpy(&tmp_short, ptr, sizeof(short)); this_str = (char*) malloc(9); sprintf(this_str, "%d", tmp_short); } } else if (sizeof(long) == size) { if(H5T_SGN_NONE == nsign) { /* if (H5Tequal(tid, H5T_NATIVE_ULONG)) */ memcpy(&tmp_ulong, ptr, sizeof(unsigned long)); this_str = (char*) malloc(23); sprintf(this_str, "%lu", tmp_ulong); } else { /* if (H5Tequal(tid, H5T_NATIVE_LONG)) */ memcpy(&tmp_long, ptr, sizeof(long)); this_str = (char*) malloc(23); sprintf(this_str, "%ld", tmp_long); } } else if (sizeof(long long) == size) { if(H5T_SGN_NONE == nsign) { /* if (H5Tequal(tid, H5T_NATIVE_ULLONG)) */ memcpy(&tmp_ullong, ptr, sizeof(unsigned long long)); this_str = (char*) malloc(25); sprintf(this_str, fmt_ullong, tmp_ullong); } else { /* if (H5Tequal(tid, H5T_NATIVE_LLONG)) */ memcpy(&tmp_llong, ptr, sizeof(long long)); this_str = (char*) malloc(25); sprintf(this_str, fmt_llong, tmp_llong); } } break; case H5T_COMPOUND: { unsigned i; n = H5Tget_nmembers(tid); h5str_append(str, " {"); for (i = 0; i < n; i++) { offset = H5Tget_member_offset(tid, i); mtid = H5Tget_member_type(tid, i); h5str_sprintf(str, container, mtid, cptr + offset, expand_data); if (i < n - 1) h5str_append(str, ", "); H5Tclose(mtid); } h5str_append(str, "} "); } break; case H5T_ENUM: { char enum_name[1024]; if (H5Tenum_nameof(tid, ptr, enum_name, sizeof enum_name) >= 0) { h5str_append(str, enum_name); } else { size_t i; nll = H5Tget_size(tid); this_str = (char*) malloc(4 * (nll + 1)); if (1 == nll) { sprintf(this_str, "0x%02x", ucptr[0]); } else { for (i = 0; i < (int)nll; i++) sprintf(this_str, "%s%02x", i ? ":" : "", ucptr[i]); } } } break; case H5T_REFERENCE: if (h5str_is_zero(ptr, size)) { h5str_append(str, "NULL"); } else { if (H5R_DSET_REG_REF_BUF_SIZE == size) { /* if (H5Tequal(tid, H5T_STD_REF_DSETREG)) */ /* * Dataset region reference -- * show the type and the referenced object */ char ref_name[1024]; hid_t region_obj; hid_t region; H5S_sel_type region_type; /* get name of the dataset the region reference points to using H5Rget_name */ region_obj = H5Rdereference(container, H5R_DATASET_REGION, ptr); if (region_obj >= 0) { region = H5Rget_region(container, H5R_DATASET_REGION, ptr); if (region >= 0) { if(expand_data) { region_type = H5Sget_select_type(region); if(region_type==H5S_SEL_POINTS) { h5str_dump_region_points_data(str, region, region_obj); } else { h5str_dump_region_blocks_data(str, region, region_obj); } } else { if(H5Rget_name(region_obj, H5R_DATASET_REGION, ptr, (char*)ref_name, 1024) >= 0) { h5str_append(str, ref_name); } region_type = H5Sget_select_type(region); if(region_type==H5S_SEL_POINTS) { h5str_append(str, " REGION_TYPE POINT"); h5str_dump_region_points(str, region, region_obj); } else { h5str_append(str, " REGION_TYPE BLOCK"); h5str_dump_region_blocks(str, region, region_obj); } } H5Sclose(region); } H5Dclose(region_obj); } } else if (H5R_OBJ_REF_BUF_SIZE == size) { /* if (H5Tequal(tid, H5T_STD_REF_OBJ)) */ /* * Object references -- show the type and OID of the referenced * object. */ H5O_info_t oi; hid_t obj; this_str = (char*) malloc(64); obj = H5Rdereference(container, H5R_OBJECT, ptr); H5Oget_info(obj, &oi); /* Print object data and close object */ sprintf(this_str, "%u-%lu", (unsigned) oi.type, oi.addr); H5Oclose(obj); } } break; case H5T_ARRAY: { int rank = 0; hsize_t i, dims[H5S_MAX_RANK], total_elmts; h5str_append(str, "[ "); mtid = H5Tget_super(tid); size = H5Tget_size(mtid); rank = H5Tget_array_ndims(tid); H5Tget_array_dims2(tid, dims); total_elmts = 1; for (i = 0; i < rank; i++) total_elmts *= dims[i]; for (i = 0; i < total_elmts; i++) { h5str_sprintf(str, container, mtid, cptr + i * size, expand_data); if (i < total_elmts - 1) h5str_append(str, ", "); } H5Tclose(mtid); h5str_append(str, "] "); } break; case H5T_VLEN: { unsigned int i; mtid = H5Tget_super(tid); size = H5Tget_size(mtid); vlptr = (hvl_t *) cptr; nll = vlptr->len; for (i = 0; i < (int)nll; i++) { h5str_sprintf(str, container, mtid, ((char *) (vlptr->p)) + i * size, expand_data); if (i < (int)nll - 1) h5str_append(str, ", "); } H5Tclose(mtid); } break; default: { /* All other types get printed as hexadecimal */ size_t i; nll = H5Tget_size(tid); this_str = (char*) malloc(4 * (nll + 1)); if (1 == nll) { sprintf(this_str, "0x%02x", ucptr[0]); } else { for (i = 0; i < (int)nll; i++) sprintf(this_str, "%s%02x", i ? ":" : "", ucptr[i]); } } break; } /* end switch */ if (this_str) { h5str_append(str, this_str); this_strlen = strlen(str->s); free(this_str); } return this_strlen; } /*------------------------------------------------------------------------- * Purpose: Print the data values from a dataset referenced by region blocks. * * Description: * This is a special case subfunction to print the data in a region reference of type blocks. * * Return: * The function returns FAIL if there was an error, otherwise SUCEED *------------------------------------------------------------------------- */ int h5str_print_region_data_blocks(hid_t region_id, h5str_t *str, int ndims, hid_t type_id, hssize_t nblocks, hsize_t *ptdata) { hsize_t *dims1 = NULL; hsize_t *start = NULL; hsize_t *count = NULL; hsize_t blkndx; hsize_t total_size[H5S_MAX_RANK]; unsigned int region_flags; /* buffer extent flags */ hsize_t numelem; hsize_t numindex; size_t jndx; unsigned indx; int type_size; int ret_value = SUCCEED; hid_t mem_space = -1; hid_t sid1 = -1; void *region_buf = NULL; /* Get the dataspace of the dataset */ if((sid1 = H5Dget_space(region_id)) >= 0) { /* Allocate space for the dimension array */ if((dims1 = (hsize_t *) malloc(sizeof(hsize_t) * ndims)) != NULL) { /* find the dimensions of each data space from the block coordinates */ numelem = 1; for (jndx = 0; jndx < ndims; jndx++) { dims1[jndx] = ptdata[jndx + ndims] - ptdata[jndx] + 1; numelem = dims1[jndx] * numelem; } /* Create dataspace for reading buffer */ if((mem_space = H5Screate_simple(ndims, dims1, NULL)) >= 0) { if((type_size = H5Tget_size(type_id)) > 0) { if((region_buf = malloc(type_size * (size_t)numelem)) != NULL) { /* Select (x , x , ..., x ) x (y , y , ..., y ) hyperslab for reading memory dataset */ /* 1 2 n 1 2 n */ if((start = (hsize_t *) malloc(sizeof(hsize_t) * ndims)) != NULL) { if((count = (hsize_t *) malloc(sizeof(hsize_t) * ndims)) != NULL) { for (blkndx = 0; blkndx < nblocks; blkndx++) { for (indx = 0; indx < ndims; indx++) { start[indx] = ptdata[indx + blkndx * ndims * 2]; count[indx] = dims1[indx]; } if(H5Sselect_hyperslab(sid1, H5S_SELECT_SET, start, NULL, count, NULL) >= 0) { if(H5Dread(region_id, type_id, mem_space, sid1, H5P_DEFAULT, region_buf) >= 0) { if(H5Sget_simple_extent_dims(mem_space, total_size, NULL) >= 0) { for (numindex = 0; numindex < numelem; numindex++) { h5str_sprintf(str, region_id, type_id, ((char*)region_buf + numindex * type_size), 1); if (numindex + 1 < numelem) h5str_append(str, ", "); } /* end for (jndx = 0; jndx < numelem; jndx++, region_elmtno++, ctx.cur_elmt++) */ } /* end if(H5Sget_simple_extent_dims(mem_space, total_size, NULL) >= 0) */ } /* end if(H5Dread(region_id, type_id, mem_space, sid1, H5P_DEFAULT, region_buf) >= 0) */ } /* end if(H5Sselect_hyperslab(sid1, H5S_SELECT_SET, start, NULL, count, NULL) >= 0) */ } /* end for (blkndx = 0; blkndx < nblocks; blkndx++) */ free(count); } /* end if((count = (hsize_t *) HDmalloc(sizeof(hsize_t) * ndims)) != NULL) */ else ret_value = -1; free(start); } /* end if((start = (hsize_t *) HDmalloc(sizeof(hsize_t) * ndims)) != NULL) */ else ret_value = -1; free(region_buf); } /* end if((region_buf = HDmalloc(type_size * (size_t)numelem)) != NULL) */ else ret_value = -1; } /* end if((type_size = H5Tget_size(type_id)) > 0) */ else ret_value = -1; if(H5Sclose(mem_space) < 0) ret_value = -1; } /* end if((mem_space = H5Screate_simple(ndims, dims1, NULL)) >= 0) */ else ret_value = -1; free(dims1); } /* end if((dims1 = (hsize_t *) HDmalloc(sizeof(hsize_t) * ndims)) != NULL) */ else ret_value = -1; if(H5Sclose(sid1) < 0) ret_value = -1; } /* end if((sid1 = H5Dget_space(region_id)) >= 0) */ else ret_value = -1; return ret_value; } int h5str_dump_region_blocks_data(h5str_t *str, hid_t region, hid_t region_id) { int ret_value = 0; hssize_t nblocks; hsize_t alloc_size; hsize_t *ptdata; hid_t dtype = -1; hid_t type_id = -1; char tmp_str[256]; int ndims = H5Sget_simple_extent_ndims(region); /* * This function fails if the region does not have blocks. */ H5E_BEGIN_TRY { nblocks = H5Sget_select_hyper_nblocks(region); } H5E_END_TRY; /* Print block information */ if (nblocks > 0) { int i; alloc_size = nblocks * ndims * 2 * sizeof(ptdata[0]); if (alloc_size == (hsize_t)((size_t) alloc_size)) { ptdata = (hsize_t *) malloc((size_t) alloc_size); H5Sget_select_hyper_blocklist(region, (hsize_t) 0, (hsize_t) nblocks, ptdata); if((dtype = H5Dget_type(region_id)) >= 0) { if((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) >= 0) { h5str_print_region_data_blocks(region_id, str, ndims, type_id, nblocks, ptdata); if(H5Tclose(type_id) < 0) ret_value = -1; } /* end if((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) >= 0) */ else ret_value = -1; if(H5Tclose(dtype) < 0) ret_value = -1; } /* end if((dtype = H5Dget_type(region_id)) >= 0) */ else ret_value = -1; free(ptdata); } /* if (alloc_size == (hsize_t)((size_t)alloc_size)) */ } /* if (nblocks > 0) */ return ret_value; } int h5str_dump_region_blocks(h5str_t *str, hid_t region, hid_t region_id) { int ret_value = 0; hssize_t nblocks; hsize_t alloc_size; hsize_t *ptdata; hid_t dtype = -1; hid_t type_id = -1; char tmp_str[256]; int ndims = H5Sget_simple_extent_ndims(region); /* * This function fails if the region does not have blocks. */ H5E_BEGIN_TRY { nblocks = H5Sget_select_hyper_nblocks(region); } H5E_END_TRY; /* Print block information */ if (nblocks > 0) { int i; alloc_size = nblocks * ndims * 2 * sizeof(ptdata[0]); if (alloc_size == (hsize_t)((size_t) alloc_size)) { ptdata = (hsize_t *) malloc((size_t) alloc_size); H5Sget_select_hyper_blocklist(region, (hsize_t) 0, (hsize_t) nblocks, ptdata); h5str_append(str, " {"); for (i = 0; i < nblocks; i++) { int j; h5str_append(str, " "); /* Start coordinates and opposite corner */ for (j = 0; j < ndims; j++) { tmp_str[0] = '\0'; sprintf(tmp_str, "%s%lu", j ? "," : "(", (unsigned long) ptdata[i * 2 * ndims + j]); h5str_append(str, tmp_str); } for (j = 0; j < ndims; j++) { tmp_str[0] = '\0'; sprintf(tmp_str, "%s%lu", j ? "," : ")-(", (unsigned long) ptdata[i * 2 * ndims + j + ndims]); h5str_append(str, tmp_str); } h5str_append(str, ") "); tmp_str[0] = '\0'; } h5str_append(str, " }"); free(ptdata); } /* if (alloc_size == (hsize_t)((size_t)alloc_size)) */ } /* if (nblocks > 0) */ return ret_value; } /*------------------------------------------------------------------------- * Purpose: Print the data values from a dataset referenced by region points. * * Description: * This is a special case subfunction to print the data in a region reference of type points. * * Return: * The function returns FAIL on error, otherwise SUCCEED *------------------------------------------------------------------------- */ int h5str_print_region_data_points(hid_t region_space, hid_t region_id, h5str_t *str, int ndims, hid_t type_id, hssize_t npoints, hsize_t *ptdata) { hsize_t *dims1 = NULL; hsize_t total_size[H5S_MAX_RANK]; size_t jndx; unsigned indx; int type_size; int ret_value = SUCCEED; unsigned int region_flags; /* buffer extent flags */ hid_t mem_space = -1; void *region_buf = NULL; char tmp_str[256]; /* Allocate space for the dimension array */ if((dims1 = (hsize_t *) malloc(sizeof(hsize_t) * ndims)) != NULL) { dims1[0] = npoints; /* Create dataspace for reading buffer */ if((mem_space = H5Screate_simple(1, dims1, NULL)) >= 0) { if((type_size = H5Tget_size(type_id)) > 0) { if((region_buf = malloc(type_size * (size_t)npoints)) != NULL) { if(H5Dread(region_id, type_id, mem_space, region_space, H5P_DEFAULT, region_buf) >= 0) { for (jndx = 0; jndx < npoints; jndx++) { if(H5Sget_simple_extent_dims(mem_space, total_size, NULL) >= 0) { h5str_sprintf(str, region_id, type_id, ((char*)region_buf + jndx * type_size), 1); if (jndx + 1 < npoints) h5str_append(str, ", "); } /* end if(H5Sget_simple_extent_dims(mem_space, total_size, NULL) >= 0) */ } /* end for (jndx = 0; jndx < npoints; jndx++, elmtno++) */ } /* end if(H5Dread(region_id, type_id, mem_space, region_space, H5P_DEFAULT, region_buf) >= 0) */ else ret_value = -1; free(region_buf); } /* end if((region_buf = HDmalloc(type_size * (size_t)npoints)) != NULL) */ else ret_value = -1; } /* end if((type_size = H5Tget_size(type_id)) > 0) */ else ret_value = -1; if(H5Sclose(mem_space) < 0) ret_value = -1; } /* end if((mem_space = H5Screate_simple(1, dims1, NULL)) >= 0) */ else ret_value = -1; free(dims1); } /* end if((dims1 = (hsize_t *) HDmalloc(sizeof(hsize_t) * ndims)) != NULL) */ else ret_value = -1; return ret_value; } int h5str_dump_region_points_data(h5str_t *str, hid_t region, hid_t region_id) { int ret_value = 0; hssize_t npoints; hsize_t alloc_size; hsize_t *ptdata; char tmp_str[256]; hid_t dtype = -1; hid_t type_id = -1; int ndims = H5Sget_simple_extent_ndims(region); /* * This function fails if the region does not have points. */ H5E_BEGIN_TRY { npoints = H5Sget_select_elem_npoints(region); } H5E_END_TRY; /* Print point information */ if (npoints > 0) { int i; alloc_size = npoints * ndims * sizeof(ptdata[0]); if (alloc_size == (hsize_t)((size_t) alloc_size)) { ptdata = (hsize_t *) malloc((size_t) alloc_size); H5Sget_select_elem_pointlist(region, (hsize_t) 0, (hsize_t) npoints, ptdata); if((dtype = H5Dget_type(region_id)) >= 0) { if((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) >= 0) { h5str_print_region_data_points(region, region_id, str, ndims, type_id, npoints, ptdata); if(H5Tclose(type_id) < 0) ret_value = -1; } /* end if((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) >= 0) */ else ret_value = -1; if(H5Tclose(dtype) < 0) ret_value = -1; } /* end if((dtype = H5Dget_type(region_id)) >= 0) */ else ret_value = -1; free(ptdata); } } return ret_value; } int h5str_dump_region_points(h5str_t *str, hid_t region, hid_t region_id) { int ret_value = 0; hssize_t npoints; hsize_t alloc_size; hsize_t *ptdata; char tmp_str[256]; hid_t dtype = -1; hid_t type_id = -1; int ndims = H5Sget_simple_extent_ndims(region); /* * This function fails if the region does not have points. */ H5E_BEGIN_TRY { npoints = H5Sget_select_elem_npoints(region); } H5E_END_TRY; /* Print point information */ if (npoints > 0) { int i; alloc_size = npoints * ndims * sizeof(ptdata[0]); if (alloc_size == (hsize_t)((size_t) alloc_size)) { ptdata = (hsize_t *) malloc((size_t) alloc_size); H5Sget_select_elem_pointlist(region, (hsize_t) 0, (hsize_t) npoints, ptdata); h5str_append(str, " {"); for (i = 0; i < npoints; i++) { int j; h5str_append(str, " "); for (j = 0; j < ndims; j++) { tmp_str[0] = '\0'; sprintf(tmp_str, "%s%lu", j ? "," : "(", (unsigned long) (ptdata[i * ndims + j])); h5str_append(str, tmp_str); } h5str_append(str, ") "); } h5str_append(str, " }"); free(ptdata); } } return ret_value; } int h5str_is_zero(const void *_mem, size_t size) { const unsigned char *mem = (const unsigned char *) _mem; while (size-- > 0) if (mem[size]) return 0; return 1; } /*------------------------------------------------------------------------- * Function: h5str_detect_vlen_str * * Purpose: Recursive check for variable length string of a datatype. * * Return: * TRUE : type conatains any variable length string * FALSE : type doesn't contain any variable length string * Negative value: error occur * *------------------------------------------------------------------------- */ htri_t h5str_detect_vlen_str(hid_t tid) { H5T_class_t tclass = H5T_NO_CLASS; htri_t ret = 0; ret = H5Tis_variable_str(tid); if((ret == 1) || (ret < 0)) goto done; tclass = H5Tget_class(tid); if(tclass == H5T_ARRAY || tclass == H5T_VLEN) { hid_t btid = H5Tget_super(tid); if(btid < 0) { ret = (htri_t)btid; goto done; } ret = h5str_detect_vlen_str(btid); if((ret == 1) || (ret < 0)) { H5Tclose(btid); goto done; } } else if(tclass == H5T_COMPOUND) { int i = 0; int n = H5Tget_nmembers(tid); if(n < 0) { n = ret; goto done; } for(i = 0; i < n; i++) { hid_t mtid = H5Tget_member_type(tid, i); ret = h5str_detect_vlen_str(mtid); if((ret == 1) || (ret < 0)) { H5Tclose(mtid); goto done; } H5Tclose(mtid); } } done: return ret; } /*------------------------------------------------------------------------- * Function: h5str_get_native_type * * Purpose: Wrapper around H5Tget_native_type() to work around * Problems with bitfields. * * Return: Success: datatype ID * Failure: FAIL *------------------------------------------------------------------------- */ hid_t h5str_get_native_type(hid_t type) { hid_t p_type; H5T_class_t type_class; type_class = H5Tget_class(type); if(type_class==H5T_BITFIELD) p_type=H5Tcopy(type); else p_type = H5Tget_native_type(type,H5T_DIR_DEFAULT); return(p_type); } /*------------------------------------------------------------------------- * Function: h5str_get_little_endian_type * * Purpose: Get a little endian type from a file type * * Return: Success: datatype ID * Failure: FAIL *------------------------------------------------------------------------- */ hid_t h5str_get_little_endian_type(hid_t tid) { hid_t p_type=-1; H5T_class_t type_class; size_t size; H5T_sign_t sign; type_class = H5Tget_class(tid); size = H5Tget_size(tid); sign = H5Tget_sign(tid); switch( type_class ) { case H5T_INTEGER: { if ( size == 1 && sign == H5T_SGN_2) p_type=H5Tcopy(H5T_STD_I8LE); else if ( size == 2 && sign == H5T_SGN_2) p_type=H5Tcopy(H5T_STD_I16LE); else if ( size == 4 && sign == H5T_SGN_2) p_type=H5Tcopy(H5T_STD_I32LE); else if ( size == 8 && sign == H5T_SGN_2) p_type=H5Tcopy(H5T_STD_I64LE); else if ( size == 1 && sign == H5T_SGN_NONE) p_type=H5Tcopy(H5T_STD_U8LE); else if ( size == 2 && sign == H5T_SGN_NONE) p_type=H5Tcopy(H5T_STD_U16LE); else if ( size == 4 && sign == H5T_SGN_NONE) p_type=H5Tcopy(H5T_STD_U32LE); else if ( size == 8 && sign == H5T_SGN_NONE) p_type=H5Tcopy(H5T_STD_U64LE); } break; case H5T_FLOAT: if ( size == 4) p_type=H5Tcopy(H5T_IEEE_F32LE); else if ( size == 8) p_type=H5Tcopy(H5T_IEEE_F64LE); break; case H5T_TIME: case H5T_BITFIELD: case H5T_OPAQUE: case H5T_STRING: case H5T_COMPOUND: case H5T_REFERENCE: case H5T_ENUM: case H5T_VLEN: case H5T_ARRAY: break; default: break; } return(p_type); } /*------------------------------------------------------------------------- * Function: h5str_get_big_endian_type * * Purpose: Get a big endian type from a file type * * Return: Success: datatype ID * Failure: FAIL *------------------------------------------------------------------------- */ hid_t h5str_get_big_endian_type(hid_t tid) { hid_t p_type=-1; H5T_class_t type_class; size_t size; H5T_sign_t sign; type_class = H5Tget_class(tid); size = H5Tget_size(tid); sign = H5Tget_sign(tid); switch( type_class ) { case H5T_INTEGER: { if ( size == 1 && sign == H5T_SGN_2) p_type=H5Tcopy(H5T_STD_I8BE); else if ( size == 2 && sign == H5T_SGN_2) p_type=H5Tcopy(H5T_STD_I16BE); else if ( size == 4 && sign == H5T_SGN_2) p_type=H5Tcopy(H5T_STD_I32BE); else if ( size == 8 && sign == H5T_SGN_2) p_type=H5Tcopy(H5T_STD_I64BE); else if ( size == 1 && sign == H5T_SGN_NONE) p_type=H5Tcopy(H5T_STD_U8BE); else if ( size == 2 && sign == H5T_SGN_NONE) p_type=H5Tcopy(H5T_STD_U16BE); else if ( size == 4 && sign == H5T_SGN_NONE) p_type=H5Tcopy(H5T_STD_U32BE); else if ( size == 8 && sign == H5T_SGN_NONE) p_type=H5Tcopy(H5T_STD_U64BE); } break; case H5T_FLOAT: if ( size == 4) p_type=H5Tcopy(H5T_IEEE_F32BE); else if ( size == 8) p_type=H5Tcopy(H5T_IEEE_F64BE); break; case H5T_TIME: case H5T_BITFIELD: case H5T_OPAQUE: case H5T_STRING: case H5T_COMPOUND: case H5T_REFERENCE: case H5T_ENUM: case H5T_VLEN: case H5T_ARRAY: break; default: break; } return(p_type); } /*------------------------------------------------------------------------- * Function: h5str_detect_vlen * * Purpose: Recursive check for any variable length data in given type. * * Return: * 1 : type conatains any variable length data * 0 : type doesn't contain any variable length data * Negative value: error occur *------------------------------------------------------------------------- */ htri_t h5str_detect_vlen(hid_t tid) { htri_t ret; /* recursive detect any vlen data values in type (compound, array ...) */ ret = H5Tdetect_class(tid, H5T_VLEN); if((ret == 1) || (ret < 0)) goto done; /* recursive detect any vlen string in type (compound, array ...) */ ret = h5str_detect_vlen_str(tid); if((ret == 1) || (ret < 0)) goto done; done: return ret; } /*------------------------------------------------------------------------- * Function: render_bin_output * * Purpose: Write one element of memory buffer to a binary file stream * * Return: Success: SUCCEED * Failure: FAIL *------------------------------------------------------------------------- */ int h5str_render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t block_nelmts) { int ret_value = 0; unsigned char *mem = (unsigned char*)_mem; size_t size; /* datum size */ hsize_t block_index; H5T_class_t type_class; if((size = H5Tget_size(tid)) > 0) { if((type_class = H5Tget_class(tid)) >= 0) { switch (type_class) { case H5T_INTEGER: case H5T_FLOAT: case H5T_ENUM: block_index = block_nelmts * size; while(block_index > 0) { size_t bytes_in = 0; /* # of bytes to write */ size_t bytes_wrote = 0; /* # of bytes written */ size_t item_size = size; /* size of items in bytes */ if(block_index > sizeof(size_t)) bytes_in = sizeof(size_t); else bytes_in = (size_t)block_index; bytes_wrote = fwrite(mem, 1, bytes_in, stream); if(bytes_wrote != bytes_in || (0 == bytes_wrote && ferror(stream))) { ret_value = -1; break; } block_index -= (hsize_t)bytes_wrote; mem = mem + bytes_wrote; } break; case H5T_STRING: { unsigned int i; H5T_str_t pad; char *s; unsigned char tempuchar; pad = H5Tget_strpad(tid); for (block_index = 0; block_index < block_nelmts; block_index++) { mem = ((unsigned char*)_mem) + block_index * size; if (H5Tis_variable_str(tid)) { s = *(char**) mem; if (s != NULL) size = strlen(s); } else { s = (char *) mem; } for (i = 0; i < size && (s[i] || pad != H5T_STR_NULLTERM); i++) { memcpy(&tempuchar, &s[i], sizeof(unsigned char)); if (1 != fwrite(&tempuchar, sizeof(unsigned char), 1, stream)) { ret_value = -1; break; } } /* i */ if(ret_value < 0) break; } /* for (block_index = 0; block_index < block_nelmts; block_index++) */ } break; case H5T_COMPOUND: { unsigned j; hid_t memb; unsigned nmembs; size_t offset; nmembs = H5Tget_nmembers(tid); for (block_index = 0; block_index < block_nelmts; block_index++) { mem = ((unsigned char*)_mem) + block_index * size; for (j = 0; j < nmembs; j++) { offset = H5Tget_member_offset(tid, j); memb = H5Tget_member_type(tid, j); if (h5str_render_bin_output(stream, container, memb, mem + offset, 1) < 0) { H5Tclose(memb); ret_value = -1; break; } H5Tclose(memb); } if(ret_value < 0) break; } } break; case H5T_ARRAY: { int k, ndims; hsize_t i, dims[H5S_MAX_RANK], temp_nelmts, nelmts; hid_t memb; /* get the array's base datatype for each element */ memb = H5Tget_super(tid); ndims = H5Tget_array_ndims(tid); H5Tget_array_dims2(tid, dims); /* calculate the number of array elements */ for (k = 0, nelmts = 1; k < ndims; k++) { temp_nelmts = nelmts; temp_nelmts *= dims[k]; nelmts = (size_t) temp_nelmts; } for (block_index = 0; block_index < block_nelmts; block_index++) { mem = ((unsigned char*)_mem) + block_index * size; /* dump the array element */ if (h5str_render_bin_output(stream, container, memb, mem, nelmts) < 0) { ret_value = -1; break; } } H5Tclose(memb); } break; case H5T_VLEN: { unsigned int i; hsize_t nelmts; hid_t memb; /* get the VL sequences's base datatype for each element */ memb = H5Tget_super(tid); for (block_index = 0; block_index < block_nelmts; block_index++) { mem = ((unsigned char*)_mem) + block_index * size; /* Get the number of sequence elements */ nelmts = ((hvl_t *) mem)->len; /* dump the array element */ if (h5str_render_bin_output(stream, container, memb, ((char *) (((hvl_t *) mem)->p)), nelmts) < 0) { ret_value = -1; break; } } H5Tclose(memb); } break; case H5T_REFERENCE: { if (H5Tequal(tid, H5T_STD_REF_DSETREG)) { /* region data */ hid_t region_id, region_space; H5S_sel_type region_type; for (block_index = 0; block_index < block_nelmts; block_index++) { mem = ((unsigned char*)_mem) + block_index * size; region_id = H5Rdereference(container, H5R_DATASET_REGION, mem); if (region_id >= 0) { region_space = H5Rget_region(container, H5R_DATASET_REGION, mem); if (region_space >= 0) { region_type = H5Sget_select_type(region_space); if(region_type == H5S_SEL_POINTS) ret_value = render_bin_output_region_points(stream, region_space, region_id, container); else ret_value = render_bin_output_region_blocks(stream, region_space, region_id, container); H5Sclose(region_space); } /* end if (region_space >= 0) */ H5Dclose(region_id); } /* end if (region_id >= 0) */ if(ret_value < 0) break; } } else if (H5Tequal(tid, H5T_STD_REF_OBJ)) { ; } } break; default: for (block_index = 0; block_index < block_nelmts; block_index++) { mem = ((unsigned char*)_mem) + block_index * size; if (size != fwrite(mem, sizeof(char), size, stream)) { ret_value = -1; break; } } break; } } /* end if((type_class = H5Tget_class(tid)) >= 0) */ else ret_value = -1; } /* end if((size = H5Tget_size(tid)) > 0) */ else ret_value = -1; return ret_value; } /*------------------------------------------------------------------------- * Purpose: Print the data values from a dataset referenced by region blocks. * * Description: * This is a special case subfunction to print the data in a region reference of type blocks. * * Return: * The function returns FAIL if there was an error, otherwise SUCEED * *------------------------------------------------------------------------- */ int render_bin_output_region_data_blocks(FILE *stream, hid_t region_id, hid_t container, int ndims, hid_t type_id, hssize_t nblocks, hsize_t *ptdata) { hsize_t *dims1 = NULL; hsize_t *start = NULL; hsize_t *count = NULL; hsize_t numelem; hsize_t numindex; hsize_t total_size[H5S_MAX_RANK]; int jndx; int type_size; hid_t mem_space = -1; void *region_buf = NULL; int blkndx; hid_t sid1 = -1; int ret_value = SUCCEED; /* Get the dataspace of the dataset */ if((sid1 = H5Dget_space(region_id)) >= 0) { /* Allocate space for the dimension array */ if((dims1 = (hsize_t *) malloc(sizeof(hsize_t) * ndims)) != NULL) { /* find the dimensions of each data space from the block coordinates */ numelem = 1; for (jndx = 0; jndx < ndims; jndx++) { dims1[jndx] = ptdata[jndx + ndims] - ptdata[jndx] + 1; numelem = dims1[jndx] * numelem; } /* Create dataspace for reading buffer */ if((mem_space = H5Screate_simple(ndims, dims1, NULL)) >= 0) { if((type_size = H5Tget_size(type_id)) > 0) { if((region_buf = malloc(type_size * (size_t)numelem)) != NULL) { /* Select (x , x , ..., x ) x (y , y , ..., y ) hyperslab for reading memory dataset */ /* 1 2 n 1 2 n */ if((start = (hsize_t *) malloc(sizeof(hsize_t) * ndims)) != NULL) { if((count = (hsize_t *) malloc(sizeof(hsize_t) * ndims)) != NULL) { for (blkndx = 0; blkndx < nblocks; blkndx++) { for (jndx = 0; jndx < ndims; jndx++) { start[jndx] = ptdata[jndx + blkndx * ndims * 2]; count[jndx] = dims1[jndx]; } if(H5Sselect_hyperslab(sid1, H5S_SELECT_SET, start, NULL, count, NULL) >= 0) { if(H5Dread(region_id, type_id, mem_space, sid1, H5P_DEFAULT, region_buf) >= 0) { if(H5Sget_simple_extent_dims(mem_space, total_size, NULL) >= 0) { ret_value = h5str_render_bin_output(stream, container, type_id, (char*)region_buf, numelem); } /* end if(H5Sget_simple_extent_dims(mem_space, total_size, NULL) >= 0) */ else { ret_value = -1; break; } } /* end if(H5Dread(region_id, type_id, mem_space, sid1, H5P_DEFAULT, region_buf) >= 0) */ else { ret_value = -1; break; } } /* end if(H5Sselect_hyperslab(sid1, H5S_SELECT_SET, start, NULL, count, NULL) >= 0) */ else { ret_value = -1; break; } /* Render the region data element end */ } /* end for (blkndx = 0; blkndx < nblocks; blkndx++) */ free(count); } /* end if((count = (hsize_t *) HDmalloc(sizeof(hsize_t) * ndims)) != NULL) */ else ret_value = -1; free(start); } /* end if((start = (hsize_t *) HDmalloc(sizeof(hsize_t) * ndims)) != NULL) */ else ret_value = -1; free(region_buf); } /* end if((region_buf = HDmalloc(type_size * (size_t)numelem)) != NULL) */ else ret_value = -1; } /* end if((type_size = H5Tget_size(type_id)) > 0) */ else ret_value = -1; if(H5Sclose(mem_space) < 0) ret_value = -1; } /* end if((mem_space = H5Screate_simple(ndims, dims1, NULL)) >= 0) */ else ret_value = -1; free(dims1); } /* end if((dims1 = (hsize_t *) HDmalloc(sizeof(hsize_t) * ndims)) != NULL) */ else ret_value = -1; if(H5Sclose(sid1) < 0) ret_value = -1; } /* end if((sid1 = H5Dget_space(region_id)) >= 0) */ else ret_value = -1; return ret_value; } /*------------------------------------------------------------------------- * Purpose: Print some values from a dataset referenced by region blocks. * * Description: * This is a special case subfunction to dump a region reference using blocks. * * Return: * The function returns False if ERROR, otherwise True * *------------------------------------------------------------------------- */ int render_bin_output_region_blocks(FILE *stream, hid_t region_space, hid_t region_id, hid_t container) { int ret_value = SUCCEED; hssize_t nblocks; hsize_t alloc_size; hsize_t *ptdata = NULL; int ndims; hid_t dtype; hid_t type_id; if((nblocks = H5Sget_select_hyper_nblocks(region_space)) > 0) { /* Print block information */ if((ndims = H5Sget_simple_extent_ndims(region_space)) >= 0) { alloc_size = nblocks * ndims * 2 * sizeof(ptdata[0]); if((ptdata = (hsize_t*) malloc((size_t) alloc_size)) != NULL) { if(H5Sget_select_hyper_blocklist(region_space, (hsize_t) 0, (hsize_t) nblocks, ptdata) >= 0) { if((dtype = H5Dget_type(region_id)) >= 0) { if((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) >= 0) { ret_value = render_bin_output_region_data_blocks(stream, region_id, container, ndims, type_id, nblocks, ptdata); if(H5Tclose(type_id) < 0) ret_value = -1; } /* end if((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) >= 0) */ else ret_value = -1; if(H5Tclose(dtype) < 0) ret_value = -1; } /* end if((dtype = H5Dget_type(region_id)) >= 0) */ else ret_value = -1; } /* end if(H5Sget_select_hyper_blocklist(region_space, (hsize_t) 0, (hsize_t) nblocks, ptdata) >= 0) */ else ret_value = -1; free(ptdata); } /* end if((ptdata = (hsize_t*) HDmalloc((size_t) alloc_size)) != NULL) */ else ret_value = -1; } /* end if((ndims = H5Sget_simple_extent_ndims(region_space)) >= 0) */ else ret_value = -1; } /* end if((nblocks = H5Sget_select_hyper_nblocks(region_space)) > 0) */ else ret_value = -1; return ret_value; } /*------------------------------------------------------------------------- * Purpose: Print the data values from a dataset referenced by region points. * * Description: * This is a special case subfunction to print the data in a region reference of type points. * * Return: * The function returns FAIL on error, otherwise SUCCEED * *------------------------------------------------------------------------- */ int render_bin_output_region_data_points(FILE *stream, hid_t region_space, hid_t region_id, hid_t container, int ndims, hid_t type_id, hssize_t npoints, hsize_t *ptdata) { hsize_t *dims1 = NULL; int jndx; int type_size; hid_t mem_space = -1; void *region_buf = NULL; int ret_value = SUCCEED; if((type_size = H5Tget_size(type_id)) > 0) { if((region_buf = malloc(type_size * (size_t)npoints)) != NULL) { /* Allocate space for the dimension array */ if((dims1 = (hsize_t *) malloc(sizeof(hsize_t) * ndims)) != NULL) { dims1[0] = npoints; if((mem_space = H5Screate_simple(1, dims1, NULL)) >= 0) { if(H5Dread(region_id, type_id, mem_space, region_space, H5P_DEFAULT, region_buf) >= 0) { if(H5Sget_simple_extent_dims(region_space, dims1, NULL) >= 0) { ret_value = h5str_render_bin_output(stream, container, type_id, (char*)region_buf, npoints); } /* end if(H5Sget_simple_extent_dims(region_space, dims1, NULL) >= 0) */ else ret_value = -1; } /* end if(H5Dread(region_id, type_id, mem_space, region_space, H5P_DEFAULT, region_buf) >= 0) */ else ret_value = -1; } /* end if((mem_space = H5Screate_simple(1, dims1, NULL)) >= 0) */ else ret_value = -1; free(dims1); } /* end if((dims1 = (hsize_t *) malloc(sizeof(hsize_t) * ndims)) != NULL) */ else ret_value = -1; free(region_buf); } /* end if((region_buf = malloc(type_size * (size_t)npoints)) != NULL) */ else ret_value = -1; if(H5Sclose(mem_space) < 0) ret_value = -1; } /* end if((type_size = H5Tget_size(type_id)) > 0) */ else ret_value = -1; return ret_value; } /*------------------------------------------------------------------------- * Purpose: Print some values from a dataset referenced by region points. * * Description: * This is a special case subfunction to dump a region reference using points. * * Return: * The function returns False if the last dimension has been reached, otherwise True * *------------------------------------------------------------------------- */ int render_bin_output_region_points(FILE *stream, hid_t region_space, hid_t region_id, hid_t container) { int ret_value = SUCCEED; hssize_t npoints; hsize_t alloc_size; hsize_t *ptdata; int ndims; hid_t dtype; hid_t type_id; if((npoints = H5Sget_select_elem_npoints(region_space)) > 0) { /* Allocate space for the dimension array */ if((ndims = H5Sget_simple_extent_ndims(region_space)) >= 0) { alloc_size = npoints * ndims * sizeof(ptdata[0]); if(NULL != (ptdata = (hsize_t *)malloc((size_t) alloc_size))) { if(H5Sget_select_elem_pointlist(region_space, (hsize_t) 0, (hsize_t) npoints, ptdata) >= 0) { if((dtype = H5Dget_type(region_id)) >= 0) { if((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) >= 0) { ret_value = render_bin_output_region_data_points(stream, region_space, region_id, container, ndims, type_id, npoints, ptdata); if(H5Tclose(type_id) < 0) ret_value = -1; } /* end if((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) >= 0) */ else ret_value = -1; if(H5Tclose(dtype) < 0) ret_value = -1; } /* end if((dtype = H5Dget_type(region_id)) >= 0) */ else ret_value = -1; } /* end if(H5Sget_select_elem_pointlist(region_space, (hsize_t) 0, (hsize_t) npoints, ptdata) >= 0) */ else ret_value = -1; free(ptdata); } /* end if(NULL != (ptdata = (hsize_t *)malloc((size_t) alloc_size))) */ else ret_value = -1; } /* end if((ndims = H5Sget_simple_extent_ndims(region_space)) >= 0) */ else ret_value = -1; } /* end if((npoints = H5Sget_select_elem_npoints(region_space)) > 0) */ else ret_value = -1; return ret_value; } int h5str_dump_simple_dset(FILE *stream, hid_t dset, int binary_order) { int ret_value = SUCCEED; hid_t f_space = -1; /* file data space */ hsize_t elmtno; /* counter */ size_t i; /* counter */ int ndims; int carry; /* counter carry value */ hsize_t zero[8]; /* vector of zeros */ unsigned int flags; /* buffer extent flags */ hsize_t total_size[H5S_MAX_RANK]; /* total size of dataset*/ /* Print info */ size_t p_type_nbytes; /* size of memory type */ hsize_t p_nelmts; /* total selected elmts */ /* Stripmine info */ hsize_t sm_size[H5S_MAX_RANK]; /* stripmine size */ hsize_t sm_nbytes; /* bytes per stripmine */ hsize_t sm_nelmts; /* elements per stripmine*/ unsigned char *sm_buf = NULL; /* buffer for raw data */ hid_t sm_space = -1; /* stripmine data space */ /* Hyperslab info */ hsize_t hs_offset[H5S_MAX_RANK]; /* starting offset */ hsize_t hs_size[H5S_MAX_RANK]; /* size this pass */ hsize_t hs_nelmts; /* elements in request */ /* VL data special information */ unsigned int vl_data = 0; /* contains VL datatypes */ hid_t p_type = -1; hid_t f_type = -1; if(dset < 0) return -1; f_type = H5Dget_type(dset); if (binary_order == 1) p_type = h5str_get_native_type(f_type); else if (binary_order == 2) p_type = h5str_get_little_endian_type(f_type); else if (binary_order == 3) p_type = h5str_get_big_endian_type(f_type); else p_type = H5Tcopy(f_type); H5Tclose(f_type); if (p_type >= 0) { if((f_space = H5Dget_space(dset)) >= 0) { ndims = H5Sget_simple_extent_ndims(f_space); if ((size_t)ndims <= (sizeof(sm_size)/sizeof(sm_size[0]))) { H5Sget_simple_extent_dims(f_space, total_size, NULL); /* calculate the number of elements we're going to print */ p_nelmts = 1; if (ndims > 0) { for (i = 0; i < ndims; i++) p_nelmts *= total_size[i]; } /* end if */ if (p_nelmts > 0) { /* Check if we have VL data in the dataset's datatype */ if (h5str_detect_vlen(p_type) != 0) vl_data = 1; /* * Determine the strip mine size and allocate a buffer. The strip mine is * a hyperslab whose size is manageable. */ sm_nbytes = p_type_nbytes = H5Tget_size(p_type); if (ndims > 0) { for (i = ndims; i > 0; --i) { hsize_t size = H5TOOLS_BUFSIZE / sm_nbytes; if ( size == 0) /* datum size > H5TOOLS_BUFSIZE */ size = 1; sm_size[i - 1] = (((total_size[i - 1]) < (size)) ? (total_size[i - 1]) : (size)); sm_nbytes *= sm_size[i - 1]; } } if(sm_nbytes > 0) { sm_buf = (unsigned char *)malloc((size_t)sm_nbytes); sm_nelmts = sm_nbytes / p_type_nbytes; sm_space = H5Screate_simple(1, &sm_nelmts, NULL); /* The stripmine loop */ memset(hs_offset, 0, sizeof hs_offset); memset(zero, 0, sizeof zero); for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_nelmts) { /* Calculate the hyperslab size */ if (ndims > 0) { for (i = 0, hs_nelmts = 1; i < ndims; i++) { hs_size[i] = (((total_size[i] - hs_offset[i]) < (sm_size[i])) ? (total_size[i] - hs_offset[i]) : (sm_size[i])); hs_nelmts *= hs_size[i]; } H5Sselect_hyperslab(f_space, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL); H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL, &hs_nelmts, NULL); } else { H5Sselect_all(f_space); H5Sselect_all(sm_space); hs_nelmts = 1; } /* Read the data */ if (H5Dread(dset, p_type, sm_space, f_space, H5P_DEFAULT, sm_buf) >= 0) { if (binary_order == 99) ret_value = h5tools_dump_simple_data(stream, dset, p_type, sm_buf, hs_nelmts); else ret_value = h5str_render_bin_output(stream, dset, p_type, sm_buf, hs_nelmts); /* Reclaim any VL memory, if necessary */ if (vl_data) H5Dvlen_reclaim(p_type, sm_space, H5P_DEFAULT, sm_buf); } else { ret_value = -1; break; } if(ret_value < 0) break; /* Calculate the next hyperslab offset */ for (i = ndims, carry = 1; i > 0 && carry; --i) { hs_offset[i - 1] += hs_size[i - 1]; if (hs_offset[i - 1] == total_size[i - 1]) hs_offset[i - 1] = 0; else carry = 0; } } if(sm_buf) free(sm_buf); } if(sm_space >= 0 && H5Sclose(sm_space) < 0) ret_value = -1; } } if(f_space >= 0 && H5Sclose(f_space) < 0) ret_value = -1; } /* end if((f_space = H5Dget_space(dset)) >= 0) */ else ret_value = -1; if (p_type >= 0) H5Tclose(p_type); } return ret_value; } int h5tools_dump_simple_data(FILE *stream, hid_t container, hid_t type, void *_mem, hsize_t nelmts) { int ret_value = 0; int line_count; unsigned char *mem = (unsigned char*)_mem; size_t size; /* datum size */ H5T_class_t type_class; hsize_t i; /*element counter */ h5str_t buffer; /*string into which to render */ if((size = H5Tget_size(type)) > 0) { for (i = 0, line_count = 0; i < nelmts; i++, line_count++) { size_t bytes_in = 0; /* # of bytes to write */ size_t bytes_wrote = 0; /* # of bytes written */ void* memref = mem + i * size; /* Render the data element*/ h5str_new(&buffer, 32 * size); bytes_in = h5str_sprintf(&buffer, container, type, memref, 1); if(i > 0) { fprintf(stream, ", "); if (line_count >= H5TOOLS_TEXT_BLOCK) { line_count = 0; fprintf(stream, "\n"); } } fprintf(stream, "%s", buffer.s); h5str_free(&buffer); } /* end for (i = 0; i < nelmts... */ fprintf(stream, "\n"); } /* end if((size = H5Tget_size(tid)) > 0) */ else ret_value = -1; return ret_value; } #ifdef __cplusplus } #endif libsis-jhdf5-java-14.12.1/source/c/hdf-java/h5util.h000077500000000000000000000035241256564762100216740ustar00rootroot00000000000000/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the files COPYING and Copyright.html. COPYING can be found at the root * * of the source code distribution tree; Copyright.html can be found at the * * root level of an installed copy of the electronic HDF5 document set and * * is linked from the top-level documents page. It can also be found at * * http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have * * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #ifndef H5UTIL_H__ #define H5UTIL_H__ #ifndef SUCCEED #define SUCCEED 0 #endif #ifndef FAIL #define FAIL (-1) #endif typedef struct h5str_t { char *s; size_t max; /* the allocated size of the string */ } h5str_t; void h5str_new (h5str_t *str, size_t len); void h5str_free (h5str_t *str); void h5str_resize (h5str_t *str, size_t new_len); char* h5str_append (h5str_t *str, const char* cstr); int h5str_sprintf(h5str_t *str, hid_t container, hid_t tid, void *buf, int expand_data); void h5str_array_free(char **strs, size_t len); int h5str_dump_simple_dset(FILE *stream, hid_t dset, int binary_order); int h5str_dump_region_blocks_data(h5str_t *str, hid_t region, hid_t region_obj); int h5str_dump_region_points_data(h5str_t *str, hid_t region, hid_t region_obj); #endif /* H5UTIL_H__ */ libsis-jhdf5-java-14.12.1/source/c/hdf-java/h5zImp.c000077500000000000000000000053411256564762100216300ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ /* * This code is the C-interface called by Java programs to access the * Reference API Functions of the HDF5 library. * * Each routine wraps a single HDF entry point, generally with the * analogous arguments and return codes. * * For details of the HDF libraries, see the HDF Documentation at: * http://hdf.ncsa.uiuc.edu/HDF5/doc/ * */ #ifdef __cplusplus extern "C" { #endif #include "hdf5.h" #include #include #include "h5jni.h" /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Zunregister * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Zunregister (JNIEnv *env, jclass clss, jint filter) { herr_t retValue; retValue = H5Zunregister((H5Z_filter_t)filter); if (retValue < 0) { h5libraryError(env); } return (jint)retValue; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Zfilter_avail * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Zfilter_1avail (JNIEnv *env, jclass clss, jint filter) { herr_t retValue; retValue = H5Zfilter_avail((H5Z_filter_t)filter); if (retValue < 0) { h5libraryError(env); } return (jint)retValue; } /********************************************************************** * * * New functions release 1.6.3 versus release 1.6.2 * * * **********************************************************************/ /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Zget_filter_info * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5Zget_1filter_1info (JNIEnv *env, jclass clss, jint filter) { herr_t status; unsigned int flags = 0; status = H5Zget_filter_info ((H5Z_filter_t) filter, (unsigned *) &flags); if (status < 0) { h5libraryError(env); } return flags; } #ifdef __cplusplus } #endif libsis-jhdf5-java-14.12.1/source/c/hdf-java/nativeData.c000077500000000000000000000767531256564762100225530ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ /* * This module contains the implementation of all the native methods * used for number conversion. This is represented by the Java * class HDFNativeData. * * These routines convert one dimensional arrays of bytes into * one-D arrays of other types (int, float, etc) and vice versa. * * These routines are called from the Java parts of the Java-C * interface. * * ***Important notes: * * 1. These routines are designed to be portable--they use the * C compiler to do the required native data manipulation. * 2. These routines copy the data at least once -- a serious * but unavoidable performance hit. */ #ifdef __cplusplus extern "C" { #endif #include #include "hdf5.h" #include "h5jni.h" /* returns int [] */ JNIEXPORT jintArray JNICALL Java_ncsa_hdf_hdf5lib_HDFNativeData_byteToInt___3B ( JNIEnv *env, jclass clss, jbyteArray bdata) /* IN: array of bytes */ { jbyte *barr; jintArray rarray; int blen; jint *iarray; jboolean bb; char *bp; jint *iap; int ii; int len; if (bdata == NULL) { h5nullArgument( env, "byteToInt: bdata is NULL?"); return NULL; } barr = ENVPTR->GetByteArrayElements(ENVPAR bdata,&bb); if (barr == NULL) { h5JNIFatalError(env, "byteToInt: pin failed"); return NULL; } blen = ENVPTR->GetArrayLength(ENVPAR bdata); len = blen/sizeof(jint); rarray = ENVPTR->NewIntArray(ENVPAR len); if (rarray == NULL) { ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); h5outOfMemory( env, "byteToInt" ); return NULL; } iarray = ENVPTR->GetIntArrayElements(ENVPAR rarray,&bb); if (iarray == NULL) { ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); h5JNIFatalError(env, "byteToInt: pin iarray failed"); return NULL; } bp = (char *)barr; iap = iarray; for (ii = 0; ii < len; ii++) { *iap = *(jint *)bp; iap++; bp += sizeof(jint); } ENVPTR->ReleaseIntArrayElements(ENVPAR rarray,iarray, 0); ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); return rarray; } /* returns float [] */ JNIEXPORT jfloatArray JNICALL Java_ncsa_hdf_hdf5lib_HDFNativeData_byteToFloat___3B ( JNIEnv *env, jclass clss, jbyteArray bdata) /* IN: array of bytes */ { jbyte *barr; jfloatArray rarray; int blen; jfloat *farray; jboolean bb; char *bp; jfloat *iap; int ii; int len; if (bdata == NULL) { h5nullArgument( env, "byteToFloat: bdata is NULL?"); return NULL; } barr = ENVPTR->GetByteArrayElements(ENVPAR bdata,&bb); if (barr == NULL) { h5JNIFatalError(env, "byteToFloat: pin failed"); return NULL; } blen = ENVPTR->GetArrayLength(ENVPAR bdata); len = blen/sizeof(jfloat); rarray = ENVPTR->NewFloatArray(ENVPAR len); if (rarray == NULL) { ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); h5outOfMemory( env, "byteToFloat" ); return NULL; } farray = ENVPTR->GetFloatArrayElements(ENVPAR rarray,&bb); if (farray == NULL) { ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); h5JNIFatalError(env, "byteToFloat: pin farray failed"); return NULL; } bp = (char *)barr; iap = farray; for (ii = 0; ii < len; ii++) { *iap = *(jfloat *)bp; iap++; bp += sizeof(jfloat); } ENVPTR->ReleaseFloatArrayElements(ENVPAR rarray,farray, 0); ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); return rarray; } /* returns short [] */ JNIEXPORT jshortArray JNICALL Java_ncsa_hdf_hdf5lib_HDFNativeData_byteToShort___3B ( JNIEnv *env, jclass clss, jbyteArray bdata) /* IN: array of bytes */ { jbyte *barr; jshortArray rarray; int blen; jshort *sarray; jboolean bb; char *bp; jshort *iap; int ii; int len; if (bdata == NULL) { h5nullArgument( env, "byteToShort: bdata is NULL?"); return NULL; } barr = ENVPTR->GetByteArrayElements(ENVPAR bdata,&bb); if (barr == NULL) { h5JNIFatalError(env, "byteToShort: pin failed"); return NULL; } blen = ENVPTR->GetArrayLength(ENVPAR bdata); len = blen/sizeof(jshort); rarray = ENVPTR->NewShortArray(ENVPAR len); if (rarray == NULL) { ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); h5outOfMemory( env, "byteToShort" ); return NULL; } sarray = ENVPTR->GetShortArrayElements(ENVPAR rarray,&bb); if (sarray == NULL) { ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); h5JNIFatalError(env, "byteToShort: pin sarray failed"); return NULL; } bp = (char *)barr; iap = sarray; for (ii = 0; ii < len; ii++) { *iap = *(jshort *)bp; iap++; bp += sizeof(jshort); } ENVPTR->ReleaseShortArrayElements(ENVPAR rarray,sarray, 0); ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); return rarray; } /* returns long [] */ JNIEXPORT jlongArray JNICALL Java_ncsa_hdf_hdf5lib_HDFNativeData_byteToLong___3B ( JNIEnv *env, jclass clss, jbyteArray bdata) /* IN: array of bytes */ { jbyte *barr; jlongArray rarray; int blen; jlong *larray; jboolean bb; char *bp; jlong *iap; int ii; int len; if (bdata == NULL) { h5nullArgument( env, "byteToLong: bdata is NULL?"); return NULL; } barr = ENVPTR->GetByteArrayElements(ENVPAR bdata,&bb); if (barr == NULL) { h5JNIFatalError(env, "byteToLong: pin failed"); return NULL; } blen = ENVPTR->GetArrayLength(ENVPAR bdata); len = blen/sizeof(jlong); rarray = ENVPTR->NewLongArray(ENVPAR len); if (rarray == NULL) { ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); h5outOfMemory( env, "byteToLong" ); return NULL; } larray = ENVPTR->GetLongArrayElements(ENVPAR rarray,&bb); if (larray == NULL) { ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); h5JNIFatalError(env, "byteToLong: pin larray failed"); return NULL; } bp = (char *)barr; iap = larray; for (ii = 0; ii < len; ii++) { *iap = *(jlong *)bp; iap++; bp += sizeof(jlong); } ENVPTR->ReleaseLongArrayElements(ENVPAR rarray,larray, 0); ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); return rarray; } /* returns double [] */ JNIEXPORT jdoubleArray JNICALL Java_ncsa_hdf_hdf5lib_HDFNativeData_byteToDouble___3B ( JNIEnv *env, jclass clss, jbyteArray bdata) /* IN: array of bytes */ { jbyte *barr; jdoubleArray rarray; int blen; jdouble *darray; jboolean bb; char *bp; jdouble *iap; int ii; int len; if (bdata == NULL) { h5nullArgument( env, "byteToDouble: bdata is NULL?"); return NULL; } barr = ENVPTR->GetByteArrayElements(ENVPAR bdata,&bb); if (barr == NULL) { h5JNIFatalError(env, "byteToDouble: pin failed"); return NULL; } blen = ENVPTR->GetArrayLength(ENVPAR bdata); len = blen/sizeof(jdouble); rarray = ENVPTR->NewDoubleArray(ENVPAR len); if (rarray == NULL) { ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); h5outOfMemory( env, "byteToDouble" ); return NULL; } darray = ENVPTR->GetDoubleArrayElements(ENVPAR rarray,&bb); if (darray == NULL) { ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); h5JNIFatalError(env, "byteToDouble: pin darray failed"); return NULL; } bp = (char *)barr; iap = darray; for (ii = 0; ii < len; ii++) { *iap = *(jdouble *)bp; iap++; bp += sizeof(jdouble); } ENVPTR->ReleaseDoubleArrayElements(ENVPAR rarray,darray,0); ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); return rarray; } /* returns int [] */ JNIEXPORT jintArray JNICALL Java_ncsa_hdf_hdf5lib_HDFNativeData_byteToInt__II_3B ( JNIEnv *env, jclass clss, jint start, jint len, jbyteArray bdata) /* IN: array of bytes */ { char *bp; jbyte *barr; jintArray rarray; int blen; jint *iarray; jint *iap; int ii; jboolean bb; if (bdata == NULL) { h5nullArgument( env, "byteToInt: bdata is NULL?"); return NULL; } barr = ENVPTR->GetByteArrayElements(ENVPAR bdata,&bb); if (barr == NULL) { h5JNIFatalError(env, "byteToInt: pin failed"); return NULL; } blen = ENVPTR->GetArrayLength(ENVPAR bdata); if ((start < 0) || ((int)(start + (len*sizeof(jint))) > blen)) { ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); h5JNIFatalError(env, "byteToInt: getLen failed"); return NULL; } bp = (char *)barr + start; rarray = ENVPTR->NewIntArray(ENVPAR len); if (rarray == NULL) { ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); h5outOfMemory( env, "byteToInt" ); return NULL; } iarray = ENVPTR->GetIntArrayElements(ENVPAR rarray,&bb); if (iarray == NULL) { ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); h5JNIFatalError(env, "byteToInt: pin iarray failed"); return NULL; } iap = iarray; for (ii = 0; ii < len; ii++) { *iap = *(jint *)bp; iap++; bp += sizeof(jint); } ENVPTR->ReleaseIntArrayElements(ENVPAR rarray,iarray, 0); ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); return rarray; } /* returns short [] */ JNIEXPORT jshortArray JNICALL Java_ncsa_hdf_hdf5lib_HDFNativeData_byteToShort__II_3B ( JNIEnv *env, jclass clss, jint start, jint len, jbyteArray bdata) /* IN: array of bytes */ { char *bp; jbyte *barr; jshortArray rarray; int blen; jshort *iarray; jshort *iap; int ii; jboolean bb; if (bdata == NULL) { h5nullArgument( env, "byteToShort: bdata is NULL?"); return NULL; } barr = ENVPTR->GetByteArrayElements(ENVPAR bdata,&bb); if (barr == NULL) { h5JNIFatalError( env, "byteToShort: getByte failed?"); return NULL; } blen = ENVPTR->GetArrayLength(ENVPAR bdata); if ((start < 0) || ((int)(start + (len*(sizeof(jshort)))) > blen)) { ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); h5badArgument( env, "byteToShort: start or len is out of bounds"); return NULL; } bp = (char *)barr + start; rarray = ENVPTR->NewShortArray(ENVPAR len); if (rarray == NULL) { ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); h5outOfMemory( env, "byteToShort" ); return NULL; } iarray = ENVPTR->GetShortArrayElements(ENVPAR rarray,&bb); if (iarray == NULL) { ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); h5JNIFatalError( env, "byteToShort: getShort failed?"); return NULL; } iap = iarray; for (ii = 0; ii < len; ii++) { *iap = *(jshort *)bp; iap++; bp += sizeof(jshort); } ENVPTR->ReleaseShortArrayElements(ENVPAR rarray,iarray, 0); ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); return rarray; } /* returns float [] */ JNIEXPORT jfloatArray JNICALL Java_ncsa_hdf_hdf5lib_HDFNativeData_byteToFloat__II_3B ( JNIEnv *env, jclass clss, jint start, jint len, jbyteArray bdata) /* IN: array of bytes */ { char *bp; jbyte *barr; jfloatArray rarray; int blen; jfloat *iarray; jfloat *iap; int ii; jboolean bb; if (bdata == NULL) { h5nullArgument( env, "byteToFloat: bdata is NULL?"); return NULL; } barr = ENVPTR->GetByteArrayElements(ENVPAR bdata,&bb); if (barr == NULL) { h5JNIFatalError( env, "byteToFloat: getByte failed?"); return NULL; } blen = ENVPTR->GetArrayLength(ENVPAR bdata); if ((start < 0) || ((int)(start + (len*(sizeof(jfloat)))) > blen)) { ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); h5badArgument( env, "byteToFloat: start or len is out of bounds"); return NULL; } bp = (char *)barr + start; rarray = ENVPTR->NewFloatArray(ENVPAR len); if (rarray == NULL) { ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); h5outOfMemory( env, "byteToFloat" ); return NULL; } iarray = ENVPTR->GetFloatArrayElements(ENVPAR rarray,&bb); if (iarray == NULL) { ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); h5JNIFatalError( env, "byteToFloat: getFloat failed?"); return NULL; } iap = iarray; for (ii = 0; ii < len; ii++) { *iap = *(jfloat *)bp; iap++; bp += sizeof(jfloat); } ENVPTR->ReleaseFloatArrayElements(ENVPAR rarray,iarray, 0); ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); return rarray; } /* returns long [] */ JNIEXPORT jlongArray JNICALL Java_ncsa_hdf_hdf5lib_HDFNativeData_byteToLong__II_3B ( JNIEnv *env, jclass clss, jint start, jint len, jbyteArray bdata) /* IN: array of bytes */ { char *bp; jbyte *barr; jlongArray rarray; int blen; jlong *iarray; jlong *iap; int ii; jboolean bb; if (bdata == NULL) { h5nullArgument( env, "byteToLong: bdata is NULL?"); return NULL; } barr = ENVPTR->GetByteArrayElements(ENVPAR bdata,&bb); if (barr == NULL) { h5JNIFatalError( env, "byteToLong: getByte failed?"); return NULL; } blen = ENVPTR->GetArrayLength(ENVPAR bdata); if ((start < 0) || ((int)(start + (len*(sizeof(jlong)))) > blen)) { ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); h5badArgument( env, "byteToLong: start or len is out of bounds"); return NULL; } bp = (char *)barr + start; rarray = ENVPTR->NewLongArray(ENVPAR len); if (rarray == NULL) { ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); h5outOfMemory( env, "byteToLong" ); return NULL; } iarray = ENVPTR->GetLongArrayElements(ENVPAR rarray,&bb); if (iarray == NULL) { ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); h5JNIFatalError( env, "byteToLong: getLong failed?"); return NULL; } iap = iarray; for (ii = 0; ii < len; ii++) { *iap = *(jlong *)bp; iap++; bp += sizeof(jlong); } ENVPTR->ReleaseLongArrayElements(ENVPAR rarray,iarray, 0); ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); return rarray; } /* returns double [] */ JNIEXPORT jdoubleArray JNICALL Java_ncsa_hdf_hdf5lib_HDFNativeData_byteToDouble__II_3B ( JNIEnv *env, jclass clss, jint start, jint len, jbyteArray bdata) /* IN: array of bytes */ { char *bp; jbyte *barr; jdoubleArray rarray; int blen; jdouble *iarray; jdouble *iap; int ii; jboolean bb; if (bdata == NULL) { h5nullArgument( env, "byteToDouble: bdata is NULL?"); return NULL; } barr = ENVPTR->GetByteArrayElements(ENVPAR bdata,&bb); if (barr == NULL) { h5JNIFatalError( env, "byteToDouble: getByte failed?"); return NULL; } blen = ENVPTR->GetArrayLength(ENVPAR bdata); if ((start < 0) || ((int)(start + (len*(sizeof(jdouble)))) > blen)) { ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); h5badArgument( env, "byteToDouble: start or len is out of bounds"); return NULL; } bp = (char *)barr + start; rarray = ENVPTR->NewDoubleArray(ENVPAR len); if (rarray == NULL) { ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); h5outOfMemory( env, "byteToDouble" ); return NULL; } iarray = ENVPTR->GetDoubleArrayElements(ENVPAR rarray,&bb); if (iarray == NULL) { ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); h5JNIFatalError( env, "byteToDouble: getDouble failed?"); return NULL; } iap = iarray; for (ii = 0; ii < len; ii++) { *iap = *(jdouble *)bp; iap++; bp += sizeof(jdouble); } ENVPTR->ReleaseDoubleArrayElements(ENVPAR rarray,iarray, 0); ENVPTR->ReleaseByteArrayElements(ENVPAR bdata,barr,JNI_ABORT); return rarray; } /* returns byte [] */ JNIEXPORT jbyteArray JNICALL Java_ncsa_hdf_hdf5lib_HDFNativeData_intToByte__II_3I (JNIEnv *env, jclass clss, jint start, jint len, jintArray idata) /* IN: array of int */ { jint *ip; jint *iarr; int ilen; jbyteArray rarray; int blen; jbyte *barray; jbyte *bap; jboolean bb; int ii; int ij; union things { int ival; char bytes[4]; } u; if (idata == NULL) { h5nullArgument( env, "intToByte: idata is NULL?"); return NULL; } iarr = ENVPTR->GetIntArrayElements(ENVPAR idata,&bb); if (iarr == NULL) { h5JNIFatalError( env, "intToByte: getInt failed?"); return NULL; } ilen = ENVPTR->GetArrayLength(ENVPAR idata); if ((start < 0) || (((start + len)) > ilen)) { ENVPTR->ReleaseIntArrayElements(ENVPAR idata,iarr,JNI_ABORT); h5badArgument( env, "intToByte: start or len is out of bounds"); return NULL; } ip = iarr + start; blen = ilen * sizeof(jint); rarray = ENVPTR->NewByteArray(ENVPAR blen); if (rarray == NULL) { ENVPTR->ReleaseIntArrayElements(ENVPAR idata,iarr,JNI_ABORT); h5outOfMemory( env, "intToByte" ); return NULL; } barray = ENVPTR->GetByteArrayElements(ENVPAR rarray,&bb); if (barray == NULL) { ENVPTR->ReleaseIntArrayElements(ENVPAR idata,iarr,JNI_ABORT); h5JNIFatalError( env, "intToByte: getByte failed?"); return NULL; } bap = barray; for (ii = 0; ii < len; ii++) { u.ival = *ip++; for (ij = 0; ij < sizeof(jint); ij++) { *bap = u.bytes[ij]; bap++; } } ENVPTR->ReleaseByteArrayElements(ENVPAR rarray,barray, 0); ENVPTR->ReleaseIntArrayElements(ENVPAR idata,iarr,JNI_ABORT); return rarray; } /* returns byte [] */ JNIEXPORT jbyteArray JNICALL Java_ncsa_hdf_hdf5lib_HDFNativeData_shortToByte__II_3S ( JNIEnv *env, jclass clss, jint start, jint len, jshortArray idata) /* IN: array of short */ { jshort *ip; jshort *iarr; int ilen; jbyteArray rarray; int blen; jbyte *barray; jbyte *bap; jboolean bb; int ii; int ij; union things { short ival; char bytes[4]; } u; if (idata == NULL) { h5nullArgument( env, "shortToByte: idata is NULL?"); return NULL; } iarr = ENVPTR->GetShortArrayElements(ENVPAR idata,&bb); if (iarr == NULL) { h5JNIFatalError( env, "shortToByte: getShort failed?"); return NULL; } ilen = ENVPTR->GetArrayLength(ENVPAR idata); if ((start < 0) || (((start + len)) > ilen)) { ENVPTR->ReleaseShortArrayElements(ENVPAR idata,iarr,JNI_ABORT); h5badArgument( env, "shortToByte: start or len is out of bounds"); return NULL; } ip = iarr + start; blen = ilen * sizeof(jshort); rarray = ENVPTR->NewByteArray(ENVPAR blen); if (rarray == NULL) { ENVPTR->ReleaseShortArrayElements(ENVPAR idata,iarr,JNI_ABORT); h5outOfMemory( env, "shortToByte" ); return NULL; } barray = ENVPTR->GetByteArrayElements(ENVPAR rarray,&bb); if (barray == NULL) { ENVPTR->ReleaseShortArrayElements(ENVPAR idata,iarr,JNI_ABORT); h5JNIFatalError( env, "shortToByte: getByte failed?"); return NULL; } bap = barray; for (ii = 0; ii < len; ii++) { u.ival = *ip++; for (ij = 0; ij < sizeof(jshort); ij++) { *bap = u.bytes[ij]; bap++; } } ENVPTR->ReleaseByteArrayElements(ENVPAR rarray,barray, 0); ENVPTR->ReleaseShortArrayElements(ENVPAR idata,iarr,JNI_ABORT); return rarray; } /* returns byte [] */ JNIEXPORT jbyteArray JNICALL Java_ncsa_hdf_hdf5lib_HDFNativeData_floatToByte__II_3F ( JNIEnv *env, jclass clss, jint start, jint len, jfloatArray idata) /* IN: array of float */ { jfloat *ip; jfloat *iarr; int ilen; jbyteArray rarray; int blen; jbyte *barray; jbyte *bap; jboolean bb; int ii; int ij; union things { float ival; char bytes[4]; } u; if (idata == NULL) { h5nullArgument( env, "floatToByte: idata is NULL?"); return NULL; } iarr = ENVPTR->GetFloatArrayElements(ENVPAR idata,&bb); if (iarr == NULL) { h5JNIFatalError( env, "floatToByte: getFloat failed?"); return NULL; } ilen = ENVPTR->GetArrayLength(ENVPAR idata); if ((start < 0) || (((start + len)) > ilen)) { ENVPTR->ReleaseFloatArrayElements(ENVPAR idata,iarr,JNI_ABORT); h5badArgument( env, "floatToByte: start or len is out of bounds"); return NULL; } ip = iarr + start; blen = ilen * sizeof(jfloat); rarray = ENVPTR->NewByteArray(ENVPAR blen); if (rarray == NULL) { ENVPTR->ReleaseFloatArrayElements(ENVPAR idata,iarr,JNI_ABORT); h5outOfMemory( env, "floatToByte" ); return NULL; } barray = ENVPTR->GetByteArrayElements(ENVPAR rarray,&bb); if (barray == NULL) { ENVPTR->ReleaseFloatArrayElements(ENVPAR idata,iarr,JNI_ABORT); h5JNIFatalError( env, "floatToByte: getByte failed?"); return NULL; } bap = barray; for (ii = 0; ii < len; ii++) { u.ival = *ip++; for (ij = 0; ij < sizeof(jfloat); ij++) { *bap = u.bytes[ij]; bap++; } } ENVPTR->ReleaseByteArrayElements(ENVPAR rarray,barray, 0); ENVPTR->ReleaseFloatArrayElements(ENVPAR idata,iarr,JNI_ABORT); return rarray; } /* returns byte [] */ JNIEXPORT jbyteArray JNICALL Java_ncsa_hdf_hdf5lib_HDFNativeData_doubleToByte__II_3D ( JNIEnv *env, jclass clss, jint start, jint len, jdoubleArray idata) /* IN: array of double */ { jdouble *ip; jdouble *iarr; int ilen; jbyteArray rarray; int blen; jbyte *barray; jbyte *bap; jboolean bb; int ii; int ij; union things { double ival; char bytes[8]; } u; if (idata == NULL) { h5nullArgument( env, "doubleToByte: idata is NULL?"); return NULL; } iarr = ENVPTR->GetDoubleArrayElements(ENVPAR idata,&bb); if (iarr == NULL) { h5JNIFatalError( env, "doubleToByte: getDouble failed?"); return NULL; } ilen = ENVPTR->GetArrayLength(ENVPAR idata); if ((start < 0) || (((start + len)) > ilen)) { ENVPTR->ReleaseDoubleArrayElements(ENVPAR idata,iarr,JNI_ABORT); h5badArgument( env, "doubleToByte: start or len is out of bounds"); return NULL; } ip = iarr + start; blen = ilen * sizeof(jdouble); rarray = ENVPTR->NewByteArray(ENVPAR blen); if (rarray == NULL) { ENVPTR->ReleaseDoubleArrayElements(ENVPAR idata,iarr,JNI_ABORT); h5outOfMemory( env, "doubleToByte" ); return NULL; } barray = ENVPTR->GetByteArrayElements(ENVPAR rarray,&bb); if (barray == NULL) { ENVPTR->ReleaseDoubleArrayElements(ENVPAR idata,iarr,JNI_ABORT); h5JNIFatalError( env, "doubleToByte: getByte failed?"); return NULL; } bap = barray; for (ii = 0; ii < len; ii++) { u.ival = *ip++; for (ij = 0; ij < sizeof(jdouble); ij++) { *bap = u.bytes[ij]; bap++; } } ENVPTR->ReleaseByteArrayElements(ENVPAR rarray,barray, 0); ENVPTR->ReleaseDoubleArrayElements(ENVPAR idata,iarr,JNI_ABORT); return rarray; } /* returns byte [] */ JNIEXPORT jbyteArray JNICALL Java_ncsa_hdf_hdf5lib_HDFNativeData_longToByte__II_3J ( JNIEnv *env, jclass clss, jint start, jint len, jlongArray idata) /* IN: array of long */ { jlong *ip; jlong *iarr; int ilen; jbyteArray rarray; int blen; jbyte *barray; jbyte *bap; jboolean bb; int ii; int ij; union things { jlong ival; char bytes[8]; } u; if (idata == NULL) { h5nullArgument( env, "longToByte: idata is NULL?"); return NULL; } iarr = ENVPTR->GetLongArrayElements(ENVPAR idata,&bb); if (iarr == NULL) { h5JNIFatalError( env, "longToByte: getLong failed?"); return NULL; } ilen = ENVPTR->GetArrayLength(ENVPAR idata); if ((start < 0) || (((start + len)) > ilen)) { ENVPTR->ReleaseLongArrayElements(ENVPAR idata,iarr,JNI_ABORT); h5badArgument( env, "longToByte: start or len is out of bounds?\n"); return NULL; } ip = iarr + start; blen = ilen * sizeof(jlong); rarray = ENVPTR->NewByteArray(ENVPAR blen); if (rarray == NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR idata,iarr,JNI_ABORT); h5outOfMemory( env, "longToByte" ); return NULL; } barray = ENVPTR->GetByteArrayElements(ENVPAR rarray,&bb); if (barray == NULL) { ENVPTR->ReleaseLongArrayElements(ENVPAR idata,iarr,JNI_ABORT); h5JNIFatalError( env, "longToByte: getByte failed?"); return NULL; } bap = barray; for (ii = 0; ii < len; ii++) { u.ival = *ip++; for (ij = 0; ij < sizeof(jlong); ij++) { *bap = u.bytes[ij]; bap++; } } ENVPTR->ReleaseByteArrayElements(ENVPAR rarray,barray, 0); ENVPTR->ReleaseLongArrayElements(ENVPAR idata,iarr,JNI_ABORT); return rarray; } /* returns byte [] */ JNIEXPORT jbyteArray JNICALL Java_ncsa_hdf_hdf5lib_HDFNativeData_intToByte__I ( JNIEnv *env, jclass clss, jint idata) /* IN: int */ { jbyteArray rarray; jbyte *barray; jbyte *bap; int ij; jboolean bb; union things { int ival; char bytes[sizeof(int)]; } u; rarray = ENVPTR->NewByteArray(ENVPAR sizeof(jint)); if (rarray == NULL) { h5outOfMemory( env, "intToByte" ); return NULL; } barray = ENVPTR->GetByteArrayElements(ENVPAR rarray,&bb); if (barray == NULL) { h5JNIFatalError( env, "intToByte: getByte failed?"); return NULL; } bap = barray; u.ival = idata; for (ij = 0; ij < sizeof(jint); ij++) { *bap = u.bytes[ij]; bap++; } ENVPTR->ReleaseByteArrayElements(ENVPAR rarray,barray, 0); return rarray; } /* returns byte [] */ JNIEXPORT jbyteArray JNICALL Java_ncsa_hdf_hdf5lib_HDFNativeData_floatToByte__F ( JNIEnv *env, jclass clss, jfloat idata) /* IN: int */ { jbyteArray rarray; jbyte *barray; jbyte *bap; jboolean bb; int ij; union things { float ival; char bytes[sizeof(float)]; } u; rarray = ENVPTR->NewByteArray(ENVPAR sizeof(jfloat)); if (rarray == NULL) { h5outOfMemory( env, "floatToByte" ); return NULL; } barray = ENVPTR->GetByteArrayElements(ENVPAR rarray,&bb); if (barray == NULL) { h5JNIFatalError( env, "floatToByte: getByte failed?"); return NULL; } bap = barray; u.ival = idata; for (ij = 0; ij < sizeof(jfloat); ij++) { *bap = u.bytes[ij]; bap++; } ENVPTR->ReleaseByteArrayElements(ENVPAR rarray,(jbyte *)barray, 0); return rarray; } /* returns byte [] */ JNIEXPORT jbyteArray JNICALL Java_ncsa_hdf_hdf5lib_HDFNativeData_shortToByte__S ( JNIEnv *env, jclass clss, jshort idata) /* IN: short */ { jbyteArray rarray; jbyte *barray; jbyte *bap; jboolean bb; int ij; union things { short ival; char bytes[sizeof(short)]; } u; rarray = ENVPTR->NewByteArray(ENVPAR sizeof(jshort)); if (rarray == NULL) { h5outOfMemory( env, "shortToByte" ); return NULL; } barray = ENVPTR->GetByteArrayElements(ENVPAR rarray,&bb); if (barray == NULL) { h5JNIFatalError( env, "shortToByte: getShort failed?"); return NULL; } bap = barray; u.ival = idata; for (ij = 0; ij < sizeof(jshort); ij++) { *bap = u.bytes[ij]; bap++; } ENVPTR->ReleaseByteArrayElements(ENVPAR rarray,(jbyte *)barray, 0); return rarray; } /* returns byte [] */ JNIEXPORT jbyteArray JNICALL Java_ncsa_hdf_hdf5lib_HDFNativeData_doubleToByte__D ( JNIEnv *env, jclass clss, jdouble idata) /* IN: double */ { jbyteArray rarray; jbyte *barray; jbyte *bap; jboolean bb; int ij; union things { double ival; char bytes[sizeof(double)]; } u; rarray = ENVPTR->NewByteArray(ENVPAR sizeof(jdouble)); if (rarray == NULL) { h5outOfMemory( env, "doubleToByte" ); return NULL; } barray = ENVPTR->GetByteArrayElements(ENVPAR rarray,&bb); if (barray == NULL) { h5JNIFatalError( env, "doubleToByte: getDouble failed?"); return NULL; } bap = barray; u.ival = idata; for (ij = 0; ij < sizeof(jdouble); ij++) { *bap = u.bytes[ij]; bap++; } ENVPTR->ReleaseByteArrayElements(ENVPAR rarray,(jbyte *)barray, 0); return rarray; } /* returns byte [] */ JNIEXPORT jbyteArray JNICALL Java_ncsa_hdf_hdf5lib_HDFNativeData_longToByte__J ( JNIEnv *env, jclass clss, jlong idata) /* IN: array of long */ { jbyteArray rarray; jbyte *barray; jbyte *bap; jboolean bb; int ij; union things { jlong ival; char bytes[sizeof(jlong)]; } u; rarray = ENVPTR->NewByteArray(ENVPAR sizeof(jlong)); if (rarray == NULL) { h5outOfMemory( env, "longToByte" ); return NULL; } barray = ENVPTR->GetByteArrayElements(ENVPAR rarray,&bb); if (barray == NULL) { h5JNIFatalError( env, "longToByte: getLong failed?"); return NULL; } bap = barray; u.ival = idata; for (ij = 0; ij < sizeof(jlong); ij++) { *bap = u.bytes[ij]; bap++; } ENVPTR->ReleaseByteArrayElements(ENVPAR rarray,(jbyte *)barray, 0); return rarray; } /* returns byte [] */ JNIEXPORT jbyteArray JNICALL Java_ncsa_hdf_hdf5lib_HDFNativeData_byteToByte__B ( JNIEnv *env, jclass clss, jbyte idata) /* IN: array of long */ { jbyteArray rarray; jbyte *barray; jbyte *bap; jboolean bb; int ij; union things { jbyte ival; char bytes[sizeof(jbyte)]; } u; rarray = ENVPTR->NewByteArray(ENVPAR sizeof(jbyte)); if (rarray == NULL) { h5outOfMemory( env, "byteToByte" ); return NULL; } barray = ENVPTR->GetByteArrayElements(ENVPAR rarray,&bb); if (barray == NULL) { h5JNIFatalError( env, "byteToByte: getByte failed?"); return NULL; } bap = barray; u.ival = idata; for (ij = 0; ij < sizeof(jbyte); ij++) { *bap = u.bytes[ij]; bap++; } ENVPTR->ReleaseByteArrayElements(ENVPAR rarray,(jbyte *)barray, 0); return rarray; } #ifdef __cplusplus } #endif libsis-jhdf5-java-14.12.1/source/c/hdf5_win_compile.diff000066400000000000000000000021001256564762100226600ustar00rootroot00000000000000diff -ruN hdf5-1.8.13.orig/compile_windows_i386.bat hdf5-1.8.13/compile_windows_i386.bat --- compile_windows_i386.bat 1970-01-01 01:00:00.000000000 +0100 +++ compile_windows_i386.bat 2013-06-22 00:04:09.000000000 +0200 @@ -0,0 +1,6 @@ +@echo off +rd /S /Q build +mkdir build +cd build +cmake -G "Visual Studio 9 2008" -DBUILD_SHARED_LIBS:BOOL=OFF -DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=ON -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING="TGZ" -DZLIB_TGZ_NAME:STRING="zlib-1.2.8.tar.gz" -DTGZPATH:STRING="u:/winbuild" .. +cmake --build . --config Release diff -ruN hdf5-1.8.13.orig/compile_windows_x64.bat hdf5-1.8.13/compile_windows_x64.bat --- compile_windows_x64.bat 1970-01-01 01:00:00.000000000 +0100 +++ compile_windows_x64.bat 2013-06-22 00:05:05.000000000 +0200 @@ -0,0 +1,6 @@ +@echo off +rd /S /Q build +mkdir build +cd build +cmake -G "Visual Studio 9 2008 Win64" -DBUILD_SHARED_LIBS:BOOL=OFF -DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=ON -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING="TGZ" -DZLIB_TGZ_NAME:STRING="zlib-1.2.8.tar.gz" -DTGZPATH:STRING="u:/winbuild" .. +cmake --build . --config Release libsis-jhdf5-java-14.12.1/source/c/hdf5_win_mt.diff000066400000000000000000002146321256564762100216670ustar00rootroot00000000000000Index: test/CMakeLists.txt =================================================================== --- test/CMakeLists.txt (revision 23770) +++ test/CMakeLists.txt (revision 23771) @@ -27,6 +27,7 @@ ) ADD_LIBRARY (${HDF5_TEST_LIB_TARGET} ${LIB_TYPE} ${TEST_LIB_SRCS} ${TEST_LIB_HEADERS}) +TARGET_C_PROPERTIES (${HDF5_TEST_LIB_TARGET} " " " ") IF (MSVC) TARGET_LINK_LIBRARIES (${HDF5_TEST_LIB_TARGET} "ws2_32.lib") ENDIF (MSVC) @@ -64,6 +65,7 @@ INCLUDE_DIRECTORIES (${HDF5_SRC_DIR}) ADD_LIBRARY (${HDF5_TEST_PLUGIN_LIB_TARGET} ${LIB_TYPE} ${HDF5_TEST_SOURCE_DIR}/${test_lib}.c) + TARGET_C_PROPERTIES (${HDF5_TEST_PLUGIN_LIB_TARGET} " " " ") TARGET_LINK_LIBRARIES (${HDF5_TEST_PLUGIN_LIB_TARGET} ${HDF5_TEST_LIB_TARGET}) H5_SET_LIB_OPTIONS ( ${HDF5_TEST_PLUGIN_LIB_TARGET} ${HDF5_TEST_PLUGIN_LIB_NAME} @@ -94,6 +96,7 @@ INCLUDE_DIRECTORIES (${HDF5_SRC_DIR}) ADD_LIBRARY (${HDF5_TEST_PLUGIN_LIB_TARGET} ${LIB_TYPE} ${HDF5_TEST_SOURCE_DIR}/${test_lib}.c) + TARGET_C_PROPERTIES (${HDF5_TEST_PLUGIN_LIB_TARGET} " " " ") TARGET_LINK_LIBRARIES (${HDF5_TEST_PLUGIN_LIB_TARGET} ${HDF5_TEST_LIB_TARGET}) H5_SET_LIB_OPTIONS ( ${HDF5_TEST_PLUGIN_LIB_TARGET} ${HDF5_TEST_PLUGIN_LIB_NAME} @@ -237,6 +240,7 @@ #-- Adding test for testhdf5 ADD_EXECUTABLE (testhdf5 ${testhdf5_SRCS}) TARGET_NAMING (testhdf5 ${LIB_TYPE}) +TARGET_C_PROPERTIES (testhdf5 " " " ") TARGET_LINK_LIBRARIES (testhdf5 ${HDF5_TEST_LIB_TARGET} ${HDF5_LIB_TARGET}) SET_TARGET_PROPERTIES (testhdf5 PROPERTIES FOLDER test) @@ -288,6 +292,7 @@ MACRO (ADD_H5_TEST file) ADD_EXECUTABLE (${file} ${HDF5_TEST_SOURCE_DIR}/${file}.c) TARGET_NAMING (${file} ${LIB_TYPE}) + TARGET_C_PROPERTIES (${file} " " " ") TARGET_LINK_LIBRARIES (${file} ${HDF5_TEST_LIB_TARGET} ${HDF5_LIB_TARGET}) SET_TARGET_PROPERTIES (${file} PROPERTIES FOLDER test) @@ -428,6 +433,7 @@ #-- Adding test for cache ADD_EXECUTABLE (cache ${HDF5_TEST_SOURCE_DIR}/cache.c ${HDF5_TEST_SOURCE_DIR}/cache_common.c) TARGET_NAMING (cache ${LIB_TYPE}) +TARGET_C_PROPERTIES (cache " " " ") TARGET_LINK_LIBRARIES (cache ${HDF5_LIB_TARGET} ${HDF5_TEST_LIB_TARGET}) SET_TARGET_PROPERTIES (cache PROPERTIES FOLDER test) ADD_TEST ( @@ -442,6 +448,7 @@ #-- Adding test for cache_api ADD_EXECUTABLE (cache_api ${HDF5_TEST_SOURCE_DIR}/cache_api.c ${HDF5_TEST_SOURCE_DIR}/cache_common.c) TARGET_NAMING (cache_api ${LIB_TYPE}) +TARGET_C_PROPERTIES (cache_api " " " ") TARGET_LINK_LIBRARIES (cache_api ${HDF5_LIB_TARGET} ${HDF5_TEST_LIB_TARGET}) SET_TARGET_PROPERTIES (cache_api PROPERTIES FOLDER test) @@ -463,6 +470,7 @@ ${HDF5_TEST_SOURCE_DIR}/ttsafe_acreate.c ) TARGET_NAMING (ttsafe ${LIB_TYPE}) +TARGET_C_PROPERTIES (ttsafe " " " ") TARGET_LINK_LIBRARIES (ttsafe ${HDF5_LIB_TARGET} ${HDF5_TEST_LIB_TARGET}) SET_TARGET_PROPERTIES (ttsafe PROPERTIES FOLDER test) @@ -482,6 +490,7 @@ IF (HDF5_ENABLE_DEPRECATED_SYMBOLS) ADD_EXECUTABLE (err_compat ${HDF5_TEST_SOURCE_DIR}/err_compat.c) TARGET_NAMING (err_compat ${LIB_TYPE}) + TARGET_C_PROPERTIES (err_compat " " " ") TARGET_LINK_LIBRARIES (err_compat ${HDF5_LIB_TARGET} ${HDF5_TEST_LIB_TARGET}) SET_TARGET_PROPERTIES (err_compat PROPERTIES FOLDER test) @@ -508,6 +517,7 @@ #-- Adding test for error_test ADD_EXECUTABLE (error_test ${HDF5_TEST_SOURCE_DIR}/error_test.c) TARGET_NAMING (error_test ${LIB_TYPE}) +TARGET_C_PROPERTIES (error_test " " " ") TARGET_LINK_LIBRARIES (error_test ${HDF5_LIB_TARGET} ${HDF5_TEST_LIB_TARGET}) SET_TARGET_PROPERTIES (error_test PROPERTIES FOLDER test) @@ -534,6 +544,7 @@ #-- Adding test for links_env ADD_EXECUTABLE (links_env ${HDF5_TEST_SOURCE_DIR}/links_env.c) TARGET_NAMING (links_env ${LIB_TYPE}) +TARGET_C_PROPERTIES (links_env " " " ") TARGET_LINK_LIBRARIES (links_env ${HDF5_LIB_TARGET} ${HDF5_TEST_LIB_TARGET}) SET_TARGET_PROPERTIES (links_env PROPERTIES FOLDER test) @@ -587,6 +598,7 @@ ADD_EXECUTABLE (plugin ${HDF5_TEST_SOURCE_DIR}/plugin.c) TARGET_NAMING (plugin ${LIB_TYPE}) + TARGET_C_PROPERTIES (plugin " " " ") TARGET_LINK_LIBRARIES (plugin ${HDF5_TEST_PLUGIN_LIB_TARGET}) SET_TARGET_PROPERTIES (plugin PROPERTIES FOLDER test) @@ -720,6 +732,7 @@ MACRO (ADD_H5_GENERATOR genfile) ADD_EXECUTABLE (${genfile} ${HDF5_TEST_SOURCE_DIR}/${genfile}.c) TARGET_NAMING (${genfile} ${LIB_TYPE}) + TARGET_C_PROPERTIES (${genfile} " " " ") TARGET_LINK_LIBRARIES (${genfile} ${HDF5_TEST_LIB_TARGET} ${HDF5_LIB_TARGET}) SET_TARGET_PROPERTIES (${genfile} PROPERTIES FOLDER generator/test) ENDMACRO (ADD_H5_GENERATOR genfile) Index: configure =================================================================== --- configure (revision 23770) +++ configure (revision 23771) @@ -31025,8 +31025,8 @@ ## Enable strict file format checks ## -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking Whether to perform strict file format checks" >&5 -$as_echo_n "checking Whether to perform strict file format checks... " >&6; }; +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether to perform strict file format checks" >&5 +$as_echo_n "checking whether to perform strict file format checks... " >&6; }; # Check whether --enable-strict-format-checks was given. if test "${enable_strict_format_checks+set}" = set; then : enableval=$enable_strict_format_checks; STRICT_CHECKS=$enableval @@ -31062,8 +31062,8 @@ ## ---------------------------------------------------------------------- ## Enable embedded library information ## -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking Whether to have library information embedded in the executables" >&5 -$as_echo_n "checking Whether to have library information embedded in the executables... " >&6; } +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether to have library information embedded in the executables" >&5 +$as_echo_n "checking whether to have library information embedded in the executables... " >&6; } # Check whether --enable-embedded-libinfo was given. if test "${enable_embedded_libinfo+set}" = set; then : enableval=$enable_embedded_libinfo; enable_embedded_libinfo=$enableval Index: testpar/CMakeLists.txt =================================================================== --- testpar/CMakeLists.txt (revision 23770) +++ testpar/CMakeLists.txt (revision 23771) @@ -28,6 +28,7 @@ #-- Adding test for testhdf5 ADD_EXECUTABLE (testphdf5 ${testphdf5_SRCS}) TARGET_NAMING (testphdf5 ${LIB_TYPE}) +TARGET_C_PROPERTIES (testphdf5 " " " ") TARGET_LINK_LIBRARIES (testphdf5 ${HDF5_TEST_LIB_TARGET} ${HDF5_LIB_TARGET} ${LINK_LIBS}) SET_TARGET_PROPERTIES (testphdf5 PROPERTIES FOLDER test/par) @@ -36,6 +37,7 @@ MACRO (ADD_H5P_TEST file) ADD_EXECUTABLE (${file} ${HDF5_TEST_PAR_SOURCE_DIR}/${file}.c) TARGET_NAMING (${file} ${LIB_TYPE}) + TARGET_C_PROPERTIES (${file} " " " ") TARGET_LINK_LIBRARIES (${file} ${HDF5_TEST_LIB_TARGET} ${HDF5_LIB_TARGET} ${LINK_LIBS}) SET_TARGET_PROPERTIES (${file} PROPERTIES FOLDER test/par) Index: src/CMakeLists.txt =================================================================== --- src/CMakeLists.txt (revision 23770) +++ src/CMakeLists.txt (revision 23771) @@ -614,6 +614,7 @@ # specific type checks inside #----------------------------------------------------------------------------- ADD_EXECUTABLE (H5detect ${HDF5_SRC_DIR}/H5detect.c) +TARGET_C_PROPERTIES (H5detect " " " ") IF (MSVC) TARGET_LINK_LIBRARIES (H5detect "ws2_32.lib") ENDIF (MSVC) @@ -627,6 +628,7 @@ ) ADD_EXECUTABLE (H5make_libsettings ${HDF5_SRC_DIR}/H5make_libsettings.c) +TARGET_C_PROPERTIES (H5make_libsettings " " " ") IF (MSVC) TARGET_LINK_LIBRARIES (H5make_libsettings "ws2_32.lib") ENDIF (MSVC) @@ -676,6 +678,7 @@ SET_SOURCE_FILES_PROPERTIES (${HDF5_BINARY_DIR}/H5overflow.h GENERATED) ADD_LIBRARY (${HDF5_LIB_TARGET} ${LIB_TYPE} ${common_SRCS} ${H5_PUBLIC_HEADERS} ${H5_PRIVATE_HEADERS}) +TARGET_C_PROPERTIES (${HDF5_LIB_TARGET} " " " ") TARGET_LINK_LIBRARIES (${HDF5_LIB_TARGET} ${LINK_LIBS}) IF (NOT WIN32) TARGET_LINK_LIBRARIES (${HDF5_LIB_TARGET} dl) Index: release_docs/USING_HDF5_CMake.txt =================================================================== --- release_docs/USING_HDF5_CMake.txt (revision 23770) +++ release_docs/USING_HDF5_CMake.txt (revision 23771) @@ -197,6 +197,7 @@ SET (example hdf_example) ADD_EXECUTABLE (${example} ${PROJECT_SOURCE_DIR}/${example}.c) +TARGET_C_PROPERTIES (${example} " " " ") TARGET_LINK_LIBRARIES (${example} ${LINK_LIBS}) ENABLE_TESTING () Index: tools/h5dump/testh5dump.sh.in =================================================================== --- tools/h5dump/testh5dump.sh.in (revision 23770) +++ tools/h5dump/testh5dump.sh.in (revision 23771) @@ -59,7 +59,9 @@ SRC_H5STAT_TESTFILES="$SRC_TOOLS/h5stat/testfiles" SRC_H5IMPORT_TESTFILES="$SRC_TOOLS/h5import/testfiles" +TEST_P_DIR=./testfiles TESTDIR=./testfiles/std +test -d $TEST_P_DIR || mkdir -p $TEST_P_DIR test -d $TESTDIR || mkdir -p $TESTDIR ###################################################################### @@ -272,6 +274,8 @@ $SRC_H5DUMP_TESTFILES/tnullspace.ddl $SRC_H5DUMP_TESTFILES/trawdatafile.ddl $SRC_H5DUMP_TESTFILES/trawdatafile.exp +$SRC_H5DUMP_TESTFILES/trawssetfile.ddl +$SRC_H5DUMP_TESTFILES/trawssetfile.exp $SRC_H5DUMP_TESTFILES/zerodim.ddl $SRC_H5DUMP_TESTFILES/tordergr1.ddl $SRC_H5DUMP_TESTFILES/tordergr2.ddl @@ -871,6 +875,7 @@ TOOLTEST2 trawdatafile.exp --enable-error-stack -y -o trawdatafile.txt packedbits.h5 TOOLTEST2 tnoddlfile.exp --enable-error-stack -O -y -o tnoddlfile.txt packedbits.h5 TOOLTEST2A twithddlfile.exp twithddl.exp --enable-error-stack --ddl=twithddl.txt -y -o twithddlfile.txt packedbits.h5 +TOOLTEST2 trawssetfile.exp --enable-error-stack -d "/dset1[1,1;;;]" -y -o trawssetfile.txt tdset.h5 # test for maximum display datasets TOOLTEST twidedisplay.ddl --enable-error-stack -w0 packedbits.h5 Index: tools/h5dump/testh5dumppbits.sh.in =================================================================== --- tools/h5dump/testh5dumppbits.sh.in (revision 23770) +++ tools/h5dump/testh5dumppbits.sh.in (revision 23771) @@ -64,7 +64,9 @@ SRC_H5STAT_TESTFILES="$SRC_TOOLS/h5stat/testfiles" SRC_H5IMPORT_TESTFILES="$SRC_TOOLS/h5import/testfiles" +TEST_P_DIR=./testfiles TESTDIR=./testfiles/pbits +test -d $TEST_P_DIR || mkdir -p $TEST_P_DIR test -d $TESTDIR || mkdir -p $TESTDIR ###################################################################### Index: tools/h5dump/testh5dumpxml.sh.in =================================================================== --- tools/h5dump/testh5dumpxml.sh.in (revision 23770) +++ tools/h5dump/testh5dumpxml.sh.in (revision 23771) @@ -50,7 +50,9 @@ SRC_H5STAT_TESTFILES="$SRC_TOOLS/h5stat/testfiles" SRC_H5IMPORT_TESTFILES="$SRC_TOOLS/h5import/testfiles" +TEST_P_DIR=./testfiles TESTDIR=./testfiles/xml +test -d $TEST_P_DIR || mkdir -p $TEST_P_DIR test -d $TESTDIR || mkdir -p $TESTDIR ###################################################################### Index: tools/h5dump/CMakeLists.txt =================================================================== --- tools/h5dump/CMakeLists.txt (revision 23770) +++ tools/h5dump/CMakeLists.txt (revision 23771) @@ -15,6 +15,7 @@ ${HDF5_TOOLS_H5DUMP_SOURCE_DIR}/h5dump_xml.c ) TARGET_NAMING (h5dump ${LIB_TYPE}) +TARGET_C_PROPERTIES (h5dump " " " ") TARGET_LINK_LIBRARIES (h5dump ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) SET_TARGET_PROPERTIES (h5dump PROPERTIES FOLDER tools) @@ -33,6 +34,7 @@ IF (HDF5_BUILD_GENERATORS AND NOT BUILD_SHARED_LIBS) ADD_EXECUTABLE (h5dumpgentest ${HDF5_TOOLS_H5DUMP_SOURCE_DIR}/h5dumpgentest.c) TARGET_NAMING (h5dumpgentest ${LIB_TYPE}) + TARGET_C_PROPERTIES (h5dumpgentest " " " ") TARGET_LINK_LIBRARIES (h5dumpgentest ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET}) SET_TARGET_PROPERTIES (h5dumpgentest PROPERTIES FOLDER generator/tools) @@ -147,6 +149,7 @@ ${HDF5_TOOLS_SRC_DIR}/testfiles/tno-subset.ddl ${HDF5_TOOLS_SRC_DIR}/testfiles/tnullspace.ddl ${HDF5_TOOLS_SRC_DIR}/testfiles/trawdatafile.ddl + ${HDF5_TOOLS_SRC_DIR}/testfiles/trawssetfile.ddl ${HDF5_TOOLS_SRC_DIR}/testfiles/zerodim.ddl ${HDF5_TOOLS_SRC_DIR}/testfiles/tordergr1.ddl ${HDF5_TOOLS_SRC_DIR}/testfiles/tordergr2.ddl @@ -198,6 +201,7 @@ tall-6.exp tnoddlfile.exp trawdatafile.exp + trawssetfile.exp tstr2bin2.exp tstr2bin6.exp twithddl.exp @@ -1250,6 +1254,9 @@ trawdatafile.out trawdatafile.out.err trawdatafile.txt + trawssetfile.out + trawssetfile.out.err + trawssetfile.txt tno-subset.out tno-subset.out.err tnullspace.out @@ -1365,7 +1372,8 @@ ADD_H5_TEST (tnoattrdata 0 --enable-error-stack -A -o tattr.h5) ADD_H5_TEST_EXPORT (trawdatafile packedbits.h5 0 --enable-error-stack -y -o) ADD_H5_TEST_EXPORT (tnoddlfile packedbits.h5 0 --enable-error-stack -O -y -o) - + ADD_H5_TEST_EXPORT (trawssetfile tdset.h5 0 --enable-error-stack -d "/dset1[1,1;;;]" -y -o) + ADD_H5_TEST_EXPORT_DDL (twithddlfile packedbits.h5 0 twithddl --enable-error-stack --ddl=twithddl.txt -y -o) # test for maximum display datasets Index: tools/h5repack/CMakeLists.txt =================================================================== --- tools/h5repack/CMakeLists.txt (revision 23770) +++ tools/h5repack/CMakeLists.txt (revision 23771) @@ -22,6 +22,7 @@ ADD_EXECUTABLE (h5repack ${REPACK_COMMON_SRCS} ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/h5repack_main.c) TARGET_NAMING (h5repack ${LIB_TYPE}) +TARGET_C_PROPERTIES (h5repack " " " ") TARGET_LINK_LIBRARIES (h5repack ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) SET_TARGET_PROPERTIES (h5repack PROPERTIES FOLDER tools) @@ -39,11 +40,13 @@ # -------------------------------------------------------------------- ADD_EXECUTABLE (testh5repack_detect_szip ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testh5repack_detect_szip.c) TARGET_NAMING (testh5repack_detect_szip ${LIB_TYPE}) + TARGET_C_PROPERTIES (testh5repack_detect_szip " " " ") TARGET_LINK_LIBRARIES (testh5repack_detect_szip ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET} ${HDF5_TEST_LIB_TARGET}) SET_TARGET_PROPERTIES (testh5repack_detect_szip PROPERTIES FOLDER tools) ADD_EXECUTABLE (h5repacktest ${REPACK_COMMON_SRCS} ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/h5repacktst.c) TARGET_NAMING (h5repacktest ${LIB_TYPE}) + TARGET_C_PROPERTIES (h5repacktest " " " ") TARGET_LINK_LIBRARIES (h5repacktest ${HDF5_TOOLS_LIB_TARGET} ${HDF5_TEST_LIB_TARGET}) SET_TARGET_PROPERTIES (h5repacktest PROPERTIES FOLDER tools) Index: tools/testfiles/trawssetfile.exp =================================================================== --- tools/testfiles/trawssetfile.exp (revision 0) +++ tools/testfiles/trawssetfile.exp (revision 23771) @@ -0,0 +1,2 @@ + + 2 \ No newline at end of file Index: tools/testfiles/trawssetfile.ddl =================================================================== --- tools/testfiles/trawssetfile.ddl (revision 0) +++ tools/testfiles/trawssetfile.ddl (revision 23771) @@ -0,0 +1,14 @@ +HDF5 "tdset.h5" { +DATASET "/dset1" { + DATATYPE H5T_STD_I32BE + DATASPACE SIMPLE { ( 10, 20 ) / ( 10, 20 ) } + SUBSET { + START ( 1, 1 ); + STRIDE ( 1, 1 ); + COUNT ( 1, 1 ); + BLOCK ( 1, 1 ); + DATA { + } + } +} +} Index: tools/h5jam/CMakeLists.txt =================================================================== --- tools/h5jam/CMakeLists.txt (revision 23770) +++ tools/h5jam/CMakeLists.txt (revision 23771) @@ -11,21 +11,25 @@ # -------------------------------------------------------------------- ADD_EXECUTABLE (h5jam ${HDF5_TOOLS_H5JAM_SOURCE_DIR}/h5jam.c) TARGET_NAMING (h5jam ${LIB_TYPE}) +TARGET_C_PROPERTIES (h5jam " " " ") TARGET_LINK_LIBRARIES (h5jam ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) SET_TARGET_PROPERTIES (h5jam PROPERTIES FOLDER tools) ADD_EXECUTABLE (getub ${HDF5_TOOLS_H5JAM_SOURCE_DIR}/getub.c) TARGET_NAMING (getub ${LIB_TYPE}) +TARGET_C_PROPERTIES (getub " " " ") TARGET_LINK_LIBRARIES (getub ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) SET_TARGET_PROPERTIES (getub PROPERTIES FOLDER tools) ADD_EXECUTABLE (tellub ${HDF5_TOOLS_H5JAM_SOURCE_DIR}/tellub.c) TARGET_NAMING (tellub ${LIB_TYPE}) +TARGET_C_PROPERTIES (tellub " " " ") TARGET_LINK_LIBRARIES (tellub ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) SET_TARGET_PROPERTIES (tellub PROPERTIES FOLDER tools) ADD_EXECUTABLE (h5unjam ${HDF5_TOOLS_H5JAM_SOURCE_DIR}/h5unjam.c) TARGET_NAMING (h5unjam ${LIB_TYPE}) +TARGET_C_PROPERTIES (h5unjam " " " ") TARGET_LINK_LIBRARIES (h5unjam ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) SET_TARGET_PROPERTIES (h5unjam PROPERTIES FOLDER tools) @@ -49,6 +53,7 @@ IF (HDF5_BUILD_GENERATORS AND NOT BUILD_SHARED_LIBS) ADD_EXECUTABLE (h5jamgentest ${HDF5_TOOLS_H5JAM_SOURCE_DIR}/h5jamgentest.c) TARGET_NAMING (h5jamgentest ${LIB_TYPE}) + TARGET_C_PROPERTIES (testhdf5 " " " ") TARGET_LINK_LIBRARIES (h5jamgentest ${HDF5_LIB_TARGET}) SET_TARGET_PROPERTIES (h5jamgentest PROPERTIES FOLDER generator/tools) Index: tools/h5diff/CMakeLists.txt =================================================================== --- tools/h5diff/CMakeLists.txt (revision 23770) +++ tools/h5diff/CMakeLists.txt (revision 23771) @@ -14,6 +14,7 @@ ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/h5diff_main.c ) TARGET_NAMING (h5diff ${LIB_TYPE}) +TARGET_C_PROPERTIES (h5diff " " " ") TARGET_LINK_LIBRARIES (h5diff ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) SET_TARGET_PROPERTIES (h5diff PROPERTIES FOLDER tools) @@ -25,6 +26,7 @@ ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/ph5diff_main.c ) TARGET_NAMING (ph5diff ${LIB_TYPE}) + TARGET_C_PROPERTIES (ph5diff " " " ") TARGET_LINK_LIBRARIES (ph5diff ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) SET_TARGET_PROPERTIES (ph5diff PROPERTIES FOLDER tools) ENDIF (H5_HAVE_PARALLEL) @@ -42,6 +44,7 @@ IF (HDF5_BUILD_GENERATORS AND NOT BUILD_SHARED_LIBS) ADD_EXECUTABLE (h5diffgentest ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/h5diffgentest.c) TARGET_NAMING (h5diffgentest ${LIB_TYPE}) + TARGET_C_PROPERTIES (h5diffgentest " " " ") TARGET_LINK_LIBRARIES (h5diffgentest ${HDF5_LIB_TARGET}) SET_TARGET_PROPERTIES (h5diffgentest PROPERTIES FOLDER generator/tools) Index: tools/lib/h5tools_dump.c =================================================================== --- tools/lib/h5tools_dump.c (revision 23770) +++ tools/lib/h5tools_dump.c (revision 23771) @@ -314,13 +314,13 @@ if (region_space >= 0) { if (h5tools_is_zero(memref, H5Tget_size(type))) { ctx->need_prefix = TRUE; - h5tools_simple_prefix(stream, info, ctx, curr_pos, 0); + h5tools_simple_prefix(rawoutstream, info, ctx, curr_pos, 0); /* Render the region element begin */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "NULL"); - dimension_break = h5tools_render_element(stream, info, + dimension_break = h5tools_render_element(rawoutstream, info, ctx, &buffer, &curr_pos, ncols, i, elmt_counter); } else { @@ -328,25 +328,25 @@ HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Rget_name failed"); ctx->need_prefix = TRUE; - h5tools_simple_prefix(stream, info, ctx, curr_pos+i, 0); + h5tools_simple_prefix(rawoutstream, info, ctx, curr_pos+i, 0); /* Render the region element begin */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, info->dset_format, ref_name); - dimension_break = h5tools_render_element(stream, info, + dimension_break = h5tools_render_element(rawoutstream, info, ctx, &buffer, &curr_pos, ncols, i, elmt_counter); region_type = H5Sget_select_type(region_space); if(region_type == H5S_SEL_POINTS) /* Print point information */ dimension_break = h5tools_dump_region_data_points( - region_space, region_id, stream, info, ctx, + region_space, region_id, rawoutstream, info, ctx, &buffer, &curr_pos, ncols, i, elmt_counter); else if(region_type == H5S_SEL_HYPERSLABS) /* Print block information */ dimension_break = h5tools_dump_region_data_blocks( - region_space, region_id, stream, info, ctx, + region_space, region_id, rawoutstream, info, ctx, &buffer, &curr_pos, ncols, i, elmt_counter); else HERROR(H5E_tools_g, H5E_tools_min_id_g, "invalid region type"); @@ -1790,7 +1790,7 @@ if(!sset) status = h5tools_dump_simple_dset(rawdatastream, info, ctx, dset, p_type); else - status = h5tools_dump_simple_subset(stream, info, ctx, dset, p_type, sset); + status = h5tools_dump_simple_subset(rawdatastream, info, ctx, dset, p_type, sset); } else /* space is H5S_NULL */ Index: tools/lib/CMakeLists.txt =================================================================== --- tools/lib/CMakeLists.txt (revision 23770) +++ tools/lib/CMakeLists.txt (revision 23771) @@ -37,8 +37,9 @@ ) ADD_LIBRARY (${HDF5_TOOLS_LIB_TARGET} ${LIB_TYPE} ${H5_TOOLS_LIB_SRCS} ${H5_TOOLS_LIB_HDRS}) +TARGET_C_PROPERTIES (${HDF5_TOOLS_LIB_TARGET} " " " ") TARGET_LINK_LIBRARIES (${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) -SET_GLOBAL_VARIABLE( HDF5_LIBRARIES_TO_EXPORT "${HDF5_LIBRARIES_TO_EXPORT};${HDF5_TOOLS_LIB_TARGET}") +SET_GLOBAL_VARIABLE (HDF5_LIBRARIES_TO_EXPORT "${HDF5_LIBRARIES_TO_EXPORT};${HDF5_TOOLS_LIB_TARGET}") H5_SET_LIB_OPTIONS ( ${HDF5_TOOLS_LIB_TARGET} ${HDF5_TOOLS_LIB_NAME} ${LIB_TYPE} Index: tools/h5copy/CMakeLists.txt =================================================================== --- tools/h5copy/CMakeLists.txt (revision 23770) +++ tools/h5copy/CMakeLists.txt (revision 23771) @@ -11,6 +11,7 @@ # -------------------------------------------------------------------- ADD_EXECUTABLE (h5copy ${HDF5_TOOLS_H5COPY_SOURCE_DIR}/h5copy.c) TARGET_NAMING (h5copy ${LIB_TYPE}) +TARGET_C_PROPERTIES (h5copy " " " ") TARGET_LINK_LIBRARIES (h5copy ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) SET_TARGET_PROPERTIES (h5copy PROPERTIES FOLDER tools) @@ -26,6 +27,7 @@ IF (HDF5_BUILD_GENERATORS AND NOT BUILD_SHARED_LIBS) ADD_EXECUTABLE (h5copygentest ${HDF5_TOOLS_H5COPY_SOURCE_DIR}/h5copygentest.c) TARGET_NAMING (h5copygentest ${LIB_TYPE}) + TARGET_C_PROPERTIES (h5copygentest " " " ") TARGET_LINK_LIBRARIES (h5copygentest ${HDF5_LIB_TARGET}) SET_TARGET_PROPERTIES (h5copygentest PROPERTIES FOLDER generator/tools) Index: tools/h5import/CMakeLists.txt =================================================================== --- tools/h5import/CMakeLists.txt (revision 23770) +++ tools/h5import/CMakeLists.txt (revision 23771) @@ -11,6 +11,7 @@ # -------------------------------------------------------------------- ADD_EXECUTABLE (h5import ${HDF5_TOOLS_H5IMPORT_SOURCE_DIR}/h5import.c) TARGET_NAMING (h5import ${LIB_TYPE}) +TARGET_C_PROPERTIES (h5import " " " ") TARGET_LINK_LIBRARIES (h5import ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) #SET_TARGET_PROPERTIES (h5import PROPERTIES COMPILE_DEFINITIONS H5DEBUGIMPORT) SET_TARGET_PROPERTIES (h5import PROPERTIES FOLDER tools) @@ -29,6 +30,7 @@ # -------------------------------------------------------------------- ADD_EXECUTABLE (h5importtest ${HDF5_TOOLS_H5IMPORT_SOURCE_DIR}/h5importtest.c) TARGET_NAMING (h5importtest ${LIB_TYPE}) + TARGET_C_PROPERTIES (h5importtest " " " ") TARGET_LINK_LIBRARIES (h5importtest ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET}) SET_TARGET_PROPERTIES (h5importtest PROPERTIES FOLDER tools) Index: tools/h5stat/CMakeLists.txt =================================================================== --- tools/h5stat/CMakeLists.txt (revision 23770) +++ tools/h5stat/CMakeLists.txt (revision 23771) @@ -11,6 +11,7 @@ # -------------------------------------------------------------------- ADD_EXECUTABLE (h5stat ${HDF5_TOOLS_H5STAT_SOURCE_DIR}/h5stat.c) TARGET_NAMING (h5stat ${LIB_TYPE}) +TARGET_C_PROPERTIES (h5stat " " " ") TARGET_LINK_LIBRARIES (h5stat ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) SET_TARGET_PROPERTIES (h5stat PROPERTIES FOLDER tools) @@ -29,6 +30,7 @@ IF (HDF5_BUILD_GENERATORS AND NOT BUILD_SHARED_LIBS) ADD_EXECUTABLE (h5stat_gentest ${HDF5_TOOLS_H5STAT_SOURCE_DIR}/h5stat_gentest.c) TARGET_NAMING (h5stat_gentest ${LIB_TYPE}) + TARGET_C_PROPERTIES (h5stat_gentest " " " ") TARGET_LINK_LIBRARIES (h5stat_gentest ${HDF5_LIB_TARGET}) SET_TARGET_PROPERTIES (h5stat_gentest PROPERTIES FOLDER generator/tools) Index: tools/h5ls/CMakeLists.txt =================================================================== --- tools/h5ls/CMakeLists.txt (revision 23770) +++ tools/h5ls/CMakeLists.txt (revision 23771) @@ -11,6 +11,7 @@ #----------------------------------------------------------------------------- ADD_EXECUTABLE (h5ls ${HDF5_TOOLS_H5LS_SOURCE_DIR}/h5ls.c) TARGET_NAMING (h5ls ${LIB_TYPE}) +TARGET_C_PROPERTIES (h5ls " " " ") TARGET_LINK_LIBRARIES (h5ls ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) SET_TARGET_PROPERTIES (h5ls PROPERTIES FOLDER tools) Index: tools/misc/CMakeLists.txt =================================================================== --- tools/misc/CMakeLists.txt (revision 23770) +++ tools/misc/CMakeLists.txt (revision 23771) @@ -12,16 +12,19 @@ #-- Misc Executables ADD_EXECUTABLE (h5debug ${HDF5_TOOLS_MISC_SOURCE_DIR}/h5debug.c) TARGET_NAMING (h5debug ${LIB_TYPE}) +TARGET_C_PROPERTIES (h5debug " " " ") TARGET_LINK_LIBRARIES (h5debug ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET}) SET_TARGET_PROPERTIES (h5debug PROPERTIES FOLDER tools) ADD_EXECUTABLE (h5repart ${HDF5_TOOLS_MISC_SOURCE_DIR}/h5repart.c) TARGET_NAMING (h5repart ${LIB_TYPE}) +TARGET_C_PROPERTIES (h5repart " " " ") TARGET_LINK_LIBRARIES (h5repart ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET}) SET_TARGET_PROPERTIES (h5repart PROPERTIES FOLDER tools) ADD_EXECUTABLE (h5mkgrp ${HDF5_TOOLS_MISC_SOURCE_DIR}/h5mkgrp.c) TARGET_NAMING (h5mkgrp ${LIB_TYPE}) +TARGET_C_PROPERTIES (h5mkgrp " " " ") TARGET_LINK_LIBRARIES (h5mkgrp ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) SET_TARGET_PROPERTIES (h5mkgrp PROPERTIES FOLDER tools) @@ -44,6 +47,7 @@ IF (HDF5_BUILD_GENERATORS AND NOT BUILD_SHARED_LIBS) ADD_EXECUTABLE (h5repart_gentest ${HDF5_TOOLS_MISC_SOURCE_DIR}/h5repart_gentest.c) TARGET_NAMING (h5repart_gentest ${LIB_TYPE}) + TARGET_C_PROPERTIES (h5repart_gentest " " " ") TARGET_LINK_LIBRARIES (h5repart_gentest ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET}) SET_TARGET_PROPERTIES (h5repart_gentest PROPERTIES FOLDER generator/tools) #ADD_TEST (NAME h5repart_gentest COMMAND $) @@ -51,6 +55,7 @@ ADD_EXECUTABLE (h5repart_test ${HDF5_TOOLS_MISC_SOURCE_DIR}/repart_test.c) TARGET_NAMING (h5repart_test ${LIB_TYPE}) + TARGET_C_PROPERTIES (h5repart_test " " " ") TARGET_LINK_LIBRARIES (h5repart_test ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET}) SET_TARGET_PROPERTIES (h5repart_test PROPERTIES FOLDER tools) Index: UserMacros.cmake =================================================================== --- UserMacros.cmake (revision 0) +++ UserMacros.cmake (revision 23771) @@ -0,0 +1,17 @@ +######################################################## +# Include file for user options +######################################################## + +#----------------------------------------------------------------------------- +# Option to Build with User Defined Values +#----------------------------------------------------------------------------- +MACRO (MACRO_USER_DEFINED_LIBS) + SET (USER_DEFINED_VALUE "FALSE") +ENDMACRO (MACRO_USER_DEFINED_LIBS) + +#------------------------------------------------------------------------------- +OPTION (BUILD_USER_DEFINED_LIBS "Build With User Defined Values" OFF) +IF (BUILD_USER_DEFINED_LIBS) + MACRO_USER_DEFINED_LIBS () +ENDIF (BUILD_USER_DEFINED_LIBS) + \ No newline at end of file Index: hl/test/CMakeLists.txt =================================================================== --- hl/test/CMakeLists.txt (revision 23770) +++ hl/test/CMakeLists.txt (revision 23771) @@ -23,6 +23,7 @@ MACRO (HL_ADD_TEST hl_name files) ADD_EXECUTABLE (hl_${hl_name} ${hl_name}.c) TARGET_NAMING (hl_${hl_name} ${LIB_TYPE}) + TARGET_C_PROPERTIES (hl_${hl_name} " " " ") TARGET_LINK_LIBRARIES (hl_${hl_name} ${HDF5_HL_LIB_TARGET} ${HDF5_LIB_TARGET} @@ -97,6 +98,7 @@ IF (HDF5_BUILD_GENERATORS AND NOT BUILD_SHARED_LIBS) ADD_EXECUTABLE (hl_gen_test_ds gen_test_ds.c) TARGET_NAMING (hl_gen_test_ds ${LIB_TYPE}) + TARGET_C_PROPERTIES (hl_gen_test_ds " " " ") TARGET_LINK_LIBRARIES (hl_gen_test_ds ${HDF5_HL_LIB_TARGET} ${HDF5_LIB_TARGET} Index: hl/tools/CMakeLists.txt =================================================================== --- hl/tools/CMakeLists.txt (revision 23770) +++ hl/tools/CMakeLists.txt (revision 23771) @@ -19,6 +19,7 @@ ADD_EXECUTABLE (gif2h5 ${GIF2H5_SRCS}) TARGET_NAMING (gif2h5 ${LIB_TYPE}) +TARGET_C_PROPERTIES (gif2h5 " " " ") TARGET_LINK_LIBRARIES (gif2h5 ${HDF5_HL_LIB_TARGET} ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET}) SET_TARGET_PROPERTIES (gif2h5 PROPERTIES FOLDER tools/hl) @@ -29,6 +30,7 @@ ) ADD_EXECUTABLE (h52gif ${hdf2gif_SRCS}) TARGET_NAMING (h52gif ${LIB_TYPE}) +TARGET_C_PROPERTIES (h52gif " " " ") TARGET_LINK_LIBRARIES (h52gif ${HDF5_HL_LIB_TARGET} ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET}) SET_TARGET_PROPERTIES (h52gif PROPERTIES FOLDER tools/hl) @@ -40,6 +42,7 @@ IF (HDF5_BUILD_GENERATORS AND NOT BUILD_SHARED_LIBS) ADD_EXECUTABLE (hl_h52gifgentest ${HDF5_HL_TOOLS_SOURCE_DIR}/gif2h5/h52gifgentst.c) TARGET_NAMING (hl_h52gifgentest ${LIB_TYPE}) + TARGET_C_PROPERTIES (hl_h52gifgentest " " " ") TARGET_LINK_LIBRARIES (hl_h52gifgentest ${HDF5_HL_LIB_TARGET} ${HDF5_LIB_TARGET}) SET_TARGET_PROPERTIES (hl_h52gifgentest PROPERTIES FOLDER generator/tools/hl) Index: hl/src/CMakeLists.txt =================================================================== --- hl/src/CMakeLists.txt (revision 23770) +++ hl/src/CMakeLists.txt (revision 23771) @@ -36,6 +36,7 @@ ) ADD_LIBRARY (${HDF5_HL_LIB_TARGET} ${LIB_TYPE} ${HL_SRCS} ${HL_HEADERS}) +TARGET_C_PROPERTIES (${HDF5_HL_LIB_TARGET} " " " ") TARGET_LINK_LIBRARIES (${HDF5_HL_LIB_TARGET} ${HDF5_LIB_TARGET}) SET_GLOBAL_VARIABLE (HDF5_LIBRARIES_TO_EXPORT "${HDF5_LIBRARIES_TO_EXPORT};${HDF5_HL_LIB_TARGET}") H5_SET_LIB_OPTIONS (${HDF5_HL_LIB_TARGET} ${HDF5_HL_LIB_NAME} ${LIB_TYPE}) Index: hl/c++/test/CMakeLists.txt =================================================================== --- hl/c++/test/CMakeLists.txt (revision 23770) +++ hl/c++/test/CMakeLists.txt (revision 23771) @@ -17,6 +17,7 @@ INCLUDE_DIRECTORIES (${HDF5_CPP_SRC_DIR}/src) ADD_EXECUTABLE (hl_ptableTest ${HDF5_HL_CPP_TEST_SOURCE_DIR}/ptableTest.cpp) + TARGET_C_PROPERTIES (hl_ptableTest " " " ") TARGET_NAMING (hl_ptableTest ${LIB_TYPE}) TARGET_LINK_LIBRARIES ( hl_ptableTest Index: hl/c++/src/CMakeLists.txt =================================================================== --- hl/c++/src/CMakeLists.txt (revision 23770) +++ hl/c++/src/CMakeLists.txt (revision 23771) @@ -10,7 +10,8 @@ SET (HDF5_HL_CPP_SRCS ${HDF5_HL_CPP_SRC_SOURCE_DIR}/H5PacketTable.cpp) SET (HDF5_HL_CPP_HDRS ${HDF5_HL_CPP_SRC_SOURCE_DIR}/H5PacketTable.h) -ADD_LIBRARY ( ${HDF5_HL_CPP_LIB_TARGET} ${LIB_TYPE} ${HDF5_HL_CPP_SRCS}) +ADD_LIBRARY (${HDF5_HL_CPP_LIB_TARGET} ${LIB_TYPE} ${HDF5_HL_CPP_SRCS}) +TARGET_C_PROPERTIES (${HDF5_HL_CPP_LIB_TARGET} " " " ") TARGET_LINK_LIBRARIES ( ${HDF5_HL_CPP_LIB_TARGET} ${HDF5_HL_LIB_TARGET} Index: hl/c++/examples/CMakeLists.txt =================================================================== --- hl/c++/examples/CMakeLists.txt (revision 23770) +++ hl/c++/examples/CMakeLists.txt (revision 23771) @@ -12,6 +12,7 @@ # -------------------------------------------------------------------- ADD_EXECUTABLE (ptExampleFL ${HDF5_HL_CPP_EXAMPLES_SOURCE_DIR}/ptExampleFL.cpp) TARGET_NAMING (ptExampleFL ${LIB_TYPE}) +TARGET_C_PROPERTIES (ptExampleFL " " " ") TARGET_LINK_LIBRARIES ( ptExampleFL ${HDF5_HL_CPP_LIB_TARGET} Index: hl/fortran/test/CMakeLists.txt =================================================================== --- hl/fortran/test/CMakeLists.txt (revision 23770) +++ hl/fortran/test/CMakeLists.txt (revision 23771) @@ -23,7 +23,7 @@ #-- Adding test for hl_f90_tstds ADD_EXECUTABLE (hl_f90_tstds tstds.f90) TARGET_NAMING (hl_f90_tstds ${LIB_TYPE}) -TARGET_FORTRAN_WIN_PROPERTIES (hl_f90_tstds "") +TARGET_FORTRAN_PROPERTIES (hl_f90_tstds " " " ") TARGET_LINK_LIBRARIES (hl_f90_tstds ${HDF5_HL_F90_LIB_TARGET} ${HDF5_F90_LIB_TARGET}) SET_TARGET_PROPERTIES (hl_f90_tstds PROPERTIES LINKER_LANGUAGE Fortran) SET_TARGET_PROPERTIES (hl_f90_tstds PROPERTIES FOLDER test/hl/fortran) @@ -33,7 +33,7 @@ #-- Adding test for hl_f90_tstlite ADD_EXECUTABLE (hl_f90_tstlite tstlite.f90) TARGET_NAMING (hl_f90_tstlite ${LIB_TYPE}) -TARGET_FORTRAN_WIN_PROPERTIES (hl_f90_tstlite "") +TARGET_FORTRAN_PROPERTIES (hl_f90_tstlite " " " ") TARGET_LINK_LIBRARIES (hl_f90_tstlite ${HDF5_HL_F90_LIB_TARGET} ${HDF5_F90_LIB_TARGET}) SET_TARGET_PROPERTIES (hl_f90_tstlite PROPERTIES LINKER_LANGUAGE Fortran) SET_TARGET_PROPERTIES (hl_f90_tstlite PROPERTIES FOLDER test/hl/fortran) @@ -43,7 +43,7 @@ #-- Adding test for hl_f90_tstimage ADD_EXECUTABLE (hl_f90_tstimage tstimage.f90) TARGET_NAMING (hl_f90_tstimage ${LIB_TYPE}) -TARGET_FORTRAN_WIN_PROPERTIES (hl_f90_tstimage "") +TARGET_FORTRAN_PROPERTIES (hl_f90_tstimage " " " ") TARGET_LINK_LIBRARIES (hl_f90_tstimage ${HDF5_HL_F90_LIB_TARGET} ${HDF5_F90_LIB_TARGET}) SET_TARGET_PROPERTIES (hl_f90_tstimage PROPERTIES LINKER_LANGUAGE Fortran) SET_TARGET_PROPERTIES (hl_f90_tstimage PROPERTIES FOLDER test/hl/fortran) @@ -53,7 +53,7 @@ #-- Adding test for hl_f90_tsttable ADD_EXECUTABLE (hl_f90_tsttable tsttable.f90) TARGET_NAMING (hl_f90_tsttable ${LIB_TYPE}) -TARGET_FORTRAN_WIN_PROPERTIES (hl_f90_tsttable "") +TARGET_FORTRAN_PROPERTIES (hl_f90_tsttable " " " ") TARGET_LINK_LIBRARIES (hl_f90_tsttable ${HDF5_HL_F90_LIB_TARGET} ${HDF5_F90_LIB_TARGET}) SET_TARGET_PROPERTIES (hl_f90_tsttable PROPERTIES LINKER_LANGUAGE Fortran) SET_TARGET_PROPERTIES (hl_f90_tsttable PROPERTIES FOLDER test/hl/fortran) Index: hl/fortran/src/CMakeLists.txt =================================================================== --- hl/fortran/src/CMakeLists.txt (revision 23770) +++ hl/fortran/src/CMakeLists.txt (revision 23771) @@ -26,6 +26,7 @@ SET (HDF5_HL_F90_HEADERS ${HDF5_HL_F90_SRC_SOURCE_DIR}/H5LTf90proto.h) ADD_LIBRARY (${HDF5_HL_F90_C_LIB_TARGET} ${LIB_TYPE} ${HDF5_HL_F90_C_SRCS} ${HDF5_HL_F90_HEADERS}) +TARGET_C_PROPERTIES (${HDF5_HL_F90_C_LIB_TARGET} " " " ") TARGET_LINK_LIBRARIES (${HDF5_HL_F90_C_LIB_TARGET} ${HDF5_F90_C_LIB_TARGET} ${HDF5_HL_LIB_TARGET}) SET_GLOBAL_VARIABLE (HDF5_LIBRARIES_TO_EXPORT "${HDF5_LIBRARIES_TO_EXPORT};${HDF5_HL_F90_C_LIB_TARGET}") H5_SET_LIB_OPTIONS (${HDF5_HL_F90_C_LIB_TARGET} ${HDF5_HL_F90_C_LIB_NAME} ${LIB_TYPE}) @@ -61,7 +62,7 @@ HDF5F90_WINDOWS ) ENDIF (WIN32 AND NOT CYGWIN) -TARGET_FORTRAN_WIN_PROPERTIES (${HDF5_HL_F90_LIB_TARGET} ${SHARED_LINK_FLAGS}) +TARGET_FORTRAN_PROPERTIES (${HDF5_HL_F90_LIB_TARGET} " " ${SHARED_LINK_FLAGS}) SET_TARGET_PROPERTIES (${HDF5_HL_F90_LIB_TARGET} PROPERTIES LINKER_LANGUAGE Fortran) TARGET_LINK_LIBRARIES (${HDF5_HL_F90_LIB_TARGET} ${HDF5_HL_F90_C_LIB_TARGET} ${HDF5_F90_LIB_TARGET}) SET_GLOBAL_VARIABLE (HDF5_LIBRARIES_TO_EXPORT "${HDF5_LIBRARIES_TO_EXPORT};${HDF5_HL_F90_LIB_TARGET}") Index: hl/fortran/examples/CMakeLists.txt =================================================================== --- hl/fortran/examples/CMakeLists.txt (revision 23770) +++ hl/fortran/examples/CMakeLists.txt (revision 23771) @@ -18,7 +18,7 @@ FOREACH (example ${examples}) ADD_EXECUTABLE (hl_f90_ex_${example} ${HDF5_HL_F90_EXAMPLES_SOURCE_DIR}/${example}.f90) TARGET_NAMING (hl_f90_ex_${example} ${LIB_TYPE}) - TARGET_FORTRAN_WIN_PROPERTIES (hl_f90_ex_${example} "") + TARGET_FORTRAN_PROPERTIES (hl_f90_ex_${example} " " " ") TARGET_LINK_LIBRARIES (hl_f90_ex_${example} ${HDF5_HL_F90_LIB_TARGET} ${HDF5_F90_LIB_TARGET} Index: hl/examples/CMakeLists.txt =================================================================== --- hl/examples/CMakeLists.txt (revision 23770) +++ hl/examples/CMakeLists.txt (revision 23771) @@ -43,6 +43,7 @@ FOREACH (example ${examples}) ADD_EXECUTABLE (hl_ex_${example} ${HDF5_HL_EXAMPLES_SOURCE_DIR}/${example}.c) TARGET_NAMING (hl_ex_${example} ${LIB_TYPE}) + TARGET_C_PROPERTIES (hl_ex_${example} " " " ") TARGET_LINK_LIBRARIES (hl_ex_${example} ${HDF5_HL_LIB_TARGET} ${HDF5_LIB_TARGET}) SET_TARGET_PROPERTIES (hl_ex_${example} PROPERTIES FOLDER examples/hl) Index: configure.ac =================================================================== --- configure.ac (revision 23770) +++ configure.ac (revision 23771) @@ -4305,7 +4305,7 @@ ## Enable strict file format checks ## AC_SUBST([STRICT_FORMAT_CHECKS]) -AC_MSG_CHECKING([Whether to perform strict file format checks]); +AC_MSG_CHECKING([whether to perform strict file format checks]); AC_ARG_ENABLE([strict-format-checks], [AS_HELP_STRING([--enable-strict-format-checks], [Enable strict file format checks, default=yes if @@ -4338,7 +4338,7 @@ ## ---------------------------------------------------------------------- ## Enable embedded library information ## -AC_MSG_CHECKING([Whether to have library information embedded in the executables]) +AC_MSG_CHECKING([whether to have library information embedded in the executables]) AC_ARG_ENABLE([embedded-libinfo], [AS_HELP_STRING([--enable-embedded-libinfo], [Enable embedded library information [default=yes]])], Index: config/cmake/ConfigureChecks.cmake =================================================================== --- config/cmake/ConfigureChecks.cmake (revision 23770) +++ config/cmake/ConfigureChecks.cmake (revision 23771) @@ -183,15 +183,15 @@ ENDIF (MINGW) SET (H5_HAVE_LIBWS2_32 1) SET (H5_HAVE_LIBWSOCK32 1) + + #----------------------------------------------------------------------------- + # These tests need to be manually SET for windows since there is currently + # something not quite correct with the actual test implementation. This affects + # the 'dt_arith' test and most likely lots of other code + # ---------------------------------------------------------------------------- + SET (H5_FP_TO_ULLONG_RIGHT_MAXIMUM "" CACHE INTERNAL "") ENDIF (WINDOWS) -#----------------------------------------------------------------------------- -# These tests need to be manually SET for windows since there is currently -# something not quite correct with the actual test implementation. This affects -# the 'dt_arith' test and most likely lots of other code -# ---------------------------------------------------------------------------- -SET (H5_FP_TO_ULLONG_RIGHT_MAXIMUM "" CACHE INTERNAL "") - # ---------------------------------------------------------------------- # END of WINDOWS Hard code Values # ---------------------------------------------------------------------- @@ -1029,7 +1029,9 @@ # integers except 'unsigned long long'. Other HP-UX systems are unknown # yet. (1/8/05 - SLU) # -H5ConversionTests (H5_LDOUBLE_TO_INTEGER_WORKS "Checking IF converting from long double to integers works") +IF (NOT MSVC) + H5ConversionTests (H5_LDOUBLE_TO_INTEGER_WORKS "Checking IF converting from long double to integers works") +ENDIF (NOT MSVC) # ----------------------------------------------------------------------- # Set flag to indicate that the machine can handle conversion from # integers to long double. (This flag should be set "yes" for all @@ -1103,7 +1105,9 @@ # where the last 2 bytes of mantissa are lost when compiler tries to do # the conversion, and Cygwin where compiler doesn't do rounding correctly.) # -H5ConversionTests (H5_ULLONG_TO_LDOUBLE_PRECISION "Checking IF converting unsigned long long to long double with precision") +IF (NOT MSVC) + H5ConversionTests (H5_ULLONG_TO_LDOUBLE_PRECISION "Checking IF converting unsigned long long to long double with precision") +ENDIF (NOT MSVC) # ---------------------------------------------------------------------- # Set the flag to indicate that the machine can handle overflow converting # all floating-point to all integer types. Index: config/cmake/HDFMacros.cmake =================================================================== --- config/cmake/HDFMacros.cmake (revision 23770) +++ config/cmake/HDFMacros.cmake (revision 23771) @@ -121,20 +121,67 @@ ENDMACRO (HDF_SET_LIB_OPTIONS) #------------------------------------------------------------------------------- -MACRO (TARGET_FORTRAN_WIN_PROPERTIES forttarget addlinkflags) - IF (WIN32 AND MSVC) +MACRO (TARGET_C_PROPERTIES wintarget addcompileflags addlinkflags) + IF (MSVC) + TARGET_MSVC_PROPERTIES (${wintarget} "${addcompileflags} ${WIN_COMPILE_FLAGS}" "${addlinkflags} ${WIN_LINK_FLAGS}") + ELSE (MSVC) IF (BUILD_SHARED_LIBS) + SET_TARGET_PROPERTIES (${wintarget} + PROPERTIES + COMPILE_FLAGS "${addcompileflags}" + LINK_FLAGS "${addlinkflags}" + ) + ELSE (BUILD_SHARED_LIBS) + SET_TARGET_PROPERTIES (${wintarget} + PROPERTIES + COMPILE_FLAGS "${addcompileflags}" + LINK_FLAGS "${addlinkflags}" + ) + ENDIF (BUILD_SHARED_LIBS) + ENDIF (MSVC) +ENDMACRO (TARGET_C_PROPERTIES) + +#------------------------------------------------------------------------------- +MACRO (TARGET_MSVC_PROPERTIES wintarget addcompileflags addlinkflags) + IF (MSVC) + IF (BUILD_SHARED_LIBS) + SET_TARGET_PROPERTIES (${wintarget} + PROPERTIES + COMPILE_FLAGS "/dll ${addcompileflags}" + LINK_FLAGS "/SUBSYSTEM:CONSOLE ${addlinkflags}" + ) + ELSE (BUILD_SHARED_LIBS) + SET_TARGET_PROPERTIES (${wintarget} + PROPERTIES + COMPILE_FLAGS "${addcompileflags}" + LINK_FLAGS "/SUBSYSTEM:CONSOLE ${addlinkflags}" + ) + ENDIF (BUILD_SHARED_LIBS) + ENDIF (MSVC) +ENDMACRO (TARGET_MSVC_PROPERTIES) + +#------------------------------------------------------------------------------- +MACRO (TARGET_FORTRAN_PROPERTIES forttarget addcompileflags addlinkflags) + IF (WIN32) + TARGET_FORTRAN_WIN_PROPERTIES (${forttarget} "${addcompileflags} ${WIN_COMPILE_FLAGS}" "${addlinkflags} ${WIN_LINK_FLAGS}") + ENDIF (WIN32) +ENDMACRO (TARGET_FORTRAN_PROPERTIES) + +#------------------------------------------------------------------------------- +MACRO (TARGET_FORTRAN_WIN_PROPERTIES forttarget addcompileflags addlinkflags) + IF (MSVC) + IF (BUILD_SHARED_LIBS) SET_TARGET_PROPERTIES (${forttarget} PROPERTIES - COMPILE_FLAGS "/dll" + COMPILE_FLAGS "/dll ${addcompileflags}" LINK_FLAGS "/SUBSYSTEM:CONSOLE ${addlinkflags}" ) ELSE (BUILD_SHARED_LIBS) SET_TARGET_PROPERTIES (${forttarget} PROPERTIES - COMPILE_FLAGS "/MD" + COMPILE_FLAGS "${addcompileflags}" LINK_FLAGS "/SUBSYSTEM:CONSOLE ${addlinkflags}" ) ENDIF (BUILD_SHARED_LIBS) - ENDIF (WIN32 AND MSVC) + ENDIF (MSVC) ENDMACRO (TARGET_FORTRAN_WIN_PROPERTIES) Index: config/cmake/UserMacros/Windows_MT.cmake =================================================================== --- config/cmake/UserMacros/Windows_MT.cmake (revision 0) +++ config/cmake/UserMacros/Windows_MT.cmake (revision 23771) @@ -0,0 +1,39 @@ +######################################################## +# Include file for user options +######################################################## + +# To use this option, copy both the macro and option code +# into the root UserMacros.cmake file. + +#----------------------------------------------------------------------------- +# Option to Build with Static CRT libraries on Windows +#------------------------------------------------------------------------------- +MACRO (TARGET_STATIC_CRT_FLAGS) + IF (MSVC AND NOT BUILD_SHARED_LIBS) + FOREACH (flag_var + CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE + CMAKE_C_FLAGS_MINSIZEREL CMAKE_C_FLAGS_RELWITHDEBINFO + CMAKE_CXX_FLAGS CMAKE_CXX_FLAGS_DEBUG CMAKE_CXX_FLAGS_RELEASE + CMAKE_CXX_FLAGS_MINSIZEREL CMAKE_CXX_FLAGS_RELWITHDEBINFO) + IF (${flag_var} MATCHES "/MD") + STRING (REGEX REPLACE "/MD" "/MT" ${flag_var} "${${flag_var}}") + ENDIF (${flag_var} MATCHES "/MD") + ENDFOREACH (flag_var) + FOREACH (flag_var + CMAKE_Fortran_FLAGS CMAKE_Fortran_FLAGS_DEBUG CMAKE_Fortran_FLAGS_RELEASE + CMAKE_Fortran_FLAGS_MINSIZEREL CMAKE_Fortran_FLAGS_RELWITHDEBINFO) + IF (${flag_var} MATCHES "/libs:dll") + STRING (REGEX REPLACE "/libs:dll" "/libs:static" ${flag_var} "${${flag_var}}") + ENDIF (${flag_var} MATCHES "/libs:dll") + ENDFOREACH (flag_var) + SET (WIN_COMPILE_FLAGS "/MT") + SET (WIN_LINK_FLAGS "/NODEFAULTLIB:MSVCRT") + ENDIF (MSVC AND NOT BUILD_SHARED_LIBS) +ENDMACRO (TARGET_STATIC_CRT_FLAGS) + +#----------------------------------------------------------------------------- +OPTION (BUILD_STATIC_CRT_LIBS "Build With Static CRT Libraries" OFF) +IF (BUILD_STATIC_CRT_LIBS) + TARGET_STATIC_CRT_FLAGS () +ENDIF (BUILD_STATIC_CRT_LIBS) + \ No newline at end of file Index: MANIFEST =================================================================== --- MANIFEST (revision 23770) +++ MANIFEST (revision 23771) @@ -1361,6 +1361,8 @@ ./tools/testfiles/topaque.h5 ./tools/testfiles/trawdatafile.ddl ./tools/testfiles/trawdatafile.exp +./tools/testfiles/trawssetfile.ddl +./tools/testfiles/trawssetfile.exp ./tools/testfiles/tsaf.ddl ./tools/testfiles/tsaf.h5 ./tools/testfiles/tscalarattrintsize.ddl @@ -2243,8 +2245,12 @@ ./config/cmake/NSIS.template.in ./config/cmake/NSIS.InstallOptions.ini.in +# CMake-specific User Files +./config/cmake/UserMacros/Windows_MT.cmake + ./CMakeLists.txt ./CTestConfig.cmake +./UserMacros.cmake ./c++/CMakeLists.txt ./c++/examples/CMakeLists.txt ./c++/src/CMakeLists.txt Index: c++/test/CMakeLists.txt =================================================================== --- c++/test/CMakeLists.txt (revision 23770) +++ c++/test/CMakeLists.txt (revision 23771) @@ -37,6 +37,7 @@ ADD_EXECUTABLE (cpp_testhdf5 ${CPP_TEST_SRCS} ) TARGET_NAMING (cpp_testhdf5 ${LIB_TYPE}) +TARGET_C_PROPERTIES (cpp_testhdf5 " " " ") TARGET_LINK_LIBRARIES (cpp_testhdf5 ${HDF5_CPP_LIB_TARGET} ${HDF5_LIB_TARGET} Index: c++/src/CMakeLists.txt =================================================================== --- c++/src/CMakeLists.txt (revision 23770) +++ c++/src/CMakeLists.txt (revision 23771) @@ -82,6 +82,7 @@ ) ADD_LIBRARY (${HDF5_CPP_LIB_TARGET} ${LIB_TYPE} ${CPP_SRCS} ${CPP_HDRS}) +TARGET_C_PROPERTIES (${HDF5_CPP_LIB_TARGET} " " " ") TARGET_LINK_LIBRARIES (${HDF5_CPP_LIB_TARGET} ${HDF5_LIB_TARGET}) SET_GLOBAL_VARIABLE (HDF5_LIBRARIES_TO_EXPORT "${HDF5_LIBRARIES_TO_EXPORT};${HDF5_CPP_LIB_TARGET}") H5_SET_LIB_OPTIONS (${HDF5_CPP_LIB_TARGET} ${HDF5_CPP_LIB_NAME} ${LIB_TYPE}) Index: c++/examples/CMakeLists.txt =================================================================== --- c++/examples/CMakeLists.txt (revision 23770) +++ c++/examples/CMakeLists.txt (revision 23771) @@ -23,6 +23,7 @@ FOREACH (example ${examples}) ADD_EXECUTABLE (cpp_ex_${example} ${HDF5_CPP_EXAMPLES_SOURCE_DIR}/${example}.cpp) TARGET_NAMING (cpp_ex_${example} ${LIB_TYPE}) + TARGET_C_PROPERTIES (cpp_ex_${example} " " " ") TARGET_LINK_LIBRARIES (cpp_ex_${example} ${HDF5_CPP_LIB_TARGET} ${HDF5_LIB_TARGET}) SET_TARGET_PROPERTIES (cpp_ex_${example} PROPERTIES FOLDER examples/cpp) ENDFOREACH (example ${examples}) Index: bin/reconfigure.system =================================================================== --- bin/reconfigure.system (revision 0) +++ bin/reconfigure.system (revision 23771) @@ -0,0 +1,143 @@ +#! /bin/sh +# +# Copyright by the Board of Trustees of the University of Illinois. +# All rights reserved. +# +# This file is part of HDF5. The full HDF5 copyright notice, including +# terms governing use, modification, and redistribution, is contained in +# the files COPYING and Copyright.html. COPYING can be found at the root +# of the source code distribution tree; Copyright.html can be found at the +# root level of an installed copy of the electronic HDF5 document set and +# is linked from the top-level documents page. It can also be found at +# http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have +# access to either file, you may request a copy from help@hdfgroup.org. +# + +# A script to reconfigure autotools for HDF5, and to recreate other +# generated files specifc to HDF5. +# If the paths of the autotools are not specified by the user, they +# are hardcoded to point to their locations on HDF5 Linux machines. +# Users can specify the locations of the autotools with the following +# variables: +# AUTOCONF, AUTOMAKE, ACLOCAL, AUTOHEADER should be the path to the +# corresponding tools. +# LIBTOOL_DIR should be the path to the base libtool directory; +# $LIBTOOL_DIR/bin/libtool should invoke libtool, while +# $LIBTOOL_DIR/share/aclocal needs to be included by aclocal. +# Be very careful when specifying these tools manually! There are a lot +# of versions that can get confused (not even counting the m4 utility)! + +# HDF5 currently uses the following versions of the autotools: +AUTOCONF_VERSION="autoconf (GNU Autoconf) 2.69" +AUTOMAKE_VERSION="automake (GNU automake) 1.12.3" +AUTOHEADER_VERSION="autoheader (GNU Autoconf) 2.69" +ACLOCAL_VERSION="aclocal (GNU automake) 1.12.3" +LIBTOOL_VERSION="(GNU libtool) 2.4.2" +M4_VERSION="m4 (GNU M4) 1.4.16" + +# +# When upgrading automake's version, don't forget to also update its +# helper utilities, especially depcomp. + + +# If paths to autotools are not specified by the user, assume tools are +# running on jam in /mnt/hdf/packages and set paths accordingly. +if test -z ${AUTOCONF}; then + AUTOCONF=/mnt/hdf/packages/autoconf/autoconf-2.69/bin/autoconf +fi +if test -z ${AUTOMAKE}; then + AUTOMAKE=/mnt/hdf/packages/automake/automake-1.12.3/bin/automake-1.12 +fi +if test -z ${AUTOHEADER}; then + AUTOHEADER=/mnt/hdf/packages/autoconf/autoconf-2.69/bin/autoheader +fi +if test -z ${ACLOCAL}; then + ACLOCAL=/mnt/hdf/packages/automake/automake-1.12.3/bin/aclocal-1.12 +fi +if test -z ${LIBTOOL}; then + LIBTOOL=/mnt/hdf/packages/libtool/libtool-2.4.2/bin/libtool +fi +if test -z ${M4}; then + M4=/mnt/hdf/packages/m4/m4-1.4.16/bin/m4 +fi + +# Check version numbers of all autotools against the "correct" versions +AC_VERS=`${AUTOCONF} --version 2>&1 | grep "^${AUTOCONF_VERSION}"` +if test -z "${AC_VERS}"; then + echo "${AUTOCONF} version is not ${AUTOCONF_VERSION}" + exit 1 +fi +AM_VERS=`${AUTOMAKE} --version 2>&1 | grep "^${AUTOMAKE_VERSION}"` +if test -z "${AM_VERS}"; then + echo "${AUTOMAKE} version is not ${AUTOMAKE_VERSION}" + exit 1 +fi +AH_VERS=`${AUTOHEADER} --version 2>&1 | grep "^${AUTOHEADER_VERSION}"` +if test -z "${AH_VERS}"; then + echo "${AUTOHEADER} version is not ${AUTOHEADER_VERSION}" + exit 1 +fi +AL_VERS=`${ACLOCAL} --version 2>&1 | grep "^${ACLOCAL_VERSION}"` +if test -z "${AL_VERS}"; then + echo "${ACLOCAL} version is not ${ACLOCAL_VERSION}" + exit 1 +fi +LT_VERS=`${LIBTOOL} --version 2>&1 | grep "${LIBTOOL_VERSION}"` +if test -z "${LT_VERS}"; then + echo "${LIBTOOL} version is not ${LIBTOOL_VERSION}" + exit 1 +fi +M4_VERS=`${M4} --version 2>&1 | grep "${M4_VERSION}"` +if test -z "${M4_VERS}"; then + echo "${M4} version is not ${M4_VERSION}" + exit 1 +fi + +# Make sure that the tools are in the path. +AUTOCONF_DIR=`dirname ${AUTOCONF}` +LIBTOOL_DIR=`dirname ${LIBTOOL}` +M4_DIR=`dirname ${M4}` +PATH=${AUTOCONF_DIR}:${M4_DIR}:$PATH + +# Run autoconf/automake commands in order + echo ${ACLOCAL} -I ${LIBTOOL_DIR}/../share/aclocal + ${ACLOCAL} -I ${LIBTOOL_DIR}/../share/aclocal || exit 1 + + echo ${AUTOHEADER} + ${AUTOHEADER} || exit 1 + + echo ${AUTOMAKE} --add-missing + ${AUTOMAKE} --add-missing || exit 1 + + echo ${AUTOCONF} + ${AUTOCONF} || exit 1 + +# Clean up top-level Makefile.in +# pmake wants an argument to be the first non-comment line it encounters +# in the Makefile. Automake wants to reorganize the Makefile. +# To work around this, we post-process the top-level Makefile.in. + sed "s/^#xxx//" Makefile.in > Makefile.in.new + mv Makefile.in.new Makefile.in + +# Run trace script +# The trace script adds H5TRACE macros to library source files. It should +# have no effect on files that don't have HDF5 API macros in them. +echo +echo " Running trace script:" +bin/trace src/H5*.c || exit 1 + +# Run make_err +# make_err automatically generates the H5E headers that create error message +# types for HDF5. +echo +echo " Running error generation script:" +bin/make_err src/H5err.txt || exit 1 + +# Run make_vers +# make_vers automatically generates the public headers that define the API version +# macros for HDF5. +echo +echo " Running API version generation script:" +bin/make_vers src/H5vers.txt || exit 1 + +exit 0 Index: bin/reconfigure.local =================================================================== --- bin/reconfigure.local (revision 0) +++ bin/reconfigure.local (revision 23771) @@ -0,0 +1,143 @@ +#! /bin/sh +# +# Copyright by the Board of Trustees of the University of Illinois. +# All rights reserved. +# +# This file is part of HDF5. The full HDF5 copyright notice, including +# terms governing use, modification, and redistribution, is contained in +# the files COPYING and Copyright.html. COPYING can be found at the root +# of the source code distribution tree; Copyright.html can be found at the +# root level of an installed copy of the electronic HDF5 document set and +# is linked from the top-level documents page. It can also be found at +# http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have +# access to either file, you may request a copy from help@hdfgroup.org. +# + +# A script to reconfigure autotools for HDF5, and to recreate other +# generated files specifc to HDF5. +# If the paths of the autotools are not specified by the user, they +# are hardcoded to point to their locations on HDF5 Linux machines. +# Users can specify the locations of the autotools with the following +# variables: +# AUTOCONF, AUTOMAKE, ACLOCAL, AUTOHEADER should be the path to the +# corresponding tools. +# LIBTOOL_DIR should be the path to the base libtool directory; +# $LIBTOOL_DIR/bin/libtool should invoke libtool, while +# $LIBTOOL_DIR/share/aclocal needs to be included by aclocal. +# Be very careful when specifying these tools manually! There are a lot +# of versions that can get confused (not even counting the m4 utility)! + +# HDF5 currently uses the following versions of the autotools: +AUTOCONF_VERSION="autoconf (GNU Autoconf) 2.69" +AUTOMAKE_VERSION="automake (GNU automake) 1.12.2" +AUTOHEADER_VERSION="autoheader (GNU Autoconf) 2.69" +ACLOCAL_VERSION="aclocal (GNU automake) 1.12.2" +LIBTOOL_VERSION="(GNU libtool) 2.4.2" +M4_VERSION="m4 (GNU M4) 1.4.16" + +# +# When upgrading automake's version, don't forget to also update its +# helper utilities, especially depcomp. + + +# If paths to autotools are not specified by the user, assume tools are +# running on jam in /mnt/hdf/packages and set paths accordingly. +if test -z ${AUTOCONF}; then + AUTOCONF=/usr/bin/autoconf +fi +if test -z ${AUTOMAKE}; then + AUTOMAKE=/usr/bin/automake-1.12 +fi +if test -z ${AUTOHEADER}; then + AUTOHEADER=/usr/bin/autoheader +fi +if test -z ${ACLOCAL}; then + ACLOCAL=/usr/bin/aclocal-1.12 +fi +if test -z ${LIBTOOL}; then + LIBTOOL=/usr/bin/libtool +fi +if test -z ${M4}; then + M4=/usr/bin/m4 +fi + +# Check version numbers of all autotools against the "correct" versions +AC_VERS=`${AUTOCONF} --version 2>&1 | grep "^${AUTOCONF_VERSION}"` +if test -z "${AC_VERS}"; then + echo "${AUTOCONF} version is not ${AUTOCONF_VERSION}" + exit 1 +fi +AM_VERS=`${AUTOMAKE} --version 2>&1 | grep "^${AUTOMAKE_VERSION}"` +if test -z "${AM_VERS}"; then + echo "${AUTOMAKE} version is not ${AUTOMAKE_VERSION}" + exit 1 +fi +AH_VERS=`${AUTOHEADER} --version 2>&1 | grep "^${AUTOHEADER_VERSION}"` +if test -z "${AH_VERS}"; then + echo "${AUTOHEADER} version is not ${AUTOHEADER_VERSION}" + exit 1 +fi +AL_VERS=`${ACLOCAL} --version 2>&1 | grep "^${ACLOCAL_VERSION}"` +if test -z "${AL_VERS}"; then + echo "${ACLOCAL} version is not ${ACLOCAL_VERSION}" + exit 1 +fi +LT_VERS=`${LIBTOOL} --version 2>&1 | grep "${LIBTOOL_VERSION}"` +if test -z "${LT_VERS}"; then + echo "${LIBTOOL} version is not ${LIBTOOL_VERSION}" + exit 1 +fi +M4_VERS=`${M4} --version 2>&1 | grep "${M4_VERSION}"` +if test -z "${M4_VERS}"; then + echo "${M4} version is not ${M4_VERSION}" + exit 1 +fi + +# Make sure that the tools are in the path. +AUTOCONF_DIR=`dirname ${AUTOCONF}` +LIBTOOL_DIR=`dirname ${LIBTOOL}` +M4_DIR=`dirname ${M4}` +PATH=${AUTOCONF_DIR}:${M4_DIR}:$PATH + +# Run autoconf/automake commands in order + echo ${ACLOCAL} -I ${LIBTOOL_DIR}/../share/aclocal + ${ACLOCAL} -I ${LIBTOOL_DIR}/../share/aclocal || exit 1 + + echo ${AUTOHEADER} + ${AUTOHEADER} || exit 1 + + echo ${AUTOMAKE} --add-missing + ${AUTOMAKE} --add-missing || exit 1 + + echo ${AUTOCONF} + ${AUTOCONF} || exit 1 + +# Clean up top-level Makefile.in +# pmake wants an argument to be the first non-comment line it encounters +# in the Makefile. Automake wants to reorganize the Makefile. +# To work around this, we post-process the top-level Makefile.in. + sed "s/^#xxx//" Makefile.in > Makefile.in.new + mv Makefile.in.new Makefile.in + +# Run trace script +# The trace script adds H5TRACE macros to library source files. It should +# have no effect on files that don't have HDF5 API macros in them. +echo +echo " Running trace script:" +bin/trace src/H5*.c || exit 1 + +# Run make_err +# make_err automatically generates the H5E headers that create error message +# types for HDF5. +echo +echo " Running error generation script:" +bin/make_err src/H5err.txt || exit 1 + +# Run make_vers +# make_vers automatically generates the public headers that define the API version +# macros for HDF5. +echo +echo " Running API version generation script:" +bin/make_vers src/H5vers.txt || exit 1 + +exit 0 Index: perform/CMakeLists.txt =================================================================== --- perform/CMakeLists.txt (revision 23770) +++ perform/CMakeLists.txt (revision 23771) @@ -23,6 +23,7 @@ ) ADD_EXECUTABLE (h5perf_serial ${h5perf_serial_SRCS}) TARGET_NAMING (h5perf_serial ${LIB_TYPE}) +TARGET_C_PROPERTIES (h5perf_serial " " " ") TARGET_LINK_LIBRARIES (h5perf_serial ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET}) SET_TARGET_PROPERTIES (h5perf_serial PROPERTIES FOLDER perform) @@ -38,6 +39,7 @@ APPEND PROPERTY COMPILE_DEFINITIONS STANDALONE ) TARGET_NAMING (h5perf_serial_alone ${LIB_TYPE}) + TARGET_C_PROPERTIES (h5perf_serial_alone " " " ") TARGET_LINK_LIBRARIES (h5perf_serial_alone ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET}) SET_TARGET_PROPERTIES (h5perf_serial_alone PROPERTIES FOLDER perform) ENDIF (HDF5_BUILD_PERFORM_STANDALONE) @@ -48,6 +50,7 @@ ) ADD_EXECUTABLE(chunk ${chunk_SRCS}) TARGET_NAMING (chunk ${LIB_TYPE}) +TARGET_C_PROPERTIES (chunk " " " ") TARGET_LINK_LIBRARIES(chunk ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET}) SET_TARGET_PROPERTIES (chunk PROPERTIES FOLDER perform) @@ -57,6 +60,7 @@ ) ADD_EXECUTABLE (iopipe ${iopipe_SRCS}) TARGET_NAMING (iopipe ${LIB_TYPE}) +TARGET_C_PROPERTIES (iopipe " " " ") TARGET_LINK_LIBRARIES (iopipe ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET}) SET_TARGET_PROPERTIES (iopipe PROPERTIES FOLDER perform) @@ -66,6 +70,7 @@ ) ADD_EXECUTABLE (overhead ${overhead_SRCS}) TARGET_NAMING (overhead ${LIB_TYPE}) +TARGET_C_PROPERTIES (overhead " " " ") TARGET_LINK_LIBRARIES (overhead ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET}) SET_TARGET_PROPERTIES (overhead PROPERTIES FOLDER perform) @@ -75,6 +80,7 @@ ) ADD_EXECUTABLE (perf_meta ${perf_meta_SRCS}) TARGET_NAMING (perf_meta ${LIB_TYPE}) +TARGET_C_PROPERTIES (perf_meta " " " ") TARGET_LINK_LIBRARIES (perf_meta ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET} ${HDF5_TEST_LIB_TARGET}) SET_TARGET_PROPERTIES (perf_meta PROPERTIES FOLDER perform) @@ -84,6 +90,7 @@ ) ADD_EXECUTABLE (zip_perf ${zip_perf_SRCS}) TARGET_NAMING (zip_perf ${LIB_TYPE}) +TARGET_C_PROPERTIES (zip_perf " " " ") TARGET_LINK_LIBRARIES (zip_perf ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) SET_TARGET_PROPERTIES (zip_perf PROPERTIES FOLDER perform) @@ -96,6 +103,7 @@ ) ADD_EXECUTABLE (h5perf ${h5perf_SRCS}) TARGET_NAMING (h5perf ${LIB_TYPE}) + TARGET_C_PROPERTIES (h5perf " " " ") TARGET_LINK_LIBRARIES (h5perf ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET} ${HDF5_TEST_LIB_TARGET}) SET_TARGET_PROPERTIES (h5perf PROPERTIES FOLDER perform) @@ -111,6 +119,7 @@ APPEND PROPERTY COMPILE_DEFINITIONS STANDALONE ) TARGET_NAMING (h5perf_alone ${LIB_TYPE}) + TARGET_C_PROPERTIES (h5perf_alone " " " ") TARGET_LINK_LIBRARIES (h5perf_alone ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET} ${HDF5_TEST_LIB_TARGET}) SET_TARGET_PROPERTIES (h5perf_alone PROPERTIES FOLDER perform) ENDIF (HDF5_BUILD_PERFORM_STANDALONE) @@ -122,6 +131,7 @@ ) ADD_EXECUTABLE (benchpar ${benchpar_SRCS}) TARGET_NAMING (benchpar ${LIB_TYPE}) + TARGET_C_PROPERTIES (benchpar " " " ") TARGET_LINK_LIBRARIES (benchpar ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET} ${HDF5_TEST_LIB_TARGET}) SET_TARGET_PROPERTIES (benchpar PROPERTIES FOLDER perform) ENDIF (HDF5_BUILD_PARALLEL_ALL) Index: fortran/test/CMakeLists.txt =================================================================== --- fortran/test/CMakeLists.txt (revision 23770) +++ fortran/test/CMakeLists.txt (revision 23771) @@ -10,6 +10,7 @@ # Add Test Lib #----------------------------------------------------------------------------- ADD_LIBRARY (${HDF5_F90_C_TEST_LIB_TARGET} ${LIB_TYPE} t.c) +TARGET_C_PROPERTIES (${HDF5_F90_C_TEST_LIB_TARGET} " " " ") TARGET_LINK_LIBRARIES (${HDF5_F90_C_TEST_LIB_TARGET} ${HDF5_F90_C_LIB_TARGET} ${HDF5_TEST_LIB_TARGET} @@ -28,7 +29,7 @@ ENDIF (BUILD_SHARED_LIBS) SET_PROPERTY (TARGET ${HDF5_F90_TEST_LIB_TARGET} APPEND PROPERTY COMPILE_DEFINITIONS HDF5F90_WINDOWS) ENDIF (WIN32 AND NOT CYGWIN) -TARGET_FORTRAN_WIN_PROPERTIES (${HDF5_F90_TEST_LIB_TARGET} ${SHARED_LINK_FLAGS}) +TARGET_FORTRAN_PROPERTIES (${HDF5_F90_TEST_LIB_TARGET} " " ${SHARED_LINK_FLAGS}) SET_TARGET_PROPERTIES (${HDF5_F90_TEST_LIB_TARGET} PROPERTIES LINKER_LANGUAGE Fortran) TARGET_LINK_LIBRARIES (${HDF5_F90_TEST_LIB_TARGET} ${HDF5_F90_C_TEST_LIB_TARGET} @@ -60,7 +61,7 @@ tH5Z.f90 ) TARGET_NAMING (testhdf5_fortran ${LIB_TYPE}) -TARGET_FORTRAN_WIN_PROPERTIES (testhdf5_fortran "") +TARGET_FORTRAN_PROPERTIES (testhdf5_fortran " " " ") TARGET_LINK_LIBRARIES (testhdf5_fortran ${HDF5_F90_TEST_LIB_TARGET} ${HDF5_F90_LIB_TARGET} @@ -84,7 +85,7 @@ tH5G_1_8.f90 ) TARGET_NAMING (testhdf5_fortran_1_8 ${LIB_TYPE}) -TARGET_FORTRAN_WIN_PROPERTIES (testhdf5_fortran_1_8 "") +TARGET_FORTRAN_PROPERTIES (testhdf5_fortran_1_8 " " " ") TARGET_LINK_LIBRARIES (testhdf5_fortran_1_8 ${HDF5_F90_TEST_LIB_TARGET} ${HDF5_F90_LIB_TARGET} @@ -112,7 +113,7 @@ tH5T_F03.f90 ) TARGET_NAMING (fortranlib_test_F03 ${LIB_TYPE}) - TARGET_FORTRAN_WIN_PROPERTIES (fortranlib_test_F03 "") + TARGET_FORTRAN_PROPERTIES (fortranlib_test_F03 " " " ") TARGET_LINK_LIBRARIES (fortranlib_test_F03 ${HDF5_F90_TEST_LIB_TARGET} ${HDF5_F90_LIB_TARGET} @@ -131,7 +132,7 @@ #-- Adding test for fflush1 ADD_EXECUTABLE (fflush1 fflush1.f90) TARGET_NAMING (fflush1 ${LIB_TYPE}) -TARGET_FORTRAN_WIN_PROPERTIES (fflush1 "") +TARGET_FORTRAN_PROPERTIES (fflush1 " " " ") TARGET_LINK_LIBRARIES (fflush1 ${HDF5_F90_LIB_TARGET} ${HDF5_F90_TEST_LIB_TARGET} @@ -148,7 +149,7 @@ #-- Adding test for fflush2 ADD_EXECUTABLE (fflush2 fflush2.f90) TARGET_NAMING (fflush2 ${LIB_TYPE}) -TARGET_FORTRAN_WIN_PROPERTIES (fflush2 "") +TARGET_FORTRAN_PROPERTIES (fflush2 " " " ") TARGET_LINK_LIBRARIES (fflush2 ${HDF5_F90_TEST_LIB_TARGET} ${HDF5_F90_LIB_TARGET} Index: fortran/testpar/CMakeLists.txt =================================================================== --- fortran/testpar/CMakeLists.txt (revision 23770) +++ fortran/testpar/CMakeLists.txt (revision 23771) @@ -17,7 +17,7 @@ mdset.f90 ) TARGET_NAMING (parallel_test ${LIB_TYPE}) -TARGET_FORTRAN_WIN_PROPERTIES (parallel_test "") +TARGET_FORTRAN_PROPERTIES (parallel_test " " " ") TARGET_LINK_LIBRARIES (parallel_test ${HDF5_F90_TEST_LIB_TARGET} ${HDF5_F90_LIB_TARGET} Index: fortran/src/CMakeLists.txt =================================================================== --- fortran/src/CMakeLists.txt (revision 23770) +++ fortran/src/CMakeLists.txt (revision 23771) @@ -133,6 +133,7 @@ ) ADD_LIBRARY (${HDF5_F90_C_LIB_TARGET} ${LIB_TYPE} ${f90CStub_C_SRCS} ${f90CStub_C_HDRS}) +TARGET_C_PROPERTIES (${HDF5_F90_C_LIB_TARGET} " " " ") TARGET_LINK_LIBRARIES (${HDF5_F90_C_LIB_TARGET} ${HDF5_LIB_TARGET} ${LINK_LIBS}) SET_GLOBAL_VARIABLE (HDF5_LIBRARIES_TO_EXPORT "${HDF5_LIBRARIES_TO_EXPORT};${HDF5_F90_C_LIB_TARGET}") H5_SET_LIB_OPTIONS (${HDF5_F90_C_LIB_TARGET} ${HDF5_F90_C_LIB_NAME} ${LIB_TYPE}) @@ -233,7 +234,7 @@ HDF5F90_WINDOWS ) ENDIF (WIN32 AND NOT CYGWIN) -TARGET_FORTRAN_WIN_PROPERTIES (${HDF5_F90_LIB_TARGET} ${SHARED_LINK_FLAGS}) +TARGET_FORTRAN_PROPERTIES (${HDF5_F90_LIB_TARGET} " " ${SHARED_LINK_FLAGS}) SET_TARGET_PROPERTIES (${HDF5_F90_LIB_TARGET} PROPERTIES LINKER_LANGUAGE Fortran) TARGET_LINK_LIBRARIES (${HDF5_F90_LIB_TARGET} ${HDF5_F90_C_LIB_TARGET} ${HDF5_LIB_TARGET}) IF (H5_HAVE_PARALLEL AND MPI_Fortran_FOUND) Index: fortran/examples/CMakeLists.txt =================================================================== --- fortran/examples/CMakeLists.txt (revision 23770) +++ fortran/examples/CMakeLists.txt (revision 23771) @@ -41,7 +41,7 @@ FOREACH (example ${examples}) ADD_EXECUTABLE (f90_ex_${example} ${HDF5_F90_EXAMPLES_SOURCE_DIR}/${example}.f90) TARGET_NAMING (f90_ex_${example} ${LIB_TYPE}) - TARGET_FORTRAN_WIN_PROPERTIES (f90_ex_${example} "") + TARGET_FORTRAN_PROPERTIES (f90_ex_${example} " " " ") IF (WIN32 AND NOT CYGWIN) SET_PROPERTY (TARGET f90_ex_${example} APPEND PROPERTY COMPILE_DEFINITIONS @@ -69,7 +69,7 @@ FOREACH (example ${F2003_examples}) ADD_EXECUTABLE (f03_ex_${example} ${HDF5_F90_EXAMPLES_SOURCE_DIR}/${example}.f90) TARGET_NAMING (f03_ex_${example} ${LIB_TYPE}) - TARGET_FORTRAN_WIN_PROPERTIES (f03_ex_${example} "") + TARGET_FORTRAN_PROPERTIES (f03_ex_${example} " " " ") IF (WIN32 AND NOT CYGWIN) SET_PROPERTY (TARGET f03_ex_${example} APPEND PROPERTY COMPILE_DEFINITIONS HDF5F90_WINDOWS @@ -95,7 +95,7 @@ IF (H5_HAVE_PARALLEL AND MPI_Fortran_FOUND) ADD_EXECUTABLE (f90_ex_ph5example ${HDF5_F90_EXAMPLES_SOURCE_DIR}/ph5example.f90) TARGET_NAMING (f90_ex_ph5example ${LIB_TYPE}) - TARGET_FORTRAN_WIN_PROPERTIES (f90_ex_ph5example "") + TARGET_FORTRAN_PROPERTIES (f90_ex_ph5example " " " ") IF (WIN32 AND NOT CYGWIN) SET_PROPERTY (TARGET f90_ex_ph5example APPEND PROPERTY COMPILE_DEFINITIONS Index: CMakeLists.txt =================================================================== --- CMakeLists.txt (revision 23770) +++ CMakeLists.txt (revision 23771) @@ -176,7 +176,7 @@ "\\1" H5_VERS_MINOR ${_h5public_h_contents}) STRING (REGEX REPLACE ".*#define[ \t]+H5_VERS_RELEASE[ \t]+([0-9]*).*$" "\\1" H5_VERS_RELEASE ${_h5public_h_contents}) -STRING (REGEX REPLACE ".*#define[ \t]+H5_VERS_SUBRELEASE[ \t]+\"([0-9A-Za-z.]*)\".*$" +STRING (REGEX REPLACE ".*#define[ \t]+H5_VERS_SUBRELEASE[ \t]+\"([0-9A-Za-z._]*)\".*$" "\\1" H5_VERS_SUBRELEASE ${_h5public_h_contents}) #MESSAGE (STATUS "VERSION: ${H5_VERS_MAJOR}.${H5_VERS_MINOR}.${H5_VERS_RELEASE}-${H5_VERS_SUBRELEASE}") @@ -190,7 +190,7 @@ "\\1" H5_SOVERS_MINOR ${_lt_vers_am_contents}) STRING (REGEX REPLACE ".*LT_VERS_AGE[ \t]+=[ \t]+([0-9]*).*$" "\\1" H5_SOVERS_RELEASE ${_lt_vers_am_contents}) -MESSAGE (STATUS "SOVERSION: ${H5_SOVERS_MAJOR}.${H5_SOVERS_MINOR}.${H5_SOVERS_RELEASE}") +MESSAGE (STATUS "SOVERSION: ${H5_SOVERS_MAJOR}.${H5_SOVERS_RELEASE}.${H5_SOVERS_MINOR}") #----------------------------------------------------------------------------- # Basic HDF5 stuff here @@ -205,7 +205,7 @@ ELSE (NOT "${H5_VERS_SUBRELEASE}" STREQUAL "") SET (HDF5_PACKAGE_VERSION_STRING "${HDF5_PACKAGE_VERSION}") ENDIF (NOT "${H5_VERS_SUBRELEASE}" STREQUAL "") -SET (HDF5_PACKAGE_SOVERSION "${H5_SOVERS_MAJOR}.${H5_SOVERS_MINOR}.${H5_SOVERS_RELEASE}") +SET (HDF5_PACKAGE_SOVERSION "${H5_SOVERS_MAJOR}.${H5_SOVERS_RELEASE}.${H5_SOVERS_MINOR}") SET (HDF5_PACKAGE_STRING "${HDF5_PACKAGE_NAME} ${HDF5_PACKAGE_VERSION_STRING}") SET (HDF5_PACKAGE_TARNAME "${HDF5_PACKAGE}${HDF_PACKAGE_EXT}") SET (HDF5_PACKAGE_URL "http://www.hdfgroup.org") @@ -358,6 +358,8 @@ IF (MSVC) SET (CMAKE_MFC_FLAG 0) + SET (WIN_COMPILE_FLAGS "/MD") + SET (WIN_LINK_FLAGS "") ENDIF (MSVC) SET (MAKE_SYSTEM) @@ -519,6 +521,11 @@ ENDIF (HDF5_USE_16_API_DEFAULT) #----------------------------------------------------------------------------- +# Include user macros +#----------------------------------------------------------------------------- +INCLUDE (UserMacros.cmake) + +#----------------------------------------------------------------------------- # Options for HDF5 Filters #----------------------------------------------------------------------------- MACRO (HDF5_SETUP_FILTERS FILTER) Index: examples/CMakeLists.txt =================================================================== --- examples/CMakeLists.txt (revision 23770) +++ examples/CMakeLists.txt (revision 23771) @@ -39,6 +39,7 @@ FOREACH (example ${examples}) ADD_EXECUTABLE (${example} ${HDF5_EXAMPLES_SOURCE_DIR}/${example}.c) TARGET_NAMING (${example} ${LIB_TYPE}) + TARGET_C_PROPERTIES (${example} " " " ") TARGET_LINK_LIBRARIES (${example} ${HDF5_LIB_TARGET}) SET_TARGET_PROPERTIES (${example} PROPERTIES FOLDER examples) ENDFOREACH (example ${examples}) @@ -46,6 +47,7 @@ IF (H5_HAVE_PARALLEL) ADD_EXECUTABLE (ph5example ${HDF5_EXAMPLES_SOURCE_DIR}/ph5example.c) TARGET_NAMING (ph5example ${LIB_TYPE}) + TARGET_C_PROPERTIES (ph5example " " " ") TARGET_LINK_LIBRARIES (ph5example ${HDF5_LIB_TARGET}) SET_TARGET_PROPERTIES (ph5example PROPERTIES FOLDER examples) ENDIF (H5_HAVE_PARALLEL) libsis-jhdf5-java-14.12.1/source/c/jhdf5/000077500000000000000000000000001256564762100176225ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/c/jhdf5/exceptionImpJHDF5.c000077500000000000000000000472441256564762100231710ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ /* * This is a utility program used by the HDF Java-C wrapper layer to * generate exceptions. This may be called from any part of the * Java-C interface. * */ #ifdef __cplusplus extern "C" { #endif #include "hdf5.h" #include #include "jni.h" /* #include "H5Eprivate.h" */ /* These types are copied from H5Eprivate.h * They should be moved to a public include file, and deleted from * here. */ #define H5E_NSLOTS 32 /*number of slots in an error stack */ /* * The list of error messages in the system is kept as an array of * error_code/message pairs, one for major error numbers and another for * minor error numbers. */ typedef struct H5E_major_mesg_t { H5E_major_t error_code; const char *str; } H5E_major_mesg_t; typedef struct H5E_minor_mesg_t { H5E_minor_t error_code; const char *str; } H5E_minor_mesg_t; /* major and minor error numbers */ typedef struct H5E_num_t { int maj_num; int min_num; } H5E_num_t; int getMajorErrorNumber(); int getMinorErrorNumber(); /* get the major and minor error numbers on the top of the erroe stack */ static herr_t walk_error_callback(unsigned n, const H5E_error_t *err_desc, void *_err_nums) { H5E_num_t *err_nums = (H5E_num_t *)_err_nums; if (err_desc) { err_nums->maj_num = err_desc->maj_num; err_nums->min_num = err_desc->min_num; } return 0; } char *defineHDF5LibraryException(int maj_num); /* * Class: ch_systemsx_cisd_hdf5_hdf5lib_H5_H5error_1off * Method: H5error_off * Signature: ()I * */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5error_1off (JNIEnv *env, jclass clss ) { return H5Eset_auto(H5E_DEFAULT, NULL, NULL); } /* * Class: ncsa_hdf_hdf5lib_H5_H5error_1off * Method: H5error_off * Signature: ()I * */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_H5_H5error_1off (JNIEnv *env, jclass clss ) { return H5Eset_auto(H5E_DEFAULT, NULL, NULL); } /* * Class: ncsa_hdf_hdf5lib_exceptions_HDFLibraryException * Method: printStackTrace0 * Signature: (Ljava/lang/Object;)V * * Call the HDF-5 library to print the HDF-5 error stack to 'file_name'. */ JNIEXPORT void JNICALL Java_ncsa_hdf_hdf5lib_exceptions_HDF5LibraryException_printStackTrace0 (JNIEnv *env, jobject obj, jstring file_name) { FILE *stream; char *file; if (file_name == NULL) H5Eprint(H5E_DEFAULT, stderr); else { #ifdef __cplusplus file = (char *)env->GetStringUTFChars(file_name,0); #else file = (char *)(*env)->GetStringUTFChars(env,file_name,0); #endif stream = fopen(file, "a+"); H5Eprint(H5E_DEFAULT, stream); #ifdef __cplusplus env->ReleaseStringUTFChars(file_name, file); #else (*env)->ReleaseStringUTFChars(env, file_name, file); #endif if (stream) fclose(stream); } } /* * Class: ncsa_hdf_hdf5lib_exceptions_HDFLibraryException * Method: getMajorErrorNumber * Signature: ()I * * Extract the HDF-5 major error number from the HDF-5 error stack. * * Note: This relies on undocumented, 'private' code in the HDF-5 * library. Later releases will have a public interface for this * purpose. */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_exceptions_HDF5LibraryException_getMajorErrorNumber (JNIEnv *env, jobject obj) { H5E_num_t err_nums; H5Ewalk(H5E_DEFAULT, H5E_WALK_DOWNWARD, walk_error_callback, &err_nums); return (int) err_nums.maj_num; } int getMajorErrorNumber() { H5E_num_t err_nums; H5Ewalk(H5E_DEFAULT, H5E_WALK_DOWNWARD, walk_error_callback, &err_nums); return (int) err_nums.maj_num; } /* * Class: ncsa_hdf_hdf5lib_exceptions_HDFLibraryException * Method: getMinorErrorNumber * Signature: ()I * * Extract the HDF-5 minor error number from the HDF-5 error stack. * * Note: This relies on undocumented, 'private' code in the HDF-5 * library. Later releases will have a public interface for this * purpose. */ JNIEXPORT jint JNICALL Java_ncsa_hdf_hdf5lib_exceptions_HDF5LibraryException_getMinorErrorNumber (JNIEnv *env, jobject obj) { return (jint) getMinorErrorNumber(); } int getMinorErrorNumber() { H5E_num_t err_nums; H5Ewalk(H5E_DEFAULT, H5E_WALK_DOWNWARD, walk_error_callback, &err_nums); return (int) err_nums.min_num; } /* * Routine to raise particular Java exceptions from C */ /* * Create and throw an 'outOfMemoryException' * * Note: This routine never returns from the 'throw', * and the Java native method immediately raises the * exception. */ jboolean h5outOfMemory( JNIEnv *env, char *functName) { jmethodID jm; jclass jc; char * args[2]; jobject ex; jstring str; int rval; #ifdef __cplusplus jc = env->FindClass("java/lang/OutOfMemoryError"); #else jc = (*env)->FindClass(env, "java/lang/OutOfMemoryError"); #endif if (jc == NULL) { return JNI_FALSE; } #ifdef __cplusplus jm = env->GetMethodID(jc, "", "(Ljava/lang/String;)V"); #else jm = (*env)->GetMethodID(env, jc, "", "(Ljava/lang/String;)V"); #endif if (jm == NULL) { return JNI_FALSE; } #ifdef __cplusplus str = (env)->NewStringUTF(functName); #else str = (*env)->NewStringUTF(env,functName); #endif args[0] = (char *)str; args[1] = 0; #ifdef __cplusplus ex = env->NewObjectA ( jc, jm, (jvalue *)args ); rval = env->Throw( (jthrowable ) ex ); #else ex = (*env)->NewObjectA ( env, jc, jm, (jvalue *)args ); rval = (*env)->Throw(env, ex ); #endif if (rval < 0) { fprintf(stderr, "FATAL ERROR: OutOfMemoryError: Throw failed\n"); return JNI_FALSE; } return JNI_TRUE; } /* * A fatal error in a JNI call * Create and throw an 'InternalError' * * Note: This routine never returns from the 'throw', * and the Java native method immediately raises the * exception. */ jboolean h5JNIFatalError( JNIEnv *env, char *functName) { jmethodID jm; jclass jc; char * args[2]; jobject ex; jstring str; int rval; #ifdef __cplusplus jc = env->FindClass("java/lang/InternalError"); #else jc = (*env)->FindClass(env, "java/lang/InternalError"); #endif if (jc == NULL) { return JNI_FALSE; } #ifdef __cplusplus jm = env->GetMethodID(jc, "", "(Ljava/lang/String;)V"); #else jm = (*env)->GetMethodID(env, jc, "", "(Ljava/lang/String;)V"); #endif if (jm == NULL) { return JNI_FALSE; } #ifdef __cplusplus str = env->NewStringUTF(functName); #else str = (*env)->NewStringUTF(env,functName); #endif args[0] = (char *)str; args[1] = 0; #ifdef __cplusplus ex = env->NewObjectA ( jc, jm, (jvalue *)args ); rval = env->Throw( (jthrowable) ex ); #else ex = (*env)->NewObjectA ( env, jc, jm, (jvalue *)args ); rval = (*env)->Throw(env, ex ); #endif if (rval < 0) { fprintf(stderr, "FATAL ERROR: JNIFatal: Throw failed\n"); return JNI_FALSE; } return JNI_TRUE; } /* * A NULL argument in an HDF5 call * Create and throw an 'NullPointerException' * * Note: This routine never returns from the 'throw', * and the Java native method immediately raises the * exception. */ jboolean h5nullArgument( JNIEnv *env, char *functName) { jmethodID jm; jclass jc; char * args[2]; jobject ex; jstring str; int rval; #ifdef __cplusplus jc = env->FindClass("java/lang/NullPointerException"); #else jc = (*env)->FindClass(env, "java/lang/NullPointerException"); #endif if (jc == NULL) { return JNI_FALSE; } #ifdef __cplusplus jm = env->GetMethodID(jc, "", "(Ljava/lang/String;)V"); #else jm = (*env)->GetMethodID(env, jc, "", "(Ljava/lang/String;)V"); #endif if (jm == NULL) { return JNI_FALSE; } #ifdef __cplusplus str = env->NewStringUTF(functName); #else str = (*env)->NewStringUTF(env,functName); #endif args[0] = (char *)str; args[1] = 0; #ifdef __cplusplus ex = env->NewObjectA ( jc, jm, (jvalue *)args ); rval = env->Throw((jthrowable) ex ); #else ex = (*env)->NewObjectA ( env, jc, jm, (jvalue *)args ); rval = (*env)->Throw(env, ex ); #endif if (rval < 0) { fprintf(stderr, "FATAL ERROR: NullPointer: Throw failed\n"); return JNI_FALSE; } return JNI_TRUE; } /* * A bad argument in an HDF5 call * Create and throw an 'IllegalArgumentException' * * Note: This routine never returns from the 'throw', * and the Java native method immediately raises the * exception. */ jboolean h5badArgument( JNIEnv *env, char *functName) { jmethodID jm; jclass jc; char * args[2]; jobject ex; jstring str; int rval; #ifdef __cplusplus jc = env->FindClass("java/lang/IllegalArgumentException"); #else jc = (*env)->FindClass(env, "java/lang/IllegalArgumentException"); #endif if (jc == NULL) { return JNI_FALSE; } #ifdef __cplusplus jm = env->GetMethodID(jc, "", "(Ljava/lang/String;)V"); #else jm = (*env)->GetMethodID(env, jc, "", "(Ljava/lang/String;)V"); #endif if (jm == NULL) { return JNI_FALSE; } #ifdef __cplusplus str = env->NewStringUTF(functName); #else str = (*env)->NewStringUTF(env,functName); #endif args[0] = (char *)str; args[1] = 0; #ifdef __cplusplus ex = env->NewObjectA ( jc, jm, (jvalue *)args ); rval = env->Throw((jthrowable) ex ); #else ex = (*env)->NewObjectA ( env, jc, jm, (jvalue *)args ); rval = (*env)->Throw(env, ex ); #endif if (rval < 0) { fprintf(stderr, "FATAL ERROR: BadArgument: Throw failed\n"); return JNI_FALSE; } return JNI_TRUE; } /* * Some feature Not implemented yet * Create and throw an 'UnsupportedOperationException' * * Note: This routine never returns from the 'throw', * and the Java native method immediately raises the * exception. */ jboolean h5unimplemented( JNIEnv *env, char *functName) { jmethodID jm; jclass jc; char * args[2]; jobject ex; jstring str; int rval; #ifdef __cplusplus jc = env->FindClass("java/lang/UnsupportedOperationException"); #else jc = (*env)->FindClass(env, "java/lang/UnsupportedOperationException"); #endif if (jc == NULL) { return JNI_FALSE; } #ifdef __cplusplus jm = env->GetMethodID(jc, "", "(Ljava/lang/String;)V"); #else jm = (*env)->GetMethodID(env, jc, "", "(Ljava/lang/String;)V"); #endif if (jm == NULL) { return JNI_FALSE; } #ifdef __cplusplus str = env->NewStringUTF(functName); #else str = (*env)->NewStringUTF(env,functName); #endif args[0] = (char *)str; args[1] = 0; #ifdef __cplusplus ex = env->NewObjectA ( jc, jm, (jvalue *)args ); rval = env->Throw((jthrowable) ex ); #else ex = (*env)->NewObjectA ( env, jc, jm, (jvalue *)args ); rval = (*env)->Throw(env, ex ); #endif if (rval < 0) { fprintf(stderr, "FATAL ERROR: Unsupported: Throw failed\n"); return JNI_FALSE; } return JNI_TRUE; } /* * h5libraryError() determines the HDF-5 major error code * and creates and throws the appropriate sub-class of * HDF5LibraryException(). This routine should be called * whenever a call to the HDF-5 library fails, i.e., when * the return is -1. * * Note: This routine never returns from the 'throw', * and the Java native method immediately raises the * exception. */ jboolean h5libraryError( JNIEnv *env ) { jmethodID jm; jclass jc; jvalue args[4]; char *exception; jobject ex; jstring min_msg_str, maj_msg_str; char *min_msg, *maj_msg; int rval, min_num, maj_num; maj_num = (int)getMajorErrorNumber(); maj_msg = (char *)H5Eget_major((H5E_major_t)maj_num); exception = (char *)defineHDF5LibraryException(maj_num); #ifdef __cplusplus jc = env->FindClass(exception); #else jc = (*env)->FindClass(env, exception); #endif if (jc == NULL) { return JNI_FALSE; } #ifdef __cplusplus jm = env->GetMethodID(jc, "", "(ILjava/lang/String;ILjava/lang/String;)V"); #else jm = (*env)->GetMethodID(env, jc, "", "(ILjava/lang/String;ILjava/lang/String;)V"); #endif if (jm == NULL) { fprintf(stderr, "FATAL ERROR: h5libraryError: Cannot find constructor\n"); return JNI_FALSE; } min_num = (int)getMinorErrorNumber(); min_msg = (char *)H5Eget_minor((H5E_minor_t)min_num); #ifdef __cplusplus maj_msg_str = env->NewStringUTF(maj_msg); min_msg_str = env->NewStringUTF(min_msg); #else maj_msg_str = (*env)->NewStringUTF(env,maj_msg); min_msg_str = (*env)->NewStringUTF(env,min_msg); #endif if (maj_msg_str == NULL || min_msg_str == NULL) { fprintf(stderr, "FATAL ERROR: h5libraryError: Out of Memory\n"); return JNI_FALSE; } args[0].i = maj_num; args[1].l = maj_msg_str; args[2].i = min_num; args[3].l = min_msg_str; #ifdef __cplusplus ex = env->NewObjectA ( jc, jm, args ); rval = env->Throw((jthrowable) ex ); #else ex = (*env)->NewObjectA ( env, jc, jm, (jvalue *)args ); rval = (*env)->Throw(env, ex ); #endif if (rval < 0) { fprintf(stderr, "FATAL ERROR: h5libraryError: Throw failed\n"); return JNI_FALSE; } return JNI_TRUE; } /* * A constant that is not defined in J2C throws an 'IllegalArgumentException'. * * Note: This routine never returns from the 'throw', * and the Java native method immediately raises the * exception. */ jboolean h5illegalConstantError(JNIEnv *env) { jmethodID jm; jclass jc; char * args[2]; jobject ex; jstring str; int rval; #ifdef __cplusplus jc = env->FindClass("java/lang/IllegalArgumentException"); #else jc = (*env)->FindClass(env, "java/lang/IllegalArgumentException"); #endif if (jc == NULL) { return JNI_FALSE; } #ifdef __cplusplus jm = env->GetMethodID(jc, "", "(Ljava/lang/String;)V"); #else jm = (*env)->GetMethodID(env, jc, "", "(Ljava/lang/String;)V"); #endif if (jm == NULL) { return JNI_FALSE; } #ifdef __cplusplus str = env->NewStringUTF("Illegal java constant"); #else str = (*env)->NewStringUTF(env,"Illegal java constant"); #endif args[0] = (char *)str; args[1] = 0; #ifdef __cplusplus ex = env->NewObjectA ( jc, jm, (jvalue *)args ); rval = env->Throw((jthrowable) ex ); #else ex = (*env)->NewObjectA ( env, jc, jm, (jvalue *)args ); rval = (*env)->Throw(env, ex ); #endif if (rval < 0) { fprintf(stderr, "FATAL ERROR: Unsupported: Throw failed\n"); return JNI_FALSE; } return JNI_TRUE; } /* raiseException(). This routine is called to generate * an arbitrary Java exception with a particular message. * * Note: This routine never returns from the 'throw', * and the Java native method immediately raises the * exception. */ jboolean h5raiseException( JNIEnv *env, char *exception, char *message) { jmethodID jm; jclass jc; char * args[2]; jobject ex; jstring str; int rval; #ifdef __cplusplus jc = env->FindClass(exception); #else jc = (*env)->FindClass(env, exception); #endif if (jc == NULL) { return JNI_FALSE; } #ifdef __cplusplus jm = env->GetMethodID(jc, "", "(Ljava/lang/String;)V"); #else jm = (*env)->GetMethodID(env, jc, "", "(Ljava/lang/String;)V"); #endif if (jm == NULL) { return JNI_FALSE; } #ifdef __cplusplus str = env->NewStringUTF(message); #else str = (*env)->NewStringUTF(env,message); #endif args[0] = (char *)str; args[1] = 0; #ifdef __cplusplus ex = env->NewObjectA ( jc, jm, (jvalue *)args ); rval = env->Throw( (jthrowable)ex ); #else ex = (*env)->NewObjectA ( env, jc, jm, (jvalue *)args ); rval = (*env)->Throw(env, ex ); #endif if (rval < 0) { fprintf(stderr, "FATAL ERROR: raiseException: Throw failed\n"); return JNI_FALSE; } return JNI_TRUE; } /* jboolean buildException( JNIEnv *env, char *exception, jint HDFerr) { jmethodID jm; jclass jc; int args[2]; jobject ex; int rval; jc = (*env)->FindClass(env, exception); if (jc == NULL) { return JNI_FALSE; } jm = (*env)->GetMethodID(env, jc, "", "(I)V"); if (jm == NULL) { return JNI_FALSE; } args[0] = HDFerr; args[1] = 0; ex = (*env)->NewObjectA ( env, jc, jm, (jvalue *)args ); rval = (*env)->Throw(env, ex ); if (rval < 0) { fprintf(stderr, "FATAL ERROR: raiseException: Throw failed\n"); return JNI_FALSE; } return JNI_TRUE; } */ /* * defineHDF5LibraryException() returns the name of the sub-class * which goes with an HDF-5 error code. */ char *defineHDF5LibraryException(int maj_num) { H5E_major_t err_num = (H5E_major_t) maj_num; if (err_num == H5E_ARGS) return "ncsa/hdf/hdf5lib/exceptions/HDF5FunctionArgumentException"; else if (err_num == H5E_RESOURCE) return "ncsa/hdf/hdf5lib/exceptions/HDF5ResourceUnavailableException"; else if (err_num == H5E_INTERNAL) return "ncsa/hdf/hdf5lib/exceptions/HDF5InternalErrorException"; else if (err_num == H5E_FILE) return "ncsa/hdf/hdf5lib/exceptions/HDF5FileInterfaceException"; else if (err_num == H5E_IO) return "ncsa/hdf/hdf5lib/exceptions/HDF5LowLevelIOException"; else if (err_num == H5E_FUNC) return "ncsa/hdf/hdf5lib/exceptions/HDF5FunctionEntryExitException"; else if (err_num == H5E_ATOM) return "ncsa/hdf/hdf5lib/exceptions/HDF5AtomException"; else if (err_num == H5E_CACHE) return "ncsa/hdf/hdf5lib/exceptions/HDF5MetaDataCacheException"; else if (err_num == H5E_BTREE) return "ncsa/hdf/hdf5lib/exceptions/HDF5BtreeException"; else if (err_num == H5E_SYM) return "ncsa/hdf/hdf5lib/exceptions/HDF5SymbolTableException"; else if (err_num == H5E_HEAP) return "ncsa/hdf/hdf5lib/exceptions/HDF5HeapException"; else if (err_num == H5E_OHDR) return "ncsa/hdf/hdf5lib/exceptions/HDF5ObjectHeaderException"; else if (err_num == H5E_DATATYPE) return "ncsa/hdf/hdf5lib/exceptions/HDF5DatatypeInterfaceException"; else if (err_num == H5E_DATASPACE) return "ncsa/hdf/hdf5lib/exceptions/HDF5DataspaceInterfaceException"; else if (err_num == H5E_DATASET) return "ncsa/hdf/hdf5lib/exceptions/HDF5DatasetInterfaceException"; else if (err_num == H5E_STORAGE) return "ncsa/hdf/hdf5lib/exceptions/HDF5DataStorageException"; else if (err_num == H5E_PLIST) return "ncsa/hdf/hdf5lib/exceptions/HDF5PropertyListInterfaceException"; else if (err_num == H5E_ATTR) return "ncsa/hdf/hdf5lib/exceptions/HDF5AttributeException"; else if (err_num == H5E_PLINE) return "ncsa/hdf/hdf5lib/exceptions/HDF5DataFiltersException"; else if (err_num == H5E_EFL) return "ncsa/hdf/hdf5lib/exceptions/HDF5ExternalFileListException"; else if (err_num == H5E_REFERENCE) return "ncsa/hdf/hdf5lib/exceptions/HDF5ReferenceException"; else return "ncsa/hdf/hdf5lib/exceptions/HDF5LibraryException"; } #ifdef __cplusplus } #endif libsis-jhdf5-java-14.12.1/source/c/jhdf5/h5ConstantsJHDF5.c000077500000000000000000000722301256564762100227270ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ #ifdef __cplusplus extern "C" { #endif #include "hdf5.h" #include "h5ConstantsJHDF5.h" #include /* * Class: ncsa_hdf_hdf5lib_H5Header converts Java constants defined * at ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.java to HDF5 runtime global variables. * Method: J2c * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_J2C (JNIEnv *env, jclass clss, jint java_constant) { switch (java_constant) { case JH5_SZIP_MAX_PIXELS_PER_BLOCK : return H5_SZIP_MAX_PIXELS_PER_BLOCK; case JH5_SZIP_NN_OPTION_MASK : return H5_SZIP_NN_OPTION_MASK; case JH5_SZIP_EC_OPTION_MASK : return H5_SZIP_EC_OPTION_MASK; case JH5_SZIP_ALLOW_K13_OPTION_MASK : return H5_SZIP_ALLOW_K13_OPTION_MASK; case JH5_SZIP_CHIP_OPTION_MASK : return H5_SZIP_CHIP_OPTION_MASK; case JH5D_ALLOC_TIME_DEFAULT : return H5D_ALLOC_TIME_DEFAULT; case JH5D_ALLOC_TIME_EARLY : return H5D_ALLOC_TIME_EARLY; case JH5D_ALLOC_TIME_ERROR : return H5D_ALLOC_TIME_ERROR; case JH5D_ALLOC_TIME_INCR : return H5D_ALLOC_TIME_INCR; case JH5D_ALLOC_TIME_LATE : return H5D_ALLOC_TIME_LATE; case JH5D_CHUNKED : return H5D_CHUNKED; case JH5D_COMPACT : return H5D_COMPACT; case JH5D_CONTIGUOUS : return H5D_CONTIGUOUS; case JH5D_FILL_TIME_ALLOC : return H5D_FILL_TIME_ALLOC; case JH5D_FILL_TIME_ERROR : return H5D_FILL_TIME_ERROR; case JH5D_FILL_TIME_NEVER : return H5D_FILL_TIME_NEVER; case JH5D_FILL_VALUE_DEFAULT : return H5D_FILL_VALUE_DEFAULT; case JH5D_FILL_VALUE_ERROR : return H5D_FILL_VALUE_ERROR; case JH5D_FILL_VALUE_UNDEFINED : return H5D_FILL_VALUE_UNDEFINED; case JH5D_FILL_VALUE_USER_DEFINED : return H5D_FILL_VALUE_USER_DEFINED; case JH5D_LAYOUT_ERROR : return H5D_LAYOUT_ERROR; case JH5D_NLAYOUTS : return H5D_NLAYOUTS; case JH5D_SPACE_STATUS_ALLOCATED : return H5D_SPACE_STATUS_ALLOCATED; case JH5D_SPACE_STATUS_ERROR : return H5D_SPACE_STATUS_ERROR; case JH5D_SPACE_STATUS_NOT_ALLOCATED : return H5D_SPACE_STATUS_NOT_ALLOCATED; case JH5D_SPACE_STATUS_PART_ALLOCATED : return H5D_SPACE_STATUS_PART_ALLOCATED; case JH5E_ALIGNMENT : return H5E_ALIGNMENT; case JH5E_ALREADYEXISTS : return H5E_ALREADYEXISTS; case JH5E_ALREADYINIT : return H5E_ALREADYINIT; case JH5E_ARGS : return H5E_ARGS; case JH5E_ATOM : return H5E_ATOM; case JH5E_ATTR : return H5E_ATTR; case JH5E_BADATOM : return H5E_BADATOM; case JH5E_BADFILE : return H5E_BADFILE; case JH5E_BADGROUP : return H5E_BADGROUP; case JH5E_BADMESG : return H5E_BADMESG; case JH5E_BADRANGE : return H5E_BADRANGE; case JH5E_BADSELECT : return H5E_BADSELECT; case JH5E_BADSIZE : return H5E_BADSIZE; case JH5E_BADTYPE : return H5E_BADTYPE; case JH5E_BADVALUE : return H5E_BADVALUE; case JH5E_BTREE : return H5E_BTREE; case JH5E_CACHE : return H5E_CACHE; case JH5E_CALLBACK : return H5E_CALLBACK; case JH5E_CANAPPLY : return H5E_CANAPPLY; /*case JH5E_CANTALLOC : return H5E_CANTALLOC; case JH5E_CANTCHANGE : return H5E_CANTCHANGE; removed from 1.6.4*/ case JH5E_CANTCLIP : return H5E_CANTCLIP; case JH5E_CANTCLOSEFILE : return H5E_CANTCLOSEFILE; case JH5E_CANTCONVERT : return H5E_CANTCONVERT; case JH5E_CANTCOPY : return H5E_CANTCOPY; case JH5E_CANTCOUNT : return H5E_CANTCOUNT; case JH5E_CANTCREATE : return H5E_CANTCREATE; case JH5E_CANTDEC : return H5E_CANTDEC; case JH5E_CANTDECODE : return H5E_CANTDECODE; case JH5E_CANTDELETE : return H5E_CANTDELETE; case JH5E_CANTENCODE : return H5E_CANTENCODE; case JH5E_CANTFLUSH : return H5E_CANTFLUSH; case JH5E_CANTFREE : return H5E_CANTFREE; case JH5E_CANTGET : return H5E_CANTGET; case JH5E_CANTINC : return H5E_CANTINC; case JH5E_CANTINIT : return H5E_CANTINIT; case JH5E_CANTINSERT : return H5E_CANTINSERT; case JH5E_CANTLIST : return H5E_CANTLIST; case JH5E_CANTLOAD : return H5E_CANTLOAD; case JH5E_CANTLOCK : return H5E_CANTLOCK; /*case JH5E_CANTMAKETREE : return H5E_CANTMAKETREE; removed from 1.8.0*/ case JH5E_CANTNEXT : return H5E_CANTNEXT; case JH5E_CANTOPENFILE : return H5E_CANTOPENFILE; case JH5E_CANTOPENOBJ : return H5E_CANTOPENOBJ; /* case JH5E_CANTRECV : return H5E_CANTRECV; removed from 1.6.4*/ case JH5E_CANTREGISTER : return H5E_CANTREGISTER; case JH5E_CANTRELEASE : return H5E_CANTRELEASE; case JH5E_CANTSELECT : return H5E_CANTSELECT; /* case JH5E_CANTSENDMDATA : return H5E_CANTSENDMDATA; removed from 1.6.4*/ case JH5E_CANTSET : return H5E_CANTSET; case JH5E_CANTSPLIT : return H5E_CANTSPLIT; case JH5E_CANTUNLOCK : return H5E_CANTUNLOCK; case JH5E_CLOSEERROR : return H5E_CLOSEERROR; case JH5E_COMPLEN : return H5E_COMPLEN; /* removed from HDF5 1.6.5 case JH5E_CWG : return H5E_CWG; */ case JH5E_DATASET : return H5E_DATASET; case JH5E_DATASPACE : return H5E_DATASPACE; case JH5E_DATATYPE : return H5E_DATATYPE; case JH5E_DUPCLASS : return H5E_DUPCLASS; case JH5E_EFL : return H5E_EFL; case JH5E_EXISTS : return H5E_EXISTS; case JH5E_FCNTL : return H5E_FCNTL; case JH5E_FILE : return H5E_FILE; case JH5E_FILEEXISTS : return H5E_FILEEXISTS; case JH5E_FILEOPEN : return H5E_FILEOPEN; /* case JH5E_FPHDF5 : return H5E_FPHDF5; removed from 1.6.4*/ case JH5E_FUNC : return H5E_FUNC; case JH5E_HEAP : return H5E_HEAP; case JH5E_INTERNAL : return H5E_INTERNAL; case JH5E_IO : return H5E_IO; case JH5E_LINK : return H5E_LINK; case JH5E_LINKCOUNT : return H5E_LINKCOUNT; case JH5E_MOUNT : return H5E_MOUNT; case JH5E_MPI : return H5E_MPI; case JH5E_MPIERRSTR : return H5E_MPIERRSTR; case JH5E_NOFILTER : return H5E_NOFILTER; case JH5E_NOIDS : return H5E_NOIDS; case JH5E_NONE_MAJOR : return H5E_NONE_MAJOR; case JH5E_NONE_MINOR : return H5E_NONE_MINOR; case JH5E_NOSPACE : return H5E_NOSPACE; case JH5E_NOTCACHED : return H5E_NOTCACHED; case JH5E_NOTFOUND : return H5E_NOTFOUND; case JH5E_NOTHDF5 : return H5E_NOTHDF5; case JH5E_OHDR : return H5E_OHDR; case JH5E_OVERFLOW : return H5E_OVERFLOW; case JH5E_PLINE : return H5E_PLINE; case JH5E_PLIST : return H5E_PLIST; case JH5E_PROTECT : return H5E_PROTECT; case JH5E_READERROR : return H5E_READERROR; case JH5E_REFERENCE : return H5E_REFERENCE; case JH5E_RESOURCE : return H5E_RESOURCE; case JH5E_RS : return H5E_RS; case JH5E_SEEKERROR : return H5E_SEEKERROR; case JH5E_SETLOCAL : return H5E_SETLOCAL; /*case JH5E_SLINK : return H5E_SLINK; removed from 1.8.0*/ case JH5E_STORAGE : return H5E_STORAGE; case JH5E_SYM : return H5E_SYM; /*case JH5E_TBBT : return H5E_TBBT; removed from 1.8.0*/ case JH5E_TRUNCATED : return H5E_TRUNCATED; case JH5E_TST : return H5E_TST; case JH5E_UNINITIALIZED : return H5E_UNINITIALIZED; case JH5E_UNSUPPORTED : return H5E_UNSUPPORTED; case JH5E_VERSION : return H5E_VERSION; case JH5E_VFL : return H5E_VFL; case JH5E_WALK_DOWNWARD : return H5E_WALK_DOWNWARD; case JH5E_WALK_UPWARD : return H5E_WALK_UPWARD; case JH5E_WRITEERROR : return H5E_WRITEERROR; case JH5F_ACC_CREAT : return H5F_ACC_CREAT; case JH5F_ACC_DEBUG : return H5F_ACC_DEBUG; case JH5F_ACC_EXCL : return H5F_ACC_EXCL; case JH5F_ACC_RDONLY : return H5F_ACC_RDONLY; case JH5F_ACC_RDWR : return H5F_ACC_RDWR; case JH5F_ACC_TRUNC : return H5F_ACC_TRUNC; case JH5F_CLOSE_DEFAULT : return H5F_CLOSE_DEFAULT; case JH5F_CLOSE_SEMI : return H5F_CLOSE_SEMI; case JH5F_CLOSE_STRONG : return H5F_CLOSE_STRONG; case JH5F_CLOSE_WEAK : return H5F_CLOSE_WEAK; case JH5F_OBJ_ALL : return H5F_OBJ_ALL; case JH5F_OBJ_DATASET : return H5F_OBJ_DATASET; case JH5F_OBJ_DATATYPE : return H5F_OBJ_DATATYPE; case JH5F_OBJ_FILE : return H5F_OBJ_FILE; case JH5F_OBJ_ATTR : return H5F_OBJ_ATTR; case JH5F_OBJ_GROUP : return H5F_OBJ_GROUP; case JH5F_SCOPE_GLOBAL : return H5F_SCOPE_GLOBAL; case JH5F_SCOPE_LOCAL : return H5F_SCOPE_LOCAL; case JH5F_UNLIMITED : return (int)H5F_UNLIMITED; case JH5F_LIBVER_EARLIEST : return H5F_LIBVER_EARLIEST; case JH5F_LIBVER_LATEST : return H5F_LIBVER_LATEST; case JH5G_DATASET : return H5G_DATASET; case JH5G_GROUP : return H5G_GROUP; case JH5G_LINK : return H5G_LINK; case JH5G_LINK_ERROR : return H5G_LINK_ERROR; case JH5G_LINK_HARD : return H5G_LINK_HARD; case JH5G_LINK_SOFT : return H5G_LINK_SOFT; case JH5G_NLIBTYPES : return H5G_NLIBTYPES; case JH5G_NTYPES : return H5G_NTYPES; case JH5G_NUSERTYPES : return H5G_NUSERTYPES; /*case JH5G_RESERVED_4 : return H5G_RESERVED_4; removed from 1.8*/ case JH5G_RESERVED_5 : return H5G_RESERVED_5; case JH5G_RESERVED_6 : return H5G_RESERVED_6; case JH5G_RESERVED_7 : return H5G_RESERVED_7; case JH5G_SAME_LOC : return H5G_SAME_LOC; case JH5G_TYPE : return H5G_TYPE; case JH5G_UNKNOWN : return H5G_UNKNOWN; /*case JH5G_USERTYPE : return H5G_USERTYPE;*/ case JH5I_ATTR : return H5I_ATTR; case JH5I_BADID : return H5I_BADID; case JH5I_DATASET : return H5I_DATASET; case JH5I_DATASPACE : return H5I_DATASPACE; case JH5I_DATATYPE : return H5I_DATATYPE; case JH5I_FILE : return H5I_FILE; /* removed from HDF5 1.6.5 case JH5I_FILE_CLOSING : return H5I_FILE_CLOSING; */ case JH5I_GENPROP_CLS : return H5I_GENPROP_CLS; case JH5I_GENPROP_LST : return H5I_GENPROP_LST; case JH5I_GROUP : return H5I_GROUP; case JH5I_INVALID_HID : return H5I_INVALID_HID; /*case JH5I_NGROUPS : return H5I_NGROUPS; removed from 1.8*/ case JH5I_REFERENCE : return H5I_REFERENCE; /* case JH5I_TEMPBUF : return H5I_TEMPBUF; removed from 1.6.4*/ case JH5I_VFL : return H5I_VFL; case JH5O_TYPE_UNKNOWN : return H5O_TYPE_UNKNOWN; case JH5O_TYPE_GROUP : return H5O_TYPE_GROUP; case JH5O_TYPE_DATASET : return H5O_TYPE_DATASET; case JH5O_TYPE_NAMED_DATATYPE : return H5O_TYPE_NAMED_DATATYPE; case JH5O_TYPE_NTYPES : return H5O_TYPE_NTYPES; case JH5L_TYPE_ERROR : return H5L_TYPE_ERROR; case JH5L_TYPE_HARD : return H5L_TYPE_HARD; case JH5L_TYPE_SOFT : return H5L_TYPE_SOFT; case JH5L_TYPE_EXTERNAL : return H5L_TYPE_EXTERNAL; case JH5L_TYPE_MAX : return H5L_TYPE_MAX; case JH5P_DATASET_CREATE : return H5P_DATASET_CREATE; case JH5P_DATASET_CREATE_DEFAULT : return H5P_DATASET_CREATE_DEFAULT; case JH5P_DATASET_XFER : return H5P_DATASET_XFER; case JH5P_DATASET_XFER_DEFAULT : return H5P_DATASET_XFER_DEFAULT; case JH5P_FILE_ACCESS : return H5P_FILE_ACCESS; case JH5P_FILE_ACCESS_DEFAULT : return H5P_FILE_ACCESS_DEFAULT; case JH5P_FILE_CREATE : return H5P_FILE_CREATE; case JH5P_FILE_CREATE_DEFAULT : return H5P_FILE_CREATE_DEFAULT; case JH5P_DEFAULT : return H5P_DEFAULT; /*case JH5P_MOUNT : return H5P_MOUNT; case JH5P_MOUNT_DEFAULT : return H5P_MOUNT_DEFAULT; removed from 1.8*/ case JH5P_NO_CLASS : return H5P_NO_CLASS; /*case JH5P_NO_CLASS_DEFAULT : return H5P_NO_CLASS_DEFAULT; removed from 1.8*/ case JH5P_ROOT : return H5P_ROOT; case JH5P_OBJECT_CREATE : return H5P_OBJECT_CREATE; case JH5P_DATASET_ACCESS : return H5P_DATASET_ACCESS; case JH5P_DATASET_ACCESS_DEFAULT : return H5P_DATASET_ACCESS_DEFAULT; case JH5P_FILE_MOUNT : return H5P_FILE_MOUNT; case JH5P_FILE_MOUNT_DEFAULT : return H5P_FILE_MOUNT_DEFAULT; case JH5P_GROUP_CREATE : return H5P_GROUP_CREATE; case JH5P_GROUP_CREATE_DEFAULT : return H5P_GROUP_CREATE_DEFAULT; case JH5P_GROUP_ACCESS : return H5P_GROUP_ACCESS; case JH5P_GROUP_ACCESS_DEFAULT : return H5P_GROUP_ACCESS_DEFAULT; case JH5P_DATATYPE_CREATE : return H5P_DATATYPE_CREATE; case JH5P_DATATYPE_CREATE_DEFAULT : return H5P_DATATYPE_CREATE_DEFAULT; case JH5P_DATATYPE_ACCESS : return H5P_DATATYPE_ACCESS; case JH5P_DATATYPE_ACCESS_DEFAULT : return H5P_DATATYPE_ACCESS_DEFAULT; case JH5P_STRING_CREATE : return H5P_STRING_CREATE; case JH5P_ATTRIBUTE_CREATE : return H5P_ATTRIBUTE_CREATE; case JH5P_ATTRIBUTE_CREATE_DEFAULT : return H5P_ATTRIBUTE_CREATE_DEFAULT; case JH5P_OBJECT_COPY : return H5P_OBJECT_COPY; case JH5P_OBJECT_COPY_DEFAULT : return H5P_OBJECT_COPY_DEFAULT; case JH5P_LINK_CREATE : return H5P_LINK_CREATE; case JH5P_LINK_CREATE_DEFAULT : return H5P_LINK_CREATE_DEFAULT; case JH5P_LINK_ACCESS : return H5P_LINK_ACCESS; case JH5P_LINK_ACCESS_DEFAULT : return H5P_LINK_ACCESS_DEFAULT; case JH5R_BADTYPE : return H5R_BADTYPE; case JH5R_DATASET_REGION : return H5R_DATASET_REGION; /*case JH5R_INTERNAL : return H5R_INTERNAL; removed from 1.8*/ case JH5R_MAXTYPE : return H5R_MAXTYPE; case JH5R_OBJ_REF_BUF_SIZE : return H5R_OBJ_REF_BUF_SIZE; case JH5R_OBJECT : return H5R_OBJECT; case JH5S_ALL : return H5S_ALL; /*case JH5S_COMPLEX : return H5S_COMPLEX; removed from 1.8*/ case JH5S_MAX_RANK : return H5S_MAX_RANK; case JH5S_NO_CLASS : return H5S_NO_CLASS; case JH5S_NULL : return H5S_NULL; case JH5S_SCALAR : return H5S_SCALAR; case JH5S_SEL_ALL : return H5S_SEL_ALL; case JH5S_SEL_ERROR : return H5S_SEL_ERROR; case JH5S_SEL_HYPERSLABS : return H5S_SEL_HYPERSLABS; case JH5S_SEL_N : return H5S_SEL_N; case JH5S_SEL_NONE : return H5S_SEL_NONE; case JH5S_SEL_POINTS : return H5S_SEL_POINTS; case JH5S_SELECT_AND : return H5S_SELECT_AND; case JH5S_SELECT_APPEND : return H5S_SELECT_APPEND; case JH5S_SELECT_INVALID : return H5S_SELECT_INVALID; case JH5S_SELECT_NOOP : return H5S_SELECT_NOOP; case JH5S_SELECT_NOTA : return H5S_SELECT_NOTA; case JH5S_SELECT_NOTB : return H5S_SELECT_NOTB; case JH5S_SELECT_OR : return H5S_SELECT_OR; case JH5S_SELECT_PREPEND : return H5S_SELECT_PREPEND; case JH5S_SELECT_SET : return H5S_SELECT_SET; case JH5S_SELECT_XOR : return H5S_SELECT_XOR; case JH5S_SIMPLE : return H5S_SIMPLE; case JH5S_UNLIMITED : return (int)H5S_UNLIMITED; case JH5T_ALPHA_B16 : return H5T_ALPHA_B16; case JH5T_ALPHA_B32 : return H5T_ALPHA_B32; case JH5T_ALPHA_B64 : return H5T_ALPHA_B64; case JH5T_ALPHA_B8 : return H5T_ALPHA_B8; case JH5T_ALPHA_F32 : return H5T_ALPHA_F32; case JH5T_ALPHA_F64 : return H5T_ALPHA_F64; case JH5T_ALPHA_I16 : return H5T_ALPHA_I16; case JH5T_ALPHA_I32 : return H5T_ALPHA_I32; case JH5T_ALPHA_I64 : return H5T_ALPHA_I64; case JH5T_ALPHA_I8 : return H5T_ALPHA_I8; case JH5T_ALPHA_U16 : return H5T_ALPHA_U16; case JH5T_ALPHA_U32 : return H5T_ALPHA_U32; case JH5T_ALPHA_U64 : return H5T_ALPHA_U64; case JH5T_ALPHA_U8 : return H5T_ALPHA_U8; case JH5T_ARRAY : return H5T_ARRAY; case JH5T_BITFIELD : return H5T_BITFIELD; case JH5T_BKG_NO : return H5T_BKG_NO; case JH5T_BKG_YES : return H5T_BKG_YES; case JH5T_C_S1 : return H5T_C_S1; case JH5T_COMPOUND : return H5T_COMPOUND; case JH5T_CONV_CONV : return H5T_CONV_CONV; case JH5T_CONV_FREE : return H5T_CONV_FREE; case JH5T_CONV_INIT : return H5T_CONV_INIT; case JH5T_CSET_ASCII : return H5T_CSET_ASCII; case JH5T_CSET_ERROR : return H5T_CSET_ERROR; case JH5T_CSET_UTF8 : return H5T_CSET_UTF8; case JH5T_CSET_RESERVED_10 : return H5T_CSET_RESERVED_10; case JH5T_CSET_RESERVED_11 : return H5T_CSET_RESERVED_11; case JH5T_CSET_RESERVED_12 : return H5T_CSET_RESERVED_12; case JH5T_CSET_RESERVED_13 : return H5T_CSET_RESERVED_13; case JH5T_CSET_RESERVED_14 : return H5T_CSET_RESERVED_14; case JH5T_CSET_RESERVED_15 : return H5T_CSET_RESERVED_15; case JH5T_CSET_RESERVED_2 : return H5T_CSET_RESERVED_2; case JH5T_CSET_RESERVED_3 : return H5T_CSET_RESERVED_3; case JH5T_CSET_RESERVED_4 : return H5T_CSET_RESERVED_4; case JH5T_CSET_RESERVED_5 : return H5T_CSET_RESERVED_5; case JH5T_CSET_RESERVED_6 : return H5T_CSET_RESERVED_6; case JH5T_CSET_RESERVED_7 : return H5T_CSET_RESERVED_7; case JH5T_CSET_RESERVED_8 : return H5T_CSET_RESERVED_8; case JH5T_CSET_RESERVED_9 : return H5T_CSET_RESERVED_9; case JH5T_DIR_ASCEND : return H5T_DIR_ASCEND; case JH5T_DIR_DEFAULT : return H5T_DIR_DEFAULT; case JH5T_DIR_DESCEND : return H5T_DIR_DESCEND; case JH5T_ENUM : return H5T_ENUM; case JH5T_FLOAT : return H5T_FLOAT; case JH5T_FORTRAN_S1 : return H5T_FORTRAN_S1; case JH5T_IEEE_F32BE : return H5T_IEEE_F32BE; case JH5T_IEEE_F32LE : return H5T_IEEE_F32LE; case JH5T_IEEE_F64BE : return H5T_IEEE_F64BE; case JH5T_IEEE_F64LE : return H5T_IEEE_F64LE; case JH5T_INTEGER : return H5T_INTEGER; case JH5T_INTEL_B16 : return H5T_INTEL_B16; case JH5T_INTEL_B32 : return H5T_INTEL_B32; case JH5T_INTEL_B64 : return H5T_INTEL_B64; case JH5T_INTEL_B8 : return H5T_INTEL_B8; case JH5T_INTEL_F32 : return H5T_INTEL_F32; case JH5T_INTEL_F64 : return H5T_INTEL_F64; case JH5T_INTEL_I16 : return H5T_INTEL_I16; case JH5T_INTEL_I32 : return H5T_INTEL_I32; case JH5T_INTEL_I64 : return H5T_INTEL_I64; case JH5T_INTEL_I8 : return H5T_INTEL_I8; case JH5T_INTEL_U16 : return H5T_INTEL_U16; case JH5T_INTEL_U32 : return H5T_INTEL_U32; case JH5T_INTEL_U64 : return H5T_INTEL_U64; case JH5T_INTEL_U8 : return H5T_INTEL_U8; case JH5T_MIPS_B16 : return H5T_MIPS_B16; case JH5T_MIPS_B32 : return H5T_MIPS_B32; case JH5T_MIPS_B64 : return H5T_MIPS_B64; case JH5T_MIPS_B8 : return H5T_MIPS_B8; case JH5T_MIPS_F32 : return H5T_MIPS_F32; case JH5T_MIPS_F64 : return H5T_MIPS_F64; case JH5T_MIPS_I16 : return H5T_MIPS_I16; case JH5T_MIPS_I32 : return H5T_MIPS_I32; case JH5T_MIPS_I64 : return H5T_MIPS_I64; case JH5T_MIPS_I8 : return H5T_MIPS_I8; case JH5T_MIPS_U16 : return H5T_MIPS_U16; case JH5T_MIPS_U32 : return H5T_MIPS_U32; case JH5T_MIPS_U64 : return H5T_MIPS_U64; case JH5T_MIPS_U8 : return H5T_MIPS_U8; case JH5T_NATIVE_B16 : return H5T_NATIVE_B16; case JH5T_NATIVE_B32 : return H5T_NATIVE_B32; case JH5T_NATIVE_B64 : return H5T_NATIVE_B64; case JH5T_NATIVE_B8 : return H5T_NATIVE_B8; case JH5T_NATIVE_CHAR : return H5T_NATIVE_CHAR; case JH5T_NATIVE_DOUBLE : return H5T_NATIVE_DOUBLE; case JH5T_NATIVE_FLOAT : return H5T_NATIVE_FLOAT; case JH5T_NATIVE_HADDR : return H5T_NATIVE_HADDR; case JH5T_NATIVE_HBOOL : return H5T_NATIVE_HBOOL; case JH5T_NATIVE_HERR : return H5T_NATIVE_HERR; case JH5T_NATIVE_HSIZE : return H5T_NATIVE_HSIZE; case JH5T_NATIVE_HSSIZE : return H5T_NATIVE_HSSIZE; case JH5T_NATIVE_INT : return H5T_NATIVE_INT; case JH5T_NATIVE_INT_FAST16 : return H5T_NATIVE_INT_FAST16; case JH5T_NATIVE_INT_FAST32 : return H5T_NATIVE_INT_FAST32; case JH5T_NATIVE_INT_FAST64 : return H5T_NATIVE_INT_FAST64; case JH5T_NATIVE_INT_FAST8 : return H5T_NATIVE_INT_FAST8; case JH5T_NATIVE_INT_LEAST16 : return H5T_NATIVE_INT_LEAST16; case JH5T_NATIVE_INT_LEAST32 : return H5T_NATIVE_INT_LEAST32; case JH5T_NATIVE_INT_LEAST64 : return H5T_NATIVE_INT_LEAST64; case JH5T_NATIVE_INT_LEAST8 : return H5T_NATIVE_INT_LEAST8; case JH5T_NATIVE_INT16 : return H5T_NATIVE_INT16; case JH5T_NATIVE_INT32 : return H5T_NATIVE_INT32; case JH5T_NATIVE_INT64 : return H5T_NATIVE_INT64; case JH5T_NATIVE_INT8 : return H5T_NATIVE_INT8; case JH5T_NATIVE_LDOUBLE : return H5T_NATIVE_LDOUBLE; case JH5T_NATIVE_LLONG : return H5T_NATIVE_LLONG; case JH5T_NATIVE_LONG : return H5T_NATIVE_LONG; case JH5T_NATIVE_OPAQUE : return H5T_NATIVE_OPAQUE; case JH5T_NATIVE_SCHAR : return H5T_NATIVE_SCHAR; case JH5T_NATIVE_SHORT : return H5T_NATIVE_SHORT; case JH5T_NATIVE_UCHAR : return H5T_NATIVE_UCHAR; case JH5T_NATIVE_UINT : return H5T_NATIVE_UINT; case JH5T_NATIVE_UINT_FAST16 : return H5T_NATIVE_UINT_FAST16; case JH5T_NATIVE_UINT_FAST32 : return H5T_NATIVE_UINT_FAST32; case JH5T_NATIVE_UINT_FAST64 : return H5T_NATIVE_UINT_FAST64; case JH5T_NATIVE_UINT_FAST8 : return H5T_NATIVE_UINT_FAST8; case JH5T_NATIVE_UINT_LEAST16 : return H5T_NATIVE_UINT_LEAST16; case JH5T_NATIVE_UINT_LEAST32 : return H5T_NATIVE_UINT_LEAST32; case JH5T_NATIVE_UINT_LEAST64 : return H5T_NATIVE_UINT_LEAST64; case JH5T_NATIVE_UINT_LEAST8 : return H5T_NATIVE_UINT_LEAST8; case JH5T_NATIVE_UINT16 : return H5T_NATIVE_UINT16; case JH5T_NATIVE_UINT32 : return H5T_NATIVE_UINT32; case JH5T_NATIVE_UINT64 : return H5T_NATIVE_UINT64; case JH5T_NATIVE_UINT8 : return H5T_NATIVE_UINT8; case JH5T_NATIVE_ULLONG : return H5T_NATIVE_ULLONG; case JH5T_NATIVE_ULONG : return H5T_NATIVE_ULONG; case JH5T_NATIVE_USHORT : return H5T_NATIVE_USHORT; case JH5T_NCLASSES : return H5T_NCLASSES; case JH5T_NO_CLASS : return H5T_NO_CLASS; case JH5T_NORM_ERROR : return H5T_NORM_ERROR; case JH5T_NORM_IMPLIED : return H5T_NORM_IMPLIED; case JH5T_NORM_MSBSET : return H5T_NORM_MSBSET; case JH5T_NORM_NONE : return H5T_NORM_NONE; case JH5T_NPAD : return H5T_NPAD; case JH5T_NSGN : return H5T_NSGN; case JH5T_OPAQUE : return H5T_OPAQUE; case JH5T_OPAQUE_TAG_MAX : return H5T_OPAQUE_TAG_MAX; case JH5T_ORDER_BE : return H5T_ORDER_BE; case JH5T_ORDER_ERROR : return H5T_ORDER_ERROR; case JH5T_ORDER_LE : return H5T_ORDER_LE; case JH5T_ORDER_NONE : return H5T_ORDER_NONE; case JH5T_ORDER_VAX : return H5T_ORDER_VAX; case JH5T_PAD_BACKGROUND : return H5T_PAD_BACKGROUND; case JH5T_PAD_ERROR : return H5T_PAD_ERROR; case JH5T_PAD_ONE : return H5T_PAD_ONE; case JH5T_PAD_ZERO : return H5T_PAD_ZERO; case JH5T_PERS_DONTCARE : return H5T_PERS_DONTCARE; case JH5T_PERS_HARD : return H5T_PERS_HARD; case JH5T_PERS_SOFT : return H5T_PERS_SOFT; case JH5T_REFERENCE : return H5T_REFERENCE; case JH5T_SGN_2 : return H5T_SGN_2; case JH5T_SGN_ERROR : return H5T_SGN_ERROR; case JH5T_SGN_NONE : return H5T_SGN_NONE; case JH5T_STD_B16BE : return H5T_STD_B16BE; case JH5T_STD_B16LE : return H5T_STD_B16LE; case JH5T_STD_B32BE : return H5T_STD_B32BE; case JH5T_STD_B32LE : return H5T_STD_B32LE; case JH5T_STD_B64BE : return H5T_STD_B64BE; case JH5T_STD_B64LE : return H5T_STD_B64LE; case JH5T_STD_B8BE : return H5T_STD_B8BE; case JH5T_STD_B8LE : return H5T_STD_B8LE; case JH5T_STD_I16BE : return H5T_STD_I16BE; case JH5T_STD_I16LE : return H5T_STD_I16LE; case JH5T_STD_I32BE : return H5T_STD_I32BE; case JH5T_STD_I32LE : return H5T_STD_I32LE; case JH5T_STD_I64BE : return H5T_STD_I64BE; case JH5T_STD_I64LE : return H5T_STD_I64LE; case JH5T_STD_I8BE : return H5T_STD_I8BE; case JH5T_STD_I8LE : return H5T_STD_I8LE; case JH5T_STD_REF_DSETREG : return H5T_STD_REF_DSETREG; case JH5T_STD_REF_OBJ : return H5T_STD_REF_OBJ; case JH5T_STD_U16BE : return H5T_STD_U16BE; case JH5T_STD_U16LE : return H5T_STD_U16LE; case JH5T_STD_U32BE : return H5T_STD_U32BE; case JH5T_STD_U32LE : return H5T_STD_U32LE; case JH5T_STD_U64BE : return H5T_STD_U64BE; case JH5T_STD_U64LE : return H5T_STD_U64LE; case JH5T_STD_U8BE : return H5T_STD_U8BE; case JH5T_STD_U8LE : return H5T_STD_U8LE; case JH5T_STR_ERROR : return H5T_STR_ERROR; case JH5T_STR_NULLPAD : return H5T_STR_NULLPAD; case JH5T_STR_NULLTERM : return H5T_STR_NULLTERM; case JH5T_STR_RESERVED_10 : return H5T_STR_RESERVED_10; case JH5T_STR_RESERVED_11 : return H5T_STR_RESERVED_11; case JH5T_STR_RESERVED_12 : return H5T_STR_RESERVED_12; case JH5T_STR_RESERVED_13 : return H5T_STR_RESERVED_13; case JH5T_STR_RESERVED_14 : return H5T_STR_RESERVED_14; case JH5T_STR_RESERVED_15 : return H5T_STR_RESERVED_15; case JH5T_STR_RESERVED_3 : return H5T_STR_RESERVED_3; case JH5T_STR_RESERVED_4 : return H5T_STR_RESERVED_4; case JH5T_STR_RESERVED_5 : return H5T_STR_RESERVED_5; case JH5T_STR_RESERVED_6 : return H5T_STR_RESERVED_6; case JH5T_STR_RESERVED_7 : return H5T_STR_RESERVED_7; case JH5T_STR_RESERVED_8 : return H5T_STR_RESERVED_8; case JH5T_STR_RESERVED_9 : return H5T_STR_RESERVED_9; case JH5T_STR_SPACEPAD : return H5T_STR_SPACEPAD; case JH5T_STRING : return H5T_STRING; case JH5T_TIME : return H5T_TIME; case JH5T_UNIX_D32BE : return H5T_UNIX_D32BE; case JH5T_UNIX_D32LE : return H5T_UNIX_D32LE; case JH5T_UNIX_D64BE : return H5T_UNIX_D64BE; case JH5T_UNIX_D64LE : return H5T_UNIX_D64LE; case JH5T_VARIABLE : return (jint) H5T_VARIABLE; case JH5T_VLEN : return H5T_VLEN; case JH5Z_CB_CONT : return H5Z_CB_CONT; case JH5Z_CB_ERROR : return H5Z_CB_ERROR; case JH5Z_CB_FAIL : return H5Z_CB_FAIL; case JH5Z_CB_NO : return H5Z_CB_NO; case JH5Z_DISABLE_EDC : return H5Z_DISABLE_EDC; case JH5Z_ENABLE_EDC : return H5Z_ENABLE_EDC; case JH5Z_ERROR_EDC : return H5Z_ERROR_EDC; case JH5Z_FILTER_DEFLATE : return H5Z_FILTER_DEFLATE; case JH5Z_FILTER_ERROR : return H5Z_FILTER_ERROR; case JH5Z_FILTER_FLETCHER32 : return H5Z_FILTER_FLETCHER32; case JH5Z_FILTER_MAX : return H5Z_FILTER_MAX; case JH5Z_FILTER_NONE : return H5Z_FILTER_NONE; case JH5Z_FILTER_RESERVED : return H5Z_FILTER_RESERVED; case JH5Z_FILTER_SHUFFLE : return H5Z_FILTER_SHUFFLE; case JH5Z_FILTER_SZIP : return H5Z_FILTER_SZIP; case JH5Z_FLAG_DEFMASK : return H5Z_FLAG_DEFMASK; case JH5Z_FLAG_INVMASK : return H5Z_FLAG_INVMASK; case JH5Z_FLAG_MANDATORY : return H5Z_FLAG_MANDATORY; case JH5Z_FLAG_OPTIONAL : return H5Z_FLAG_OPTIONAL; case JH5Z_FLAG_REVERSE : return H5Z_FLAG_REVERSE; case JH5Z_FLAG_SKIP_EDC : return H5Z_FLAG_SKIP_EDC; case JH5Z_MAX_NFILTERS : return H5Z_MAX_NFILTERS; case JH5Z_NO_EDC : return H5Z_NO_EDC; case JH5Z_FILTER_CONFIG_ENCODE_ENABLED : return H5Z_FILTER_CONFIG_ENCODE_ENABLED; case JH5Z_FILTER_CONFIG_DECODE_ENABLED : return H5Z_FILTER_CONFIG_DECODE_ENABLED; case JH5Z_SO_INT : return H5Z_SO_INT; case JH5Z_SO_FLOAT_DSCALE : return H5Z_SO_FLOAT_DSCALE; case JH5Z_SO_FLOAT_ESCALE : return H5Z_SO_FLOAT_ESCALE; default: h5illegalConstantError(env); return -1; } } #ifdef __cplusplus } #endif libsis-jhdf5-java-14.12.1/source/c/jhdf5/h5ConstantsJHDF5.h000077500000000000000000000355771256564762100227510ustar00rootroot00000000000000/* * The Java constants defined at ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.java * * The values are arbitrary, but it is very important that this * file has the same values as HDF5Constants.java. */ #include "hdf5.h" #define JH5_SZIP_MAX_PIXELS_PER_BLOCK 1000 #define JH5_SZIP_NN_OPTION_MASK 1010 #define JH5_SZIP_EC_OPTION_MASK 1020 #define JH5_SZIP_ALLOW_K13_OPTION_MASK 1021 #define JH5_SZIP_CHIP_OPTION_MASK 1022 #define JH5D_ALLOC_TIME_DEFAULT 1030 #define JH5D_ALLOC_TIME_EARLY 1040 #define JH5D_ALLOC_TIME_ERROR 1050 #define JH5D_ALLOC_TIME_INCR 1060 #define JH5D_ALLOC_TIME_LATE 1070 #define JH5D_CHUNKED 1080 #define JH5D_COMPACT 1090 #define JH5D_CONTIGUOUS 1100 #define JH5D_FILL_TIME_ALLOC 1110 #define JH5D_FILL_TIME_ERROR 1120 #define JH5D_FILL_TIME_NEVER 1130 #define JH5D_FILL_VALUE_DEFAULT 1140 #define JH5D_FILL_VALUE_ERROR 1150 #define JH5D_FILL_VALUE_UNDEFINED 1160 #define JH5D_FILL_VALUE_USER_DEFINED 1170 #define JH5D_LAYOUT_ERROR 1180 #define JH5D_NLAYOUTS 1190 #define JH5D_SPACE_STATUS_ALLOCATED 1200 #define JH5D_SPACE_STATUS_ERROR 1210 #define JH5D_SPACE_STATUS_NOT_ALLOCATED 1220 #define JH5D_SPACE_STATUS_PART_ALLOCATED 1230 #define JH5E_ALIGNMENT 1240 #define JH5E_ALREADYEXISTS 1250 #define JH5E_ALREADYINIT 1260 #define JH5E_ARGS 1270 #define JH5E_ATOM 1280 #define JH5E_ATTR 1290 #define JH5E_BADATOM 1300 #define JH5E_BADFILE 1310 #define JH5E_BADGROUP 1320 #define JH5E_BADMESG 1330 #define JH5E_BADRANGE 1340 #define JH5E_BADSELECT 1350 #define JH5E_BADSIZE 1360 #define JH5E_BADTYPE 1370 #define JH5E_BADVALUE 1380 #define JH5E_BTREE 1390 #define JH5E_CACHE 1400 #define JH5E_CALLBACK 1410 #define JH5E_CANAPPLY 1420 /*#define JH5E_CANTALLOC 1430 removed from 1.6.4 */ /*#define JH5E_CANTCHANGE 1440 removed from 1.6.4 */ #define JH5E_CANTCLIP 1450 #define JH5E_CANTCLOSEFILE 1460 #define JH5E_CANTCONVERT 1470 #define JH5E_CANTCOPY 1480 #define JH5E_CANTCOUNT 1490 #define JH5E_CANTCREATE 1500 #define JH5E_CANTDEC 1510 #define JH5E_CANTDECODE 1520 #define JH5E_CANTDELETE 1530 #define JH5E_CANTENCODE 1540 #define JH5E_CANTFLUSH 1550 #define JH5E_CANTFREE 1560 #define JH5E_CANTGET 1570 #define JH5E_CANTINC 1580 #define JH5E_CANTINIT 1590 #define JH5E_CANTINSERT 1600 #define JH5E_CANTLIST 1610 #define JH5E_CANTLOAD 1620 #define JH5E_CANTLOCK 1630 #define JH5E_CANTMAKETREE 1640 #define JH5E_CANTNEXT 1650 #define JH5E_CANTOPENFILE 1660 #define JH5E_CANTOPENOBJ 1670 /*#define JH5E_CANTRECV 1680 removed from 1.6.4 */ #define JH5E_CANTREGISTER 1690 #define JH5E_CANTRELEASE 1700 #define JH5E_CANTSELECT 1710 /*#define JH5E_CANTSENDMDATA 1720 removed from 1.6.4 */ #define JH5E_CANTSET 1730 #define JH5E_CANTSPLIT 1740 #define JH5E_CANTUNLOCK 1750 #define JH5E_CLOSEERROR 1760 #define JH5E_COMPLEN 1770 /*#define JH5E_CWG 1780 removed from 1.6.5 */ #define JH5E_DATASET 1790 #define JH5E_DATASPACE 1800 #define JH5E_DATATYPE 1810 #define JH5E_DUPCLASS 1820 #define JH5E_EFL 1830 #define JH5E_EXISTS 1840 #define JH5E_FCNTL 1850 #define JH5E_FILE 1860 #define JH5E_FILEEXISTS 1870 #define JH5E_FILEOPEN 1880 /*#define JH5E_FPHDF5 1890 removed from 1.6.4 */ #define JH5E_FUNC 1900 #define JH5E_HEAP 1910 #define JH5E_INTERNAL 1920 #define JH5E_IO 1930 #define JH5E_LINK 1940 #define JH5E_LINKCOUNT 1950 #define JH5E_MOUNT 1960 #define JH5E_MPI 1970 #define JH5E_MPIERRSTR 1980 #define JH5E_NOFILTER 1990 #define JH5E_NOIDS 2000 #define JH5E_NONE_MAJOR 2010 #define JH5E_NONE_MINOR 2020 #define JH5E_NOSPACE 2030 #define JH5E_NOTCACHED 2040 #define JH5E_NOTFOUND 2050 #define JH5E_NOTHDF5 2060 #define JH5E_OHDR 2070 #define JH5E_OVERFLOW 2080 #define JH5E_PLINE 2090 #define JH5E_PLIST 2100 #define JH5E_PROTECT 2110 #define JH5E_READERROR 2120 #define JH5E_REFERENCE 2130 #define JH5E_RESOURCE 2140 #define JH5E_RS 2150 #define JH5E_SEEKERROR 2160 #define JH5E_SETLOCAL 2170 /*#define JH5E_SLINK 2180 removed from 1.8.0 */ #define JH5E_STORAGE 2190 #define JH5E_SYM 2200 /*#define JH5E_TBBT 2210 removed from 1.8.0 */ #define JH5E_TRUNCATED 2220 #define JH5E_TST 2230 #define JH5E_UNINITIALIZED 2240 #define JH5E_UNSUPPORTED 2250 #define JH5E_VERSION 2260 #define JH5E_VFL 2270 #define JH5E_WALK_DOWNWARD 2280 #define JH5E_WALK_UPWARD 2290 #define JH5E_WRITEERROR 2300 #define JH5F_ACC_CREAT 2310 #define JH5F_ACC_DEBUG 2320 #define JH5F_ACC_EXCL 2330 #define JH5F_ACC_RDONLY 2340 #define JH5F_ACC_RDWR 2350 #define JH5F_ACC_TRUNC 2360 #define JH5F_CLOSE_DEFAULT 2370 #define JH5F_CLOSE_SEMI 2380 #define JH5F_CLOSE_STRONG 2390 #define JH5F_CLOSE_WEAK 2400 #define JH5F_OBJ_ALL 2410 #define JH5F_OBJ_ATTR 2415 #define JH5F_OBJ_DATASET 2420 #define JH5F_OBJ_DATATYPE 2430 #define JH5F_OBJ_FILE 2440 #define JH5F_OBJ_GROUP 2450 #define JH5F_OBJ_LOCAL 2455 #define JH5F_SCOPE_DOWN 2460 #define JH5F_SCOPE_GLOBAL 2470 #define JH5F_SCOPE_LOCAL 2480 #define JH5F_UNLIMITED 2490 #define JH5F_LIBVER_EARLIEST 2494 #define JH5F_LIBVER_LATEST 2495 #define JH5G_DATASET 2500 #define JH5G_GROUP 2510 #define JH5G_LINK 2520 #define JH5G_LINK_ERROR 2530 #define JH5G_LINK_HARD 2540 #define JH5G_LINK_SOFT 2550 #define JH5G_NLIBTYPES 2560 #define JH5G_NTYPES 2570 #define JH5G_NUSERTYPES 2580 /*#define JH5G_RESERVED_4 2590 removed from 1.8.0 */ #define JH5G_RESERVED_5 2600 #define JH5G_RESERVED_6 2610 #define JH5G_RESERVED_7 2620 #define JH5G_SAME_LOC 2630 #define JH5G_TYPE 2640 #define JH5G_UNKNOWN 2650 #define JH5G_USERTYPE 2660 #define JH5I_ATTR 2670 #define JH5I_BADID 2680 #define JH5I_DATASET 2690 #define JH5I_DATASPACE 2700 #define JH5I_DATATYPE 2710 #define JH5I_FILE 2720 #define JH5I_FILE_CLOSING 2730 #define JH5I_GENPROP_CLS 2740 #define JH5I_GENPROP_LST 2750 #define JH5I_GROUP 2760 #define JH5I_INVALID_HID 2770 /*#define JH5I_NGROUPS 2780 removed from 1.8.0 */ #define JH5I_REFERENCE 2790 /*#define JH5I_TEMPBUF 2800 removed from 1.8.0 */ #define JH5I_VFL 2810 #define JH5O_TYPE_UNKNOWN 5510 #define JH5O_TYPE_GROUP 5520 #define JH5O_TYPE_DATASET 5530 #define JH5O_TYPE_NAMED_DATATYPE 5540 #define JH5O_TYPE_NTYPES 5550 #define JH5L_TYPE_ERROR 5560 #define JH5L_TYPE_HARD 5570 #define JH5L_TYPE_SOFT 5580 #define JH5L_TYPE_EXTERNAL 5590 #define JH5L_TYPE_MAX 5600 #define JH5P_DATASET_CREATE 2820 #define JH5P_DATASET_CREATE_DEFAULT 2830 #define JH5P_DATASET_XFER 2840 #define JH5P_DATASET_XFER_DEFAULT 2850 #define JH5P_DEFAULT 2860 #define JH5P_FILE_ACCESS 2870 #define JH5P_FILE_ACCESS_DEFAULT 2880 #define JH5P_FILE_CREATE 2890 #define JH5P_FILE_CREATE_DEFAULT 2900 /*#define JH5P_MOUNT 2910 #define JH5P_MOUNT_DEFAULT 2920 removed from 1.8.0 */ #define JH5P_NO_CLASS 2930 /*#define JH5P_NO_CLASS_DEFAULT 2940 removed from 1.8.0 */ #define JH5P_ROOT 6000 #define JH5P_OBJECT_CREATE 6010 #define JH5P_DATASET_ACCESS 6020 #define JH5P_DATASET_ACCESS_DEFAULT 6030 #define JH5P_FILE_MOUNT 6040 #define JH5P_FILE_MOUNT_DEFAULT 6050 #define JH5P_GROUP_CREATE 6060 #define JH5P_GROUP_CREATE_DEFAULT 6070 #define JH5P_GROUP_ACCESS 6080 #define JH5P_GROUP_ACCESS_DEFAULT 6090 #define JH5P_DATATYPE_CREATE 6100 #define JH5P_DATATYPE_CREATE_DEFAULT 6110 #define JH5P_DATATYPE_ACCESS 6120 #define JH5P_DATATYPE_ACCESS_DEFAULT 6130 #define JH5P_STRING_CREATE 6140 #define JH5P_ATTRIBUTE_CREATE 6150 #define JH5P_ATTRIBUTE_CREATE_DEFAULT 6160 #define JH5P_OBJECT_COPY 6170 #define JH5P_OBJECT_COPY_DEFAULT 6180 #define JH5P_LINK_CREATE 6190 #define JH5P_LINK_CREATE_DEFAULT 6200 #define JH5P_LINK_ACCESS 6210 #define JH5P_LINK_ACCESS_DEFAULT 6220 #define JH5R_BADTYPE 2950 #define JH5R_DATASET_REGION 2960 /*#define JH5R_INTERNAL 2970 removed from 1.8.0 */ #define JH5R_MAXTYPE 2980 #define JH5R_OBJ_REF_BUF_SIZE 2990 #define JH5R_OBJECT 3000 #define JH5S_ALL 3010 /*#define JH5S_COMPLEX 3020 removed from 1.8.0 */ #define JH5S_MAX_RANK 3030 #define JH5S_NO_CLASS 3040 #define JH5S_NULL 3045 #define JH5S_SCALAR 3050 #define JH5S_SEL_ALL 3060 #define JH5S_SEL_ERROR 3070 #define JH5S_SEL_HYPERSLABS 3080 #define JH5S_SEL_N 3090 #define JH5S_SEL_NONE 3100 #define JH5S_SEL_POINTS 3110 #define JH5S_SELECT_AND 3120 #define JH5S_SELECT_APPEND 3130 #define JH5S_SELECT_INVALID 3140 #define JH5S_SELECT_NOOP 3150 #define JH5S_SELECT_NOTA 3160 #define JH5S_SELECT_NOTB 3170 #define JH5S_SELECT_OR 3180 #define JH5S_SELECT_PREPEND 3190 #define JH5S_SELECT_SET 3200 #define JH5S_SELECT_XOR 3210 #define JH5S_SIMPLE 3220 #define JH5S_UNLIMITED 3230 #define JH5T_ALPHA_B16 3240 #define JH5T_ALPHA_B32 3250 #define JH5T_ALPHA_B64 3260 #define JH5T_ALPHA_B8 3270 #define JH5T_ALPHA_F32 3280 #define JH5T_ALPHA_F64 3290 #define JH5T_ALPHA_I16 3300 #define JH5T_ALPHA_I32 3310 #define JH5T_ALPHA_I64 3320 #define JH5T_ALPHA_I8 3330 #define JH5T_ALPHA_U16 3340 #define JH5T_ALPHA_U32 3350 #define JH5T_ALPHA_U64 3360 #define JH5T_ALPHA_U8 3370 #define JH5T_ARRAY 3380 #define JH5T_BITFIELD 3390 #define JH5T_BKG_NO 3400 #define JH5T_BKG_YES 3410 #define JH5T_C_S1 3420 #define JH5T_COMPOUND 3430 #define JH5T_CONV_CONV 3440 #define JH5T_CONV_FREE 3450 #define JH5T_CONV_INIT 3460 #define JH5T_CSET_ASCII 3470 #define JH5T_CSET_ERROR 3480 #define JH5T_CSET_UTF8 3490 #define JH5T_CSET_RESERVED_10 3500 #define JH5T_CSET_RESERVED_11 3510 #define JH5T_CSET_RESERVED_12 3520 #define JH5T_CSET_RESERVED_13 3530 #define JH5T_CSET_RESERVED_14 3540 #define JH5T_CSET_RESERVED_15 3550 #define JH5T_CSET_RESERVED_2 3560 #define JH5T_CSET_RESERVED_3 3570 #define JH5T_CSET_RESERVED_4 3580 #define JH5T_CSET_RESERVED_5 3590 #define JH5T_CSET_RESERVED_6 3600 #define JH5T_CSET_RESERVED_7 3610 #define JH5T_CSET_RESERVED_8 3620 #define JH5T_CSET_RESERVED_9 3630 #define JH5T_DIR_ASCEND 3640 #define JH5T_DIR_DEFAULT 3650 #define JH5T_DIR_DESCEND 3660 #define JH5T_ENUM 3670 #define JH5T_FLOAT 3680 #define JH5T_FORTRAN_S1 3690 #define JH5T_IEEE_F32BE 3700 #define JH5T_IEEE_F32LE 3710 #define JH5T_IEEE_F64BE 3720 #define JH5T_IEEE_F64LE 3730 #define JH5T_INTEGER 3740 #define JH5T_INTEL_B16 3750 #define JH5T_INTEL_B32 3760 #define JH5T_INTEL_B64 3770 #define JH5T_INTEL_B8 3780 #define JH5T_INTEL_F32 3790 #define JH5T_INTEL_F64 3800 #define JH5T_INTEL_I16 3810 #define JH5T_INTEL_I32 3820 #define JH5T_INTEL_I64 3830 #define JH5T_INTEL_I8 3840 #define JH5T_INTEL_U16 3850 #define JH5T_INTEL_U32 3860 #define JH5T_INTEL_U64 3870 #define JH5T_INTEL_U8 3880 #define JH5T_MIPS_B16 3890 #define JH5T_MIPS_B32 3900 #define JH5T_MIPS_B64 3910 #define JH5T_MIPS_B8 3920 #define JH5T_MIPS_F32 3930 #define JH5T_MIPS_F64 3940 #define JH5T_MIPS_I16 3950 #define JH5T_MIPS_I32 3960 #define JH5T_MIPS_I64 3970 #define JH5T_MIPS_I8 3980 #define JH5T_MIPS_U16 3990 #define JH5T_MIPS_U32 4000 #define JH5T_MIPS_U64 4010 #define JH5T_MIPS_U8 4020 #define JH5T_NATIVE_B16 4030 #define JH5T_NATIVE_B32 4040 #define JH5T_NATIVE_B64 4050 #define JH5T_NATIVE_B8 4060 #define JH5T_NATIVE_CHAR 4070 #define JH5T_NATIVE_DOUBLE 4080 #define JH5T_NATIVE_FLOAT 4090 #define JH5T_NATIVE_HADDR 4100 #define JH5T_NATIVE_HBOOL 4110 #define JH5T_NATIVE_HERR 4120 #define JH5T_NATIVE_HSIZE 4130 #define JH5T_NATIVE_HSSIZE 4140 #define JH5T_NATIVE_INT 4150 #define JH5T_NATIVE_INT_FAST16 4160 #define JH5T_NATIVE_INT_FAST32 4170 #define JH5T_NATIVE_INT_FAST64 4180 #define JH5T_NATIVE_INT_FAST8 4190 #define JH5T_NATIVE_INT_LEAST16 4200 #define JH5T_NATIVE_INT_LEAST32 4210 #define JH5T_NATIVE_INT_LEAST64 4220 #define JH5T_NATIVE_INT_LEAST8 4230 #define JH5T_NATIVE_INT16 4240 #define JH5T_NATIVE_INT32 4250 #define JH5T_NATIVE_INT64 4260 #define JH5T_NATIVE_INT8 4270 #define JH5T_NATIVE_LDOUBLE 4280 #define JH5T_NATIVE_LLONG 4290 #define JH5T_NATIVE_LONG 4300 #define JH5T_NATIVE_OPAQUE 4310 #define JH5T_NATIVE_SCHAR 4320 #define JH5T_NATIVE_SHORT 4330 #define JH5T_NATIVE_UCHAR 4340 #define JH5T_NATIVE_UINT 4350 #define JH5T_NATIVE_UINT_FAST16 4360 #define JH5T_NATIVE_UINT_FAST32 4370 #define JH5T_NATIVE_UINT_FAST64 4380 #define JH5T_NATIVE_UINT_FAST8 4390 #define JH5T_NATIVE_UINT_LEAST16 4400 #define JH5T_NATIVE_UINT_LEAST32 4410 #define JH5T_NATIVE_UINT_LEAST64 4420 #define JH5T_NATIVE_UINT_LEAST8 4430 #define JH5T_NATIVE_UINT16 4440 #define JH5T_NATIVE_UINT32 4450 #define JH5T_NATIVE_UINT64 4460 #define JH5T_NATIVE_UINT8 4470 #define JH5T_NATIVE_ULLONG 4480 #define JH5T_NATIVE_ULONG 4490 #define JH5T_NATIVE_USHORT 4500 #define JH5T_NCLASSES 4510 #define JH5T_NO_CLASS 4520 #define JH5T_NORM_ERROR 4530 #define JH5T_NORM_IMPLIED 4540 #define JH5T_NORM_MSBSET 4550 #define JH5T_NORM_NONE 4560 #define JH5T_NPAD 4570 #define JH5T_NSGN 4580 #define JH5T_OPAQUE 4590 #define JH5T_OPAQUE_TAG_MAX 4595 #define JH5T_ORDER_BE 4600 #define JH5T_ORDER_ERROR 4610 #define JH5T_ORDER_LE 4620 #define JH5T_ORDER_NONE 4630 #define JH5T_ORDER_VAX 4640 #define JH5T_PAD_BACKGROUND 4650 #define JH5T_PAD_ERROR 4660 #define JH5T_PAD_ONE 4670 #define JH5T_PAD_ZERO 4680 #define JH5T_PERS_DONTCARE 4690 #define JH5T_PERS_HARD 4700 #define JH5T_PERS_SOFT 4710 #define JH5T_REFERENCE 4720 #define JH5T_SGN_2 4730 #define JH5T_SGN_ERROR 4740 #define JH5T_SGN_NONE 4750 #define JH5T_STD_B16BE 4760 #define JH5T_STD_B16LE 4770 #define JH5T_STD_B32BE 4780 #define JH5T_STD_B32LE 4790 #define JH5T_STD_B64BE 4800 #define JH5T_STD_B64LE 4810 #define JH5T_STD_B8BE 4820 #define JH5T_STD_B8LE 4830 #define JH5T_STD_I16BE 4840 #define JH5T_STD_I16LE 4850 #define JH5T_STD_I32BE 4860 #define JH5T_STD_I32LE 4870 #define JH5T_STD_I64BE 4880 #define JH5T_STD_I64LE 4890 #define JH5T_STD_I8BE 4900 #define JH5T_STD_I8LE 4910 #define JH5T_STD_REF_DSETREG 4920 #define JH5T_STD_REF_OBJ 4930 #define JH5T_STD_U16BE 4940 #define JH5T_STD_U16LE 4950 #define JH5T_STD_U32BE 4960 #define JH5T_STD_U32LE 4970 #define JH5T_STD_U64BE 4980 #define JH5T_STD_U64LE 4990 #define JH5T_STD_U8BE 5000 #define JH5T_STD_U8LE 5010 #define JH5T_STR_ERROR 5020 #define JH5T_STR_NULLPAD 5030 #define JH5T_STR_NULLTERM 5040 #define JH5T_STR_RESERVED_10 5050 #define JH5T_STR_RESERVED_11 5060 #define JH5T_STR_RESERVED_12 5070 #define JH5T_STR_RESERVED_13 5080 #define JH5T_STR_RESERVED_14 5090 #define JH5T_STR_RESERVED_15 5100 #define JH5T_STR_RESERVED_3 5110 #define JH5T_STR_RESERVED_4 5120 #define JH5T_STR_RESERVED_5 5130 #define JH5T_STR_RESERVED_6 5140 #define JH5T_STR_RESERVED_7 5150 #define JH5T_STR_RESERVED_8 5160 #define JH5T_STR_RESERVED_9 5170 #define JH5T_STR_SPACEPAD 5180 #define JH5T_STRING 5190 #define JH5T_TIME 5200 #define JH5T_UNIX_D32BE 5210 #define JH5T_UNIX_D32LE 5220 #define JH5T_UNIX_D64BE 5230 #define JH5T_UNIX_D64LE 5240 #define JH5T_VARIABLE 5245 #define JH5T_VLEN 5250 #define JH5Z_CB_CONT 5260 #define JH5Z_CB_ERROR 5270 #define JH5Z_CB_FAIL 5280 #define JH5Z_CB_NO 5290 #define JH5Z_DISABLE_EDC 5300 #define JH5Z_ENABLE_EDC 5310 #define JH5Z_ERROR_EDC 5320 #define JH5Z_FILTER_DEFLATE 5330 #define JH5Z_FILTER_ERROR 5340 #define JH5Z_FILTER_FLETCHER32 5350 #define JH5Z_FILTER_MAX 5360 #define JH5Z_FILTER_NONE 5370 #define JH5Z_FILTER_RESERVED 5380 #define JH5Z_FILTER_SHUFFLE 5390 #define JH5Z_FILTER_SZIP 5400 #define JH5Z_FLAG_DEFMASK 5410 #define JH5Z_FLAG_INVMASK 5420 #define JH5Z_FLAG_MANDATORY 5430 #define JH5Z_FLAG_OPTIONAL 5440 #define JH5Z_FLAG_REVERSE 5450 #define JH5Z_FLAG_SKIP_EDC 5460 #define JH5Z_MAX_NFILTERS 5470 #define JH5Z_NO_EDC 5480 #define JH5Z_SO_INT 5481 #define JH5Z_SO_FLOAT_DSCALE 5482 #define JH5Z_SO_FLOAT_ESCALE 5483 #define JH5Z_FILTER_CONFIG_ENCODE_ENABLED 5490 #define JH5Z_FILTER_CONFIG_DECODE_ENABLED 5500libsis-jhdf5-java-14.12.1/source/c/jhdf5/h5ImpJHDF5.c000077500000000000000000000152011256564762100214730ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ #ifdef __cplusplus extern "C" { #endif /* * This code is the C-interface called by Java programs to access the * general library functions of the HDF5 library. * * Each routine wraps a single HDF entry point, generally with the * analogous arguments and return codes. * * For details of the HDF libraries, see the HDF Documentation at: * http://hdf.ncsa.uiuc.edu/HDF5/doc/ * */ #include "hdf5.h" #include #include /* #include */ extern jboolean h5JNIFatalError( JNIEnv *env, char *functName); extern jboolean h5nullArgument( JNIEnv *env, char *functName); extern jboolean h5libraryError( JNIEnv *env ); extern jboolean h5raiseException( JNIEnv *env, char *exception, char *message); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5open * Signature: ()I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5open (JNIEnv *env, jclass clss) { herr_t retVal = -1; retVal = H5open(); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5close * Signature: ()I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5close (JNIEnv *env, jclass clss) { herr_t retVal = -1; retVal = H5close(); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5dont_atexit * Signature: ()I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5dont_1atexit (JNIEnv *env, jclass clss) { int retVal = H5dont_atexit(); if (retVal < 0) { h5libraryError(env); } return retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5get_libversion * Signature: ([I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5get_1libversion (JNIEnv *env, jclass clss, jintArray libversion) { unsigned *theArray = NULL; jboolean isCopy; int status; if (libversion == NULL) { h5nullArgument( env, "H5get_version: libversion is NULL"); } #ifdef __cplusplus theArray = (unsigned *)env->GetIntArrayElements(libversion,&isCopy); #else theArray = (unsigned *)(*env)->GetIntArrayElements(env,libversion,&isCopy); #endif if (theArray == NULL) { h5JNIFatalError( env, "H5get_libversion: input not pinned"); return -1; } status = H5get_libversion(&(theArray[0]), &(theArray[1]), &(theArray[2])); if (status < 0) { #ifdef __cplusplus env->ReleaseIntArrayElements(libversion,(jint *)theArray,JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env,libversion,(jint *)theArray,JNI_ABORT); #endif h5libraryError(env); } else { #ifdef __cplusplus env->ReleaseIntArrayElements(libversion,(jint *)theArray,JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env,libversion,(jint *)theArray,0); #endif } return (jint)status; } #ifdef notdef /* struct sigaction { int sa_flags; void (*sa_handler)(); sigset_t sa_mask; void (*sa_sigaction)(int, siginfo_t *, void *); }; int sigaction(int sig, struct sigaction *act, struct sigaction *oact); */ void catch_abrt() { /* Raise Java exception */ printf("raise exception....\n"); } #endif /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5check_version * Signature: (III)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5check_1version (JNIEnv *env, jclass clss, jint majnum, jint minnum, jint relnum) { int status; /* * In principle, we want to catch the 'abort' signal, and * do something other than crash. * Look up how to do this portably. */ /* int res; struct sigaction ctchit; struct sigaction old; ctchit.sa_handler = catch_abrt; */ /* res = sigaction(SIGABRT, &ctchit, &old); if (res != 0) { printf("sigaction failed\n"); return(-1); } */ /* catch the signal? */ status = H5check_version((unsigned)majnum, (unsigned)minnum, (unsigned)relnum); /* res = sigaction(SIGABRT, &old, 0); if (res != 0) { printf("sigaction failed\n"); return(-1); } */ return status; } /* * This is the only routine from H5E currently implemente, so * there is no separate file h5eImp.c */ /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5check_version * Signature: (III)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Eclear (JNIEnv *env, jclass clss ) { herr_t res = -1; res = H5Eclear(H5E_DEFAULT) ; if (res < 0) { h5raiseException( env, "ncsa/hdf/hdf5lib/exceptions/HDF5LibraryException", "H5Eclear Failed"); } return (jint) res; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5garbage_collect * Signature: ()I * * ** New in HDF5.1.2.2: if linking with earlier version * of HDF5, configure with --enable-hdf5_1_2_1 * */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5garbage_1collect (JNIEnv *env, jclass clss) { herr_t retVal = -1; #ifndef USE_H5_1_2_1 retVal = H5garbage_collect(); if (retVal < 0) { h5libraryError(env); } #endif return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5set_free_list_limits(int reg_global_lim, int reg_list_lim, * int arr_global_lim, int arr_list_lim, int blk_global_lim, * int blk_list_lim ) * Signature: ()I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5set_1free_1list_1limits (JNIEnv *env, jclass clss,jint reg_global_lim, jint reg_list_lim, jint arr_global_lim, jint arr_list_lim, jint blk_global_lim, jint blk_list_lim ) { int retVal = H5set_free_list_limits((int)reg_global_lim, (int)reg_list_lim, (int)arr_global_lim, (int)arr_list_lim, (int)blk_global_lim, (int)blk_list_lim); if (retVal < 0) { h5libraryError(env); } return retVal; } #ifdef __cplusplus } #endif libsis-jhdf5-java-14.12.1/source/c/jhdf5/h5aImpJHDF5.c000077500000000000000000000712401256564762100216410ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ /* * This code is the C-interface called by Java programs to access the * Attribute API Functions of the HDF5 library. * * Each routine wraps a single HDF entry point, generally with the * analogous arguments and return codes. * * For details of the HDF libraries, see the HDF Documentation at: * http://hdf.ncsa.uiuc.edu/HDF5/doc/ * */ #ifdef __cplusplus extern "C" { #endif #include "hdf5.h" #include "h5utilJHDF5.h" #include #include #include extern jboolean h5outOfMemory( JNIEnv *env, char *functName); extern jboolean h5JNIFatalError( JNIEnv *env, char *functName); extern jboolean h5nullArgument( JNIEnv *env, char *functName); extern jboolean h5badArgument( JNIEnv *env, char *functName); extern jboolean h5libraryError( JNIEnv *env ); herr_t H5AreadVL_str_jhdf5 (JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf); herr_t H5AreadVL_num_jhdf5 (JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf); herr_t H5AreadVL_comp_jhdf5 (JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Aexists */ JNIEXPORT jboolean JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Aexists (JNIEnv *env, jclass clss, jint obj_id, jstring attribute_name) { htri_t exists; char *aName; jboolean isCopy; if (attribute_name == NULL) { h5nullArgument( env, "H5Aexists: attribute_name is NULL"); return -1; } aName = (char *)(*env)->GetStringUTFChars(env,attribute_name,&isCopy); if (aName == NULL) { h5JNIFatalError( env, "H5Aexists: attribute_name not pinned"); return -1; } exists = H5Aexists( (hid_t) obj_id, aName ); if (exists < 0) { h5libraryError(env); } (*env)->ReleaseStringUTFChars(env,attribute_name,aName); return exists; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Acreate * Signature: (ILjava/lang/String;III)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Acreate (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint type_id, jint space_id, jint create_plist_id, jint access_plist_id) { herr_t status; char* aName; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Acreate: name is NULL"); return -1; } #ifdef __cplusplus aName = (char *)env->GetStringUTFChars(name,&isCopy); #else aName = (char *)(*env)->GetStringUTFChars(env,name,&isCopy); #endif if (aName == NULL) { h5JNIFatalError( env, "H5Acreate: aName is not pinned"); return -1; } status = H5Acreate((hid_t)loc_id, aName, (hid_t)type_id, (hid_t)space_id, (hid_t)create_plist_id, (hid_t)access_plist_id); #ifdef __cplusplus env->ReleaseStringUTFChars(name,aName); #else (*env)->ReleaseStringUTFChars(env,name,aName); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Aopen_name * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Aopen_1name (JNIEnv *env, jclass clss, jint loc_id, jstring name) { herr_t status; char* aName; jboolean isCopy; if (name == NULL) { h5nullArgument( env,"H5Aopen_name: name is NULL"); return -1; } #ifdef __cplusplus aName = (char *)env->GetStringUTFChars(name,&isCopy); #else aName = (char *)(*env)->GetStringUTFChars(env,name,&isCopy); #endif if (aName == NULL) { h5JNIFatalError( env,"H5Aopen_name: name is not pinned"); return -1; } status = H5Aopen_name((hid_t)loc_id, aName); #ifdef __cplusplus env->ReleaseStringUTFChars(name,aName); #else (*env)->ReleaseStringUTFChars(env,name,aName); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Aopen_idx * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Aopen_1idx (JNIEnv *env, jclass clss, jint loc_id, jint idx) { herr_t retVal = -1; retVal = H5Aopen_idx((hid_t)loc_id, (unsigned int) idx ); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Awrite * Signature: (II[B)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Awrite__II_3B (JNIEnv *env, jclass clss, jint attr_id, jint mem_type_id, jbyteArray buf) { herr_t status; jbyte *byteP; if (buf == NULL) { h5nullArgument( env,"H5Awrite: buf is NULL"); return -1; } #ifdef __cplusplus byteP = env->GetByteArrayElements(buf,NULL); #else byteP = (*env)->GetByteArrayElements(env,buf,NULL); #endif if (byteP == NULL) { h5JNIFatalError( env,"H5Awrite: buf is not pinned"); return -1; } status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, byteP); #ifdef __cplusplus env->ReleaseByteArrayElements(buf,byteP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,buf,byteP,JNI_ABORT); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Awrite * Signature: (II[S)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Awrite__II_3S (JNIEnv *env, jclass clss, jint attr_id, jint mem_type_id, jshortArray buf) { herr_t status; jshort *byteP; if (buf == NULL) { h5nullArgument( env,"H5Awrite: buf is NULL"); return -1; } #ifdef __cplusplus byteP = env->GetShortArrayElements(buf,NULL); #else byteP = (*env)->GetShortArrayElements(env,buf,NULL); #endif if (byteP == NULL) { h5JNIFatalError( env,"H5Awrite: buf is not pinned"); return -1; } status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, byteP); #ifdef __cplusplus env->ReleaseShortArrayElements(buf,byteP,JNI_ABORT); #else (*env)->ReleaseShortArrayElements(env,buf,byteP,JNI_ABORT); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Awrite * Signature: (II[I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Awrite__II_3I (JNIEnv *env, jclass clss, jint attr_id, jint mem_type_id, jintArray buf) { herr_t status; jint *byteP; if (buf == NULL) { h5nullArgument( env,"H5Awrite: buf is NULL"); return -1; } #ifdef __cplusplus byteP = env->GetIntArrayElements(buf,NULL); #else byteP = (*env)->GetIntArrayElements(env,buf,NULL); #endif if (byteP == NULL) { h5JNIFatalError( env,"H5Awrite: buf is not pinned"); return -1; } status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, byteP); #ifdef __cplusplus env->ReleaseIntArrayElements(buf,byteP,JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env,buf,byteP,JNI_ABORT); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Awrite * Signature: (II[J)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Awrite__II_3J (JNIEnv *env, jclass clss, jint attr_id, jint mem_type_id, jlongArray buf) { herr_t status; jlong *byteP; if (buf == NULL) { h5nullArgument( env,"H5Awrite: buf is NULL"); return -1; } #ifdef __cplusplus byteP = env->GetLongArrayElements(buf,NULL); #else byteP = (*env)->GetLongArrayElements(env,buf,NULL); #endif if (byteP == NULL) { h5JNIFatalError( env,"H5Awrite: buf is not pinned"); return -1; } status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, byteP); #ifdef __cplusplus env->ReleaseLongArrayElements(buf,byteP,JNI_ABORT); #else (*env)->ReleaseLongArrayElements(env,buf,byteP,JNI_ABORT); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Awrite * Signature: (II[F)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Awrite__II_3F (JNIEnv *env, jclass clss, jint attr_id, jint mem_type_id, jfloatArray buf) { herr_t status; jfloat *byteP; if (buf == NULL) { h5nullArgument( env,"H5Awrite: buf is NULL"); return -1; } #ifdef __cplusplus byteP = env->GetFloatArrayElements(buf,NULL); #else byteP = (*env)->GetFloatArrayElements(env,buf,NULL); #endif if (byteP == NULL) { h5JNIFatalError( env,"H5Awrite: buf is not pinned"); return -1; } status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, byteP); #ifdef __cplusplus env->ReleaseFloatArrayElements(buf,byteP,JNI_ABORT); #else (*env)->ReleaseFloatArrayElements(env,buf,byteP,JNI_ABORT); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Awrite * Signature: (II[D)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Awrite__II_3D (JNIEnv *env, jclass clss, jint attr_id, jint mem_type_id, jdoubleArray buf) { herr_t status; jdouble *byteP; if (buf == NULL) { h5nullArgument( env,"H5Awrite: buf is NULL"); return -1; } #ifdef __cplusplus byteP = env->GetDoubleArrayElements(buf,NULL); #else byteP = (*env)->GetDoubleArrayElements(env,buf,NULL); #endif if (byteP == NULL) { h5JNIFatalError( env,"H5Awrite: buf is not pinned"); return -1; } status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, byteP); #ifdef __cplusplus env->ReleaseDoubleArrayElements(buf,byteP,JNI_ABORT); #else (*env)->ReleaseDoubleArrayElements(env,buf,byteP,JNI_ABORT); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5AwriteString * Signature: (II[B)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5AwriteString (JNIEnv *env, jclass clss, jint attr_id, jint mem_type_id, jobjectArray buf) { herr_t status; jboolean isCopy; char* * wdata; jsize size; jint i, j; if ( buf == NULL ) { h5nullArgument( env, "H5AwriteString: buf is NULL"); return -1; } size = (*env)->GetArrayLength(env, (jarray) buf); wdata = malloc(size * sizeof (char *)); if (!wdata) { h5outOfMemory( env, "H5AwriteString: cannot allocate buffer"); return -1; } memset(wdata, 0, size * sizeof(char *)); for (i = 0; i < size; ++i) { jstring obj = (jstring) (*env)->GetObjectArrayElement(env, (jobjectArray) buf, i); if (obj != 0) { jsize length = (*env)->GetStringUTFLength(env, obj); const char * utf8 = (*env)->GetStringUTFChars(env, obj, 0); if (utf8) { wdata[i] = malloc(strlen(utf8)+1); if (!wdata[i]) { status = -1; // can't allocate memory, cleanup for (j = 0; j < i; ++i) { if(wdata[j]) { free(wdata[j]); } } free(wdata); (*env)->ReleaseStringUTFChars(env, obj, utf8); (*env)->DeleteLocalRef(env, obj); h5outOfMemory( env, "H5DwriteString: cannot allocate buffer"); return -1; } strcpy(wdata[i], utf8); } (*env)->ReleaseStringUTFChars(env, obj, utf8); (*env)->DeleteLocalRef(env, obj); } } status = H5Awrite((hid_t)attr_id, (hid_t)mem_type_id, wdata); // now free memory for (i = 0; i < size; ++i) { if(wdata[i]) { free(wdata[i]); } } free(wdata); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Aread * Signature: (II[B)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Aread__II_3B (JNIEnv *env, jclass clss, jint attr_id, jint mem_type_id, jbyteArray buf) { herr_t status; jbyte *byteP; if (buf == NULL) { h5nullArgument( env,"H5Aread: buf is NULL"); return -1; } #ifdef __cplusplus byteP = env->GetByteArrayElements(buf,NULL); #else byteP = (*env)->GetByteArrayElements(env,buf,NULL); #endif if (byteP == NULL) { h5JNIFatalError( env,"H5Aread: buf is not pinned"); return -1; } status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, byteP); if (status < 0) { #ifdef __cplusplus env->ReleaseByteArrayElements(buf,byteP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,buf,byteP,JNI_ABORT); #endif h5libraryError(env); } else { #ifdef __cplusplus env->ReleaseByteArrayElements(buf,byteP,0); #else (*env)->ReleaseByteArrayElements(env,buf,byteP,0); #endif } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Aread * Signature: (II[S)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Aread__II_3S (JNIEnv *env, jclass clss, jint attr_id, jint mem_type_id, jshortArray buf) { herr_t status; jshort *byteP; if (buf == NULL) { h5nullArgument( env,"H5Aread: buf is NULL"); return -1; } #ifdef __cplusplus byteP = env->GetShortArrayElements(buf,NULL); #else byteP = (*env)->GetShortArrayElements(env,buf,NULL); #endif if (byteP == NULL) { h5JNIFatalError( env,"H5Aread: buf is not pinned"); return -1; } status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, byteP); if (status < 0) { #ifdef __cplusplus env->ReleaseShortArrayElements(buf,byteP,JNI_ABORT); #else (*env)->ReleaseShortArrayElements(env,buf,byteP,JNI_ABORT); #endif h5libraryError(env); } else { #ifdef __cplusplus env->ReleaseShortArrayElements(buf,byteP,0); #else (*env)->ReleaseShortArrayElements(env,buf,byteP,0); #endif } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Aread * Signature: (II[I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Aread__II_3I (JNIEnv *env, jclass clss, jint attr_id, jint mem_type_id, jintArray buf) { herr_t status; jint *byteP; if (buf == NULL) { h5nullArgument( env,"H5Aread: buf is NULL"); return -1; } #ifdef __cplusplus byteP = env->GetIntArrayElements(buf,NULL); #else byteP = (*env)->GetIntArrayElements(env,buf,NULL); #endif if (byteP == NULL) { h5JNIFatalError( env,"H5Aread: buf is not pinned"); return -1; } status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, byteP); if (status < 0) { #ifdef __cplusplus env->ReleaseIntArrayElements(buf,byteP,JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env,buf,byteP,JNI_ABORT); #endif h5libraryError(env); } else { #ifdef __cplusplus env->ReleaseIntArrayElements(buf,byteP,0); #else (*env)->ReleaseIntArrayElements(env,buf,byteP,0); #endif } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Aread * Signature: (II[J)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Aread__II_3J (JNIEnv *env, jclass clss, jint attr_id, jint mem_type_id, jlongArray buf) { herr_t status; jlong *byteP; if (buf == NULL) { h5nullArgument( env,"H5Aread: buf is NULL"); return -1; } #ifdef __cplusplus byteP = env->GetLongArrayElements(buf,NULL); #else byteP = (*env)->GetLongArrayElements(env,buf,NULL); #endif if (byteP == NULL) { h5JNIFatalError( env,"H5Aread: buf is not pinned"); return -1; } status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, byteP); if (status < 0) { #ifdef __cplusplus env->ReleaseLongArrayElements(buf,byteP,JNI_ABORT); #else (*env)->ReleaseLongArrayElements(env,buf,byteP,JNI_ABORT); #endif h5libraryError(env); } else { #ifdef __cplusplus env->ReleaseLongArrayElements(buf,byteP,0); #else (*env)->ReleaseLongArrayElements(env,buf,byteP,0); #endif } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Aread * Signature: (II[F)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Aread__II_3F (JNIEnv *env, jclass clss, jint attr_id, jint mem_type_id, jfloatArray buf) { herr_t status; jfloat *byteP; if (buf == NULL) { h5nullArgument( env,"H5Aread: buf is NULL"); return -1; } #ifdef __cplusplus byteP = env->GetFloatArrayElements(buf,NULL); #else byteP = (*env)->GetFloatArrayElements(env,buf,NULL); #endif if (byteP == NULL) { h5JNIFatalError( env,"H5Aread: buf is not pinned"); return -1; } status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, byteP); if (status < 0) { #ifdef __cplusplus env->ReleaseFloatArrayElements(buf,byteP,JNI_ABORT); #else (*env)->ReleaseFloatArrayElements(env,buf,byteP,JNI_ABORT); #endif h5libraryError(env); } else { #ifdef __cplusplus env->ReleaseFloatArrayElements(buf,byteP,0); #else (*env)->ReleaseFloatArrayElements(env,buf,byteP,0); #endif } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Aread * Signature: (II[D)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Aread__II_3D (JNIEnv *env, jclass clss, jint attr_id, jint mem_type_id, jdoubleArray buf) { herr_t status; jdouble *byteP; if (buf == NULL) { h5nullArgument( env,"H5Aread: buf is NULL"); return -1; } #ifdef __cplusplus byteP = env->GetDoubleArrayElements(buf,NULL); #else byteP = (*env)->GetDoubleArrayElements(env,buf,NULL); #endif if (byteP == NULL) { h5JNIFatalError( env,"H5Aread: buf is not pinned"); return -1; } status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, byteP); if (status < 0) { #ifdef __cplusplus env->ReleaseDoubleArrayElements(buf,byteP,JNI_ABORT); #else (*env)->ReleaseDoubleArrayElements(env,buf,byteP,JNI_ABORT); #endif h5libraryError(env); } else { #ifdef __cplusplus env->ReleaseDoubleArrayElements(buf,byteP,0); #else (*env)->ReleaseDoubleArrayElements(env,buf,byteP,0); #endif } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Aget_space * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Aget_1space (JNIEnv *env, jclass clss, jint attr_id) { hid_t retVal = -1; retVal = H5Aget_space((hid_t)attr_id); if (retVal < 0) { /* throw exception */ h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Aget_type * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Aget_1type (JNIEnv *env, jclass clss, jint attr_id) { hid_t retVal = -1; retVal = H5Aget_type((hid_t)attr_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Aget_name * Signature: (IJLjava/lang/String;)J */ JNIEXPORT jlong JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Aget_1name (JNIEnv *env, jclass clss, jint attr_id, jlong buf_size, jobjectArray name) { char *aName; jstring str; hssize_t size; long bs; bs = (long)buf_size; if (bs == 0) { /* we are only supposed to find out the size */ size = H5Aget_name((hid_t)attr_id, 0, NULL); if (size < 0) { h5libraryError(env); return -1; } else { return size; } } if (bs <= 0) { h5badArgument( env, "H5Aget_name: buf_size <= 0"); return -1; } aName = (char*)malloc(sizeof(char)*bs); if (aName == NULL) { h5outOfMemory( env, "H5Aget_name: malloc failed"); return -1; } size = H5Aget_name((hid_t)attr_id, (size_t)buf_size, aName); if (size < 0) { free(aName); h5libraryError(env); return -1; } /* successful return -- save the string; */ #ifdef __cplusplus str = env->NewStringUTF(aName); #else str = (*env)->NewStringUTF(env,aName); #endif if (str == NULL) { free(aName); h5JNIFatalError( env,"H5Aget_name: return string failed"); return -1; } free(aName); /* Note: throws ArrayIndexOutOfBoundsException, ArrayStoreException */ #ifdef __cplusplus env->SetObjectArrayElement(name,0,str); #else (*env)->SetObjectArrayElement(env,name,0,str); #endif return (jlong)size; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Aget_num_attrs * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Aget_1num_1attrs (JNIEnv *env, jclass clss, jint loc_id) { int retVal = -1; retVal = H5Aget_num_attrs((hid_t)loc_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Adelete * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Adelete (JNIEnv *env, jclass clss, jint loc_id, jstring name) { herr_t status; char* aName; jboolean isCopy; if (name == NULL) { h5nullArgument( env,"H5Adelete: name is NULL"); return -1; } #ifdef __cplusplus aName = (char *)env->GetStringUTFChars(name,&isCopy); #else aName = (char *)(*env)->GetStringUTFChars(env,name,&isCopy); #endif if (aName == NULL) { h5JNIFatalError( env,"H5Adelete: name is not pinned"); return -1; } status = H5Adelete((hid_t)loc_id, aName ); #ifdef __cplusplus env->ReleaseStringUTFChars(name,aName); #else (*env)->ReleaseStringUTFChars(env,name,aName); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Aclose * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Aclose (JNIEnv *env, jclass clss, jint attr_id) { herr_t retVal = 0; if (attr_id > 0) retVal = H5Aclose((hid_t)attr_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Aread * Signature: (II[B)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5AreadVL (JNIEnv *env, jclass clss, jint attr_id, jint mem_type_id, jobjectArray buf) { if ( buf == NULL ) { h5nullArgument( env, "H5AreadVL: buf is NULL"); return -1; } if (H5Tis_variable_str((hid_t)mem_type_id) > 0) { return (jint) H5AreadVL_str_jhdf5 (env, (hid_t)attr_id, (hid_t)mem_type_id, buf); } else if (H5Tget_class((hid_t)mem_type_id) == H5T_COMPOUND) { return (jint) H5AreadVL_comp_jhdf5 (env, (hid_t)attr_id, (hid_t)mem_type_id, buf); } else { return (jint) H5AreadVL_num_jhdf5 (env, (hid_t)attr_id, (hid_t)mem_type_id, buf); } } herr_t H5AreadVL_num_jhdf5 (JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf) { herr_t status; int i, n; size_t max_len=0; h5str_t h5str; jstring jstr; hvl_t *rdata; size_t size; hid_t sid; hsize_t dims[H5S_MAX_RANK]; n = (*env)->GetArrayLength(env, buf); rdata = (hvl_t *)calloc(n, sizeof(hvl_t)); if (rdata == NULL) { h5outOfMemory( env, "H5AreadVL: failed to allocate buff for read"); return -1; } status = H5Aread(aid, tid, rdata); dims[0] = n; sid = H5Screate_simple(1, dims, NULL); if (status < 0) { H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, rdata); H5Sclose(sid); free(rdata); h5libraryError(env); return -1; } for (i=0; ilen > max_len) max_len = (rdata+i)->len; } size = H5Tget_size(tid); memset(&h5str, 0, sizeof(h5str_t)); h5str_new_jhdf5(&h5str, 4*size); if (h5str.s == NULL) { H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, rdata); H5Sclose(sid); free(rdata); h5JNIFatalError( env, "H5AreadVL: failed to allocate string buf"); return -1; } for (i=0; iNewStringUTF(env, h5str.s); (*env)->SetObjectArrayElement(env, buf, i, jstr); } h5str_free_jhdf5(&h5str); H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, rdata); H5Sclose(sid); if (rdata) free(rdata); return status; } herr_t H5AreadVL_comp_jhdf5 (JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf) { herr_t status; int i, n; size_t max_len=0; h5str_t h5str; jstring jstr; char *rdata; size_t size; size = H5Tget_size(tid); n = (*env)->GetArrayLength(env, buf); rdata = (char *)malloc(n*size); if (rdata == NULL) { h5outOfMemory( env, "H5AreadVL: failed to allocate buff for read"); return -1; } status = H5Aread(aid, tid, rdata); if (status < 0) { free(rdata); h5libraryError(env); return -1; } memset(&h5str, 0, sizeof(h5str_t)); h5str_new_jhdf5(&h5str, 4*size); if (h5str.s == NULL) { free(rdata); h5outOfMemory( env, "H5AreadVL: failed to allocate string buf"); return -1; } for (i=0; iNewStringUTF(env, h5str.s); (*env)->SetObjectArrayElement(env, buf, i, jstr); } h5str_free_jhdf5(&h5str); free(rdata); return status; } herr_t H5AreadVL_str_jhdf5 (JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf) { herr_t status=-1; jstring jstr; char **strs; int i, n; hsize_t dims[H5S_MAX_RANK]; n = (*env)->GetArrayLength(env, buf); strs =(char **)calloc(n, sizeof(char *)); if (strs == NULL) { h5outOfMemory( env, "H5AreadVL: failed to allocate buff for read variable length strings"); return -1; } status = H5Aread(aid, tid, strs); if (status < 0) { for (i=0; iNewStringUTF(env, strs[i]); (*env)->SetObjectArrayElement(env, buf, i, jstr); free(strs[i]); } free(strs); return status; } /* * Copies the content of one dataset to another dataset * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Acopy * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Acopy (JNIEnv *env, jclass clss, jint src_id, jint dst_id) { jbyte *buf; herr_t retVal = -1; hid_t src_did = (hid_t)src_id; hid_t dst_did = (hid_t)dst_id; hid_t tid=-1; hid_t sid=-1; hsize_t total_size = 0; sid = H5Aget_space(src_did); if (sid < 0) { h5libraryError(env); return -1; } tid = H5Aget_type(src_did); if (tid < 0) { H5Sclose(sid); h5libraryError(env); return -1; } total_size = H5Sget_simple_extent_npoints(sid) * H5Tget_size(tid); H5Sclose(sid); buf = (jbyte *)malloc( (int) (total_size * sizeof(jbyte))); if (buf == NULL) { H5Tclose(tid); h5outOfMemory( env, "H5Acopy: malloc failed"); return -1; } retVal = H5Aread(src_did, tid, buf); H5Tclose(tid); if (retVal < 0) { free(buf); h5libraryError(env); return (jint)retVal; } tid = H5Aget_type(dst_did); if (tid < 0) { free(buf); h5libraryError(env); return -1; } retVal = H5Awrite(dst_did, tid, buf); H5Tclose(tid); free(buf); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } #ifdef __cplusplus } #endif libsis-jhdf5-java-14.12.1/source/c/jhdf5/h5dImpJHDF5.c000077500000000000000000001165611256564762100216520ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ /* * This code is the C-interface called by Java programs to access the * Dataset Object API Functions of HDF5 library. * * Each routine wraps a single HDF entry point, generally with the * analogous arguments and return codes. * * For details of the HDF libraries, see the HDF Documentation at: * http://hdf.ncsa.uiuc.edu/&isCopy/doc/ * */ #ifdef __cplusplus extern "C" { #endif #include "hdf5.h" #include "h5utilJHDF5.h" #include #include #include extern jboolean h5outOfMemory( JNIEnv *env, char *functName); extern jboolean h5JNIFatalError( JNIEnv *env, char *functName); extern jboolean h5nullArgument( JNIEnv *env, char *functName); extern jboolean h5libraryError( JNIEnv *env ); herr_t H5DreadVL_str_jhdf5 (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf); herr_t H5DreadVL_num_jhdf5 (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dcreate * Signature: (ILjava/lang/String;III)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dcreate (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint type_id, jint space_id, jint link_create_plist_id, jint dset_create_plist_id, jint dset_access_plist_id) { herr_t status; char* file; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Dcreate: name is NULL"); return -1; } #ifdef __cplusplus file = (char *)env->GetStringUTFChars(name,&isCopy); #else file = (char *)(*env)->GetStringUTFChars(env,name,&isCopy); #endif if (file == NULL) { h5JNIFatalError( env, "H5Dcreate: file name not pinned"); return -1; } status = H5Dcreate((hid_t)loc_id, file, (hid_t)type_id, (hid_t)space_id, (hid_t)link_create_plist_id, (hid_t) dset_create_plist_id, (hid_t)dset_access_plist_id); #ifdef __cplusplus env->ReleaseStringUTFChars(name,file); #else (*env)->ReleaseStringUTFChars(env,name,file); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dchdir_ext * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dchdir_1ext (JNIEnv *env, jclass clss, jstring dir_name) { hid_t status; char* file; jboolean isCopy; if (dir_name == NULL) { h5nullArgument( env, "H5Dchdir_ext: dir_name is NULL"); return -1; } #ifdef __cplusplus file = (char *)env->GetStringUTFChars(dir_name,&isCopy); #else file = (char *)(*env)->GetStringUTFChars(env,dir_name,&isCopy); #endif if (file == NULL) { h5JNIFatalError( env, "H5Dchdir_ext: file dir not pinned"); return -1; } status = chdir ( file ); #ifdef __cplusplus env->ReleaseStringUTFChars(dir_name,file); #else (*env)->ReleaseStringUTFChars(env,dir_name,file); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dgetdir_1ext * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dgetdir_1ext (JNIEnv *env, jclass clss, jstring dir_name, jint buf_size) { char *aName; jstring str; if (buf_size <= 0) { h5badArgument( env, "H5Dgetcwd: buf_size <= 0"); return -1; } aName = (char*)malloc(sizeof(char)*buf_size); if (aName == NULL) { h5outOfMemory( env, "H5Dgetcwd: malloc failed"); return -1; } getcwd( (char *)aName, (size_t)buf_size); str = (*env)->NewStringUTF(env,aName); if (str == NULL) { free(aName); h5outOfMemory( env,"H5Dgetcwd: return string failed"); return -1; } free(aName); (*env)->SetObjectArrayElement(env,dir_name,0,str); return 0; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dopen * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dopen (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint access_plist_id) { hid_t status; char* file; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Dopen: name is NULL"); return -1; } #ifdef __cplusplus file = (char *)env->GetStringUTFChars(name,&isCopy); #else file = (char *)(*env)->GetStringUTFChars(env,name,&isCopy); #endif if (file == NULL) { h5JNIFatalError( env, "H5Dopen: file name not pinned"); return -1; } status = H5Dopen((hid_t)loc_id, file, (hid_t) access_plist_id); #ifdef __cplusplus env->ReleaseStringUTFChars(name,file); #else (*env)->ReleaseStringUTFChars(env,name,file); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dget_space * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dget_1space (JNIEnv *env, jclass clss, jint dataset_id) { hid_t retVal = -1; retVal = H5Dget_space((hid_t)dataset_id ); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dget_type * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dget_1type (JNIEnv *env, jclass clss, jint dataset_id) { hid_t retVal = -1; retVal = H5Dget_type((hid_t)dataset_id ); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dget_create_plist * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dget_1create_1plist (JNIEnv *env, jclass clss, jint dataset_id) { hid_t retVal = -1; retVal = H5Dget_create_plist((hid_t)dataset_id ); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dread * Signature: (IIIII[B)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dread (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jbyteArray buf) { herr_t status; jbyte *byteP; jboolean isCopy; if ( buf == NULL ) { h5nullArgument( env, "H5Dread: buf is NULL"); return -1; } #ifdef __cplusplus byteP = env->GetPrimitiveArrayCritical(buf,&isCopy); #else byteP = (*env)->GetPrimitiveArrayCritical(env,buf,&isCopy); #endif if (byteP == NULL) { h5JNIFatalError( env, "H5Dread: buf not pinned"); return -1; } status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)xfer_plist_id, byteP); if (status < 0) { #ifdef __cplusplus env->ReleasePrimitiveArrayCritical(buf,byteP,JNI_ABORT); #else (*env)->ReleasePrimitiveArrayCritical(env,buf,byteP,JNI_ABORT); #endif h5libraryError(env); } else { #ifdef __cplusplus env->ReleasePrimitiveArrayCritical(buf,byteP,0); #else (*env)->ReleasePrimitiveArrayCritical(env,buf,byteP,0); #endif } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dwrite * Signature: (IIIII[B)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dwrite (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jbyteArray buf) { herr_t status; jbyte *byteP; jboolean isCopy; if ( buf == NULL ) { h5nullArgument( env, "H5Dwrite: buf is NULL"); return -1; } #ifdef __cplusplus byteP = env->GetPrimitiveArrayCritical(buf,&isCopy); #else byteP = (*env)->GetPrimitiveArrayCritical(env,buf,&isCopy); #endif if (byteP == NULL) { h5JNIFatalError( env, "H5Dwrite: buf not pinned"); return -1; } status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)xfer_plist_id, byteP); #ifdef __cplusplus env->ReleasePrimitiveArrayCritical(buf,byteP,JNI_ABORT); #else (*env)->ReleasePrimitiveArrayCritical(env,buf,byteP,JNI_ABORT); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dextend * Signature: (IB)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dextend (JNIEnv *env, jclass clss, jint dataset_id, jbyteArray size) { herr_t status; jbyte *P; jboolean isCopy; hsize_t *sa; int i; int rank; hsize_t *lp; jlong *jlp; if ( size == NULL ) { h5nullArgument( env, "H5Dextend: array of sizes is NULL"); return -1; } /* * Future: check that the array has correct * rank (same as dataset dataset_id) */ #ifdef __cplusplus P = env->GetByteArrayElements(size,&isCopy); #else P = (*env)->GetByteArrayElements(env,size,&isCopy); #endif if (P == NULL) { h5JNIFatalError( env, "H5Dextend: array not pinned"); return -1; } #ifdef __cplusplus i = env->GetArrayLength(size); #else i = (*env)->GetArrayLength(env,size); #endif rank = i / sizeof(jlong); sa = lp = (hsize_t *)malloc(rank * sizeof(hsize_t)); if (sa == NULL) { #ifdef __cplusplus env->ReleaseByteArrayElements(size,P,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,size,P,JNI_ABORT); #endif h5outOfMemory(env, "H5Dextend: size not converted to hsize_t"); return -1; } jlp = (jlong *)P; for (i = 0; i < rank; i++) { *lp = (hsize_t)*jlp; lp++; jlp++; } status = H5Dextend((hid_t)dataset_id, (hsize_t *)sa); #ifdef __cplusplus env->ReleaseByteArrayElements(size,P,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,size,P,JNI_ABORT); #endif free(sa); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dset_1extent * Signature: (IB)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dset_1extent (JNIEnv *env, jclass clss, jint dataset_id, jbyteArray size) { herr_t status; jbyte *P; jboolean isCopy; hsize_t *sa; int i; int rank; hsize_t *lp; jlong *jlp; if ( size == NULL ) { h5nullArgument( env, "H5Dextend: array of sizes is NULL"); return -1; } /* * Future: check that the array has correct * rank (same as dataset dataset_id) */ #ifdef __cplusplus P = env->GetByteArrayElements(size,&isCopy); #else P = (*env)->GetByteArrayElements(env,size,&isCopy); #endif if (P == NULL) { h5JNIFatalError( env, "H5Dextend: array not pinned"); return -1; } #ifdef __cplusplus i = env->GetArrayLength(size); #else i = (*env)->GetArrayLength(env,size); #endif rank = i / sizeof(jlong); sa = lp = (hsize_t *)malloc(rank * sizeof(hsize_t)); if (sa == NULL) { #ifdef __cplusplus env->ReleaseByteArrayElements(size,P,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,size,P,JNI_ABORT); #endif h5outOfMemory(env, "H5Dextend: size not converted to hsize_t"); return -1; } jlp = (jlong *)P; for (i = 0; i < rank; i++) { *lp = (hsize_t)*jlp; lp++; jlp++; } status = H5Dset_extent((hid_t)dataset_id, (hsize_t *)sa); #ifdef __cplusplus env->ReleaseByteArrayElements(size,P,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,size,P,JNI_ABORT); #endif free(sa); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dclose * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dclose (JNIEnv *env, jclass clss, jint dataset_id) { hid_t retVal = 0; if (dataset_id > 0) retVal = H5Dclose((hid_t)dataset_id ); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dget_storage_size * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dget_1storage_1size (JNIEnv *env, jclass clss, jint dataset_id) { hsize_t retVal = (hsize_t)-1; retVal = H5Dget_storage_size((hid_t)dataset_id ); /* probably returns '0' if fails--don't do an exception if (retVal < 0) { h5libraryError(env); } */ return (jlong)retVal; } /* * Copies the content of one dataset to another dataset * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dcopy * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dcopy (JNIEnv *env, jclass clss, jint src_id, jint dst_id) { jbyte *buf; herr_t retVal = -1; hid_t src_did = (hid_t)src_id; hid_t dst_did = (hid_t)dst_id; hid_t tid=-1; hid_t sid=-1; hsize_t total_size = 0; sid = H5Dget_space(src_did); if (sid < 0) { h5libraryError(env); return -1; } tid = H5Dget_type(src_did); if (tid < 0) { H5Sclose(sid); h5libraryError(env); return -1; } total_size = H5Sget_simple_extent_npoints(sid) * H5Tget_size(tid); H5Sclose(sid); buf = (jbyte *)calloc( (int) (total_size), sizeof(jbyte)); if (buf == NULL) { H5Tclose(tid); h5outOfMemory( env, "H5Dcopy: malloc failed"); return -1; } retVal = H5Dread(src_did, tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf); H5Tclose(tid); if (retVal < 0) { free(buf); h5libraryError(env); return (jint)retVal; } tid = H5Dget_type(dst_did); if (tid < 0) { free(buf); h5libraryError(env); return -1; } retVal = H5Dwrite(dst_did, tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf); H5Tclose(tid); free(buf); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Copies the content of one dataset to another dataset * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dvlen_get_buf_size * Signature: (III[I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dvlen_1get_1buf_1size (JNIEnv *env, jclass clss, jint dataset_id, jint type_id, jint space_id, jintArray size ) { herr_t status; jint *P; jboolean isCopy; hsize_t sz; if ( size == NULL ) { h5nullArgument( env, "H5Dvlen_get_buf_size: size is NULL"); return -1; } #ifdef __cplusplus P = env->GetIntArrayElements(size,&isCopy); #else P = (*env)->GetIntArrayElements(env,size,&isCopy); #endif if (P == NULL) { h5JNIFatalError( env, "H5Dvlen_get_buf_size: array not pinned"); return -1; } status = (jint)H5Dvlen_get_buf_size((hid_t) dataset_id, (hid_t) type_id, (hid_t) space_id, (hsize_t *)&sz); if (status < 0) { #ifdef __cplusplus env->ReleaseIntArrayElements(size,P,JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env,size,P,JNI_ABORT); #endif h5libraryError(env); } else { P[0] = (jint)sz; #ifdef __cplusplus env->ReleaseIntArrayElements(size,P,0); #else (*env)->ReleaseIntArrayElements(env,size,P,0); #endif } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dvlen_reclaim * Signature: (IIIII[B)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dvlen_1reclaim (JNIEnv *env, jclass clss, jint type_id, jint space_id, jint xfer_plist_id, jbyteArray buf) { herr_t status; jbyte *byteP; jboolean isCopy; if ( buf == NULL ) { h5nullArgument( env, "H5Dwrite: buf is NULL"); return -1; } #ifdef __cplusplus byteP = env->GetByteArrayElements(buf,&isCopy); #else byteP = (*env)->GetByteArrayElements(env,buf,&isCopy); #endif if (byteP == NULL) { h5JNIFatalError( env, "H5Dwrite: buf not pinned"); return -1; } status = H5Dvlen_reclaim((hid_t)type_id, (hid_t)space_id, (hid_t)xfer_plist_id, byteP); #ifdef __cplusplus env->ReleaseByteArrayElements(buf,byteP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,buf,byteP,JNI_ABORT); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /*************************************************************** * New APIs for HDF5.1.6 * ***************************************************************/ /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dget_space_status(hid_t dset_id, H5D_space_status_t *status) * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dget_1space_1status (JNIEnv *env, jclass clss, jint dset_id, jintArray status) { herr_t retVal = -1; jint *theArray; jboolean isCopy; H5D_space_status_t space_status; if (status == NULL) { /* exception ? */ h5nullArgument( env, "H5Dget_space_status: status is NULL"); return -1; } #ifdef __cplusplus theArray = (jint *)env->GetIntArrayElements(status,&isCopy); #else theArray = (jint *)(*env)->GetIntArrayElements(env,status,&isCopy); #endif if (theArray == NULL) { h5JNIFatalError( env, "H5Dget_space_status: status not pinned"); return -1; } retVal = H5Dget_space_status((hid_t)dset_id, &space_status ); if (retVal < 0) { #ifdef __cplusplus env->ReleaseIntArrayElements(status,theArray,JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env,status,theArray,JNI_ABORT); #endif h5libraryError(env); } else { theArray[0] = space_status; #ifdef __cplusplus env->ReleaseIntArrayElements(status,theArray,0); #else (*env)->ReleaseIntArrayElements(env,status,theArray,0); #endif } return (jint)retVal; } /* //////////////////////////////////////////////////////////////////// // // // New APIs for read data from library // // Using H5Dread(..., Object buf) requires function calls // // theArray.emptyBytes() and theArray.arrayify( buf), which // // triples the actual memory needed by the data set. // // Using the following APIs solves the problem. // // // //////////////////////////////////////////////////////////////////// */ /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Dread_short * Signature: (IIIII[S)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dread__IIIII_3S (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jshortArray buf) { herr_t status; jshort *buffP; jboolean isCopy; if ( buf == NULL ) { h5nullArgument( env, "H5Dread: buf is NULL"); return -1; } #ifdef __cplusplus buffP = env->GetPrimitiveArrayCritical(buf,&isCopy); #else buffP = (*env)->GetPrimitiveArrayCritical(env,buf,&isCopy); #endif if (buffP == NULL) { h5JNIFatalError( env, "H5Dread: buf not pinned"); return -1; } status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); if (status < 0) { #ifdef __cplusplus env->ReleasePrimitiveArrayCritical(buf,buffP,JNI_ABORT); #else (*env)->ReleasePrimitiveArrayCritical(env,buf,buffP,JNI_ABORT); #endif h5libraryError(env); } else { #ifdef __cplusplus env->ReleasePrimitiveArrayCritical(buf,buffP,0); #else (*env)->ReleasePrimitiveArrayCritical(env,buf,buffP,0); #endif } return (jint)status; } JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dread__IIIII_3I (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jintArray buf) { herr_t status; jint *buffP; jboolean isCopy; if ( buf == NULL ) { h5nullArgument( env, "H5Dread: buf is NULL"); return -1; } #ifdef __cplusplus buffP = env->GetPrimitiveArrayCritical(buf,&isCopy); #else buffP = (*env)->GetPrimitiveArrayCritical(env,buf,&isCopy); #endif if (buffP == NULL) { h5JNIFatalError( env, "H5Dread: buf not pinned"); return -1; } status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); if (status < 0) { #ifdef __cplusplus env->ReleasePrimitiveArrayCritical(buf,buffP,JNI_ABORT); #else (*env)->ReleasePrimitiveArrayCritical(env,buf,buffP,JNI_ABORT); #endif h5libraryError(env); } else { #ifdef __cplusplus env->ReleasePrimitiveArrayCritical(buf,buffP,0); #else (*env)->ReleasePrimitiveArrayCritical(env,buf,buffP,0); #endif } return (jint)status; } JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dread__IIIII_3J (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jlongArray buf) { herr_t status; jlong *buffP; jboolean isCopy; if ( buf == NULL ) { h5nullArgument( env, "H5Dread: buf is NULL"); return -1; } #ifdef __cplusplus buffP = env->GetPrimitiveArrayCritical(buf,&isCopy); #else buffP = (*env)->GetPrimitiveArrayCritical(env,buf,&isCopy); #endif if (buffP == NULL) { h5JNIFatalError( env, "H5Dread: buf not pinned"); return -1; } status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); if (status < 0) { #ifdef __cplusplus env->ReleasePrimitiveArrayCritical(buf,buffP,JNI_ABORT); #else (*env)->ReleasePrimitiveArrayCritical(env,buf,buffP,JNI_ABORT); #endif h5libraryError(env); } else { #ifdef __cplusplus env->ReleasePrimitiveArrayCritical(buf,buffP,0); #else (*env)->ReleasePrimitiveArrayCritical(env,buf,buffP,0); #endif } return (jint)status; } JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dread__IIIII_3F (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jfloatArray buf) { herr_t status; jfloat *buffP; jboolean isCopy; if ( buf == NULL ) { h5nullArgument( env, "H5Dread: buf is NULL"); return -1; } #ifdef __cplusplus buffP = env->GetPrimitiveArrayCritical(buf,&isCopy); #else buffP = (*env)->GetPrimitiveArrayCritical(env,buf,&isCopy); #endif if (buffP == NULL) { h5JNIFatalError( env, "H5Dread: buf not pinned"); return -1; } status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); if (status < 0) { #ifdef __cplusplus env->ReleasePrimitiveArrayCritical(buf,buffP,JNI_ABORT); #else (*env)->ReleasePrimitiveArrayCritical(env,buf,buffP,JNI_ABORT); #endif h5libraryError(env); } else { #ifdef __cplusplus env->ReleasePrimitiveArrayCritical(buf,buffP,0); #else (*env)->ReleasePrimitiveArrayCritical(env,buf,buffP,0); #endif } return (jint)status; } JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dread__IIIII_3D (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jdoubleArray buf) { herr_t status; jdouble *buffP; jboolean isCopy; if ( buf == NULL ) { h5nullArgument( env, "H5Dread: buf is NULL"); return -1; } #ifdef __cplusplus buffP = env->GetPrimitiveArrayCritical(buf,&isCopy); #else buffP = (*env)->GetPrimitiveArrayCritical(env,buf,&isCopy); #endif if (buffP == NULL) { h5JNIFatalError( env, "H5Dread: buf not pinned"); return -1; } status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); if (status < 0) { #ifdef __cplusplus env->ReleasePrimitiveArrayCritical(buf,buffP,JNI_ABORT); #else (*env)->ReleasePrimitiveArrayCritical(env,buf,buffP,JNI_ABORT); #endif h5libraryError(env); } else { #ifdef __cplusplus env->ReleasePrimitiveArrayCritical(buf,buffP,0); #else (*env)->ReleasePrimitiveArrayCritical(env,buf,buffP,0); #endif } return (jint)status; } JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dread_1string (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jobjectArray j_buf) { herr_t status; jstring jstr; char *c_buf; char *cstr; char cterm; size_t str_len, i, n; c_buf = cstr = NULL; if ( j_buf == NULL) { h5nullArgument( env, "H5Dread_string: buf is NULL"); return -1; } n = (*env)->GetArrayLength(env, j_buf); if ( n<=0) { h5nullArgument( env, "H5Dread_string: buf length <=0"); return -1; } if ( (str_len = H5Tget_size((hid_t)mem_type_id)) <=0 ) { h5libraryError(env); } /* Note: we need one additional character at the end of the buffer for the final '\0'. */ if ( (c_buf = (char *)calloc(n + 1, str_len)) == NULL) { if (cstr) free (cstr); cstr = NULL; h5outOfMemory(env, "H5Dread_string: memory allocation failed."); return -1; } status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)xfer_plist_id, c_buf); if (status < 0) { if (c_buf) free (c_buf); c_buf = NULL; h5libraryError(env); return -1; } cstr = c_buf; for (i=0; iNewStringUTF(env, cstr); (*env)->SetObjectArrayElement(env, j_buf, i, jstr); *(cstr + str_len) = cterm; cstr += str_len; } if (c_buf) { free(c_buf); } return (jint)status; } /** * Read VLEN data into array of arrays. * Object[] buf contains VL arrays of data points * Currently only deal with variable length of atomic data types */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5DreadVL (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jobjectArray buf) { htri_t isStr=0; if ( buf == NULL ) { h5nullArgument( env, "H5DreadVL: buf is NULL"); return -1; } if (H5Tget_class((hid_t)mem_type_id) == H5T_COMPOUND) { hid_t nested_tid = H5Tget_member_type((hid_t)mem_type_id, 0); while (H5Tget_class(nested_tid) == H5T_COMPOUND) { nested_tid = H5Tget_member_type(nested_tid, 0); } isStr = H5Tis_variable_str(nested_tid); } else { isStr = H5Tis_variable_str((hid_t)mem_type_id); } if (isStr > 0) { return (jint) H5DreadVL_str_jhdf5 (env, (hid_t)dataset_id, (hid_t)mem_type_id, (hid_t) mem_space_id,(hid_t) file_space_id, (hid_t)xfer_plist_id, buf); } else if (isStr == 0) { return (jint) H5DreadVL_num_jhdf5 (env, (hid_t)dataset_id, (hid_t)mem_type_id, (hid_t) mem_space_id,(hid_t) file_space_id, (hid_t)xfer_plist_id, buf); } else { return -1; } } herr_t H5DreadVL_num_jhdf5 (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf) { herr_t status; int i, n; size_t max_len=0; h5str_t h5str; jstring jstr; hvl_t *rdata; size_t size; n = (*env)->GetArrayLength(env, buf); rdata = (hvl_t *)calloc(n, sizeof(hvl_t)); if (rdata == NULL) { h5outOfMemory( env, "H5DreadVL: failed to allocate buff for read"); return -1; } status = H5Dread(did, tid, mem_sid, file_sid, xfer_plist_id, rdata); if (status < 0) { H5Dvlen_reclaim(tid, mem_sid, H5P_DEFAULT, rdata); free(rdata); h5libraryError(env); return -1; } max_len = 1; for (i=0; ilen > max_len) max_len = (rdata+i)->len; } size = H5Tget_size(tid)*max_len; memset(&h5str, 0, sizeof(h5str_t)); h5str_new_jhdf5(&h5str, 4*size); if (h5str.s == NULL) { H5Dvlen_reclaim(tid, mem_sid, H5P_DEFAULT, rdata); free(rdata); h5outOfMemory( env, "H5DreadVL: failed to allocate string buf"); return -1; } for (i=0; iNewStringUTF(env, h5str.s); (*env)->SetObjectArrayElement(env, buf, i, jstr); } h5str_free_jhdf5(&h5str); H5Dvlen_reclaim(tid, mem_sid, H5P_DEFAULT, rdata); free(rdata); return status; } herr_t H5DreadVL_str_jhdf5 (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf) { herr_t status=-1; jstring jstr; char **strs; int i, n; n = (*env)->GetArrayLength(env, buf); strs = (char **) calloc(n, sizeof(char *)); if (strs == NULL) { h5outOfMemory( env, "H5DreadVL: failed to allocate buff for read variable length strings"); return -1; } status = H5Dread(did, tid, mem_sid, file_sid, xfer_plist_id, strs); if (status < 0) { H5Dvlen_reclaim(tid, mem_sid, H5P_DEFAULT, strs); free(strs); h5libraryError(env); return -1; } for (i=0; iNewStringUTF(env, strs[i]); (*env)->SetObjectArrayElement(env, buf, i, jstr); } H5Dvlen_reclaim(tid, mem_sid, H5P_DEFAULT, strs); free(strs); return status; } JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dread_1reg_1ref (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jobjectArray buf) { herr_t status; int i, n; h5str_t h5str; jstring jstr; hdset_reg_ref_t *ref_data; size_t size; hid_t region = -1; hid_t did = (hid_t) dataset_id; hid_t tid = (hid_t) mem_type_id; hid_t mem_sid = (hid_t) mem_space_id; hid_t file_sid = (hid_t) file_space_id; n = (*env)->GetArrayLength(env, buf); size = sizeof(hdset_reg_ref_t); /*H5Tget_size(tid);*/ ref_data = calloc(size, n); if (ref_data == NULL) { h5outOfMemory( env, "H5Dread_reg_ref: failed to allocate buff for read"); return -1; } status = H5Dread(did, tid, mem_sid, file_sid, xfer_plist_id, ref_data); if (status < 0) { free(ref_data); h5libraryError(env); return -1; } memset(&h5str, 0, sizeof(h5str_t)); h5str_new_jhdf5(&h5str, 1024); for (i=0; iNewStringUTF(env, h5str.s); (*env)->SetObjectArrayElement(env, buf, i, jstr); } h5str_free_jhdf5(&h5str); free(ref_data); return status; } JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dwrite__IIIII_3S (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jshortArray buf) { herr_t status; jshort *buffP; jboolean isCopy; if ( buf == NULL ) { h5nullArgument( env, "H5Dwrite: buf is NULL"); return -1; } #ifdef __cplusplus buffP = env->GetPrimitiveArrayCritical(buf,&isCopy); #else buffP = (*env)->GetPrimitiveArrayCritical(env,buf,&isCopy); #endif if (buffP == NULL) { h5JNIFatalError( env, "H5Dwrite: buf not pinned"); return -1; } status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); #ifdef __cplusplus env->ReleasePrimitiveArrayCritical(buf,buffP,JNI_ABORT); #else (*env)->ReleasePrimitiveArrayCritical(env,buf,buffP,JNI_ABORT); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dwrite__IIIII_3I (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jintArray buf) { herr_t status; jint *buffP; jboolean isCopy; if ( buf == NULL ) { h5nullArgument( env, "H5Dwrite: buf is NULL"); return -1; } #ifdef __cplusplus buffP = env->GetPrimitiveArrayCritical(buf,&isCopy); #else buffP = (*env)->GetPrimitiveArrayCritical(env,buf,&isCopy); #endif if (buffP == NULL) { h5JNIFatalError( env, "H5Dwrite: buf not pinned"); return -1; } status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); #ifdef __cplusplus env->ReleasePrimitiveArrayCritical(buf,buffP,JNI_ABORT); #else (*env)->ReleasePrimitiveArrayCritical(env,buf,buffP,JNI_ABORT); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dwrite__IIIII_3J (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jlongArray buf) { herr_t status; jlong *buffP; jboolean isCopy; if ( buf == NULL ) { h5nullArgument( env, "H5Dwrite: buf is NULL"); return -1; } #ifdef __cplusplus buffP = env->GetPrimitiveArrayCritical(buf,&isCopy); #else buffP = (*env)->GetPrimitiveArrayCritical(env,buf,&isCopy); #endif if (buffP == NULL) { h5JNIFatalError( env, "H5Dwrite: buf not pinned"); return -1; } status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); #ifdef __cplusplus env->ReleasePrimitiveArrayCritical(buf,buffP,JNI_ABORT); #else (*env)->ReleasePrimitiveArrayCritical(env,buf,buffP,JNI_ABORT); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dwrite__IIIII_3F (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jfloatArray buf) { herr_t status; jfloat *buffP; jboolean isCopy; if ( buf == NULL ) { h5nullArgument( env, "H5Dwrite: buf is NULL"); return -1; } #ifdef __cplusplus buffP = env->GetPrimitiveArrayCritical(buf,&isCopy); #else buffP = (*env)->GetPrimitiveArrayCritical(env,buf,&isCopy); #endif if (buffP == NULL) { h5JNIFatalError( env, "H5Dwrite: buf not pinned"); return -1; } status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); #ifdef __cplusplus env->ReleasePrimitiveArrayCritical(buf,buffP,JNI_ABORT); #else (*env)->ReleasePrimitiveArrayCritical(env,buf,buffP,JNI_ABORT); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dwrite__IIIII_3D (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jdoubleArray buf) { herr_t status; jdouble *buffP; jboolean isCopy; if ( buf == NULL ) { h5nullArgument( env, "H5Dwrite: buf is NULL"); return -1; } #ifdef __cplusplus buffP = env->GetPrimitiveArrayCritical(buf,&isCopy); #else buffP = (*env)->GetPrimitiveArrayCritical(env,buf,&isCopy); #endif if (buffP == NULL) { h5JNIFatalError( env, "H5Dwrite: buf not pinned"); return -1; } status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)xfer_plist_id, buffP); #ifdef __cplusplus env->ReleasePrimitiveArrayCritical(buf,buffP,JNI_ABORT); #else (*env)->ReleasePrimitiveArrayCritical(env,buf,buffP,JNI_ABORT); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } // Rosetta Biosoftware /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5DwriteString * Signature: (IIIII[Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5DwriteString (JNIEnv *env, jclass clss, jint dataset_id, jint mem_type_id, jint mem_space_id, jint file_space_id, jint xfer_plist_id, jobjectArray buf) { herr_t status; jboolean isCopy; char* * wdata; jsize size; jint i, j; if ( buf == NULL ) { h5nullArgument( env, "H5DwriteString: buf is NULL"); return -1; } size = (*env)->GetArrayLength(env, (jarray) buf); wdata = malloc(size * sizeof (char *)); if (!wdata) { h5outOfMemory( env, "H5DwriteString: cannot allocate buffer"); return -1; } memset(wdata, 0, size * sizeof(char *)); for (i = 0; i < size; ++i) { jstring obj = (jstring) (*env)->GetObjectArrayElement(env, (jobjectArray) buf, i); if (obj != 0) { jsize length = (*env)->GetStringUTFLength(env, obj); const char * utf8 = (*env)->GetStringUTFChars(env, obj, 0); if (utf8) { wdata[i] = malloc(strlen(utf8)+1); if (!wdata[i]) { status = -1; // can't allocate memory, cleanup for (j = 0; j < i; ++i) { if(wdata[j]) { free(wdata[j]); } } free(wdata); (*env)->ReleaseStringUTFChars(env, obj, utf8); (*env)->DeleteLocalRef(env, obj); h5outOfMemory( env, "H5DwriteString: cannot allocate buffer"); return -1; } strcpy(wdata[i], utf8); } (*env)->ReleaseStringUTFChars(env, obj, utf8); (*env)->DeleteLocalRef(env, obj); } } status = H5Dwrite((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id, (hid_t)xfer_plist_id, wdata); // now free memory for (i = 0; i < size; ++i) { if(wdata[i]) { free(wdata[i]); } } free(wdata); if (status < 0) { h5libraryError(env); } return (jint)status; } #ifdef __cplusplus } #endif libsis-jhdf5-java-14.12.1/source/c/jhdf5/h5fImpJHDF5.c000077500000000000000000000343711256564762100216520ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ /* * This code is the C-interface called by Java programs to access the * file interface functions of the HDF5 library. * * Each routine wraps a single HDF entry point, generally with the * analogous arguments and return codes. * * For details of the HDF libraries, see the HDF Documentation at: * http://hdf.ncsa.uiuc.edu/HDF5/doc/ * */ #ifdef __cplusplus extern "C" { #endif #include "hdf5.h" #include #include extern jboolean h5JNIFatalError( JNIEnv *env, char *functName); extern jboolean h5nullArgument( JNIEnv *env, char *functName); extern jboolean h5libraryError( JNIEnv *env ); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fopen * Signature: (Ljava/lang/String;II)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Fopen (JNIEnv *env, jclass clss, jstring name, jint flags, jint access_id) { hid_t status; char* file; jboolean isCopy; if (name == NULL) { /* exception -- bad argument? */ h5nullArgument( env, "H5Fopen: name is NULL"); return -1; } #ifdef __cplusplus file = (char *)env->GetStringUTFChars(name,&isCopy); #else file = (char *)(*env)->GetStringUTFChars(env,name,&isCopy); #endif if (file == NULL) { /* exception -- out of memory? */ h5JNIFatalError( env, "H5Fopen: file name not pinned"); return -1; } status = H5Fopen(file, (unsigned) flags, (hid_t) access_id ); #ifdef __cplusplus env->ReleaseStringUTFChars(name,file); #else (*env)->ReleaseStringUTFChars(env,name,file); #endif if (status < 0) { /* throw exception */ h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fcreate * Signature: (Ljava/lang/String;III)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Fcreate (JNIEnv *env, jclass clss, jstring name, jint flags, jint create_id, jint access_id) { hid_t status; char* file; jboolean isCopy; if (name == NULL) { /* exception -- bad argument? */ h5nullArgument( env, "H5Fcreate: name is NULL"); return -1; } #ifdef __cplusplus file = (char *)env->GetStringUTFChars(name,&isCopy); #else file = (char *)(*env)->GetStringUTFChars(env,name,&isCopy); #endif if (file == NULL) { /* exception -- out of memory? */ h5JNIFatalError( env, "H5Fcreate: file name is not pinned"); return -1; } status = H5Fcreate(file, flags, create_id, access_id); #ifdef __cplusplus env->ReleaseStringUTFChars(name,file); #else (*env)->ReleaseStringUTFChars(env,name,file); #endif if (status < 0) { /* throw exception */ h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fflush * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Fflush (JNIEnv *env, jclass clss, jint object_id, jint scope) { herr_t retVal = -1; retVal = H5Fflush((hid_t) object_id, (H5F_scope_t) scope ); if (retVal < 0) { /* throw exception */ h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fis_hdf5 * Signature: (Ljava/lang/String;)B */ JNIEXPORT jboolean JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Fis_1hdf5 (JNIEnv *env, jclass clss, jstring name) { htri_t retVal = 0; char * file; jboolean isCopy; if (name == NULL) { /* exception -- bad argument? */ h5nullArgument( env, "H5Fis_hdf5: name is NULL"); return JNI_FALSE; } #ifdef __cplusplus file = (char *)env->GetStringUTFChars(name,&isCopy); #else file = (char *)(*env)->GetStringUTFChars(env,name,&isCopy); #endif if (file == NULL) { /* exception -- out of memory? */ h5JNIFatalError( env, "H5Fis_hdf5: file name is not pinned"); return JNI_FALSE; } retVal = H5Fis_hdf5(file); #ifdef __cplusplus env->ReleaseStringUTFChars(name,file); #else (*env)->ReleaseStringUTFChars(env,name,file); #endif if (retVal > 0) { return JNI_TRUE; } else if (retVal == 0) { return JNI_FALSE; } else { /* raise exception here -- return value is irrelevant */ h5libraryError(env); return JNI_FALSE; } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fget_create_plist * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Fget_1create_1plist (JNIEnv *env, jclass clss, jint file_id) { hid_t retVal = -1; retVal = H5Fget_create_plist((hid_t) file_id ); if (retVal < 0) { /* throw exception */ h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fget_access_plist * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Fget_1access_1plist (JNIEnv *env, jclass clss, jint file_id) { hid_t retVal = -1; retVal = H5Fget_access_plist((hid_t) file_id); if (retVal < 0) { /* throw exception */ h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fclose * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Fclose (JNIEnv *env, jclass clss, jint file_id) { herr_t status = 0; if (file_id > 0) status = H5Fclose((hid_t) file_id ); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fmount * Signature: (ILjava/lang/String;II)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Fmount (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint child_id, jint plist_id) { herr_t status; char* file; jboolean isCopy; if (name == NULL) { /* exception -- bad argument? */ h5nullArgument( env, "H5Fmount: name is NULL"); return -1; } #ifdef __cplusplus file = (char *)env->GetStringUTFChars(name,&isCopy); #else file = (char *)(*env)->GetStringUTFChars(env,name,&isCopy); #endif if (file == NULL) { /* exception -- out of memory? */ h5JNIFatalError( env, "H5Fmount: file name is not pinned"); return -1; } status = H5Fmount((hid_t) loc_id, file, (hid_t) child_id, (hid_t) plist_id ); #ifdef __cplusplus env->ReleaseStringUTFChars(name,file); #else (*env)->ReleaseStringUTFChars(env,name,file); #endif if (status < 0) { /* throw exception */ h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Funmount * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Funmount (JNIEnv *env, jclass clss, jint loc_id, jstring name) { herr_t status; char* file; jboolean isCopy; if (name == NULL) { /* exception -- bad argument? */ h5nullArgument( env, "H5Funmount: name is NULL"); return -1; } #ifdef __cplusplus file = (char *)env->GetStringUTFChars(name,&isCopy); #else file = (char *)(*env)->GetStringUTFChars(env,name,&isCopy); #endif if (file == NULL) { h5JNIFatalError( env, "H5Funmount: file name is not pinned"); /* exception -- out of memory? */ return -1; } status = H5Funmount((hid_t) loc_id, file ); #ifdef __cplusplus env->ReleaseStringUTFChars(name,file); #else (*env)->ReleaseStringUTFChars(env,name,file); #endif if (status < 0) { /* throw exception */ h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Freopen * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Freopen (JNIEnv *env, jclass clss, jint file_id) { herr_t retVal = -1; retVal = H5Freopen((hid_t)file_id); if (retVal < 0) { /* throw exception */ h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fget_obj_ids(hid_t file_id, unsigned int types, int maxObjs, hid_t *obj_id_list ) * Signature: (I[J[J)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Fget_1obj_1ids (JNIEnv *env, jclass clss, jint file_id, jint types, jint obj_count, jintArray obj_id_list) { herr_t status=-1; jint *obj_id_listP; jboolean isCopy; int i; if ( obj_id_list == NULL ) { h5nullArgument( env, "H5Fget_obj_ids: obj_id_list is NULL"); return -1; } obj_id_listP = (*env)->GetIntArrayElements(env,obj_id_list,&isCopy); if (obj_id_listP == NULL) { h5JNIFatalError( env, "H5Fget_obj_ids: obj_id_list not pinned"); return -1; } status = H5Fget_obj_ids((hid_t)file_id, (unsigned int)types, (int)obj_count, (hid_t*)obj_id_listP); if (status < 0) { (*env)->ReleaseIntArrayElements(env,obj_id_list,obj_id_listP,JNI_ABORT); h5libraryError(env); } else { (*env)->ReleaseIntArrayElements(env,obj_id_list,obj_id_listP,0); } return (jint)status; } /* bug on 64-bit machines JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Fget_1obj_1ids (JNIEnv *env, jclass clss, jint file_id, jint types, jint maxObjs, jintArray obj_id_list) { herr_t status; jint *obj_id_listP; jboolean isCopy; hid_t *id_list; int rank; int i; status = -1; if ( obj_id_list == NULL ) { h5nullArgument( env, "H5Fget_obj_ids: obj_id_list is NULL"); return -1; } #ifdef __cplusplus obj_id_listP = env->GetIntArrayElements(obj_id_list,&isCopy); #else obj_id_listP = (*env)->GetIntArrayElements(env,obj_id_list,&isCopy); #endif if (obj_id_listP == NULL) { h5JNIFatalError( env, "H5Fget_obj_ids: obj_id_list not pinned"); return -1; } #ifdef __cplusplus rank = (int)env->GetArrayLength(obj_id_list); #else rank = (int)(*env)->GetArrayLength(env,obj_id_list); #endif id_list = (hid_t *)malloc( rank * sizeof(hid_t)); if (id_list == NULL) { #ifdef __cplusplus env->ReleaseIntArrayElements(obj_id_list,obj_id_listP,JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env,obj_id_list,obj_id_listP,JNI_ABORT); #endif h5outOfMemory(env, "H5Fget_obj_ids: obj_id_list not converted to hid_t"); return -1; } status = H5Fget_obj_ids((hid_t)file_id, (unsigned int)types, (int)maxObjs, id_list); if (status < 0) { #ifdef __cplusplus env->ReleaseIntArrayElements(obj_id_list,obj_id_listP,JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env,obj_id_list,obj_id_listP,JNI_ABORT); #endif free(id_list); h5libraryError(env); } else { for (i = 0; i < rank; i++) { obj_id_listP[i] = id_list[i]; } free(id_list); #ifdef __cplusplus env->ReleaseIntArrayElements(obj_id_list,obj_id_listP,0); #else (*env)->ReleaseIntArrayElements(env,obj_id_list,obj_id_listP,0); #endif } return (jint)status; } */ /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Fget_obj_count(hid_t file_id, unsigned int types ) * Signature: (I[J[J)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Fget_1obj_1count (JNIEnv *env, jclass clss, jint file_id, jint types ) { herr_t status; status = -1; status = H5Fget_obj_count((hid_t)file_id, (unsigned int)types ); if (status < 0) { h5libraryError(env); } return (jint)status; } /********************************************************************** * * * New functions release 1.6.3 versus release 1.6.2 * * * **********************************************************************/ /* * Class: ncsa_hdf_hdf5lib_H5 * Signature: ssize_t H5Fget_name (hid_t obj_id, char *name, size_t size) * Purpose: */ JNIEXPORT jlong JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Fget_1name (JNIEnv *env, jclass clss, jint obj_id, jstring name, jint buf_size) { char *aName; jstring str; ssize_t size; if (buf_size <= 0) { h5badArgument( env, "H5Fget_name: buf_size <= 0"); return -1; } aName = (char*)malloc(sizeof(char)*buf_size); if (aName == NULL) { h5outOfMemory( env, "H5Fget_name: malloc failed"); return -1; } size = H5Fget_name ((hid_t) obj_id, (char *)aName, (size_t)buf_size); if (size < 0) { free(aName); h5libraryError(env); /* exception, returns immediately */ } /* successful return -- save the string; */ #ifdef __cplusplus str = env->NewStringUTF(aName); #else str = (*env)->NewStringUTF(env,aName); #endif if (str == NULL) { free(aName); h5outOfMemory( env,"H5Fget_name: return string failed"); return -1; } free(aName); /* Note: throws ArrayIndexOutOfBoundsException, ArrayStoreException */ #ifdef __cplusplus env->SetObjectArrayElement(name,0,str); #else (*env)->SetObjectArrayElement(env,name,0,str); #endif return (jlong)size; } /* * Class: ncsa_hdf_hdf5lib_H5 * Signature: herr_t H5Fget_filesize (hid_t file_id, hsize_t * size) * Purpose: */ JNIEXPORT jlong JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Fget_1filesize (JNIEnv *env, jclass clss, jint file_id) { herr_t status; hsize_t size = 0; status = H5Fget_filesize ((hid_t) file_id, (hsize_t *) &size); if (status < 0) { h5libraryError(env); } return (jlong) size; } #ifdef __cplusplus } #endif libsis-jhdf5-java-14.12.1/source/c/jhdf5/h5gImpJHDF5.c000077500000000000000000000750441256564762100216550ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ /* * This code is the C-interface called by Java programs to access the * Group Object API Functions of the HDF5 library. * * Each routine wraps a single HDF entry point, generally with the * analogous arguments and return codes. * * For details of the HDF libraries, see the HDF Documentation at: * http://hdf.ncsa.uiuc.edu/HDF5/doc/ * */ #ifdef __cplusplus extern "C" { #endif #include "hdf5.h" /* missing definitions from hdf5.h */ #ifndef FALSE #define FALSE 0 #endif #ifndef TRUE #define TRUE (!FALSE) #endif /* delete TRUE and FALSE when fixed in HDF5 */ #include #include #include #ifdef __cplusplus herr_t obj_info_all(hid_t loc_id, const char *name, void *opdata); herr_t H5Gget_obj_info_all( JNIEnv *env, hid_t loc_id, char *group_name, char **objname, int *type ); #else static herr_t obj_info_all(hid_t loc_id, const char *name, void *opdata); static herr_t H5Gget_obj_info_all( JNIEnv *env, hid_t loc_id, char *group_name, char **objname, int *type ); #endif extern jboolean h5outOfMemory( JNIEnv *env, char *functName); extern jboolean h5JNIFatalError( JNIEnv *env, char *functName); extern jboolean h5nullArgument( JNIEnv *env, char *functName); extern jboolean h5badArgument( JNIEnv *env, char *functName); extern jboolean h5libraryError( JNIEnv *env ); typedef struct info_all { JNIEnv *env; char **objname; int *type; int count; } info_all_t; /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gcreate * Signature: (ILjava/lang/String;I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Gcreate (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint link_create_plist_id, jint group_create_plist_id, jint group_access_plist_id) { hid_t status; char* gName; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Gcreate: name is NULL"); return -1; } #ifdef __cplusplus gName = (char *)env->GetStringUTFChars(name,&isCopy); #else gName = (char *)(*env)->GetStringUTFChars(env,name,&isCopy); #endif if (gName == NULL) { h5JNIFatalError( env, "H5Gcreate: file name not pinned"); return -1; } status = H5Gcreate((hid_t)loc_id, gName, (hid_t)link_create_plist_id, (hid_t)group_create_plist_id, (hid_t)group_access_plist_id); #ifdef __cplusplus env->ReleaseStringUTFChars(name,gName); #else (*env)->ReleaseStringUTFChars(env,name,gName); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gopen * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Gopen (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint access_plist_id) { herr_t status; char* gName; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Gopen: name is NULL"); return -1; } #ifdef __cplusplus gName = (char *)env->GetStringUTFChars(name,&isCopy); #else gName = (char *)(*env)->GetStringUTFChars(env,name,&isCopy); #endif if (gName == NULL) { h5JNIFatalError( env, "H5Gopen: file name not pinned"); return -1; } status = H5Gopen((hid_t)loc_id, gName, (hid_t) access_plist_id); #ifdef __cplusplus env->ReleaseStringUTFChars(name,gName); #else (*env)->ReleaseStringUTFChars(env,name,gName); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gclose * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Gclose (JNIEnv *env, jclass clss, jint group_id) { herr_t retVal = 0; if (group_id > 0) retVal = H5Gclose((hid_t)group_id) ; if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Glink * Signature: (IILjava/lang/String;Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Glink (JNIEnv *env, jclass clss, jint loc_id, jint link_type, jstring current_name, jstring new_name) { herr_t status; char *cName, *nName; jboolean isCopy; if (current_name == NULL) { h5nullArgument( env, "H5Glink: current_name is NULL"); return -1; } if (new_name == NULL) { h5nullArgument( env, "H5Glink: new_name is NULL"); return -1; } #ifdef __cplusplus cName = (char *)env->GetStringUTFChars(current_name,&isCopy); #else cName = (char *)(*env)->GetStringUTFChars(env,current_name,&isCopy); #endif if (cName == NULL) { h5JNIFatalError( env, "H5Glink: current_name not pinned"); return -1; } #ifdef __cplusplus nName = (char *)env->GetStringUTFChars(new_name,&isCopy); #else nName = (char *)(*env)->GetStringUTFChars(env,new_name,&isCopy); #endif if (nName == NULL) { #ifdef __cplusplus env->ReleaseStringUTFChars(current_name,cName); #else (*env)->ReleaseStringUTFChars(env,current_name,cName); #endif h5JNIFatalError( env, "H5Glink: new_name not pinned"); return -1; } status = H5Glink((hid_t)loc_id, (H5G_link_t)link_type, cName, nName); #ifdef __cplusplus env->ReleaseStringUTFChars(new_name,nName); env->ReleaseStringUTFChars(current_name,cName); #else (*env)->ReleaseStringUTFChars(env,new_name,nName); (*env)->ReleaseStringUTFChars(env,current_name,cName); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Glink * Signature: (IILjava/lang/String;Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Glink2 (JNIEnv *env, jclass clss, jint current_loc_id, jstring current_name, jint link_type, jint new_loc_id, jstring new_name) { herr_t status; char *cName, *nName; jboolean isCopy; if (current_name == NULL) { h5nullArgument( env, "H5Glink2: current_name is NULL"); return -1; } if (new_name == NULL) { h5nullArgument( env, "H5Glink2: new_name is NULL"); return -1; } #ifdef __cplusplus cName = (char *)env->GetStringUTFChars(current_name,&isCopy); #else cName = (char *)(*env)->GetStringUTFChars(env,current_name,&isCopy); #endif if (cName == NULL) { h5JNIFatalError( env, "H5Glink2: current_name not pinned"); return -1; } #ifdef __cplusplus nName = (char *)env->GetStringUTFChars(new_name,&isCopy); #else nName = (char *)(*env)->GetStringUTFChars(env,new_name,&isCopy); #endif if (nName == NULL) { #ifdef __cplusplus env->ReleaseStringUTFChars(current_name,cName); #else (*env)->ReleaseStringUTFChars(env,current_name,cName); #endif h5JNIFatalError( env, "H5Glink2: new_name not pinned"); return -1; } status = H5Glink2((hid_t)current_loc_id, cName, (H5G_link_t)link_type, (hid_t)new_loc_id, nName); #ifdef __cplusplus env->ReleaseStringUTFChars(new_name,nName); env->ReleaseStringUTFChars(current_name,cName); #else (*env)->ReleaseStringUTFChars(env,new_name,nName); (*env)->ReleaseStringUTFChars(env,current_name,cName); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gunlink * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Gunlink (JNIEnv *env, jclass clss, jint loc_id, jstring name) { herr_t status; char* gName; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Gunlink: name is NULL"); return -1; } #ifdef __cplusplus gName = (char *)env->GetStringUTFChars(name,&isCopy); #else gName = (char *)(*env)->GetStringUTFChars(env,name,&isCopy); #endif if (gName == NULL) { h5JNIFatalError( env, "H5Gunlink: name not pinned"); return -1; } status = H5Gunlink((hid_t)loc_id, gName ); #ifdef __cplusplus env->ReleaseStringUTFChars(name,gName); #else (*env)->ReleaseStringUTFChars(env,name,gName); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gmove * Signature: (ILjava/lang/String;Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Gmove (JNIEnv *env, jclass clss, jint loc_id, jstring src, jstring dst) { herr_t status; char *sName, *dName; jboolean isCopy; if (src == NULL) { h5nullArgument( env, "H5Gmove: src is NULL"); return -1; } if (dst == NULL) { h5nullArgument( env, "H5Gmove: dst is NULL"); return -1; } #ifdef __cplusplus sName = (char *)env->GetStringUTFChars(src,&isCopy); #else sName = (char *)(*env)->GetStringUTFChars(env,src,&isCopy); #endif if (sName == NULL) { h5JNIFatalError( env, "H5Gmove: src not pinned"); return -1; } #ifdef __cplusplus dName = (char *)env->GetStringUTFChars(dst,&isCopy); #else dName = (char *)(*env)->GetStringUTFChars(env,dst,&isCopy); #endif if (dName == NULL) { #ifdef __cplusplus env->ReleaseStringUTFChars(src,sName); #else (*env)->ReleaseStringUTFChars(env,src,sName); #endif h5JNIFatalError( env, "H5Gmove: dst not pinned"); return -1; } status = H5Gmove((hid_t)loc_id, sName, dName ); #ifdef __cplusplus env->ReleaseStringUTFChars(dst,dName); env->ReleaseStringUTFChars(src,sName); #else (*env)->ReleaseStringUTFChars(env,dst,dName); (*env)->ReleaseStringUTFChars(env,src,sName); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gget_objinfo * Signature: (ILjava/lang/String;Z[J[I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Gget_1objinfo (JNIEnv *env, jclass clss, jint loc_id, jstring name, jboolean follow_link, jlongArray fileno, jlongArray objno, jintArray link_info, jlongArray mtime) { char* gName; jboolean isCopy; herr_t retVal; jint *linkInfo; jlong *fileInfo, *objInfo, *timeInfo; hbool_t follow; H5G_stat_t h5gInfo; if (name == NULL) { h5nullArgument( env, "H5Gget_objinfo: name is NULL"); return -1; } if (follow_link == JNI_TRUE) { follow = TRUE; /* HDF5 'TRUE' */ } else if (follow_link == JNI_FALSE) { follow = FALSE; /* HDF5 'FALSE' */ } else { h5badArgument( env, "H5Gget_objinfo: follow_link is invalid"); } if (fileno == NULL) { h5nullArgument( env, "H5Gget_objinfo: fileno is NULL"); return -1; } #ifdef __cplusplus if (env->GetArrayLength(fileno) < 2) { h5badArgument( env, "H5Gget_objinfo: fileno input array < 2"); } #else if ((*env)->GetArrayLength(env, fileno) < 2) { h5badArgument( env, "H5Gget_objinfo: fileno input array < 2"); } #endif if (objno == NULL) { h5nullArgument( env, "H5Gget_objinfo: objno is NULL"); return -1; } #ifdef __cplusplus if (env->GetArrayLength(objno) < 2) { h5badArgument( env, "H5Gget_objinfo: objno input array < 2"); } #else if ((*env)->GetArrayLength(env, objno) < 2) { h5badArgument( env, "H5Gget_objinfo: objno input array < 2"); } #endif if (link_info == NULL) { h5nullArgument( env, "H5Gget_objinfo: link_info is NULL"); return -1; } #ifdef __cplusplus if (env->GetArrayLength(link_info) < 3) { h5badArgument( env, "H5Gget_objinfo: link_info input array < 3"); } #else if ((*env)->GetArrayLength(env, link_info) < 3) { h5badArgument( env, "H5Gget_objinfo: link_info input array < 3"); } #endif if (mtime == NULL) { h5nullArgument( env, "H5Gget_objinfo: mtime is NULL"); return -1; } #ifdef __cplusplus gName = (char *)env->GetStringUTFChars(name,&isCopy); #else gName = (char *)(*env)->GetStringUTFChars(env,name,&isCopy); #endif if (gName == NULL) { h5JNIFatalError( env, "H5Gget_object: name not pinned"); return -1; } #ifdef __cplusplus fileInfo = (jlong *)env->GetLongArrayElements(fileno,&isCopy); #else fileInfo = (jlong *)(*env)->GetLongArrayElements(env,fileno,&isCopy); #endif if (fileInfo == NULL) { #ifdef __cplusplus env->ReleaseStringUTFChars(name,gName); #else (*env)->ReleaseStringUTFChars(env,name,gName); #endif h5JNIFatalError( env, "H5Gget_object: fileno not pinned"); return -1; } #ifdef __cplusplus objInfo = (jlong *)env->GetLongArrayElements(objno,&isCopy); #else objInfo = (jlong *)(*env)->GetLongArrayElements(env,objno,&isCopy); #endif if (objInfo == NULL) { #ifdef __cplusplus env->ReleaseLongArrayElements(fileno,fileInfo,JNI_ABORT); env->ReleaseStringUTFChars(name,gName); #else (*env)->ReleaseLongArrayElements(env,fileno,fileInfo,JNI_ABORT); (*env)->ReleaseStringUTFChars(env,name,gName); #endif h5JNIFatalError( env, "H5Gget_object: objno not pinned"); return -1; } #ifdef __cplusplus linkInfo = (jint *)env->GetIntArrayElements(link_info,&isCopy); #else linkInfo = (jint *)(*env)->GetIntArrayElements(env,link_info,&isCopy); #endif if (linkInfo == NULL) { #ifdef __cplusplus env->ReleaseLongArrayElements(objno,objInfo,JNI_ABORT); env->ReleaseLongArrayElements(fileno,fileInfo,JNI_ABORT); env->ReleaseStringUTFChars(name,gName); #else (*env)->ReleaseLongArrayElements(env,objno,objInfo,JNI_ABORT); (*env)->ReleaseLongArrayElements(env,fileno,fileInfo,JNI_ABORT); (*env)->ReleaseStringUTFChars(env,name,gName); #endif h5JNIFatalError( env, "H5Gget_object: link_info not pinned"); return -1; } #ifdef __cplusplus timeInfo = (jlong *)env->GetLongArrayElements(mtime,&isCopy); #else timeInfo = (jlong *)(*env)->GetLongArrayElements(env,mtime,&isCopy); #endif if (timeInfo == NULL) { #ifdef __cplusplus env->ReleaseIntArrayElements(link_info,linkInfo,JNI_ABORT); env->ReleaseLongArrayElements(objno,objInfo,JNI_ABORT); env->ReleaseLongArrayElements(fileno,fileInfo,JNI_ABORT); env->ReleaseStringUTFChars(name,gName); #else (*env)->ReleaseIntArrayElements(env,link_info,linkInfo,JNI_ABORT); (*env)->ReleaseLongArrayElements(env,objno,objInfo,JNI_ABORT); (*env)->ReleaseLongArrayElements(env,fileno,fileInfo,JNI_ABORT); (*env)->ReleaseStringUTFChars(env,name,gName); #endif h5JNIFatalError( env, "H5Gget_object: mtime not pinned"); return -1; } retVal = H5Gget_objinfo((hid_t)loc_id, gName, follow, &h5gInfo); if (retVal < 0) { #ifdef __cplusplus env->ReleaseLongArrayElements(mtime,timeInfo,JNI_ABORT); env->ReleaseLongArrayElements(objno,objInfo,JNI_ABORT); env->ReleaseLongArrayElements(fileno,fileInfo,JNI_ABORT); env->ReleaseIntArrayElements(link_info,linkInfo,JNI_ABORT); env->ReleaseStringUTFChars(name,gName); #else (*env)->ReleaseLongArrayElements(env,mtime,timeInfo,JNI_ABORT); (*env)->ReleaseLongArrayElements(env,objno,objInfo,JNI_ABORT); (*env)->ReleaseLongArrayElements(env,fileno,fileInfo,JNI_ABORT); (*env)->ReleaseIntArrayElements(env,link_info,linkInfo,JNI_ABORT); (*env)->ReleaseStringUTFChars(env,name,gName); #endif h5libraryError(env); } else { fileInfo[0] = (jlong)h5gInfo.fileno[0]; fileInfo[1] = (jlong)h5gInfo.fileno[1]; objInfo[0] = (jlong)h5gInfo.objno[0]; objInfo[1] = (jlong)h5gInfo.objno[1]; timeInfo[0] = (jlong)h5gInfo.mtime; linkInfo[0] = (jint)h5gInfo.nlink; linkInfo[1] = (jint)h5gInfo.type; linkInfo[2] = (jint)h5gInfo.linklen; #ifdef __cplusplus env->ReleaseLongArrayElements(mtime,timeInfo,0); env->ReleaseLongArrayElements(objno,objInfo,0); env->ReleaseLongArrayElements(fileno,fileInfo,0); env->ReleaseIntArrayElements(link_info,linkInfo,0); env->ReleaseStringUTFChars(name,gName); #else (*env)->ReleaseLongArrayElements(env,mtime,timeInfo,0); (*env)->ReleaseLongArrayElements(env,objno,objInfo,0); (*env)->ReleaseLongArrayElements(env,fileno,fileInfo,0); (*env)->ReleaseIntArrayElements(env,link_info,linkInfo,0); (*env)->ReleaseStringUTFChars(env,name,gName); #endif } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gget_linkval * Signature: (ILjava/lang/String;I[Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Gget_1linkval (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint size, jobjectArray value) { char* gName; jboolean isCopy; char *lValue; jstring str; herr_t status; if (size < 0) { h5badArgument( env, "H5Gget_linkval: size < 0"); return -1; } if (name == NULL) { h5nullArgument( env, "H5Gget_linkval: name is NULL"); return -1; } lValue = (char *) malloc(sizeof(char)*size); if (lValue == NULL) { h5outOfMemory( env, "H5Gget_linkval: malloc failed "); return -1; } #ifdef __cplusplus gName = (char *)env->GetStringUTFChars(name,&isCopy); #else gName = (char *)(*env)->GetStringUTFChars(env,name,&isCopy); #endif if (gName == NULL) { free(lValue); h5JNIFatalError( env, "H5Gget_linkval: name not pinned"); return -1; } status = H5Gget_linkval((hid_t)loc_id, gName, (size_t)size, lValue); #ifdef __cplusplus env->ReleaseStringUTFChars(name,gName); #else (*env)->ReleaseStringUTFChars(env,name,gName); #endif if (status >= 0) { /* may throw OutOfMemoryError */ #ifdef __cplusplus str = env->NewStringUTF(lValue); #else str = (*env)->NewStringUTF(env,lValue); #endif if (str == NULL) { /* exception -- fatal JNI error */ free(lValue); h5outOfMemory( env, "H5Gget_linkval: return string not created"); return -1; } /* the SetObjectArrayElement may raise exceptions... */ #ifdef __cplusplus env->SetObjectArrayElement(value,0,(jobject)str); #else (*env)->SetObjectArrayElement(env,value,0,(jobject)str); #endif free(lValue); } else { free(lValue); h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gset_comment * Signature: (ILjava/lang/String;Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Gset_1comment (JNIEnv *env, jclass clss, jint loc_id, jstring name, jstring comment) { herr_t status; char *gName, *gComment; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Gset_comment: name is NULL"); return -1; } if (comment == NULL) { h5nullArgument( env, "H5Gset_comment: comment is NULL"); return -1; } #ifdef __cplusplus gName = (char *)env->GetStringUTFChars(name,&isCopy); #else gName = (char *)(*env)->GetStringUTFChars(env,name,&isCopy); #endif if (gName == NULL) { h5JNIFatalError( env, "H5Gset_comment: name not pinned"); return -1; } #ifdef __cplusplus gComment = (char *)env->GetStringUTFChars(comment,&isCopy); #else gComment = (char *)(*env)->GetStringUTFChars(env,comment,&isCopy); #endif if (gComment == NULL) { #ifdef __cplusplus env->ReleaseStringUTFChars(name,gName); #else (*env)->ReleaseStringUTFChars(env,name,gName); #endif h5JNIFatalError( env, "H5Gset_comment: comment not pinned"); return -1; } status = H5Gset_comment((hid_t)loc_id, gName, gComment); #ifdef __cplusplus env->ReleaseStringUTFChars(comment,gComment); env->ReleaseStringUTFChars(name,gName); #else (*env)->ReleaseStringUTFChars(env,comment,gComment); (*env)->ReleaseStringUTFChars(env,name,gName); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gget_comment * Signature: (ILjava/lang/String;I[Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Gget_1comment (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint bufsize, jobjectArray comment) { char* gName; jboolean isCopy; char *gComment; jstring str; jint status; if (bufsize <= 0) { h5badArgument( env, "H5Gget_comment: bufsize <= 0"); return -1; } if (name == NULL) { h5nullArgument( env, "H5Gget_comment: name is NULL"); return -1; } if (comment == NULL) { h5nullArgument( env, "H5Gget_comment: comment is NULL"); return -1; } gComment = (char *)malloc(sizeof(char)*bufsize); if (gComment == NULL) { /* exception -- out of memory */ h5outOfMemory( env, "H5Gget_comment: malloc failed"); return -1; } #ifdef __cplusplus gName = (char *)env->GetStringUTFChars(name,&isCopy); #else gName = (char *)(*env)->GetStringUTFChars(env,name,&isCopy); #endif if (gName == NULL) { free(gComment); h5JNIFatalError( env, "H5Gget_comment: name not pinned"); return -1; } status = H5Gget_comment((hid_t)loc_id, gName, (size_t)bufsize, gComment); #ifdef __cplusplus env->ReleaseStringUTFChars(name,gName); #else (*env)->ReleaseStringUTFChars(env,name,gName); #endif if (status >= 0) { /* may throw OutOfMemoryError */ #ifdef __cplusplus str = env->NewStringUTF(gComment); #else str = (*env)->NewStringUTF(env,gComment); #endif if (str == NULL) { free(gComment); h5outOfMemory( env, "H5Gget_comment: return string not allocated"); return -1; } /* The SetObjectArrayElement may raise exceptions */ #ifdef __cplusplus env->SetObjectArrayElement(comment,0,(jobject)str); #else (*env)->SetObjectArrayElement(env,comment,0,(jobject)str); #endif free(gComment); } else { free(gComment); h5libraryError(env); } return (jint)status; } /*************************************************************** * New APIs for HDF5.1.6 * ***************************************************************/ /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gget_num_objs * Signature: (I[J[J)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Gget_1num_1objs (JNIEnv *env, jclass clss, jint loc_id, jlongArray num_obj) { int status; jlong *num_objP; jboolean isCopy; hsize_t *num_obja; int i; int rank; if (num_obj == NULL) { h5nullArgument( env, "H5Gget_num_objs: num_obj is NULL"); return -1; } #ifdef __cplusplus num_objP = env->GetLongArrayElements(num_obj,&isCopy); #else num_objP = (*env)->GetLongArrayElements(env,num_obj,&isCopy); #endif if (num_objP == NULL) { h5JNIFatalError(env, "H5Gget_num_objs: num_obj not pinned"); return -1; } #ifdef __cplusplus rank = (int) env->GetArrayLength(num_obj); #else rank = (int) (*env)->GetArrayLength(env,num_obj); #endif num_obja = (hsize_t *)malloc( rank * sizeof(hsize_t)); if (num_obja == NULL) { #ifdef __cplusplus env->ReleaseLongArrayElements(num_obj,num_objP,JNI_ABORT); #else (*env)->ReleaseLongArrayElements(env,num_obj,num_objP,JNI_ABORT); #endif h5outOfMemory(env, "H5Gget_num_objs: num_obj not converted to hsize_t"); return -1; } status = H5Gget_num_objs(loc_id, (hsize_t *)num_obja); if (status < 0) { #ifdef __cplusplus env->ReleaseLongArrayElements(num_obj,num_objP,JNI_ABORT); #else (*env)->ReleaseLongArrayElements(env,num_obj,num_objP,JNI_ABORT); #endif free(num_obja); h5libraryError(env); } else { for (i = 0; i < rank; i++) { num_objP[i] = num_obja[i]; } free(num_obja); #ifdef __cplusplus env->ReleaseLongArrayElements(num_objs,num_objP,0); #else (*env)->ReleaseLongArrayElements(env,num_obj,num_objP,0); #endif } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gget_objname_by_idx(hid_t group_id, hsize_t idx, char *name, size_t* size ) * Signature: (IJLjava/lang/String;)J */ JNIEXPORT jlong JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Gget_1objname_1by_1idx (JNIEnv *env, jclass clss, jint group_id, jlong idx, jobjectArray name, jlong buf_size) { char *aName; jstring str; hssize_t size; long bs; bs = (long)buf_size; if (bs <= 0) { h5badArgument( env, "H5Gget_objname_by_idx: buf_size <= 0"); return -1; } aName = (char*)malloc(sizeof(char)*bs); if (aName == NULL) { h5outOfMemory( env, "H5Gget_objname_by_idx: malloc failed"); return -1; } size = H5Gget_objname_by_idx((hid_t)group_id, (hsize_t)idx, aName, (size_t)buf_size); if (size < 0) { free(aName); h5libraryError(env); /* exception, returns immediately */ } /* successful return -- save the string; */ #ifdef __cplusplus str = env->NewStringUTF(aName); #else str = (*env)->NewStringUTF(env,aName); #endif if (str == NULL) { free(aName); h5outOfMemory( env,"H5Gget_objname_by_idx: return string failed"); return -1; } free(aName); /* Note: throws ArrayIndexOutOfBoundsException, ArrayStoreException */ #ifdef __cplusplus env->SetObjectArrayElement(name,0,str); #else (*env)->SetObjectArrayElement(env,name,0,str); #endif return (jlong)size; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gget_objtype_by_idx(hid_t group_id, hsize_t idx ) * Signature: (IJLjava/lang/String;)J */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Gget_1objtype_1by_1idx (JNIEnv *env, jclass clss, jint group_id, jlong idx) { int type; type = H5Gget_objtype_by_idx((hid_t)group_id, (hsize_t)idx ); if (type < 0) { h5libraryError(env); } return (jint)type; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gget_info(hid_t group_id, H5G_info_t group_info ) */ JNIEXPORT jlong JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Gget_1nlinks (JNIEnv *env, jclass clss, jint group_id) { H5G_info_t group_info; int status; status = H5Gget_info((hid_t)group_id, &group_info ); if (status < 0) { h5libraryError(env); return -1; } return group_info.nlinks; } /* ///////////////////////////////////////////////////////////////////////////////// // // // Add these methods so that we don't need to call H5Gget_objtype_by_idx // in a loop to get information for all the object in a group, which takes // a lot of time to finish if the number of objects is more than 10,000 // ///////////////////////////////////////////////////////////////////////////////// */ /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Gget_obj_info_all */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Gget_1obj_1info_1all (JNIEnv *env, jclass clss, jint loc_id, jstring group_name, jobjectArray objName, jintArray oType, jint n) { herr_t status; char *gName=NULL; char **oName=NULL; jboolean isCopy; jstring str; jint *tarr; int i; if (group_name == NULL) { h5nullArgument( env, "H5Gget_obj_info_all: group_name is NULL"); return -1; } if (oType == NULL) { h5nullArgument( env, "H5Gget_obj_info_all: oType is NULL"); return -1; } gName = (char *)(*env)->GetStringUTFChars(env,group_name,&isCopy); if (gName == NULL) { h5JNIFatalError( env, "H5Gget_obj_info_all: group_name not pinned"); return -1; } tarr = (*env)->GetIntArrayElements(env,oType,&isCopy); if (tarr == NULL) { (*env)->ReleaseStringUTFChars(env,group_name,gName); h5JNIFatalError( env, "H5Gget_obj_info_all: type not pinned"); return -1; } oName = malloc(n * sizeof (*oName)); if (oName == NULL) { (*env)->ReleaseStringUTFChars(env,group_name,gName); (*env)->ReleaseIntArrayElements(env,oType,tarr,0); h5outOfMemory(env, "H5Gget_obj_info_all: malloc failed"); return -1; } status = H5Gget_obj_info_all( env, (hid_t) loc_id, gName, oName, (int *)tarr ); (*env)->ReleaseStringUTFChars(env,group_name,gName); if (status < 0) { (*env)->ReleaseIntArrayElements(env,oType,tarr,JNI_ABORT); h5str_array_free_jhdf5(oName, n); h5libraryError(env); } else { (*env)->ReleaseIntArrayElements(env,oType,tarr,0); for (i=0; iNewStringUTF(env,*(oName+i)); (*env)->SetObjectArrayElement(env,objName,i,(jobject)str); } } /* for (i=0; itype+info->count) = -1; *(info->objname+info->count) = NULL; } else { *(info->type+info->count) = ib.type; *(info->objname+info->count) = (char *) malloc(strlen(name)+1); if (*(info->objname+info->count) == NULL) { h5outOfMemory(info->env, "H5Gget_link_info_all: malloc failed"); return -1; } strcpy(*(info->objname+info->count), name); } info->count++; return 0; } #ifdef __cplusplus } #endif libsis-jhdf5-java-14.12.1/source/c/jhdf5/h5iImpJHDF5.c000077500000000000000000000124451256564762100216530ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ /* * This code is the C-interface called by Java programs to access the * Identifier API Functions of the HDF5 library. * * Each routine wraps a single HDF entry point, generally with the * analogous arguments and return codes. * * For details of the HDF libraries, see the HDF Documentation at: * http://hdf.ncsa.uiuc.edu/HDF5/doc/ * */ #ifdef __cplusplus extern "C" { #endif #include "hdf5.h" #include #include extern jboolean h5libraryError( JNIEnv *env ); /* * Class: ncsa_hdf_hdf5lib_H5Header * Method: H5Gget_linkval * Signature: (ILjava/lang/String;I[Ljava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Iget_1type (JNIEnv *env, jclass clss, jint obj_id) { H5I_type_t retVal = H5I_BADID; retVal = H5Iget_type((hid_t)obj_id); if (retVal == H5I_BADID) { h5libraryError(env); } return (jint)retVal; } /********************************************************************** * * * New functions release 1.6.2 versus release 1.6.1 * * * **********************************************************************/ /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Iget_name(hid_t obj_id, char *name, size_t size ) * Signature: (IJLjava/lang/String;)J */ JNIEXPORT jlong JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Iget_1name (JNIEnv *env, jclass clss, jint obj_id, jobjectArray name, jlong buf_size) { char *aName; jstring str; hssize_t size; size_t bs; bs = (size_t)buf_size; if (bs <= 0) { h5badArgument( env, "H5Iget_name: buf_size <= 0"); return -1; } aName = (char*)malloc(sizeof(char)*(bs+1)); if (aName == NULL) { h5outOfMemory( env, "H5Iget_name: malloc failed"); return -1; } size = H5Iget_name((hid_t)obj_id, aName, bs); if (size < 0) { free(aName); h5libraryError(env); return -1; } /* successful return -- save the string; */ #ifdef __cplusplus str = env->NewStringUTF(aName); #else str = (*env)->NewStringUTF(env,aName); #endif if (str == NULL) { free(aName); h5outOfMemory( env,"H5Iget_name: return string failed"); return -1; } free(aName); /* Note: throws ArrayIndexOutOfBoundsException, ArrayStoreException */ #ifdef __cplusplus env->SetObjectArrayElement(name,0,str); #else (*env)->SetObjectArrayElement(env,name,0,str); #endif return (jlong)size; } /* * Class: ncsa_hdf_hdf5lib_H5 * Signature: int H5Iget_ref(hid_t obj_id) * Purpose: Retrieves the reference count for an object */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Iget_1ref (JNIEnv *env, jclass clss, jint obj_id) { int retVal = -1; retVal = H5Iget_ref( (hid_t)obj_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Signature: int H5Iinc_ref(hid_t obj_id) * Purpose: Increments the reference count for an object */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Iinc_1ref (JNIEnv *env, jclass clss, jint obj_id) { int retVal = -1; retVal = H5Iinc_ref( (hid_t)obj_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Signature: int H5Idec_ref(hid_t obj_id) * Purpose: Decrements the reference count for an object */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Idec_1ref (JNIEnv *env, jclass clss, jint obj_id) { int retVal = -1; retVal = H5Idec_ref( (hid_t)obj_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /********************************************************************** * * * New functions release 1.6.3 versus release 1.6.2 * * * **********************************************************************/ /* * Class: ncsa_hdf_hdf5lib_H5 * Signature: hid_t H5Iget_file_id (hid_t obj_id) * Purpose: */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Iget_1file_1id (JNIEnv *env, jclass clss, jint obj_id) { hid_t file_id = 0; file_id = H5Iget_file_id ((hid_t) obj_id); if (file_id < 0) { h5libraryError(env); } return (jint) file_id; } #ifdef __cplusplus } #endif libsis-jhdf5-java-14.12.1/source/c/jhdf5/h5lImpJHDF5.c000066400000000000000000000554441256564762100216610ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ /* * This code is the C-interface called by Java programs to access the * Group Object API Functions of the HDF5 library. * * Each routine wraps a single HDF entry point, generally with the * analogous arguments and return codes. * * For details of the HDF libraries, see the HDF Documentation at: * http://hdf.ncsa.uiuc.edu/HDF5/doc/ * */ #ifdef __cplusplus extern "C" { #endif #include "hdf5.h" #include "h5utilJHDF5.h" /* missing definitions from hdf5.h */ #ifndef FALSE #define FALSE 0 #endif #ifndef TRUE #define TRUE (!FALSE) #endif /* delete TRUE and FALSE when fixed in HDF5 */ #include #include #include extern jboolean h5outOfMemory( JNIEnv *env, char *functName); extern jboolean h5JNIFatalError( JNIEnv *env, char *functName); extern jboolean h5nullArgument( JNIEnv *env, char *functName); extern jboolean h5badArgument( JNIEnv *env, char *functName); extern jboolean h5libraryError( JNIEnv *env ); extern int getMinorErrorNumber(); #ifdef __cplusplus herr_t link_info_all(hid_t loc_id, const char *name, const H5L_info_t *link_info, void *opdata); herr_t H5Lget_link_info_all( JNIEnv *env, hid_t loc_id, char *group_name, char **names, int *type, char **linknames ); herr_t link_names_all(hid_t loc_id, const char *name, const H5L_info_t *link_info, void *opdata); herr_t H5Lget_link_names_all( JNIEnv *env, hid_t loc_id, char *group_name, char **names ); #else static herr_t link_info_all(hid_t loc_id, const char *name, const H5L_info_t *link_info, void *opdata); static herr_t H5Lget_link_info_all( JNIEnv *env, hid_t loc_id, char *group_name, char **names, int *type, char **linknames ); static herr_t link_names_all(hid_t loc_id, const char *name, const H5L_info_t *link_info, void *opdata); static herr_t H5Lget_link_names_all( JNIEnv *env, hid_t loc_id, char *group_name, char **names ); #endif typedef struct link_info_all { JNIEnv *env; char **name; int *type; char **linkname; int count; } link_info_all_t; char *get_external_link( JNIEnv *env, const char *linkval_buf, size_t size ) { const char *filename; const char *obj_path; char *external_link_buf; const char *prefix = "EXTERNAL::"; H5Lunpack_elink_val(linkval_buf, size, NULL, &filename, &obj_path); external_link_buf = (char *) malloc(strlen(prefix) + strlen(filename) + strlen(obj_path) + 3); if (external_link_buf == NULL) { h5outOfMemory(env, "get_external_link: malloc failed"); return NULL; } strcpy(external_link_buf, prefix); strcat(external_link_buf, filename); strcat(external_link_buf, "::"); strcat(external_link_buf, obj_path); return external_link_buf; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lcreate_hard * Signature: (ILjava/lang/String;ILjava/lang/String;II)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Lcreate_1hard (JNIEnv *env, jclass clss, jint obj_loc_id, jstring obj_name, jint link_loc_id, jstring link_name, jint lcpl_id, jint lapl_id) { herr_t status; char *oName, *lName; jboolean isCopy; if (obj_name == NULL) { h5nullArgument( env, "H5Lcreate_hard: obj_name is NULL"); return -1; } if (link_name == NULL) { h5nullArgument( env, "H5Lcreate_hard: link_name is NULL"); return -1; } #ifdef __cplusplus oName = (char *)env->GetStringUTFChars(obj_name,&isCopy); #else oName = (char *)(*env)->GetStringUTFChars(env,obj_name,&isCopy); #endif if (oName == NULL) { h5JNIFatalError( env, "H5Lcreate_hard: obj_name not pinned"); return -1; } #ifdef __cplusplus lName = (char *)env->GetStringUTFChars(link_name,&isCopy); #else lName = (char *)(*env)->GetStringUTFChars(env,link_name,&isCopy); #endif if (lName == NULL) { #ifdef __cplusplus env->ReleaseStringUTFChars(obj_name,oName); #else (*env)->ReleaseStringUTFChars(env,obj_name,oName); #endif h5JNIFatalError( env, "H5Lcreate_hard: link_name not pinned"); return -1; } status = H5Lcreate_hard((hid_t)obj_loc_id, oName, (hid_t)link_loc_id, lName, lcpl_id, lapl_id); #ifdef __cplusplus env->ReleaseStringUTFChars(link_name,lName); env->ReleaseStringUTFChars(obj_name,oName); #else (*env)->ReleaseStringUTFChars(env,link_name,lName); (*env)->ReleaseStringUTFChars(env,obj_name,oName); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lcreate_soft * Signature: (Ljava/lang/String;ILjava/lang/String;II)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Lcreate_1soft (JNIEnv *env, jclass clss, jstring target_path, jint link_loc_id, jstring link_name, jint lcpl_id, jint lapl_id) { herr_t status; char *tPath, *lName; jboolean isCopy; if (target_path == NULL) { h5nullArgument( env, "H5Lcreate_soft: target_path is NULL"); return -1; } if (link_name == NULL) { h5nullArgument( env, "H5Lcreate_soft: link_name is NULL"); return -1; } #ifdef __cplusplus tPath = (char *)env->GetStringUTFChars(target_path,&isCopy); #else tPath = (char *)(*env)->GetStringUTFChars(env,target_path,&isCopy); #endif if (tPath == NULL) { h5JNIFatalError( env, "H5Lcreate_soft: target_path not pinned"); return -1; } #ifdef __cplusplus lName = (char *)env->GetStringUTFChars(link_name,&isCopy); #else lName = (char *)(*env)->GetStringUTFChars(env,link_name,&isCopy); #endif if (lName == NULL) { #ifdef __cplusplus env->ReleaseStringUTFChars(target_path,tPath); #else (*env)->ReleaseStringUTFChars(env,target_path,tPath); #endif h5JNIFatalError( env, "H5Lcreate_soft: link_name not pinned"); return -1; } status = H5Lcreate_soft(tPath, (hid_t)link_loc_id, lName, lcpl_id, lapl_id); #ifdef __cplusplus env->ReleaseStringUTFChars(link_name,lName); env->ReleaseStringUTFChars(target_path,tPath); #else (*env)->ReleaseStringUTFChars(env,link_name,lName); (*env)->ReleaseStringUTFChars(env,target_path,tPath); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lcreate_external * Signature: (Ljava/lang/String;Ljava/lang/String;ILjava/lang/String;II)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Lcreate_1external (JNIEnv *env, jclass clss, jstring file_name, jstring obj_name, jint link_loc_id, jstring link_name, jint lcpl_id, jint lapl_id) { herr_t status; char *fName, *oName, *lName; jboolean isCopy; if (file_name == NULL) { h5nullArgument( env, "H5Lcreate_external: file_name is NULL"); return -1; } if (obj_name == NULL) { h5nullArgument( env, "H5Lcreate_external: obj_name is NULL"); return -1; } if (link_name == NULL) { h5nullArgument( env, "H5Lcreate_external: link_name is NULL"); return -1; } #ifdef __cplusplus fName = (char *)env->GetStringUTFChars(file_name,&isCopy); #else fName = (char *)(*env)->GetStringUTFChars(env,file_name,&isCopy); #endif if (fName == NULL) { h5JNIFatalError( env, "H5Lcreate_external: file_name not pinned"); return -1; } #ifdef __cplusplus oName = (char *)env->GetStringUTFChars(obj_name,&isCopy); #else oName = (char *)(*env)->GetStringUTFChars(env,obj_name,&isCopy); #endif if (oName == NULL) { #ifdef __cplusplus env->ReleaseStringUTFChars(file_name,fName); #else (*env)->ReleaseStringUTFChars(env,file_name,fName); #endif h5JNIFatalError( env, "H5Lcreate_external: obj_name not pinned"); return -1; } #ifdef __cplusplus lName = (char *)env->GetStringUTFChars(link_name,&isCopy); #else lName = (char *)(*env)->GetStringUTFChars(env,link_name,&isCopy); #endif if (lName == NULL) { #ifdef __cplusplus env->ReleaseStringUTFChars(file_name,fName); env->ReleaseStringUTFChars(obj_name,oName); #else (*env)->ReleaseStringUTFChars(env,file_name,fName); (*env)->ReleaseStringUTFChars(env,obj_name,oName); #endif h5JNIFatalError( env, "H5Lcreate_external: link_name not pinned"); return -1; } status = H5Lcreate_external(fName, oName, (hid_t)link_loc_id, lName, lcpl_id, lapl_id); #ifdef __cplusplus env->ReleaseStringUTFChars(file_name,fName); env->ReleaseStringUTFChars(link_name,lName); env->ReleaseStringUTFChars(obj_name,oName); #else (*env)->ReleaseStringUTFChars(env,file_name,fName); (*env)->ReleaseStringUTFChars(env,link_name,lName); (*env)->ReleaseStringUTFChars(env,obj_name,oName); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lmove * Signature: (ILjava/lang/String;ILjava/lang/String;II)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Lmove (JNIEnv *env, jclass clss, jint src_loc_id, jstring src_name, jint dest_loc_id, jstring dest_name, jint lcpl_id, jint lapl_id) { herr_t status; char *srcName, *dstName; jboolean isCopy; if (src_name == NULL) { h5nullArgument( env, "H5Lmove: src_name is NULL"); return -1; } if (dest_name == NULL) { h5nullArgument( env, "H5Lmove: dest_name is NULL"); return -1; } #ifdef __cplusplus srcName = (char *)env->GetStringUTFChars(src_name,&isCopy); #else srcName = (char *)(*env)->GetStringUTFChars(env,src_name,&isCopy); #endif if (srcName == NULL) { h5JNIFatalError( env, "H5Lmove: src_name not pinned"); return -1; } #ifdef __cplusplus dstName = (char *)env->GetStringUTFChars(dest_name,&isCopy); #else dstName = (char *)(*env)->GetStringUTFChars(env,dest_name,&isCopy); #endif if (dstName == NULL) { #ifdef __cplusplus env->ReleaseStringUTFChars(src_name,srcName); #else (*env)->ReleaseStringUTFChars(env,src_name,srcName); #endif h5JNIFatalError( env, "H5Lmove: dest_name not pinned"); return -1; } status = H5Lmove((hid_t)src_loc_id, srcName, (hid_t)dest_loc_id, dstName, lcpl_id, lapl_id); #ifdef __cplusplus env->ReleaseStringUTFChars(dest_name,dstName); env->ReleaseStringUTFChars(src_name,srcName); #else (*env)->ReleaseStringUTFChars(env,dest_name,dstName); (*env)->ReleaseStringUTFChars(env,src_name,srcName); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lget_link_info */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Lget_1link_1info (JNIEnv *env, jclass clss, jint loc_id, jstring object_name, jobjectArray linkName, jboolean exception_when_non_existent) { jint type; herr_t status; int minor_err_num; char *oName; char *linkval_buf; char *linkname_buf; jboolean isCopy; jstring str; H5L_info_t link_info; H5O_info_t obj_info; if (object_name == NULL) { h5nullArgument( env, "H5Lget_link_info: object_name is NULL"); return -1; } #ifdef __cplusplus oName = (char *)env->GetStringUTFChars(object_name,&isCopy); #else oName = (char *)(*env)->GetStringUTFChars(env,object_name,&isCopy); #endif if (oName == NULL) { h5JNIFatalError( env, "H5Lget_link_info: object_name not pinned"); return -1; } type = H5Lget_info( (hid_t) loc_id, oName, &link_info, H5P_DEFAULT ); if (type < 0) { #ifdef __cplusplus env->ReleaseStringUTFChars(object_name,oName); #else (*env)->ReleaseStringUTFChars(env,object_name,oName); #endif if (exception_when_non_existent == JNI_FALSE) { minor_err_num = getMinorErrorNumber(); /* * Note: H5E_CANTINSERT is thrown by the dense group lookup, see H5Gdense:534. That is * probably a wrong error code, but we have to deal with it here anyway. */ if (minor_err_num == H5E_NOTFOUND || minor_err_num == H5E_CANTINSERT) { return -1; } } h5libraryError(env); } else { str = NULL; if (link_info.type == H5L_TYPE_HARD) { status = H5Oget_info_by_name(loc_id, oName, &obj_info, H5P_DEFAULT); (*env)->ReleaseStringUTFChars(env,object_name,oName); if (status < 0 ) { h5libraryError(env); return -1; } else { type = obj_info.type; } } else { type = H5O_TYPE_NTYPES + link_info.type; if (linkName != NULL) { linkval_buf = (char*) malloc(link_info.u.val_size); if (linkval_buf == NULL) { h5outOfMemory(env, "H5Lget_link_info: malloc failed"); return -1; } if (H5Lget_val(loc_id, oName, linkval_buf, link_info.u.val_size, H5P_DEFAULT) < 0) { h5libraryError(env); return -1; } if (link_info.type == H5L_TYPE_EXTERNAL) { linkname_buf = get_external_link(env, linkval_buf, link_info.u.val_size); free(linkval_buf); } else { linkname_buf = linkval_buf; } str = (*env)->NewStringUTF(env,linkname_buf); (*env)->SetObjectArrayElement(env,linkName,0,(jobject)str); } } } return (jint)type; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lexists */ JNIEXPORT jboolean JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Lexists (JNIEnv *env, jclass clss, jint loc_id, jstring link_name) { htri_t exists; char *lName; jboolean isCopy; if (link_name == NULL) { h5nullArgument( env, "H5Lexists: link_name is NULL"); return -1; } lName = (char *)(*env)->GetStringUTFChars(env,link_name,&isCopy); if (lName == NULL) { h5JNIFatalError( env, "H5Lexists: link_name not pinned"); return -1; } exists = H5Lexists( (hid_t) loc_id, lName, H5P_DEFAULT ); if (exists < 0) { if (getMinorErrorNumber() == H5E_NOTFOUND) { exists = 0; } else { h5libraryError(env); } } (*env)->ReleaseStringUTFChars(env,link_name,lName); return exists; } /* ///////////////////////////////////////////////////////////////////////////////// // // // Add these methods so that we don't need to call H5Lget_info // in a loop to get information for all the object in a group, which takes // a lot of time to finish if the number of objects is more than 10,000 // ///////////////////////////////////////////////////////////////////////////////// */ /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lget_link_names_all */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Lget_1link_1names_1all (JNIEnv *env, jclass clss, jint loc_id, jstring group_name, jobjectArray objName, jint n) { herr_t status; char *gName=NULL; char **oName=NULL; char **lName=NULL; jboolean isCopy; jstring str; jint *tarr; int i; if (group_name == NULL) { h5nullArgument( env, "H5Lget_link_info_all: group_name is NULL"); return -1; } gName = (char *)(*env)->GetStringUTFChars(env,group_name,&isCopy); if (gName == NULL) { h5JNIFatalError( env, "H5Lget_link_info_all: group_name not pinned"); return -1; } oName = malloc(n * sizeof (*oName)); if (oName == NULL) { (*env)->ReleaseStringUTFChars(env,group_name,gName); h5outOfMemory(env, "H5Lget_link_info_all: malloc failed"); return -1; } for (i=0; iReleaseStringUTFChars(env,group_name,gName); if (status < 0) { h5str_array_free_jhdf5(oName, n); h5libraryError(env); } else { for (i=0; iNewStringUTF(env,*(oName+i)); (*env)->SetObjectArrayElement(env,objName,i,(jobject)str); } } /* for (i=0; iname+info->count) = (char *) malloc(strlen(name)+1); if (*(info->name+info->count) == NULL) { h5outOfMemory(info->env, "H5Lget_link_info_all: malloc failed"); return -1; } strcpy(*(info->name+info->count), name); info->count++; return 0; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Lget_link_info_all */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Lget_1link_1info_1all (JNIEnv *env, jclass clss, jint loc_id, jstring group_name, jobjectArray objName, jintArray oType, jobjectArray linkName, jint n) { herr_t status; char *gName=NULL; char **oName=NULL; char **lName=NULL; jboolean isCopy; jstring str; jint *tarr; int i; if (group_name == NULL) { h5nullArgument( env, "H5Lget_link_info_all: group_name is NULL"); return -1; } if (oType == NULL) { h5nullArgument( env, "H5Lget_link_info_all: oType is NULL"); return -1; } gName = (char *)(*env)->GetStringUTFChars(env,group_name,&isCopy); if (gName == NULL) { h5JNIFatalError( env, "H5Lget_link_info_all: group_name not pinned"); return -1; } tarr = (*env)->GetIntArrayElements(env,oType,&isCopy); if (tarr == NULL) { (*env)->ReleaseStringUTFChars(env,group_name,gName); h5JNIFatalError( env, "H5Lget_link_info_all: type not pinned"); return -1; } oName = malloc(n * sizeof (*oName)); if (oName == NULL) { (*env)->ReleaseStringUTFChars(env,group_name,gName); (*env)->ReleaseIntArrayElements(env,oType,tarr,0); h5outOfMemory(env, "H5Lget_link_info_all: malloc failed"); return -1; } for (i=0; iReleaseStringUTFChars(env,group_name,gName); (*env)->ReleaseIntArrayElements(env,oType,tarr,0); h5str_array_free_jhdf5(oName, n); h5outOfMemory(env, "H5Lget_link_info_all: malloc failed"); return -1; } for (i=0; iReleaseStringUTFChars(env,group_name,gName); if (status < 0) { (*env)->ReleaseIntArrayElements(env,oType,tarr,JNI_ABORT); h5str_array_free_jhdf5(oName, n); if (lName != NULL) { h5str_array_free_jhdf5(lName, n); } h5libraryError(env); } else { (*env)->ReleaseIntArrayElements(env,oType,tarr,0); for (i=0; iNewStringUTF(env,*(oName+i)); (*env)->SetObjectArrayElement(env,objName,i,(jobject)str); } } /* for (i=0; iNewStringUTF(env,*(lName+i)); (*env)->SetObjectArrayElement(env,linkName,i,(jobject)str); } } /* for (i=0; iname+info->count) = (char *) malloc(strlen(name)+1); if (*(info->name+info->count) == NULL) { h5outOfMemory(info->env, "H5Lget_link_info_all: malloc failed"); return -1; } strcpy(*(info->name+info->count), name); if (link_info->type == H5L_TYPE_HARD) { if (info->linkname != NULL) { *(info->linkname+info->count) = NULL; } if ( H5Oget_info_by_name(loc_id, name, &obj_info, H5P_DEFAULT) < 0 ) { *(info->type+info->count) = H5O_TYPE_UNKNOWN; } else { *(info->type+info->count) = obj_info.type; } } else { *(info->type+info->count) = H5O_TYPE_NTYPES + link_info->type; if (info->linkname != NULL) { linkval_buf = (char*) malloc(link_info->u.val_size); if (linkval_buf == NULL) { h5outOfMemory(info->env, "H5Lget_link_info_all: malloc failed"); return -1; } if (H5Lget_val(loc_id, name, linkval_buf, link_info->u.val_size, H5P_DEFAULT) < 0) { h5libraryError(info->env); free(linkval_buf); return -1; } if (link_info->type == H5L_TYPE_EXTERNAL) { *(info->linkname+info->count) = get_external_link( info->env, linkval_buf, link_info->u.val_size ); free(linkval_buf); } else { *(info->linkname+info->count) = linkval_buf; } } } info->count++; return 0; } libsis-jhdf5-java-14.12.1/source/c/jhdf5/h5oImpJHDF5.c000066400000000000000000000160621256564762100216550ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ /* * This code is the C-interface called by Java programs to access the * Group Object API Functions of the HDF5 library. * * Each routine wraps a single HDF entry point, generally with the * analogous arguments and return codes. * * For details of the HDF libraries, see the HDF Documentation at: * http://hdf.ncsa.uiuc.edu/HDF5/doc/ * */ #ifdef __cplusplus extern "C" { #endif #include "hdf5.h" /* missing definitions from hdf5.h */ #ifndef FALSE #define FALSE 0 #endif #ifndef TRUE #define TRUE (!FALSE) #endif /* delete TRUE and FALSE when fixed in HDF5 */ #include #include /* * Class: ncsa_hdf_hdf5lib_H5 * Method: HOGopen * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Oopen (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint access_plist_id) { herr_t status; char* gName; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Oopen: name is NULL"); return -1; } #ifdef __cplusplus gName = (char *)env->GetStringUTFChars(name,&isCopy); #else gName = (char *)(*env)->GetStringUTFChars(env,name,&isCopy); #endif if (gName == NULL) { h5JNIFatalError( env, "H5Oopen: file name not pinned"); return -1; } status = H5Oopen((hid_t)loc_id, gName, (hid_t) access_plist_id); #ifdef __cplusplus env->ReleaseStringUTFChars(name,gName); #else (*env)->ReleaseStringUTFChars(env,name,gName); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Oclose * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Oclose (JNIEnv *env, jclass clss, jint group_id) { herr_t retVal = 0; if (group_id > 0) retVal = H5Oclose((hid_t)group_id) ; if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: HOcopy * Signature: (ILjava/lang/String;)ILjava/lang/String;)II */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Ocopy (JNIEnv *env, jclass clss, jint src_loc_id, jstring src_name, jint dst_loc_id, jstring dst_name, jint object_copy_plist, jint link_creation_plist) { herr_t status; char *srcName, *dstName; jboolean isCopy; if (src_name == NULL) { h5nullArgument( env, "H5Ocopy: src_name is NULL"); return -1; } if (dst_name == NULL) { h5nullArgument( env, "H5Ocopy: dst_name is NULL"); return -1; } #ifdef __cplusplus srcName = (char *)env->GetStringUTFChars(src_name,&isCopy); #else srcName = (char *)(*env)->GetStringUTFChars(env,src_name,&isCopy); #endif if (srcName == NULL) { h5JNIFatalError( env, "H5Ocopy: source object name not pinned"); return -1; } #ifdef __cplusplus dstName = (char *)env->GetStringUTFChars(dst_name,&isCopy); #else dstName = (char *)(*env)->GetStringUTFChars(env,dst_name,&isCopy); #endif if (dstName == NULL) { #ifdef __cplusplus env->ReleaseStringUTFChars(src_name,srcName); #else (*env)->ReleaseStringUTFChars(env,src_name,srcName); #endif h5JNIFatalError( env, "H5Ocopy: destination object name not pinned"); return -1; } status = H5Ocopy((hid_t)src_loc_id, srcName, (hid_t)dst_loc_id, dstName, (hid_t)object_copy_plist, (hid_t)link_creation_plist); #ifdef __cplusplus env->ReleaseStringUTFChars(src_name,srcName); env->ReleaseStringUTFChars(dst_name,dstName); #else (*env)->ReleaseStringUTFChars(env,src_name,srcName); (*env)->ReleaseStringUTFChars(env,dst_name,dstName); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Oget_info_by_name */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Oget_1info_1by_1name (JNIEnv *env, jclass clss, jint loc_id, jstring object_name, jlongArray info, jboolean exception_when_non_existent) { jint type; herr_t status; jlong *infoP, *infoPP; jint info_len; int minor_err_num; char *oName; jboolean isCopy; H5O_info_t obj_info; if (object_name == NULL) { h5nullArgument( env, "H5Oget_info_by_name: object_name is NULL"); return -1; } if (info != NULL) { #ifdef __cplusplus info_len = env->GetArrayLength(info); #else info_len = (*env)->GetArrayLength(env,info); #endif if (info_len != 5) { h5badArgument( env, "H5Oget_info_by_name: info is not an array of length 5"); } } #ifdef __cplusplus oName = (char *)env->GetStringUTFChars(object_name,&isCopy); #else oName = (char *)(*env)->GetStringUTFChars(env,object_name,&isCopy); #endif if (oName == NULL) { h5JNIFatalError( env, "H5Oget_info_by_name: object_name not pinned"); return -1; } status = H5Oget_info_by_name(loc_id, oName, &obj_info, H5P_DEFAULT); (*env)->ReleaseStringUTFChars(env,object_name,oName); if (status < 0) { if (exception_when_non_existent == JNI_FALSE) { minor_err_num = getMinorErrorNumber(); /* * Note: H5E_CANTINSERT is thrown by the dense group lookup, see H5Gdense:534. That is * probably a wrong error code, but we have to deal with it here anyway. */ if (minor_err_num == H5E_NOTFOUND || minor_err_num == H5E_CANTINSERT) { return -1; } } h5libraryError(env); return -1; } else { type = obj_info.type; if (info != NULL) { #ifdef __cplusplus infoP = env->GetPrimitiveArrayCritical(info,&isCopy); #else infoP = (*env)->GetPrimitiveArrayCritical(env,info,&isCopy); #endif if (infoP == NULL) { h5JNIFatalError( env, "H5Oget_info_by_name: info not pinned"); return -1; } infoPP = infoP; *infoPP++ = obj_info.fileno; *infoPP++ = obj_info.addr; *infoPP++ = obj_info.rc; *infoPP++ = obj_info.ctime; *infoPP++ = obj_info.num_attrs; #ifdef __cplusplus env->ReleasePrimitiveArrayCritical(info,infoP,0); #else (*env)->ReleasePrimitiveArrayCritical(env,info,infoP,0); #endif } } return (jint) type; } libsis-jhdf5-java-14.12.1/source/c/jhdf5/h5pImpJHDF5.c000077500000000000000000002761771256564762100217000ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ /* * This code is the C-interface called by Java programs to access the * Property List API Functions of the HDF5 library. * * Each routine wraps a single HDF entry point, generally with the * analogous arguments and return codes. * * For details of the HDF libraries, see the HDF Documentation at: * http://hdf.ncsa.uiuc.edu/HDF5/doc/ * */ #ifdef __cplusplus extern "C" { #endif #include "hdf5.h" /* missing definitions from hdf5.h */ #ifndef FALSE #define FALSE 0 #endif #ifndef TRUE #define TRUE (!FALSE) #endif /* delete TRUE and FALSE when fixed in HDF5 */ #include #include extern jboolean h5outOfMemory( JNIEnv *env, char *functName); extern jboolean h5JNIFatalError( JNIEnv *env, char *functName); extern jboolean h5nullArgument( JNIEnv *env, char *functName); extern jboolean h5badArgument( JNIEnv *env, char *functName); extern jboolean h5libraryError( JNIEnv *env ); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pcreate * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pcreate (JNIEnv *env, jclass clss, jint type) { herr_t retVal = -1; retVal = H5Pcreate((hid_t)type ); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pclose * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pclose (JNIEnv *env, jclass clss, jint plist) { herr_t retVal = 0; if (plist > 0) retVal = H5Pclose((hid_t)plist ); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_class * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1class (JNIEnv *env, jclass clss, jint plist) { hid_t retVal = H5P_NO_CLASS; retVal = H5Pget_class((hid_t) plist ); if (retVal == H5P_NO_CLASS) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pcopy * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pcopy (JNIEnv *env, jclass clss, jint plist) { hid_t retVal = -1; retVal = H5Pcopy((hid_t)plist); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_version * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1version (JNIEnv *env, jclass clss, jint plist, jintArray version_info) { herr_t status; jint *theArray; jboolean isCopy; if (version_info == NULL) { h5nullArgument( env, "H5Pget_version: version_info input array is NULL"); return -1; } #ifdef __cplusplus if (env->GetArrayLength(version_info) < 4) { h5badArgument( env, "H5Pget_version: version_info input array < 4"); return -1; } theArray = (jint *)env->GetIntArrayElements(version_info,&isCopy); #else if ((*env)->GetArrayLength(env, version_info) < 4) { h5badArgument( env, "H5Pget_version: version_info input array < 4"); return -1; } theArray = (jint *)(*env)->GetIntArrayElements(env,version_info,&isCopy); #endif if (theArray == NULL) { h5JNIFatalError( env, "H5Pget_version: version_info not pinned"); return -1; } status = H5Pget_version((hid_t)plist, (unsigned *) &(theArray[0]), (unsigned *) &(theArray[1]), (unsigned *) &(theArray[2]), (unsigned *) &(theArray[3])); if (status < 0) { #ifdef __cplusplus env->ReleaseIntArrayElements(version_info,theArray,JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env,version_info,theArray,JNI_ABORT); #endif h5libraryError(env); } else { if (theArray[0] < 0 || theArray[1] < 0 || theArray[2] < 0 || theArray[3] < 0) { h5raiseException( env, "java/lang/RuntimeException", "H5Pget_version: parameter overflow"); return -1; } #ifdef __cplusplus env->ReleaseIntArrayElements(version_info,theArray,0); #else (*env)->ReleaseIntArrayElements(env,version_info,theArray,0); #endif } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_userblock * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1userblock (JNIEnv *env, jclass clss, jint plist, jlong size) { long sz; herr_t retVal = -1; sz = (long)size; retVal = H5Pset_userblock((hid_t)plist, (hsize_t)sz ); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_userblock * Signature: (I[J)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1userblock (JNIEnv *env, jclass clss, jint plist, jlongArray size) { herr_t status; jlong *theArray; jboolean isCopy; hsize_t s; if (size == NULL) { /* exception ? */ h5nullArgument( env, "H5Pget_userblock: size is NULL"); return -1; } #ifdef __cplusplus theArray = (jlong *)env->GetLongArrayElements(size,&isCopy); #else theArray = (jlong *)(*env)->GetLongArrayElements(env,size,&isCopy); #endif if (theArray == NULL) { h5JNIFatalError( env, "H5Pget_userblock: size not pinned"); return -1; } status = H5Pget_userblock((hid_t)plist, &s); if (status < 0) { #ifdef __cplusplus env->ReleaseLongArrayElements(size,theArray,JNI_ABORT); #else (*env)->ReleaseLongArrayElements(env,size,theArray,JNI_ABORT); #endif h5libraryError(env); } else { theArray[0] = s; #ifdef __cplusplus env->ReleaseLongArrayElements(size,theArray,0); #else (*env)->ReleaseLongArrayElements(env,size,theArray,0); #endif } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_sizes * Signature: (III)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1sizes (JNIEnv *env, jclass clss, jint plist, jint sizeof_addr, jint sizeof_size) { herr_t retVal = -1; retVal = H5Pset_sizes((hid_t)plist, (size_t)sizeof_addr, (size_t)sizeof_size); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_sizes * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1sizes (JNIEnv *env, jclass clss, jint plist, jintArray size) { herr_t status; jint *theArray; jboolean isCopy; size_t ss; size_t sa; if (size == NULL) { h5nullArgument( env, "H5Pget_sizes: size is NULL"); return -1; } #ifdef __cplusplus if (env->GetArrayLength(size) < 2) { h5badArgument( env, "H5Pget_sizes: size input array < 2 elements"); } theArray = (jint *)env->GetIntArrayElements(size,&isCopy); #else if ((*env)->GetArrayLength(env, size) < 2) { h5badArgument( env, "H5Pget_sizes: size input array < 2 elements"); } theArray = (jint *)(*env)->GetIntArrayElements(env,size,&isCopy); #endif if (theArray == NULL) { h5JNIFatalError( env, "H5Pget_sizes: size not pinned"); return -1; } status = H5Pget_sizes((hid_t)plist, &sa, &ss); if (status < 0) { #ifdef __cplusplus env->ReleaseIntArrayElements(size,theArray,JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env,size,theArray,JNI_ABORT); #endif h5libraryError(env); } else { theArray[0] = sa; theArray[1] = ss; #ifdef __cplusplus env->ReleaseIntArrayElements(size,theArray,0); #else (*env)->ReleaseIntArrayElements(env,size,theArray,0); #endif } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_sym_k * Signature: (III)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1sym_1k (JNIEnv *env, jclass clss, jint plist, jint ik, jint lk) { herr_t retVal = -1; retVal = H5Pset_sym_k((hid_t)plist, (int)ik, (int)lk); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_sym_k * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1sym_1k (JNIEnv *env, jclass clss, jint plist, jintArray size) { herr_t status; jint *theArray; jboolean isCopy; if (size == NULL) { h5nullArgument( env, "H5Pget_sym_k: size is NULL"); return -1; } #ifdef __cplusplus if (env->GetArrayLength(size) < 2) { h5badArgument( env, "H5Pget_sym_k: size < 2 elements"); } theArray = (jint *)env->GetIntArrayElements(size,&isCopy); #else if ((*env)->GetArrayLength(env, size) < 2) { h5badArgument( env, "H5Pget_sym_k: size < 2 elements"); } theArray = (jint *)(*env)->GetIntArrayElements(env,size,&isCopy); #endif if (theArray == NULL) { h5JNIFatalError( env, "H5Pget_sym_k: size not pinned"); return -1; } status = H5Pget_sym_k((hid_t)plist, (unsigned *) &(theArray[0]), (unsigned *) &(theArray[1])); if (status < 0) { #ifdef __cplusplus env->ReleaseIntArrayElements(size,theArray,JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env,size,theArray,JNI_ABORT); #endif h5libraryError(env); } else { #ifdef __cplusplus env->ReleaseIntArrayElements(size,theArray,0); #else (*env)->ReleaseIntArrayElements(env,size,theArray,0); #endif } if (theArray[0] < 0 || theArray[1] < 0) { h5raiseException( env, "java/lang/RuntimeException", "H5Pget_sym_k: parameter overflow"); return -1; } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_istore_k * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1istore_1k (JNIEnv *env, jclass clss, jint plist, jint ik) { herr_t retVal = -1; retVal = H5Pset_istore_k((hid_t)plist, (int)ik ); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_istore_k * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1istore_1k (JNIEnv *env, jclass clss, jint plist, jintArray ik) { herr_t status; jint *theArray; jboolean isCopy; if (ik == NULL) { h5nullArgument( env, "H5Pget_store_k: ik is NULL"); return -1; } #ifdef __cplusplus theArray = (jint *)env->GetIntArrayElements(ik,&isCopy); #else theArray = (jint *)(*env)->GetIntArrayElements(env,ik,&isCopy); #endif if (theArray == NULL) { h5JNIFatalError( env, "H5Pget_store_k: size not pinned"); return -1; } status = H5Pget_istore_k((hid_t)plist, (unsigned *) &(theArray[0])); if (status < 0) { #ifdef __cplusplus env->ReleaseIntArrayElements(ik,theArray,JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env,ik,theArray,JNI_ABORT); #endif h5libraryError(env); } else { #ifdef __cplusplus env->ReleaseIntArrayElements(ik,theArray,0); #else (*env)->ReleaseIntArrayElements(env,ik,theArray,0); #endif } if (theArray[0] < 0) { h5raiseException( env, "java/lang/RuntimeException", "H5Pget_istore_k: parameter overflow"); return -1; } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_layout * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1layout (JNIEnv *env, jclass clss, jint plist, jint layout) { herr_t retVal = -1; retVal = H5Pset_layout((hid_t)plist, (H5D_layout_t)layout ); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_layout * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1layout (JNIEnv *env, jclass clss, jint plist) { H5D_layout_t retVal = H5D_LAYOUT_ERROR; retVal = H5Pget_layout((hid_t)plist); if (retVal == H5D_LAYOUT_ERROR) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_libver_bounds * Signature: (III)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1libver_1bounds (JNIEnv *env, jclass clss, jint plist, jint low, jint high) { herr_t retVal; retVal = H5Pset_libver_bounds((hid_t)plist, (H5F_libver_t)low, (H5F_libver_t)high); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_libver_bounds * Signature: ([I)I */ JNIEXPORT jintArray JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1libver_1bounds (JNIEnv *env, jclass clss, jint plist) { herr_t retVal; jintArray iarray; jint bounds[2]; retVal = H5Pget_libver_bounds((hid_t)plist, (H5F_libver_t*)bounds, (H5F_libver_t*)(bounds+1)); if (retVal < 0) { h5libraryError(env); return NULL; } #ifdef __cplusplus iarray = env->NewIntArray(2); #else iarray = (*env)->NewIntArray(env,2); #endif if (iarray == NULL) { h5outOfMemory( env, "H5Pget_libver_bounds" ); return NULL; } #ifdef __cplusplus env->SetIntArrayRegion(iarray,0,2,bounds); #else (*env)->SetIntArrayRegion(env,iarray,0,2,bounds); #endif return iarray; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_chunk * Signature: (II[B)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1chunk (JNIEnv *env, jclass clss, jint plist, jint ndims, jbyteArray dim) { herr_t status; jbyte *theArray; jboolean isCopy; hsize_t *da; int i; hsize_t *lp; jlong *jlp; int rank; if (dim == NULL) { h5nullArgument( env, "H5Pset_chunk: dim array is NULL"); return -1; } #ifdef __cplusplus i = env->GetArrayLength(dim); #else i = (*env)->GetArrayLength(env, dim); #endif rank = i / sizeof(jlong); if (rank < ndims) { h5badArgument( env, "H5Pset_chunk: dims array < ndims"); } #ifdef __cplusplus theArray = (jbyte *)env->GetByteArrayElements(dim,&isCopy); #else theArray = (jbyte *)(*env)->GetByteArrayElements(env,dim,&isCopy); #endif if (theArray == NULL) { h5JNIFatalError( env, "H5Pset_chunk: dim array not pinned"); return -1; } da = lp = (hsize_t *)malloc(rank * sizeof(hsize_t)); if (da == NULL) { #ifdef __cplusplus env->ReleaseByteArrayElements(dim,theArray,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,dim,theArray,JNI_ABORT); #endif h5outOfMemory(env, "H5Pset_chunk: dims not converted to hsize_t"); return -1; } jlp = (jlong *)theArray; for (i = 0; i < rank; i++) { *lp = (hsize_t)*jlp; lp++; jlp++; } status = H5Pset_chunk((hid_t)plist, (int)ndims, da); #ifdef __cplusplus env->ReleaseByteArrayElements(dim,theArray,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,dim,theArray,JNI_ABORT); #endif free(da); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_chunk * Signature: (II[J)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1chunk (JNIEnv *env, jclass clss, jint plist, jint max_ndims, jlongArray dims) { herr_t status; jlong *theArray; jboolean isCopy; hsize_t *da; int i; if (dims == NULL) { h5nullArgument( env, "H5Pget_chunk: dims is NULL"); return -1; } #ifdef __cplusplus if (env->GetArrayLength(dims) < max_ndims) { h5badArgument( env, "H5Pget_chunk: dims array < max_ndims"); } theArray = (jlong *)env->GetLongArrayElements(dims,&isCopy); #else if ((*env)->GetArrayLength(env, dims) < max_ndims) { h5badArgument( env, "H5Pget_chunk: dims array < max_ndims"); } theArray = (jlong *)(*env)->GetLongArrayElements(env,dims,&isCopy); #endif if (theArray == NULL) { h5JNIFatalError( env, "H5Pget_chunk: input dims not pinned"); return -1; } da = (hsize_t *)malloc( max_ndims * sizeof(hsize_t)); if (da == NULL) { #ifdef __cplusplus env->ReleaseLongArrayElements(dims, theArray,JNI_ABORT); #else (*env)->ReleaseLongArrayElements(env,dims, theArray,JNI_ABORT); #endif h5outOfMemory(env, "H5Pget_chunk: dims not converted to hsize_t"); return -1; } status = H5Pget_chunk((hid_t)plist, (int)max_ndims, da); if (status < 0) { #ifdef __cplusplus env->ReleaseLongArrayElements(dims, theArray,JNI_ABORT); #else (*env)->ReleaseLongArrayElements(env,dims, theArray,JNI_ABORT); #endif free (da); h5libraryError(env); } else { for (i= 0; i < max_ndims; i++) { theArray[i] = da[i]; } free (da); #ifdef __cplusplus env->ReleaseLongArrayElements(dims, theArray,0); #else (*env)->ReleaseLongArrayElements(env,dims, theArray,0); #endif } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_alignment * Signature: (IJJ)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1alignment (JNIEnv *env, jclass clss, jint plist, jlong threshold, jlong alignment) { long thr; long align; herr_t retVal = -1; thr = (long)threshold; align = (long)alignment; retVal = H5Pset_alignment((hid_t)plist, (hsize_t)thr, (hsize_t)align); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_alignment * Signature: (I[J)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1alignment (JNIEnv *env, jclass clss, jint plist, jlongArray alignment) { herr_t status; jlong *theArray; jboolean isCopy; hsize_t t; hsize_t a; if (alignment == NULL) { h5nullArgument( env, "H5Pget_alignment: input alignment is NULL"); return -1; } #ifdef __cplusplus if (env->GetArrayLength(alignment) < 2) { h5badArgument( env, "H5Pget_alignment: allingment input array < 2"); } theArray = (jlong *)env->GetLongArrayElements(alignment,&isCopy); #else if ((*env)->GetArrayLength(env, alignment) < 2) { h5badArgument( env, "H5Pget_alignment: allingment input array < 2"); } theArray = (jlong *)(*env)->GetLongArrayElements(env,alignment,&isCopy); #endif if (theArray == NULL) { h5JNIFatalError( env, "H5Pget_alignment: input array not pinned"); return -1; } status = H5Pget_alignment((hid_t)plist, &t, &a); if (status < 0) { #ifdef __cplusplus env->ReleaseLongArrayElements(alignment, theArray,JNI_ABORT); #else (*env)->ReleaseLongArrayElements(env,alignment, theArray,JNI_ABORT); #endif h5libraryError(env); } else { theArray[0] = t; theArray[1] = a; #ifdef __cplusplus env->ReleaseLongArrayElements(alignment, theArray,0); #else (*env)->ReleaseLongArrayElements(env,alignment, theArray,0); #endif } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_external * Signature: (ILjava/lang/String;JJ)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1external (JNIEnv *env, jclass clss, jint plist, jstring name, jlong offset, jlong size) { herr_t status; char* file; jboolean isCopy; long off; long sz; off = (long)offset; sz = (long)size; if (name == NULL) { h5nullArgument( env, "H5Pset_external: name is NULL"); return -1; } #ifdef __cplusplus file = (char *)env->GetStringUTFChars(name,&isCopy); #else file = (char *)(*env)->GetStringUTFChars(env,name,&isCopy); #endif if (file == NULL) { h5JNIFatalError( env, "H5Pset_external: name not pinned"); return -1; } status = H5Pset_external((hid_t)plist, file, (off_t)off, (hsize_t)sz); #ifdef __cplusplus env->ReleaseStringUTFChars(name,file); #else (*env)->ReleaseStringUTFChars(env,name,file); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_external_count * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1external_1count (JNIEnv *env, jclass clss, jint plist) { int retVal = -1; retVal = H5Pget_external_count((hid_t)plist); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_external * Signature: (III[Ljava/lang/String;[J[J)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1external (JNIEnv *env, jclass clss, jint plist, jint idx, jint name_size, jobjectArray name, jlongArray size) { herr_t status; jlong *theArray; jboolean isCopy; char *file; jstring str; off_t o; hsize_t s; if (name_size < 0) { h5badArgument( env, "H5Pget_external: name_size < 0"); return -1; } else if (name_size == 0) { file = NULL; } else { file = (char *)malloc(sizeof(char)*name_size); } if (size != NULL) { #ifdef __cplusplus if (env->GetArrayLength(size) < 2) { free(file); h5badArgument( env, "H5Pget_external: size input array < 2"); } theArray = (jlong *)env->GetLongArrayElements(size,&isCopy); #else if ((*env)->GetArrayLength(env, size) < 2) { free(file); h5badArgument( env, "H5Pget_external: size input array < 2"); } theArray = (jlong *)(*env)->GetLongArrayElements(env,size,&isCopy); #endif if (theArray == NULL) { free(file); h5JNIFatalError( env, "H5Pget_external: size array not pinned"); return -1; } } status = H5Pget_external((hid_t) plist, (int)idx, (size_t)name_size, file, (off_t *)&o, (hsize_t *)&s); if (status < 0) { if (size != NULL) { #ifdef __cplusplus env->ReleaseLongArrayElements(size,theArray,JNI_ABORT); #else (*env)->ReleaseLongArrayElements(env,size,theArray,JNI_ABORT); #endif } free(file); h5libraryError(env); return -1; } if (size != NULL) { theArray[0] = o; theArray[1] = s; #ifdef __cplusplus env->ReleaseLongArrayElements(size,theArray,0); #else (*env)->ReleaseLongArrayElements(env,size,theArray,0); #endif } if (file != NULL) { /* NewStringUTF may throw OutOfMemoryError */ #ifdef __cplusplus str = env->NewStringUTF(file); #else str = (*env)->NewStringUTF(env,file); #endif if (str == NULL) { free(file); h5outOfMemory( env, "H5Pget_external: return array not created"); return -1; } /* SetObjectArrayElement may raise exceptions */ #ifdef __cplusplus env->SetObjectArrayElement(name,0,(jobject)str); #else (*env)->SetObjectArrayElement(env,name,0,(jobject)str); #endif free(file); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_fill_value * Signature: (II[B)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1fill_1value (JNIEnv *env, jclass clss, jint plist_id, jint type_id, jbyteArray value) { /* unimplemented( env, "H5Pset_fill_value: not implemented yet"); return -1; */ jint status; jbyte *byteP; jboolean isCopy; #ifdef __cplusplus byteP = env->GetByteArrayElements(value,&isCopy); #else byteP = (*env)->GetByteArrayElements(env,value,&isCopy); #endif status = H5Pset_fill_value((hid_t)plist_id, (hid_t)type_id, byteP); #ifdef __cplusplus env->ReleaseByteArrayElements(value,byteP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,value,byteP,JNI_ABORT); #endif return status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_fill_value * Signature: (II[B)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1fill_1value (JNIEnv *env, jclass clss, jint plist_id, jint type_id, jbyteArray value) { jint status; jbyte *byteP; jboolean isCopy; #ifdef __cplusplus byteP = env->GetByteArrayElements(value,&isCopy); #else byteP = (*env)->GetByteArrayElements(env,value,&isCopy); #endif status = H5Pget_fill_value((hid_t)plist_id, (hid_t)type_id, byteP); #ifdef __cplusplus if (status < 0) env->ReleaseByteArrayElements(value,byteP,JNI_ABORT); else env->ReleaseByteArrayElements(value,byteP,0); #else if (status < 0) (*env)->ReleaseByteArrayElements(env,value,byteP,JNI_ABORT); else (*env)->ReleaseByteArrayElements(env,value,byteP,0); #endif return status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_filter * Signature: (IIII[I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1filter (JNIEnv *env, jclass clss, jint plist, jint filter, jint flags, jint cd_nelmts, jintArray cd_values) { herr_t status; jint *theArray; jboolean isCopy; if (cd_values == NULL) status = H5Pset_filter((hid_t)plist, (H5Z_filter_t)filter, (unsigned int)flags, (size_t)cd_nelmts, NULL); else { #ifdef __cplusplus theArray = (jint *)env->GetIntArrayElements(cd_values,&isCopy); #else theArray = (jint *)(*env)->GetIntArrayElements(env,cd_values,&isCopy); #endif if (theArray == NULL) { h5JNIFatalError(env, "H5Pset_filter: input array not pinned"); return -1; } status = H5Pset_filter((hid_t)plist, (H5Z_filter_t)filter, (unsigned int)flags, (size_t)cd_nelmts, (const unsigned int *)theArray); #ifdef __cplusplus env->ReleaseIntArrayElements(cd_values,theArray,JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env,cd_values,theArray,JNI_ABORT); #endif } if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_nfilters * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1nfilters (JNIEnv *env, jclass clss, jint plist) { int retVal = -1; retVal = H5Pget_nfilters((hid_t)plist); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_filter * Signature: (II[I[IILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1filter (JNIEnv *env, jclass clss, jint plist, jint filter_number, jintArray flags, jintArray cd_nelmts, jintArray cd_values, jint namelen, jobjectArray name) { herr_t status; jint *flagsArray, *cd_nelmtsArray, *cd_valuesArray; jboolean isCopy; char *filter; jstring str; if (namelen <= 0) { h5badArgument( env, "H5Pget_filter: namelen <= 0"); return -1; } if (flags == NULL) { h5badArgument( env, "H5Pget_filter: flags is NULL"); return -1; } if (cd_nelmts == NULL) { h5badArgument( env, "H5Pget_filter: cd_nelmts is NULL"); return -1; } if (cd_values == NULL) { h5badArgument( env, "H5Pget_filter: cd_values is NULL"); return -1; } filter = (char *)malloc(sizeof(char)*namelen); if (filter == NULL) { h5outOfMemory( env, "H5Pget_filter: namelent malloc failed"); return -1; } #ifdef __cplusplus flagsArray = (jint *)env->GetIntArrayElements(flags,&isCopy); #else flagsArray = (jint *)(*env)->GetIntArrayElements(env,flags,&isCopy); #endif if (flagsArray == NULL) { free(filter); h5JNIFatalError(env, "H5Pget_filter: flags array not pinned"); return -1; } #ifdef __cplusplus cd_nelmtsArray = (jint *)env->GetIntArrayElements(cd_nelmts,&isCopy); #else cd_nelmtsArray = (jint *)(*env)->GetIntArrayElements(env,cd_nelmts,&isCopy); #endif if (cd_nelmtsArray == NULL) { #ifdef __cplusplus env->ReleaseIntArrayElements(flags,flagsArray,JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env,flags,flagsArray,JNI_ABORT); #endif free(filter); h5JNIFatalError(env, "H5Pget_filter: nelmts array not pinned"); return -1; } #ifdef __cplusplus cd_valuesArray = (jint *)env->GetIntArrayElements(cd_values,&isCopy); #else cd_valuesArray = (jint *)(*env)->GetIntArrayElements(env,cd_values,&isCopy); #endif if (cd_valuesArray == NULL) { #ifdef __cplusplus env->ReleaseIntArrayElements(cd_nelmts,cd_nelmtsArray,JNI_ABORT); env->ReleaseIntArrayElements(flags,flagsArray,JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env,cd_nelmts,cd_nelmtsArray,JNI_ABORT); (*env)->ReleaseIntArrayElements(env,flags,flagsArray,JNI_ABORT); #endif free(filter); h5JNIFatalError(env, "H5Pget_filter: elmts array not pinned"); return -1; } status = H5Pget_filter((hid_t)plist, (int)filter_number, (unsigned int *)flagsArray, (size_t *)cd_nelmtsArray, (unsigned int *)cd_valuesArray, (size_t)namelen, filter, (unsigned int*)NULL); if (status < 0) { #ifdef __cplusplus env->ReleaseIntArrayElements(cd_values,cd_valuesArray,JNI_ABORT); env->ReleaseIntArrayElements(cd_nelmts,cd_nelmtsArray,JNI_ABORT); env->ReleaseIntArrayElements(flags,flagsArray,JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env,cd_values,cd_valuesArray,JNI_ABORT); (*env)->ReleaseIntArrayElements(env,cd_nelmts,cd_nelmtsArray,JNI_ABORT); (*env)->ReleaseIntArrayElements(env,flags,flagsArray,JNI_ABORT); #endif free(filter); h5libraryError(env); } else { #ifdef __cplusplus env->ReleaseIntArrayElements(cd_values,cd_valuesArray,0); env->ReleaseIntArrayElements(cd_nelmts,cd_nelmtsArray,0); env->ReleaseIntArrayElements(flags,flagsArray,0); /* NewStringUTF may throw OutOfMemoryError */ str = env->NewStringUTF(filter); #else (*env)->ReleaseIntArrayElements(env,cd_values,cd_valuesArray,0); (*env)->ReleaseIntArrayElements(env,cd_nelmts,cd_nelmtsArray,0); (*env)->ReleaseIntArrayElements(env,flags,flagsArray,0); /* NewStringUTF may throw OutOfMemoryError */ str = (*env)->NewStringUTF(env,filter); #endif if (str == NULL) { free(filter); h5JNIFatalError(env, "H5Pget_filter: return string not pinned"); return -1; } free(filter); /* SetObjectArrayElement may throw exceptiosn */ #ifdef __cplusplus env->SetObjectArrayElement(name,0,(jobject)str); #else (*env)->SetObjectArrayElement(env,name,0,(jobject)str); #endif } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_driver * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1driver (JNIEnv *env, jclass clss, jint plist) { hid_t retVal = -1; retVal = H5Pget_driver((hid_t) plist); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } #ifdef removed /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_stdio * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1stdio (JNIEnv *env, jclass clss, jint plist) { herr_t retVal = -1; retVal = H5Pset_stdio((hid_t)plist); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_stdio * Signature: (I)B */ JNIEXPORT jboolean JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1stdio (JNIEnv *env, jclass clss, jint plist) { herr_t retValue; retValue = H5Pget_stdio((hid_t)plist); if (retValue >= 0) { return JNI_TRUE; } else { return JNI_FALSE; } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_sec2 * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1sec2 (JNIEnv *env, jclass clss, jint plist) { herr_t retVal = -1; retVal = H5Pset_sec2((hid_t) plist); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_sec2 * Signature: (I)B */ JNIEXPORT jboolean JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1sec2 (JNIEnv *env, jclass clss, jint plist) { herr_t retValue; retValue = H5Pget_sec2((hid_t)plist); if (retValue >= 0) { return JNI_TRUE; } else { return JNI_FALSE; } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_core * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1core (JNIEnv *env, jclass clss, jint plist, jint increment) { herr_t retVal = -1; retVal = H5Pset_core((hid_t)plist, (size_t)increment); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_core * Signature: (I[I)B */ JNIEXPORT jboolean JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1core (JNIEnv *env, jclass clss, jint plist, jintArray increment) { jboolean isCopy; herr_t status; jint *theArray = NULL; if (increment != NULL) { theArray = (jint *)(*env)->GetIntArrayElements(env,increment,&isCopy); if (theArray == NULL) { h5JNIFatalError(env, "H5Pget_core: input array not pinned"); return JNI_FALSE; } } status = H5Pget_core((hid_t)plist, (size_t *)&(theArray[0])); if (status < 0) { (*env)->ReleaseIntArrayElements(env,increment,theArray,JNI_ABORT); return JNI_FALSE; } else { (*env)->ReleaseIntArrayElements(env,increment,theArray,0); return JNI_TRUE; } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_split * Signature: (ILjava/lang/String;ILjava/lang/String;I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1split (JNIEnv *env, jclass clss, jint plist, jstring meta_ext, jint meta_plist, jstring raw_ext, jint raw_plist) { herr_t status; char *meta, *raw; jboolean isCopy; if (meta_ext == NULL) { meta = (char *)NULL; } else { meta = (char *)(*env)->GetStringUTFChars(env,meta_ext,&isCopy); if (meta == NULL) { h5JNIFatalError(env, "H5Pset_split: meta not pinned"); return -1; } } if (raw_ext == NULL) { raw = (char *)NULL; } else { raw = (char *)(*env)->GetStringUTFChars(env,raw_ext,&isCopy); if (raw == NULL) { (*env)->ReleaseStringUTFChars(env,meta_ext,meta); h5JNIFatalError(env, "H5Pset_split: raw not pinned"); return -1; } } status = H5Pset_split((hid_t)plist, meta, (hid_t)meta_plist, raw, (hid_t)raw_plist); (*env)->ReleaseStringUTFChars(env,raw_ext,raw); (*env)->ReleaseStringUTFChars(env,meta_ext,meta); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_split * Signature: (II[Ljava/lang/String;[II[Ljava/lang/String;[I)B */ JNIEXPORT jboolean JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1split (JNIEnv *env, jclass clss, jint plist, jint meta_ext_size, jobjectArray meta_ext, jintArray meta_properties, jint raw_ext_size, jobjectArray raw_ext, jintArray raw_properties) { jint status; jint *metaArray, *rawArray; jboolean isCopy; char *meta, *raw; jstring meta_str, raw_str; if (meta_ext == NULL) { metaArray = NULL; } else { if (meta_ext_size <=0 ) { h5badArgument( env, "H5Pget_split: meta_ext_size <=0"); } meta = (char *)malloc(sizeof(char)*meta_ext_size); if (meta == NULL) { h5JNIFatalError(env, "H5Pget_split: meta not pinned"); return -1; } } if (raw_ext == NULL ) { rawArray = NULL; } else { if (raw_ext_size <=0 ) { h5badArgument( env, "H5Pget_split: raw_ext_size <=0"); return -1; } raw = (char *)malloc(sizeof(char)*raw_ext_size); if (raw == NULL) { free(meta); h5JNIFatalError(env, "H5Pget_split: raw not pinned"); return -1; } } metaArray = (jint *)(*env)->GetIntArrayElements(env,meta_properties,&isCopy); if (metaArray == NULL) { free(raw); free(meta); h5JNIFatalError(env, "H5Pget_split: metaArray not pinned"); return -1; } rawArray = (jint *)(*env)->GetIntArrayElements(env,raw_properties,&isCopy); if (rawArray == NULL) { (*env)->ReleaseIntArrayElements(env,meta_properties,metaArray,JNI_ABORT); free(raw); free(meta); h5JNIFatalError(env, "H5Pget_split: rawArray not pinned"); return -1; } status = H5Pget_split((hid_t)plist, (size_t)meta_ext_size, meta, (hid_t *)metaArray, (size_t)raw_ext_size, raw, (hid_t *)rawArray); if (status < 0) { (*env)->ReleaseIntArrayElements(env,raw_properties,rawArray,JNI_ABORT); (*env)->ReleaseIntArrayElements(env,meta_properties,metaArray,JNI_ABORT); free(raw); free(meta); h5libraryError(env); } else { (*env)->ReleaseIntArrayElements(env,raw_properties,rawArray,0); (*env)->ReleaseIntArrayElements(env,meta_properties,metaArray,0); /* NewStringUTF may throw OutOfMemoryError */ meta_str = (*env)->NewStringUTF(env,meta); if (meta_str == NULL) { free(raw); free(meta); h5JNIFatalError(env, "H5Pget_split: return meta_str not pinned"); return -1; } /* SetObjectArrayElement may throw exceptions */ (*env)->SetObjectArrayElement(env,meta_ext,0,(jobject)meta_str); free(meta); /* NewStringUTF may throw OutOfMemoryError */ raw_str = (*env)->NewStringUTF(env,raw); if (meta_str == NULL) { free(raw); h5JNIFatalError(env, "H5Pget_split: return raw_str not pinned"); return -1; } /* SetObjectArrayElement may throw exceptions */ (*env)->SetObjectArrayElement(env,raw_ext,0,(jobject)raw_str); free(raw); } return (jint)status; } #endif /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_cache * Signature: (IIID)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1cache (JNIEnv *env, jclass clss, jint plist, jint mdc_nelmts, jint rdcc_nelmts, jint rdcc_nbytes, jdouble rdcc_w0) { herr_t retVal = -1; retVal = H5Pset_cache((hid_t)plist, (int)mdc_nelmts, (int)rdcc_nelmts, (size_t)rdcc_nbytes, (double) rdcc_w0); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_cache * Signature: (I[I[I[D)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1cache (JNIEnv *env, jclass clss, jint plist, jintArray mdc_nelmts, jintArray rdcc_nelmts, jintArray rdcc_nbytes, jdoubleArray rdcc_w0) { herr_t status; jint mode; jdouble *w0Array; jint *mdc_nelmtsArray, *rdcc_nelmtsArray, *nbytesArray; jboolean isCopy; if (mdc_nelmts == NULL) { h5nullArgument( env, "H5Pget_gache: mdc_nelmts is NULL"); return -1; } #ifdef __cplusplus mdc_nelmtsArray = (jint *)env->GetIntArrayElements(mdc_nelmts,&isCopy); #else mdc_nelmtsArray = (jint *)(*env)->GetIntArrayElements(env,mdc_nelmts,&isCopy); #endif if (mdc_nelmtsArray == NULL) { h5JNIFatalError(env, "H5Pget_cache: mdc_nelmts array not pinned"); return -1; } if (rdcc_w0 == NULL) { w0Array = (jdouble *)NULL; } else { #ifdef __cplusplus w0Array = (jdouble *)env->GetDoubleArrayElements(rdcc_w0,&isCopy); #else w0Array = (jdouble *)(*env)->GetDoubleArrayElements(env,rdcc_w0,&isCopy); #endif if (w0Array == NULL) { #ifdef __cplusplus env->ReleaseIntArrayElements(mdc_nelmts,mdc_nelmtsArray,JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env,mdc_nelmts,mdc_nelmtsArray,JNI_ABORT); #endif h5JNIFatalError(env, "H5Pget_cache: w0_array array not pinned"); return -1; } } if (rdcc_nelmts == NULL) { rdcc_nelmtsArray = (jint *) NULL; } else { #ifdef __cplusplus rdcc_nelmtsArray = (jint *)env->GetIntArrayElements(rdcc_nelmts,&isCopy); #else rdcc_nelmtsArray = (jint *)(*env)->GetIntArrayElements(env,rdcc_nelmts,&isCopy); #endif if (rdcc_nelmtsArray == NULL) { #ifdef __cplusplus env->ReleaseIntArrayElements(mdc_nelmts,mdc_nelmtsArray,JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env,mdc_nelmts,mdc_nelmtsArray,JNI_ABORT); #endif /* exception -- out of memory */ if (w0Array != NULL) { #ifdef __cplusplus env->ReleaseDoubleArrayElements(rdcc_w0,w0Array,JNI_ABORT); #else (*env)->ReleaseDoubleArrayElements(env,rdcc_w0,w0Array,JNI_ABORT); #endif } h5JNIFatalError(env, "H5Pget_cache: rdcc_nelmts array not pinned"); return -1; } } if (rdcc_nbytes == NULL) { nbytesArray = (jint *) NULL; } else { #ifdef __cplusplus nbytesArray = (jint *)env->GetIntArrayElements(rdcc_nbytes,&isCopy); #else nbytesArray = (jint *)(*env)->GetIntArrayElements(env,rdcc_nbytes,&isCopy); #endif if (nbytesArray == NULL) { #ifdef __cplusplus env->ReleaseIntArrayElements(mdc_nelmts,mdc_nelmtsArray,JNI_ABORT); if (w0Array != NULL) { env->ReleaseDoubleArrayElements(rdcc_w0,w0Array,JNI_ABORT); } if (rdcc_nelmtsArray != NULL) { env->ReleaseIntArrayElements(rdcc_nelmts,rdcc_nelmtsArray,JNI_ABORT); } #else (*env)->ReleaseIntArrayElements(env,mdc_nelmts,mdc_nelmtsArray,JNI_ABORT); if (w0Array != NULL) { (*env)->ReleaseDoubleArrayElements(env,rdcc_w0,w0Array,JNI_ABORT); } if (rdcc_nelmtsArray != NULL) { (*env)->ReleaseIntArrayElements(env,rdcc_nelmts,rdcc_nelmtsArray,JNI_ABORT); } #endif h5JNIFatalError(env, "H5Pget_cache: nbytesArray array not pinned"); return -1; } } status = H5Pget_cache((hid_t)plist, (int *)mdc_nelmtsArray, (size_t *)rdcc_nelmtsArray, (size_t *)nbytesArray, w0Array); if (status < 0) { mode = JNI_ABORT; } else { mode = 0; /* commit and free */ } #ifdef __cplusplus env->ReleaseIntArrayElements(mdc_nelmts,mdc_nelmtsArray,mode); #else (*env)->ReleaseIntArrayElements(env,mdc_nelmts,mdc_nelmtsArray,mode); #endif if (rdcc_nelmtsArray != NULL) { #ifdef __cplusplus env->ReleaseIntArrayElements(rdcc_nelmts,rdcc_nelmtsArray,mode); #else (*env)->ReleaseIntArrayElements(env,rdcc_nelmts,rdcc_nelmtsArray,mode); #endif } if (nbytesArray != NULL) { #ifdef __cplusplus env->ReleaseIntArrayElements(rdcc_nbytes,nbytesArray,mode); #else (*env)->ReleaseIntArrayElements(env,rdcc_nbytes,nbytesArray,mode); #endif } if (w0Array != NULL) { #ifdef __cplusplus env->ReleaseDoubleArrayElements(rdcc_w0,w0Array,mode); #else (*env)->ReleaseDoubleArrayElements(env,rdcc_w0,w0Array,mode); #endif } if (status < 0) { h5libraryError(env); } return (jint)status; } #ifdef notdef /* DON'T IMPLEMENT THIS!!! */ /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_buffer * Signature: (II[B[B)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1buffer (JNIEnv *env, jclass clss, jint plist, jint size, jbyteArray tconv, jbyteArray bkg) { jint status; jbyte *tconvP, *bkgP; jboolean isCopy; if (tconv == NULL) tconvP = (jbyte *)NULL; else tconvP = (*env)->GetByteArrayElements(env,tconv,&isCopy); if (bkg == NULL) bkgP = (jbyte *)NULL; else bkgP = (*env)->GetByteArrayElements(env,bkg,&isCopy); status = H5Pset_buffer((hid_t)plist, (size_t)size, tconvP, bkgP); if (tconv != NULL) (*env)->ReleaseByteArrayElements(env,tconv,tconvP,JNI_ABORT); if (bkg != NULL) (*env)->ReleaseByteArrayElements(env,bkg,bkgP,JNI_ABORT); return status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_buffer * Signature: (I[B[B)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1buffer (JNIEnv *env, jclass clss, jint plist, jbyteArray tconv, jbyteArray bkg) { jint status; jbyte *tconvP, *bkgP; jboolean isCopy; tconvP = (*env)->GetByteArrayElements(env,tconv,&isCopy); bkgP = (*env)->GetByteArrayElements(env,bkg,&isCopy); status = H5Pget_buffer((hid_t)plist, tconvP, bkgP); if (status < 0) { (*env)->ReleaseByteArrayElements(env,tconv,tconvP,JNI_ABORT); (*env)->ReleaseByteArrayElements(env,bkg,bkgP,JNI_ABORT); } else { (*env)->ReleaseByteArrayElements(env,tconv,tconvP,0); (*env)->ReleaseByteArrayElements(env,bkg,bkgP,0); } return status; } #endif /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_preserve * Signature: (IB)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1preserve (JNIEnv *env, jclass clss, jint plist, jboolean status) { hbool_t st; herr_t retVal = -1; if (status == JNI_TRUE) { st = TRUE; } else if (status == JNI_FALSE) { st = FALSE; } else { /* exception -- bad argument */ h5badArgument( env, "H5Pset_preserve: status not TRUE or FALSE"); return -1; } retVal = H5Pset_preserve((hid_t)plist, (hbool_t)st); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_preserve * Signature: (I)B */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1preserve (JNIEnv *env, jclass clss, jint plist) { herr_t retValue; retValue = H5Pget_preserve((hid_t)plist); if (retValue < 0) { h5libraryError(env); return JNI_FALSE; } return (jint)retValue; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_deflate * Signature: (II)B */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1deflate (JNIEnv *env, jclass clss, jint plist, jint level) { herr_t retValue; retValue = H5Pset_deflate((hid_t)plist, (int)level); if (retValue < 0) { h5libraryError(env); return JNI_FALSE; } return (jint)retValue; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_nbit * Signature: (I)B */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1nbit (JNIEnv *env, jclass clss, jint plist) { herr_t retValue; retValue = H5Pset_nbit((hid_t)plist); if (retValue < 0) { h5libraryError(env); return JNI_FALSE; } return (jint)retValue; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_scaleoffset * Signature: (III)B */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1scaleoffset (JNIEnv *env, jclass clss, jint plist, jint scale_type, jint scale_factor) { herr_t retValue; retValue = H5Pset_scaleoffset((hid_t)plist, scale_type, scale_factor); if (retValue < 0) { h5libraryError(env); return JNI_FALSE; } return (jint)retValue; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_gc_references * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1gc_1references (JNIEnv *env, jclass clss, jint fapl_id, jboolean gc_ref) { herr_t retVal; unsigned gc_ref_val; if (gc_ref == JNI_TRUE) { gc_ref_val = 1; } else { gc_ref_val = 0; } retVal = H5Pset_gc_references((hid_t)fapl_id, gc_ref_val); if (retVal < 0) { h5libraryError(env); return -1; } return (jint)retVal; } #ifdef remove #ifdef USE_H5_1_2_1 #define GET_GC H5Pget_gc_reference #else #define GET_GC H5Pget_gc_references #endif #endif /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_gc_references * Signature: (I[Z)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1gc_1references (JNIEnv *env, jclass clss, jint fapl_id, jbooleanArray gc_ref) { herr_t status; jboolean *theArray; jboolean isCopy; unsigned gc_ref_val = 0; if (gc_ref == NULL) { h5nullArgument( env, "H5Pget_gc_references: gc_ref input array is NULL"); return -1; } #ifdef __cplusplus theArray = (jboolean *)env->GetBooleanArrayElements(gc_ref,&isCopy); #else theArray = (jboolean *)(*env)->GetBooleanArrayElements(env,gc_ref,&isCopy); #endif if (theArray == NULL) { h5JNIFatalError( env, "H5Pget_gc_references: gc_ref not pinned"); return -1; } status = H5Pget_gc_references((hid_t)fapl_id, (unsigned *)&gc_ref_val); #ifdef removed status = GET_GC((hid_t)fapl_id, (unsigned *)&gc_ref_val); #endif if (status < 0) { #ifdef __cplusplus env->ReleaseBooleanArrayElements(gc_ref,theArray,JNI_ABORT); #else (*env)->ReleaseBooleanArrayElements(env,gc_ref,theArray,JNI_ABORT); #endif h5libraryError(env); } else { if (gc_ref_val == 1) { theArray[0] = JNI_TRUE; } else { theArray[0] = JNI_FALSE; } #ifdef __cplusplus env->ReleaseBooleanArrayElements(gc_ref,theArray,0); #else (*env)->ReleaseBooleanArrayElements(env,gc_ref,theArray,0); #endif } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_btree_ratios * Signature: (IDDD)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1btree_1ratios (JNIEnv *env, jclass clss, jint plist_id, jdouble left, jdouble middle, jdouble right) { herr_t status; status = H5Pset_btree_ratios((hid_t)plist_id, (double)left,(double)middle, (double)right); if (status < 0) { h5libraryError(env); return -1; } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_btree_ratios * Signature: (I[D[D[D)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1btree_1ratios (JNIEnv *env, jclass clss, jint plist_id, jdoubleArray left, jdoubleArray middle, jdoubleArray right) { herr_t status; jdouble *leftP, *middleP, *rightP; jboolean isCopy; if (left == NULL) { h5nullArgument( env, "H5Pget_btree_ratios: left input array is NULL"); return -1; } if (middle == NULL) { h5nullArgument( env, "H5Pget_btree_ratios: middle input array is NULL"); return -1; } if (right == NULL) { h5nullArgument( env, "H5Pget_btree_ratios: right input array is NULL"); return -1; } #ifdef __cplusplus leftP = (jdouble *)env->GetDoubleArrayElements(left,&isCopy); #else leftP = (jdouble *)(*env)->GetDoubleArrayElements(env,left,&isCopy); #endif if (leftP == NULL) { h5JNIFatalError( env, "H5Pget_btree_ratios: left not pinned"); return -1; } #ifdef __cplusplus middleP = (jdouble *)env->GetDoubleArrayElements(middle,&isCopy); #else middleP = (jdouble *)(*env)->GetDoubleArrayElements(env,middle,&isCopy); #endif if (middleP == NULL) { #ifdef __cplusplus env->ReleaseDoubleArrayElements(left,leftP,JNI_ABORT); #else (*env)->ReleaseDoubleArrayElements(env,left,leftP,JNI_ABORT); #endif h5JNIFatalError( env, "H5Pget_btree_ratios: middle not pinned"); return -1; } #ifdef __cplusplus rightP = (jdouble *)env->GetDoubleArrayElements(right,&isCopy); #else rightP = (jdouble *)(*env)->GetDoubleArrayElements(env,right,&isCopy); #endif if (rightP == NULL) { #ifdef __cplusplus env->ReleaseDoubleArrayElements(left,leftP,JNI_ABORT); env->ReleaseDoubleArrayElements(middle,middleP,JNI_ABORT); #else (*env)->ReleaseDoubleArrayElements(env,left,leftP,JNI_ABORT); (*env)->ReleaseDoubleArrayElements(env,middle,middleP,JNI_ABORT); #endif h5JNIFatalError( env, "H5Pget_btree_ratios: middle not pinned"); return -1; } status = H5Pget_btree_ratios((hid_t)plist_id, (double *)leftP, (double *)middleP, (double *)rightP); if (status < 0) { #ifdef __cplusplus env->ReleaseDoubleArrayElements(left,leftP,JNI_ABORT); env->ReleaseDoubleArrayElements(middle,middleP,JNI_ABORT); env->ReleaseDoubleArrayElements(right,rightP,JNI_ABORT); #else (*env)->ReleaseDoubleArrayElements(env,left,leftP,JNI_ABORT); (*env)->ReleaseDoubleArrayElements(env,middle,middleP,JNI_ABORT); (*env)->ReleaseDoubleArrayElements(env,right,rightP,JNI_ABORT); #endif h5libraryError(env); } else { #ifdef __cplusplus env->ReleaseDoubleArrayElements(left,leftP,0); env->ReleaseDoubleArrayElements(middle,middleP,0); env->ReleaseDoubleArrayElements(right,rightP,0); #else (*env)->ReleaseDoubleArrayElements(env,left,leftP,0); (*env)->ReleaseDoubleArrayElements(env,middle,middleP,0); (*env)->ReleaseDoubleArrayElements(env,right,rightP,0); #endif } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_small_data_block_size * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1small_1data_1block_1size (JNIEnv *env, jclass clss, jint plist, jlong size) { long sz; herr_t retVal = -1; sz = (long)size; retVal = H5Pset_small_data_block_size((hid_t)plist, (hsize_t)sz ); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_small_data_block_size * Signature: (I[J)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1small_1data_1block_1size (JNIEnv *env, jclass clss, jint plist, jlongArray size) { herr_t status; jlong *theArray; jboolean isCopy; hsize_t s; if (size == NULL) { /* exception ? */ h5nullArgument( env, "H5Pget_small_user_block_size: size is NULL"); return -1; } #ifdef __cplusplus theArray = (jlong *)env->GetLongArrayElements(size,&isCopy); #else theArray = (jlong *)(*env)->GetLongArrayElements(env,size,&isCopy); #endif if (theArray == NULL) { h5JNIFatalError( env, "H5Pget_userblock: size not pinned"); return -1; } status = H5Pget_small_data_block_size((hid_t)plist, &s); if (status < 0) { #ifdef __cplusplus env->ReleaseLongArrayElements(size,theArray,JNI_ABORT); #else (*env)->ReleaseLongArrayElements(env,size,theArray,JNI_ABORT); #endif h5libraryError(env); } else { theArray[0] = s; #ifdef __cplusplus env->ReleaseLongArrayElements(size,theArray,0); #else (*env)->ReleaseLongArrayElements(env,size,theArray,0); #endif } return (jint)status; } /*************************************************************** * New APIs for HDF5.1.6 * ***************************************************************/ /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_alloc_time(hid_t plist_id, H5D_alloc_time_t alloc_time ) * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1alloc_1time (JNIEnv *env, jclass clss, jint plist, jint alloc_time) { herr_t retVal = -1; retVal = H5Pset_alloc_time((hid_t)plist, (H5D_alloc_time_t)alloc_time ); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_alloc_time(hid_t plist_id, H5D_alloc_time_t *alloc_time ) * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1alloc_1time (JNIEnv *env, jclass clss, jint plist, jintArray alloc_time) { herr_t retVal = -1; jint *theArray; jboolean isCopy; H5D_alloc_time_t time; if (alloc_time == NULL) { /* exception ? */ h5nullArgument( env, "H5Pget_alloc_time: alloc_time is NULL"); return -1; } #ifdef __cplusplus theArray = (jint *)env->GetIntArrayElements(alloc_time,&isCopy); #else theArray = (jint *)(*env)->GetIntArrayElements(env,alloc_time,&isCopy); #endif if (theArray == NULL) { h5JNIFatalError( env, "H5Pget_alloc_time: alloc_time not pinned"); return -1; } retVal = H5Pget_alloc_time((hid_t)plist, &time ); if (retVal < 0) { #ifdef __cplusplus env->ReleaseIntArrayElements(alloc_time,theArray,JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env,alloc_time,theArray,JNI_ABORT); #endif h5libraryError(env); } else { theArray[0] = time; #ifdef __cplusplus env->ReleaseIntArrayElements(alloc_time,theArray,0); #else (*env)->ReleaseIntArrayElements(env,alloc_time,theArray,0); #endif } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_fill_time(hid_t plist_id, H5D_fill_time_t fill_time ) * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1fill_1time (JNIEnv *env, jclass clss, jint plist, jint fill_time) { herr_t retVal = -1; retVal = H5Pset_fill_time((hid_t)plist, (H5D_fill_time_t)fill_time ); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_fill_time(hid_t plist_id, H5D_fill_time_t *fill_time ) * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1fill_1time (JNIEnv *env, jclass clss, jint plist, jintArray fill_time) { herr_t retVal = -1; jint *theArray; jboolean isCopy; H5D_fill_time_t time; if (fill_time == NULL) { /* exception ? */ h5nullArgument( env, "H5Pget_fill_time: fill_time is NULL"); return -1; } #ifdef __cplusplus theArray = (jint *)env->GetIntArrayElements(fill_time,&isCopy); #else theArray = (jint *)(*env)->GetIntArrayElements(env,fill_time,&isCopy); #endif if (theArray == NULL) { h5JNIFatalError( env, "H5Pget_fill_time: fill_time not pinned"); return -1; } retVal = H5Pget_fill_time((hid_t)plist, &time ); if (retVal < 0) { #ifdef __cplusplus env->ReleaseIntArrayElements(fill_time,theArray,JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env,fill_time,theArray,JNI_ABORT); #endif h5libraryError(env); } else { theArray[0] = time; #ifdef __cplusplus env->ReleaseIntArrayElements(fill_time,theArray,0); #else (*env)->ReleaseIntArrayElements(env,fill_time,theArray,0); #endif } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pfill_value_defined(hid_t plist_id, H5D_fill_value_t *status ) * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pfill_1value_1defined (JNIEnv *env, jclass clss, jint plist, jintArray status) { herr_t retVal = -1; jint *theArray; jboolean isCopy; H5D_fill_value_t value; if (status == NULL) { /* exception ? */ h5nullArgument( env, "H5Pfill_value_defined: status is NULL"); return -1; } #ifdef __cplusplus theArray = (jint *)env->GetIntArrayElements(status,&isCopy); #else theArray = (jint *)(*env)->GetIntArrayElements(env,status,&isCopy); #endif if (theArray == NULL) { h5JNIFatalError( env, "H5Pfill_value_defined: status not pinned"); return -1; } retVal = H5Pfill_value_defined((hid_t)plist, &value ); if (retVal < 0) { #ifdef __cplusplus env->ReleaseIntArrayElements(status,theArray,JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env,status,theArray,JNI_ABORT); #endif h5libraryError(env); } else { theArray[0] = value; #ifdef __cplusplus env->ReleaseIntArrayElements(status,theArray,0); #else (*env)->ReleaseIntArrayElements(env,status,theArray,0); #endif } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_fletcher32(hid_t plist) * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1fletcher32 (JNIEnv *env, jclass clss, jint plist) { herr_t retVal = -1; retVal = H5Pset_fletcher32((hid_t)plist); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_edc_check(hid_t plist, H5Z_EDC_t check) * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1edc_1check (JNIEnv *env, jclass clss, jint plist, jint check) { herr_t retVal = -1; retVal = H5Pset_edc_check((hid_t)plist, (H5Z_EDC_t)check ); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_edc_check(hid_t plist) * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1edc_1check (JNIEnv *env, jclass clss, jint plist) { H5Z_EDC_t retVal = -1; retVal = H5Pget_edc_check((hid_t)plist); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_shuffle(hid_t plist_id) * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1shuffle (JNIEnv *env, jclass clss, jint plist) { herr_t retVal = -1; retVal = H5Pset_shuffle((hid_t)plist); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_szip(hid_t plist, unsigned int options_mask, unsigned int pixels_per_block) * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1szip (JNIEnv *env, jclass clss, jint plist, jint options_mask, jint pixels_per_block) { herr_t retVal = -1; retVal = H5Pset_szip((hid_t)plist, (unsigned int)options_mask, (unsigned int)pixels_per_block); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_hyper_vector_size(hid_t dxpl_id, size_t vector_size ) * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1hyper_1vector_1size (JNIEnv *env, jclass clss, jint plist, jlong vector_size) { herr_t retVal = -1; retVal = H5Pset_hyper_vector_size((hid_t)plist, (size_t)vector_size); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_hyper_vector_size(hid_t dxpl_id, size_t *vector_size ) * Signature: (IJ)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1hyper_1vector_1size (JNIEnv *env, jclass clss, jint plist, jlongArray vector_size) { herr_t retVal = -1; jlong *theArray; size_t size; jboolean isCopy; if (vector_size == NULL) { /* exception ? */ h5nullArgument( env, "H5Pget_hyper_vector_size: vector_size is NULL"); return -1; } #ifdef __cplusplus theArray = (jlong *)env->GetLongArrayElements(vector_size,&isCopy); #else theArray = (jlong *)(*env)->GetLongArrayElements(env,vector_size,&isCopy); #endif if (theArray == NULL) { h5JNIFatalError( env, "H5Pget_hyper_vector_size: vector_size not pinned"); return -1; } retVal = H5Pget_hyper_vector_size((hid_t)plist, &size); if (retVal < 0) { #ifdef __cplusplus env->ReleaseLongArrayElements(vector_size,theArray,JNI_ABORT); #else (*env)->ReleaseLongArrayElements(env,vector_size,theArray,JNI_ABORT); #endif h5libraryError(env); } else { theArray[0] = size; #ifdef __cplusplus env->ReleaseLongArrayElements(vector_size,theArray,0); #else (*env)->ReleaseLongArrayElements(env,vector_size,theArray,0); #endif } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pall_filters_avail(hid_t dcpl_id) * Signature: (I)J */ JNIEXPORT jboolean JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pall_1filters_1avail (JNIEnv *env, jclass clss, jint dcpl_id) { htri_t bval; bval = H5Pall_filters_avail((hid_t)dcpl_id); if (bval > 0) { return JNI_TRUE; } else if (bval == 0) { return JNI_FALSE; } else { h5libraryError(env); return JNI_FALSE; } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pmodify_filter(hid_t plist, H5Z_filter_t filter, * unsigned int flags, size_t cd_nelmts, const unsigned int cd_values[] ) * Signature: (III[J)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pmodify_1filter (JNIEnv *env, jclass clss, jint plist, jint filter, jint flags, jlong cd_nelmts, jintArray cd_values) { herr_t status; jint *cd_valuesP; jboolean isCopy; if (cd_values == NULL) { h5nullArgument( env, "H5Pmodify_filter: cd_values is NULL"); return -1; } #ifdef __cplusplus cd_valuesP = (*env)->GetIntArrayElements(cd_values,&isCopy); #else cd_valuesP = (*env)->GetIntArrayElements(env,cd_values,&isCopy); #endif if (cd_valuesP == NULL) { h5JNIFatalError(env, "H5Pmodify_filter: cd_values not pinned"); return -1; } status = H5Pmodify_filter((hid_t)plist, (H5Z_filter_t)filter,(const unsigned int)flags, (size_t)cd_nelmts, (unsigned int *)cd_valuesP); #ifdef __cplusplus (*env)->ReleaseIntArrayElements(cd_values, cd_valuesP, JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env, cd_values, cd_valuesP, JNI_ABORT); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_filter_by_id( hid_t plist_id, H5Z_filter_t filter, * unsigned int *flags, size_t *cd_nelmts, unsigned int cd_values[], * size_t namelen, char *name[] ) * Signature: (III[J)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1filter_1by_1id (JNIEnv *env, jclass clss, jint plist, jint filter, jintArray flags, jlongArray cd_nelmts, jintArray cd_values, jlong namelen, jobjectArray name) { herr_t status; int i=0; jint *cd_valuesP, *flagsP; jlong *cd_nelmsP; jboolean isCopy; size_t *nelmsP; int rank; long bs; char *aName; jstring str; bs = (long)namelen; if (bs <= 0) { h5badArgument( env, "H5Pget_filter_by_id: namelen <= 0"); return -1; } if (flags == NULL) { h5nullArgument( env, "H5Pget_filter_by_id: flags is NULL"); return -1; } if (cd_nelmts == NULL) { h5nullArgument( env, "H5Pget_filter_by_id: cd_nelms is NULL"); return -1; } if (cd_values == NULL) { h5nullArgument( env, "H5Pget_filter_by_id: cd_values is NULL"); return -1; } if (name == NULL) { h5nullArgument( env, "H5Pget_filter_by_id: name is NULL"); return -1; } aName = (char*)malloc(sizeof(char)*bs); if (aName == NULL) { h5outOfMemory( env, "H5Pget_filter_by_id: malloc failed"); return -1; } #ifdef __cplusplus flagsP = (*env)->GetIntArrayElements(flags,&isCopy); #else flagsP = (*env)->GetIntArrayElements(env,flags,&isCopy); #endif if (flagsP == NULL) { free(aName); h5JNIFatalError(env, "H5Pget_filter_by_id: flags not pinned"); return -1; } #ifdef __cplusplus cd_nelmsP = (*env)->GetLongArrayElements(cd_nelmts,&isCopy); #else cd_nelmsP = (*env)->GetLongArrayElements(env,cd_nelmts,&isCopy); #endif if (cd_nelmsP == NULL) { free(aName); h5JNIFatalError(env, "H5Pget_filter_by_id: cd_nelms not pinned"); return -1; } nelmsP = (size_t *)malloc( sizeof(size_t)); if (nelmsP == NULL) { #ifdef __cplusplus (*env)->ReleaseIntArrayElements(flags,flagsP,JNI_ABORT); (*env)->ReleaseLongArrayElements(cd_nelmts,cd_nelmsP,JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env,flags,flagsP,JNI_ABORT); (*env)->ReleaseLongArrayElements(env,cd_nelmts,cd_nelmsP,JNI_ABORT); #endif free(aName); h5outOfMemory(env, "H5Pget_filter_by_id: cd_nelmts array not converted to unsigned int."); return -1; } #ifdef __cplusplus cd_valuesP = (*env)->GetIntArrayElements(cd_values,&isCopy); rank = (*env)->GetArrayLength(env, cd_values); #else cd_valuesP = (*env)->GetIntArrayElements(env,cd_values,&isCopy); rank = (*env)->GetArrayLength(env, cd_values); #endif if (cd_valuesP == NULL) { #ifdef __cplusplus (*env)->ReleaseIntArrayElements(flags,flagsP,JNI_ABORT); (*env)->ReleaseLongArrayElements(cd_nelmts,cd_nelmsP,JNI_ABORT); (*env)->ReleaseIntArrayElements(cd_values,cd_valuesP,JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env,flags,flagsP,JNI_ABORT); (*env)->ReleaseLongArrayElements(env,cd_nelmts,cd_nelmsP,JNI_ABORT); (*env)->ReleaseIntArrayElements(env,cd_values,cd_valuesP,JNI_ABORT); #endif free(aName); free(nelmsP); h5JNIFatalError(env, "H5Pget_filter_by_id: cd_values array not pinned."); return -1; } status = H5Pget_filter_by_id( (hid_t)plist, (H5Z_filter_t)filter, (unsigned int *)flagsP, (size_t *)nelmsP, (unsigned int *)cd_valuesP, (size_t)namelen, (char *)aName, (unsigned int*)NULL); if (status < 0) { #ifdef __cplusplus (*env)->ReleaseIntArrayElements(flags,flagsP,JNI_ABORT); (*env)->ReleaseLongArrayElements(cd_nelmts,cd_nelmsP,JNI_ABORT); (*env)->ReleaseIntArrayElements(cd_values,cd_valuesP,JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env,flags,flagsP,JNI_ABORT); (*env)->ReleaseLongArrayElements(env,cd_nelmts,cd_nelmsP,JNI_ABORT); (*env)->ReleaseIntArrayElements(env,cd_values,cd_valuesP,JNI_ABORT); #endif h5libraryError(env); } else { #ifdef __cplusplus cd_nelmsP[0] = nelmsP[0]; str = env->NewStringUTF(aName); (*env)->ReleaseIntArrayElements(flags,flagsP,0); (*env)->ReleaseLongArrayElements(cd_nelmts,cd_nelmsP,0); (*env)->ReleaseIntArrayElements(cd_values,cd_valuesP,0); #else str = (*env)->NewStringUTF(env, aName); (*env)->ReleaseIntArrayElements(env,flags,flagsP,0); (*env)->ReleaseLongArrayElements(env,cd_nelmts,cd_nelmsP,0); (*env)->ReleaseIntArrayElements(env,cd_values,cd_valuesP,0); #endif } free(aName); free(nelmsP); return (jint)status; } #ifdef __cplusplus } #endif /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_fclose_degree * Signature: (IJI)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1fclose_1degree (JNIEnv *env, jclass clss, jint plist, jint fc_degree) { herr_t retVal = -1; retVal = H5Pset_fclose_degree((hid_t) plist, (H5F_close_degree_t) fc_degree); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_fclose_degree * Signature: (IJI)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1fclose_1degree (JNIEnv *env, jclass clss, jint plist) { H5F_close_degree_t degree; herr_t retVal = -1; retVal = H5Pget_fclose_degree((hid_t) plist, °ree); if (retVal < 0) { h5libraryError(env); } return (jint)degree; } /********************************************************************** * * * File access properties * * * **********************************************************************/ /* * Class: ncsa_hdf_hdf5lib_H5 * Signature: herr_t H5Pset_fapl_family ( hid_t fapl_id, hsize_t memb_size, hid_t memb_fapl_id ) * Purpose: Sets the file access property list to use the family driver */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1fapl_1family (JNIEnv *env, jclass clss, jint plist, jlong memb_size, jint memb_plist) { long ms; herr_t retVal = -1; ms = (long)memb_size; retVal = H5Pset_fapl_family((hid_t)plist, (hsize_t)ms, (hid_t)memb_plist); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Signature: herr_t H5Pget_fapl_family ( hid_t fapl_id, hsize_t *memb_size, hid_t *memb_fapl_id ) * Purpose: Returns file access property list information */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1family (JNIEnv *env, jclass clss, jint tid, jlongArray memb_size, jintArray memb_plist) { herr_t status; jlong *sizeArray; jint *plistArray; jboolean isCopy; hsize_t *sa; int i; int rank; if (memb_size == NULL) { h5nullArgument( env, "H5Pget_family: memb_size is NULL"); return -1; } if (memb_plist == NULL) { h5nullArgument( env, "H5Pget_family: memb_plist is NULL"); return -1; } sizeArray = (jlong *)(*env)->GetLongArrayElements(env,memb_size,&isCopy); if (sizeArray == NULL) { h5JNIFatalError(env, "H5Pget_family: sizeArray not pinned"); return -1; } rank = (*env)->GetArrayLength(env, memb_size); sa = (hsize_t *)malloc( rank * sizeof(hsize_t)); if (sa == NULL) { (*env)->ReleaseLongArrayElements(env,memb_size,sizeArray,JNI_ABORT); h5outOfMemory(env, "H5Screate-simple: dims not converted to hsize_t"); return -1; } plistArray = (jint *)(*env)->GetIntArrayElements(env,memb_plist,&isCopy); if (plistArray == NULL) { (*env)->ReleaseLongArrayElements(env,memb_size,sizeArray,JNI_ABORT); h5JNIFatalError(env, "H5Pget_family: plistArray not pinned"); return -1; } status = H5Pget_fapl_family ((hid_t)tid, sa, (hid_t *)plistArray); if (status < 0) { free(sa); (*env)->ReleaseLongArrayElements(env,memb_size,sizeArray,JNI_ABORT); (*env)->ReleaseIntArrayElements(env,memb_plist,plistArray,JNI_ABORT); h5libraryError(env); } else { for (i= 0; i < rank; i++) { sa[i] = sizeArray[i]; } free(sa); (*env)->ReleaseLongArrayElements(env,memb_size,sizeArray,0); (*env)->ReleaseIntArrayElements(env,memb_plist,plistArray,0); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Signature: herr_t H5Pset_fapl_core( hid_t fapl_id, size_t increment, hbool_t backing_store ) * Purpose: Modifies the file access property list to use the H5FD_CORE driver */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1fapl_1core (JNIEnv *env, jclass clss, jint fapl_id, jint increment, jboolean backing_store) { herr_t retVal = -1; retVal = H5Pset_fapl_core( (hid_t) fapl_id, (size_t) increment, (hbool_t) backing_store ); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Signature: herr_t H5Pget_fapl_core( hid_t fapl_id, size_t *increment, hbool_t *backing_store ) * Purpose: Queries core file driver properties */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1fapl_1core (JNIEnv *env, jclass clss, jint fapl_id, jintArray increment, jbooleanArray backing_store) { herr_t status; jint *incArray; jboolean *backArray; jboolean isCopy; if (increment == NULL) { h5nullArgument( env, "H5Pget_fapl_core: increment is NULL"); return -1; } if (backing_store == NULL) { h5nullArgument( env, "H5Pget_fapl_core: backing_store is NULL"); return -1; } incArray = (jint *)(*env)->GetIntArrayElements(env,increment,&isCopy); if (incArray == NULL) { h5JNIFatalError(env, "H5Pget_fapl_core: incArray not pinned"); return -1; } backArray = (jboolean *)(*env)->GetBooleanArrayElements(env,backing_store,&isCopy); if (backArray == NULL) { (*env)->ReleaseIntArrayElements(env,increment,incArray,JNI_ABORT); h5JNIFatalError(env, "H5Pget_fapl_core: backArray not pinned"); return -1; } status = H5Pget_fapl_core( (hid_t) fapl_id, (size_t *)incArray, (hbool_t *)backArray ); if (status < 0) { (*env)->ReleaseIntArrayElements(env,increment,incArray,JNI_ABORT); (*env)->ReleaseBooleanArrayElements(env,backing_store,backArray,JNI_ABORT); h5libraryError(env); } else { (*env)->ReleaseIntArrayElements(env,increment,incArray,0); (*env)->ReleaseBooleanArrayElements(env,backing_store,backArray,0); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Signature: herr_t H5Pset_family_offset ( hid_t fapl_id, hsize_t offset ) * Purpose: Sets offset property for low-level access to a file in a family of files */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1family_1offset (JNIEnv *env, jclass clss, jint fapl_id, jlong offset) { herr_t retVal = -1; retVal = H5Pset_family_offset ( (hid_t) fapl_id, (hsize_t) offset ); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Signature: herr_t H5Pget_family_offset ( hid_t fapl_id, hsize_t *offset ) * Purpose: Retrieves a data offset from the file access property list */ JNIEXPORT jlong JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1family_1offset (JNIEnv *env, jclass clss, jint fapl_id) { hsize_t offset = -1; herr_t retVal = -1; retVal = H5Pget_family_offset ( (hid_t) fapl_id, &offset ); if (retVal < 0) { h5libraryError(env); } return (jlong)offset; } /* * Class: ncsa_hdf_hdf5lib_H5 * Signature: herr_t H5Pset_fapl_log( hid_t fapl_id, const char *logfile, unsigned int flags, size_t buf_size ) * Purpose: Sets up the use of the logging driver */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1fapl_1log (JNIEnv *env, jclass clss, jint fapl_id, jstring logfile, jint flags, jint buf_size) { herr_t retVal = -1; char * pLogfile; jboolean isCopy; if (logfile == NULL) { h5nullArgument( env, "H5Pset_fapl_log: logfile is NULL"); return -1; } pLogfile = (char *)(*env)->GetStringUTFChars(env,logfile,&isCopy); if (pLogfile == NULL) { h5JNIFatalError(env, "H5Pset_fapl_log: logfile not pinned"); return -1; } retVal = H5Pset_fapl_log( (hid_t) fapl_id, (const char *)pLogfile, (unsigned int) flags, (size_t) buf_size ); if (retVal < 0) { h5libraryError(env); } (*env)->ReleaseStringUTFChars(env, logfile, pLogfile); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /********************************************************************** * * * New functions release 1.6.3 versus release 1.6.2 * * * **********************************************************************/ /* * Class: ncsa_hdf_hdf5lib_H5 * Signature: herr_t H5Premove_filter (hid_t obj_id, H5Z_filter_t filter) * Purpose: */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5P1remove_1filter (JNIEnv *env, jclass clss, jint obj_id, jint filter) { herr_t status; status = H5Premove_filter ((hid_t) obj_id, (H5Z_filter_t) filter); if (status < 0) { h5libraryError(env); } return status; } /********************************************************************** * * Modified by Peter Cao on July 26, 2006: Some of the Generic Property APIs have callback function pointers, which Java does not support. Only the Generic Property APIs without function pointers are implemented * * **********************************************************************/ /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pcreate_list * Signature: hid_t H5Pcreate_list( hid_t class) */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pcreate_1list (JNIEnv *env, jclass clss, jint cls) { hid_t retVal = -1; retVal = H5Pcopy((hid_t)cls); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset * Signature: herr_t H5Pset( hid_t plid, const char *name, void *value) */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset (JNIEnv *env, jclass clss, jint plid, jstring name, jint val) { char* cstr; jboolean isCopy; hid_t retVal = -1; if (name == NULL) { h5nullArgument( env, "H5Pset: name is NULL"); return -1; } cstr = (char *)(*env)->GetStringUTFChars(env,name,&isCopy); if (cstr == NULL) { h5JNIFatalError( env, "H5Pset: name not pinned"); return -1; } retVal = H5Pset((hid_t)plid, cstr, &val); (*env)->ReleaseStringUTFChars(env,name,cstr); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pexist * Signature: htri_t H5Pexist( hid_t id, const char *name ) */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pexist (JNIEnv *env, jclass clss, jint plid, jstring name) { char* cstr; jboolean isCopy; hid_t retVal = -1; if (name == NULL) { h5nullArgument( env, "H5Pexist: name is NULL"); return -1; } cstr = (char *)(*env)->GetStringUTFChars(env,name,&isCopy); if (cstr == NULL) { h5JNIFatalError( env, "H5Pexist: name not pinned"); return -1; } retVal = H5Pexist((hid_t)plid, cstr); (*env)->ReleaseStringUTFChars(env,name,cstr); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_size * Signature: int H5Pget_size( hid_t id, const char *name, size_t *size ) */ JNIEXPORT jlong JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1size (JNIEnv *env, jclass clss, jint plid, jstring name) { char* cstr; jboolean isCopy; hid_t retVal = -1; size_t size; if (name == NULL) { h5nullArgument( env, "H5Pget_size: name is NULL"); return -1; } cstr = (char *)(*env)->GetStringUTFChars(env,name,&isCopy); if (cstr == NULL) { h5JNIFatalError( env, "H5Pget_size: name not pinned"); return -1; } retVal = H5Pget_size((hid_t)plid, cstr, &size); (*env)->ReleaseStringUTFChars(env,name,cstr); if (retVal < 0) { h5libraryError(env); } return (jlong) size; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_nprops * Signature: int H5Pget_nprops( hid_t id, size_t *nprops ) */ JNIEXPORT jlong JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1nprops (JNIEnv *env, jclass clss, jint plid) { hid_t retVal = -1; size_t nprops; retVal = H5Pget_nprops((hid_t)plid, &nprops); if (retVal < 0) { h5libraryError(env); } return (jlong) nprops; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_class_name * Signature: char * H5Pget_class_name( hid_t pcid ) */ JNIEXPORT jstring JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1class_1name (JNIEnv *env, jclass clss, jint plid) { char *c_str; jstring j_str; c_str = H5Pget_class_name((hid_t)plid); if (c_str < 0) { h5libraryError(env); } j_str = (*env)->NewStringUTF(env,c_str); if (j_str == NULL) { h5outOfMemory( env,"H5Pget_class_name: return string failed"); } return j_str; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_class_parent * Signature: hid_t H5Pget_class_parent( hid_t pcid ) */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1class_1parent (JNIEnv *env, jclass clss, jint plid) { hid_t retVal = -1; retVal = H5Pget_class_parent((hid_t)plid); if (retVal < 0) { h5libraryError(env); } return (jint) retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pisa_class * Signature: htri_t H5Pisa_class( hid_t plist, hid_t pclass ) */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pisa_1class (JNIEnv *env, jclass clss, jint plid, jint pcls) { htri_t retVal = -1; retVal = H5Pisa_class((hid_t)plid, (hid_t)pcls); if (retVal < 0) { h5libraryError(env); } return (jint) retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget * Signature: herr_t H5Pget( hid_t plid, const char *name, void *value ) */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget (JNIEnv *env, jclass clss, jint plid, jstring name) { char* cstr; jboolean isCopy; jint val; jint retVal = -1; if (name == NULL) { h5nullArgument( env, "H5Pget: name is NULL"); return -1; } cstr = (char *)(*env)->GetStringUTFChars(env,name,&isCopy); if (cstr == NULL) { h5JNIFatalError( env, "H5Pget: name not pinned"); return -1; } retVal = H5Pget((hid_t)plid, cstr, &val); (*env)->ReleaseStringUTFChars(env,name,cstr); if (retVal < 0) { h5libraryError(env); } return (jint)val; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pequal * Signature: htri_t H5Pequal( hid_t id1, hid_t id2 ) */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pequal (JNIEnv *env, jclass clss, jint plid1, jint plid2) { htri_t retVal = -1; retVal = H5Pequal((hid_t)plid1, (hid_t)plid2); if (retVal < 0) { h5libraryError(env); } return (jint) retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pcopy_prop * Signature: herr_t H5Pcopy_prop( hid_t dst_id, hid_t src_id, const char *name ) */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pcopy_1prop (JNIEnv *env, jclass clss, jint dst_plid, jint src_plid, jstring name) { char* cstr; jboolean isCopy; jint retVal = -1; if (name == NULL) { h5nullArgument( env, "H5Pcopy_prop: name is NULL"); return -1; } cstr = (char *)(*env)->GetStringUTFChars(env,name,&isCopy); if (cstr == NULL) { h5JNIFatalError( env, "H5Pcopy_prop: name not pinned"); return -1; } retVal = H5Pcopy_prop((hid_t)dst_plid, (hid_t)src_plid, cstr); (*env)->ReleaseStringUTFChars(env,name,cstr); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Premove * Signature: herr_t H5Premove( hid_t plid; const char *name ) */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Premove (JNIEnv *env, jclass clss, jint plid, jstring name) { char* cstr; jboolean isCopy; jint retVal = -1; if (name == NULL) { h5nullArgument( env, "H5Premove: name is NULL"); return -1; } cstr = (char *)(*env)->GetStringUTFChars(env,name,&isCopy); if (cstr == NULL) { h5JNIFatalError( env, "H5Premove: name not pinned"); return -1; } retVal = H5Premove((hid_t)plid, cstr); (*env)->ReleaseStringUTFChars(env,name,cstr); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Punregister * Signature: herr_t H5Punregister( H5P_class_t class, const char *name ) */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Punregister (JNIEnv *env, jclass clss, jint plid, jstring name) { char* cstr; jboolean isCopy; jint retVal = -1; if (name == NULL) { h5nullArgument( env, "H5Punregister: name is NULL"); return -1; } cstr = (char *)(*env)->GetStringUTFChars(env,name,&isCopy); if (cstr == NULL) { h5JNIFatalError( env, "H5Punregister: name not pinned"); return -1; } retVal = H5Punregister((hid_t)plid, cstr); (*env)->ReleaseStringUTFChars(env,name,cstr); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pclose_list * Signature: herr_t H5Pclose_class( hid_t plist ) */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pclose_1class (JNIEnv *env, jclass clss, jint plid) { hid_t retVal = -1; retVal = H5Pclose_class((hid_t)plid); if (retVal < 0) { h5libraryError(env); } return (jint) retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_create_intermediate_group * Signature: herr_t H5Pset_create_intermediate_group( hid_t lcpl_id, unsigned crt_intermed_group ) */ JNIEXPORT void JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1create_1intermediate_1group (JNIEnv *env, jclass clss, jint lcpl_id, jboolean crt_intermed_group) { hid_t retVal = -1; retVal = H5Pset_create_intermediate_group((hid_t) lcpl_id, crt_intermed_group ? 1 : 0); if (retVal < 0) { h5libraryError(env); } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_create_intermediate_group * Signature: herr_t H5Pget_create_intermediate_group( hid_t lcpl_id, unsigned *crt_intermed_group ) */ JNIEXPORT jboolean JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1create_1intermediate_1group (JNIEnv *env, jclass clss, jint lcpl_id) { hid_t retVal = -1; unsigned crt_intermed_group; retVal = H5Pget_create_intermediate_group((hid_t) lcpl_id, &crt_intermed_group); if (retVal < 0) { h5libraryError(env); } return crt_intermed_group ? JNI_TRUE : JNI_FALSE; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_local_heap_size_hint * Signature: herr_t H5Pset_local_heap_size_hint( hid_t gcpl_id, size_t size_hint ) */ JNIEXPORT void JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1local_1heap_1size_1hint (JNIEnv *env, jclass clss, jint gcpl_id, jint size_hint) { hid_t retVal = -1; retVal = H5Pset_local_heap_size_hint((hid_t) gcpl_id, size_hint); if (retVal < 0) { h5libraryError(env); } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_local_heap_size_hint * Signature: herr_t H5Pget_local_heap_size_hint( hid_t gcpl_id, size_t *size_hint ) */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1local_1heap_1size_1hint (JNIEnv *env, jclass clss, jint gcpl_id) { hid_t retVal = -1; size_t size_hint; retVal = H5Pget_local_heap_size_hint((hid_t) gcpl_id, &size_hint); if (retVal < 0) { h5libraryError(env); } return size_hint; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_link_phase_change * Signature: herr_t H5Pset_link_phase_change( hid_t gcpl_id, unsigned max_compact, unsigned min_dense ) */ JNIEXPORT void JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1link_1phase_1change (JNIEnv *env, jclass clss, jint gcpl_id, jint max_compact, jint min_dense) { hid_t retVal = -1; retVal = H5Pset_link_phase_change((hid_t) gcpl_id, max_compact, min_dense); if (retVal < 0) { h5libraryError(env); } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_link_phase_change * Signature: herr_t H5Pget_link_phase_change( hid_t gcpl_id, unsigned *max_compact, unsigned *min_dense ) */ JNIEXPORT jintArray JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1link_1phase_1change (JNIEnv *env, jclass clss, jint gcpl_id) { hid_t retVal = -1; jintArray iarray; jint max_compact_min_dense[2]; retVal = H5Pget_link_phase_change((hid_t) gcpl_id, (unsigned*) max_compact_min_dense, (unsigned*) (max_compact_min_dense + 1)); if (retVal < 0) { h5libraryError(env); } if (max_compact_min_dense[0] < 0 || max_compact_min_dense[1] < 0) { h5raiseException( env, "java/lang/RuntimeException", "H5Pget_link_phase_change: parameter overflow"); return NULL; } #ifdef __cplusplus iarray = env->NewIntArray(2); #else iarray = (*env)->NewIntArray(env,2); #endif if (iarray == NULL) { h5outOfMemory( env, "H5Pget_link_phase_change" ); return NULL; } #ifdef __cplusplus env->SetIntArrayRegion(iarray,0,2,max_compact_min_dense); #else (*env)->SetIntArrayRegion(env,iarray,0,2,max_compact_min_dense); #endif return iarray; } H5T_conv_ret_t abort_on_overflow_cb(int except_type, hid_t *src_id, hid_t *dst_id, void *src_buf, void *dst_buf, void *op_data) { if (except_type == H5T_CONV_EXCEPT_RANGE_HI || except_type == H5T_CONV_EXCEPT_RANGE_LOW) { return H5T_CONV_ABORT; } return H5T_CONV_UNHANDLED; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pcreate_xfer_abort_overflow * Signature: hid_t H5Pcreate_xfer_abort_overflow() */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pcreate_1xfer_1abort_1overflow (JNIEnv *env, jclass clss) { hid_t plist; herr_t status; plist = H5Pcreate(H5P_DATASET_XFER); status = H5Pset_type_conv_cb(plist, (H5T_conv_except_func_t) abort_on_overflow_cb, NULL); if (status < 0) { return status; } return plist; } H5T_conv_ret_t abort_cb(int except_type, hid_t *src_id, hid_t *dst_id, void *src_buf, void *dst_buf, void *op_data) { return H5T_CONV_ABORT; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pcreate_xfer_abort * Signature: hid_t H5Pcreate_xfer_abort() */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pcreate_1xfer_1abort (JNIEnv *env, jclass clss) { hid_t plist; herr_t status; plist = H5Pcreate(H5P_DATASET_XFER); status = H5Pset_type_conv_cb(plist, (H5T_conv_except_func_t) abort_cb, NULL); if (status < 0) { return status; } return plist; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pget_char_encoding(hid_t cpl_id) * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1char_1encoding (JNIEnv *env, jclass clss, jint cpl_id) { H5T_cset_t encoding; herr_t retVal; retVal = H5Pget_char_encoding((hid_t)cpl_id, &encoding); if (retVal >= 0) { return (jint) encoding; } else { h5libraryError(env); return retVal; } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Pset_char_encoding(hid_t cpl_id) * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1char_1encoding (JNIEnv *env, jclass clss, jint cpl_id, jint encoding) { herr_t retVal; retVal = H5Pset_char_encoding((hid_t)cpl_id, (H5T_cset_t)encoding); if (retVal < 0) { h5libraryError(env); } return retVal; } libsis-jhdf5-java-14.12.1/source/c/jhdf5/h5rImpJHDF5.c000077500000000000000000000443251256564762100216660ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ /* * This code is the C-interface called by Java programs to access the * Reference API Functions of the HDF5 library. * * Each routine wraps a single HDF entry point, generally with the * analogous arguments and return codes. * * For details of the HDF libraries, see the HDF Documentation at: * http://hdf.ncsa.uiuc.edu/HDF5/doc/ * */ #ifdef __cplusplus extern "C" { #endif #include "hdf5.h" #include #include extern jboolean h5JNIFatalError( JNIEnv *env, char *functName); extern jboolean h5nullArgument( JNIEnv *env, char *functName); extern jboolean h5badArgument( JNIEnv *env, char *functName); extern jboolean h5libraryError( JNIEnv *env ); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Rcreate * Signature: ([BILjava/lang/String;II)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Rcreate___3BILjava_lang_String_2II (JNIEnv *env, jclass clss, jbyteArray ref, jint loc_id, jstring name, jint ref_type, jint space_id) { char* rName; herr_t status; jbyte *refP; if (ref == NULL) { h5nullArgument( env, "H5Rcreate: ref is NULL"); return -1; } if (name == NULL) { h5nullArgument( env, "H5Rcreate: name is NULL"); return -1; } if (ref_type == H5R_OBJECT) { #ifdef __cplusplus if (env->GetArrayLength(ref) < 8) { h5badArgument( env, "H5Rcreate: ref input array < 8"); return -1; } #else if ((*env)->GetArrayLength(env, ref) < 8) { h5badArgument( env, "H5Rcreate: ref input array < 8"); return -1; } #endif } else if (ref_type == H5R_DATASET_REGION) { #ifdef __cplusplus if (env->GetArrayLength( ref) < 12) { h5badArgument( env, "H5Rcreate: region ref input array < 12"); return -1; } #else if ((*env)->GetArrayLength(env, ref) < 12) { h5badArgument( env, "H5Rcreate: region ref input array < 12"); return -1; } #endif } else { h5badArgument( env, "H5Rcreate: ref_type unknown type "); return -1; } #ifdef __cplusplus refP = (jbyte *)env->GetByteArrayElements(ref,NULL); #else refP = (jbyte *)(*env)->GetByteArrayElements(env,ref,NULL); #endif if (refP == NULL) { h5JNIFatalError(env, "H5Rcreate: ref not pinned"); return -1; } #ifdef __cplusplus rName = (char *)env->GetStringUTFChars(name,NULL); #else rName = (char *)(*env)->GetStringUTFChars(env,name,NULL); #endif if (rName == NULL) { #ifdef __cplusplus env->ReleaseByteArrayElements(ref,refP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,ref,refP,JNI_ABORT); #endif h5JNIFatalError(env, "H5Rcreate: name not pinned"); return -1; } status = H5Rcreate(refP, loc_id, rName, (H5R_type_t)ref_type, space_id); #ifdef __cplusplus env->ReleaseStringUTFChars(name,rName); #else (*env)->ReleaseStringUTFChars(env,name,rName); #endif if (status < 0) { #ifdef __cplusplus env->ReleaseByteArrayElements(ref,refP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,ref,refP,JNI_ABORT); #endif h5libraryError(env); return -1; } #ifdef __cplusplus env->ReleaseByteArrayElements(ref,refP,0); #else (*env)->ReleaseByteArrayElements(env,ref,refP,0); #endif return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Rcreate * Signature: (ILjava/lang/String;)[J */ JNIEXPORT jlongArray JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Rcreate__I_3Ljava_lang_String_2 (JNIEnv *env, jclass clss, jint loc_id, jobjectArray names) { char* rName; herr_t status; jint arrayLen; jlongArray array; jlong* arrayP; jlong* arrayPR; jstring name; int i; if (names == NULL) { h5nullArgument( env, "H5Rcreate: names is NULL"); return NULL; } #ifdef __cplusplus arrayLen = env->GetArrayLength(names); array = env->NewLongArray(arrayLen); if (array == NULL) { return NULL; } arrayP = (long *)env->GetLongArrayElements(array,NULL); #else arrayLen = (*env)->GetArrayLength(env,names); array = (*env)->NewLongArray(env,arrayLen); if (array == NULL) { return NULL; } arrayP = (jlong *)(*env)->GetLongArrayElements(env,array,NULL); #endif if (arrayP == NULL) { h5JNIFatalError(env, "H5Rcreate: array not pinned"); return NULL; } for (i = 0,arrayPR=arrayP; i < arrayLen; ++i,++arrayPR) { #ifdef __cplusplus name = env->GetObjectArrayElement(names,i); #else name = (*env)->GetObjectArrayElement(env,names,i); #endif if (name == NULL) { #ifdef __cplusplus env->ReleaseLongArrayElements(array,arrayP,JNI_ABORT); #else (*env)->ReleaseLongArrayElements(env,array,arrayP,JNI_ABORT); #endif return NULL; } #ifdef __cplusplus rName = (char *)env->GetStringUTFChars(name,NULL); #else rName = (char *)(*env)->GetStringUTFChars(env,name,NULL); #endif if (rName == NULL) { #ifdef __cplusplus env->ReleaseLongArrayElements(array,arrayP,JNI_ABORT); #else (*env)->ReleaseLongArrayElements(env,array,arrayP,JNI_ABORT); #endif h5JNIFatalError(env, "H5Rcreate: name not pinned"); return NULL; } status = H5Rcreate(arrayPR, loc_id, rName, H5R_OBJECT, -1); #ifdef __cplusplus env->ReleaseStringUTFChars(name,rName); #else (*env)->ReleaseStringUTFChars(env,name,rName); #endif if (status < 0) { #ifdef __cplusplus env->ReleaseLongArrayElements(array,arrayP,0); #else (*env)->ReleaseLongArrayElements(env,array,arrayP,0); #endif h5libraryError(env); return NULL; } } /* for (i=0...)*/ #ifdef __cplusplus env->ReleaseLongArrayElements(array,arrayP,0); #else (*env)->ReleaseLongArrayElements(env,array,arrayP,0); #endif return array; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Rdereference * Signature: (IIJ)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Rdereference__IJ (JNIEnv *env, jclass clss, jint dataset, jlong ref) { hid_t id; id = H5Rdereference((hid_t)dataset, H5R_OBJECT, &ref); if (id < 0) { h5libraryError(env); } return (jint) id; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Rdereference * Signature: (II[B)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Rdereference__II_3B (JNIEnv *env, jclass clss, jint dataset, jint ref_type, jbyteArray ref ) { jboolean isCopy; jbyte *refP; herr_t status; if (ref == NULL) { h5nullArgument( env, "H5Rdereference: ref is NULL"); return -1; } #ifdef __cplusplus if ((ref_type == H5R_OBJECT) && env->GetArrayLength(ref) < 8) { h5badArgument( env, "H5Rdereference: obj ref input array < 8"); } else if ((ref_type == H5R_DATASET_REGION) && env->GetArrayLength(ref) < 12) { h5badArgument( env, "H5Rdereference: region ref input array < 12"); } refP = (jbyte *)env->GetByteArrayElements(ref,&isCopy); #else if ((ref_type == H5R_OBJECT) && (*env)->GetArrayLength(env, ref) < 8) { h5badArgument( env, "H5Rdereference: obj ref input array < 8"); } else if ((ref_type == H5R_DATASET_REGION) && (*env)->GetArrayLength(env, ref) < 12) { h5badArgument( env, "H5Rdereference: region ref input array < 12"); } refP = (jbyte *)(*env)->GetByteArrayElements(env,ref,&isCopy); #endif if (refP == NULL) { h5JNIFatalError(env, "H5Rderefernce: ref not pinned"); return -1; } status = H5Rdereference((hid_t)dataset, (H5R_type_t)ref_type, refP); #ifdef __cplusplus env->ReleaseByteArrayElements(ref,refP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,ref,refP,JNI_ABORT); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Rget_region * Signature: (II[B)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Rget_1region (JNIEnv *env, jclass clss, jint dataset, jint ref_type, jbyteArray ref ) { hid_t status; jboolean isCopy; jbyte *refP; if (ref_type != H5R_DATASET_REGION) { h5badArgument( env, "H5Rget_region: bad ref_type "); return -1; } if (ref == NULL) { h5nullArgument( env, "H5Rget_region: ref is NULL"); return -1; } #ifdef __cplusplus if ( env->GetArrayLength(ref) < 12) { h5badArgument( env, "H5Rget_region: region ref input array < 12"); } refP = (jbyte *)env->GetByteArrayElements(ref,&isCopy); #else if ( (*env)->GetArrayLength(env, ref) < 12) { h5badArgument( env, "H5Rget_region: region ref input array < 12"); } refP = (jbyte *)(*env)->GetByteArrayElements(env,ref,&isCopy); #endif if (refP == NULL) { h5JNIFatalError(env, "H5Rget_region: ref not pinned"); return -1; } status = H5Rget_region((hid_t)dataset, (H5R_type_t)ref_type, refP); #ifdef __cplusplus env->ReleaseByteArrayElements(ref,refP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,ref,refP,JNI_ABORT); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5G_obj_t H5Rget_obj_type(hid_t id, H5R_type_t ref_type, void *_ref) * Signature: (I[B)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Rget_1obj_1type (JNIEnv *env, jclass clss, jint loc_id, jint ref_type, jbyteArray ref) { herr_t status; H5O_type_t obj_type; jboolean isCopy; jbyte *refP; if (ref == NULL) { h5nullArgument( env, "H5Rget_object_type: ref is NULL"); return -1; } #ifdef __cplusplus refP = (jbyte *)env->GetByteArrayElements(ref,&isCopy); #else refP = (jbyte *)(*env)->GetByteArrayElements(env,ref,&isCopy); #endif if (refP == NULL) { h5JNIFatalError(env, "H5Rget_object_type: ref not pinned"); return -1; } status = H5Rget_obj_type((hid_t)loc_id, (H5R_type_t)ref_type, refP, &obj_type); #ifdef __cplusplus env->ReleaseByteArrayElements(ref,refP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,ref,refP,JNI_ABORT); #endif if (status < 0) { h5libraryError(env); } return (jint)obj_type; } #ifdef __cplusplus } #endif /* * Class: ncsa_hdf_hdf5lib_H5 * Method: String H5Rget_name(hid_t id, H5R_type_t ref_type, void *ref) * Signature: (I[B)Ljava/lang/String; */ JNIEXPORT jstring JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Rget_1name__II_3B (JNIEnv *env, jclass clss, jint loc_id, jint ref_type, jbyteArray ref) { ssize_t size; H5O_type_t obj_type; jbyte *refP; char *rName; int rname_buf_size = 128; jstring str; if (ref == NULL) { h5nullArgument( env, "H5Rget_name: ref is NULL"); return NULL; } #ifdef __cplusplus refP = (jbyte *)env->GetByteArrayElements(ref, NULL); #else refP = (jbyte *)(*env)->GetByteArrayElements(env,ref, NULL); #endif if (refP == NULL) { h5JNIFatalError(env, "H5Rget_name: ref not pinned"); return NULL; } rName = (char*) malloc(sizeof(char) * rname_buf_size); if (rName == NULL) { #ifdef __cplusplus env->ReleaseByteArrayElements(ref,refP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,ref,refP,JNI_ABORT); #endif h5outOfMemory(env, "H5Rget_name: malloc failed"); return NULL; } size = H5Rget_name((hid_t)loc_id, (H5R_type_t)ref_type, refP, rName, rname_buf_size); if (size < 0) { free(rName); #ifdef __cplusplus env->ReleaseByteArrayElements(ref,refP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,ref,refP,JNI_ABORT); #endif h5libraryError(env); return NULL; } if (size >= rname_buf_size) { free(rName); rname_buf_size = size + 1; rName = (char*) malloc(sizeof(char) * rname_buf_size); size = H5Rget_name((hid_t)loc_id, (H5R_type_t)ref_type, refP, rName, rname_buf_size); if (size < 0) { free(rName); #ifdef __cplusplus env->ReleaseByteArrayElements(ref,refP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,ref,refP,JNI_ABORT); #endif h5libraryError(env); return NULL; } } rName[size] = '\0'; #ifdef __cplusplus env->ReleaseByteArrayElements(ref,refP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,ref,refP,JNI_ABORT); #endif /* successful return -- save the string; */ #ifdef __cplusplus str = env->NewStringUTF(rName); #else str = (*env)->NewStringUTF(env,rName); #endif free(rName); if (str == NULL) { return NULL; } return str; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: String H5Rget_name(hid_t id, jlong ref) * Signature: (I[B)Ljava/lang/String; */ JNIEXPORT jstring JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Rget_1name__IJ (JNIEnv *env, jclass clss, jint loc_id, jlong ref) { ssize_t size; H5O_type_t obj_type; char *rName; int rname_buf_size = 128; jstring str; rName = (char*) malloc(sizeof(char) * rname_buf_size); if (rName == NULL) { h5outOfMemory(env, "H5Rget_name: malloc failed"); return NULL; } size = H5Rget_name((hid_t)loc_id, H5R_OBJECT, &ref, rName, rname_buf_size); if (size < 0) { free(rName); h5libraryError(env); return NULL; } if (size >= rname_buf_size) { free(rName); rname_buf_size = size + 1; rName = (char*) malloc(sizeof(char) * rname_buf_size); size = H5Rget_name((hid_t)loc_id, H5R_OBJECT, &ref, rName, rname_buf_size); if (size < 0) { free(rName); h5libraryError(env); return NULL; } } rName[size] = '\0'; /* successful return -- save the string; */ #ifdef __cplusplus str = env->NewStringUTF(rName); #else str = (*env)->NewStringUTF(env,rName); #endif free(rName); if (str == NULL) { return NULL; } return str; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: String[] H5Rget_name(hid_t id, H5R_type_t ref_type, long *_ref) * Signature: (I[B)Ljava/lang/String; */ JNIEXPORT jobjectArray JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Rget_1name__I_3J (JNIEnv *env, jclass clss, jint loc_id, jlongArray ref) { ssize_t size; H5O_type_t obj_type; jlong *refP, *refPR; char *rName; int rname_buf_size = 128; jclass stringClass; jint arrayLen; jobjectArray array; jstring str; int i; if (ref == NULL) { h5nullArgument( env, "H5Rget_name: ref is NULL"); return NULL; } #ifdef __cplusplus refP = (jlong *)env->GetLongArrayElements(ref, NULL); #else refP = (jlong *)(*env)->GetLongArrayElements(env,ref, NULL); #endif if (refP == NULL) { h5JNIFatalError(env, "H5Rget_name: ref not pinned"); return NULL; } #ifdef __cplusplus arrayLen = env->GetArrayLength(ref); stringClass = env->FindClass("java/lang/String"); array = env->NewObjectArray(arrayLen, stringClass, NULL); #else arrayLen = (*env)->GetArrayLength(env, ref); stringClass = (*env)->FindClass(env, "java/lang/String"); array = (*env)->NewObjectArray(env, arrayLen, stringClass, NULL); #endif if (array == NULL) { return NULL; } rName = (char*) malloc(sizeof(char) * rname_buf_size); if (rName == NULL) { #ifdef __cplusplus env->ReleaseLongArrayElements(ref,refP,JNI_ABORT); #else (*env)->ReleaseLongArrayElements(env,ref,refP,JNI_ABORT); #endif h5outOfMemory(env, "H5Rget_name: malloc failed"); return NULL; } for (i = 0,refPR = refP; i < arrayLen; ++i,++refPR) { size = H5Rget_name((hid_t)loc_id, H5R_OBJECT, refPR, rName, rname_buf_size); if (size < 0) { free(rName); #ifdef __cplusplus env->ReleaseLongArrayElements(ref,refP,JNI_ABORT); #else (*env)->ReleaseLongArrayElements(env,ref,refP,JNI_ABORT); #endif h5libraryError(env); return NULL; } if (size >= rname_buf_size) { free(rName); rname_buf_size = size + 1; rName = (char*) malloc(sizeof(char) * rname_buf_size); size = H5Rget_name((hid_t)loc_id, H5R_OBJECT, refP, rName, rname_buf_size); if (size < 0) { free(rName); #ifdef __cplusplus env->ReleaseLongArrayElements(ref,refP,JNI_ABORT); #else (*env)->ReleaseLongArrayElements(env,ref,refP,JNI_ABORT); #endif h5libraryError(env); return NULL; } } rName[size] = '\0'; /* successful return -- save the string; */ #ifdef __cplusplus str = env->NewStringUTF(rName); #else str = (*env)->NewStringUTF(env,rName); #endif if (str == NULL) { free(rName); #ifdef __cplusplus env->ReleaseLongArrayElements(ref,refP,JNI_ABORT); #else (*env)->ReleaseLongArrayElements(env,ref,refP,JNI_ABORT); #endif return NULL; } #ifdef __cplusplus env->SetObjectArrayElement(array, i, str); #else (*env)->SetObjectArrayElement(env, array, i, str); #endif } /* for (i = 0...) */ #ifdef __cplusplus env->ReleaseLongArrayElements(ref,refP,JNI_ABORT); #else (*env)->ReleaseLongArrayElements(env,ref,refP,JNI_ABORT); #endif free(rName); return array; } #ifdef __cplusplus } #endif libsis-jhdf5-java-14.12.1/source/c/jhdf5/h5sImpJHDF5.c000077500000000000000000001101771256564762100216660ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ /* * This code is the C-interface called by Java programs to access the * Dataspace Object API Functions of the HDF5 library. * * Each routine wraps a single HDF entry point, generally with the * analogous arguments and return codes. * * For details of the HDF libraries, see the HDF Documentation at: * http://hdf.ncsa.uiuc.edu/HDF5/doc/ * */ #ifdef __cplusplus extern "C" { #endif #include "hdf5.h" #include #include extern jboolean h5outOfMemory( JNIEnv *env, char *functName); extern jboolean h5JNIFatalError( JNIEnv *env, char *functName); extern jboolean h5nullArgument( JNIEnv *env, char *functName); extern jboolean h5badArgument( JNIEnv *env, char *functName); extern jboolean h5libraryError( JNIEnv *env ); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Screate * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Screate (JNIEnv *env, jclass clss, jint type) { hid_t retVal = -1; retVal = H5Screate((H5S_class_t)type); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Screate_simple * Signature: (I[B[B)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Screate_1simple (JNIEnv *env, jclass clss, jint rank, jbyteArray dims, jbyteArray maxdims) { hid_t status; jbyte *dimsP, *maxdimsP; jboolean isCopy; hsize_t *sa; hsize_t *msa; int i; hsize_t *lp; jlong *jlp; if (dims == NULL) { h5nullArgument( env, "H5Screate_simple: dims is NULL"); return -1; } #ifdef __cplusplus dimsP = env->GetByteArrayElements(dims,&isCopy); #else dimsP = (*env)->GetByteArrayElements(env,dims,&isCopy); #endif if (dimsP == NULL) { h5JNIFatalError(env, "H5Screate-simple: dims not pinned"); return -1; } sa = lp = (hsize_t *)malloc(rank * sizeof(hsize_t)); if (sa == NULL) { #ifdef __cplusplus env->ReleaseByteArrayElements(dims,dimsP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,dims,dimsP,JNI_ABORT); #endif h5outOfMemory(env, "H5Screate-simple: dims not converted to hsize_t"); return -1; } jlp = (jlong *)dimsP; for (i = 0; i < rank; i++) { *lp = (hsize_t)*jlp; lp++; jlp++; } if (maxdims == NULL) { maxdimsP = NULL; msa = (hsize_t *)maxdimsP; } else { #ifdef __cplusplus maxdimsP = env->GetByteArrayElements(maxdims,&isCopy); #else maxdimsP = (*env)->GetByteArrayElements(env,maxdims,&isCopy); #endif if (maxdimsP == NULL) { #ifdef __cplusplus env->ReleaseByteArrayElements(dims,dimsP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,dims,dimsP,JNI_ABORT); #endif h5JNIFatalError(env, "H5Screate-simple: maxdims not pinned"); return -1; } msa = lp = (hsize_t *)malloc(rank * sizeof(hsize_t)); if (msa == NULL) { #ifdef __cplusplus env->ReleaseByteArrayElements(dims,dimsP,JNI_ABORT); env->ReleaseByteArrayElements(maxdims,maxdimsP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,dims,dimsP,JNI_ABORT); (*env)->ReleaseByteArrayElements(env,maxdims,maxdimsP,JNI_ABORT); #endif free (sa); h5outOfMemory(env, "H5Screate-simple: dims not converted to hsize_t"); return -1; } jlp = (jlong *)maxdimsP; for (i = 0; i < rank; i++) { *lp = (hsize_t)*jlp; lp++; jlp++; } } status = H5Screate_simple(rank, (const hsize_t *)sa, (const hsize_t *)msa); if (maxdimsP != NULL) { #ifdef __cplusplus env->ReleaseByteArrayElements(maxdims,maxdimsP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,maxdims,maxdimsP,JNI_ABORT); #endif free (msa); } #ifdef __cplusplus env->ReleaseByteArrayElements(dims,dimsP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,dims,dimsP,JNI_ABORT); #endif free (sa); if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Scopy * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Scopy (JNIEnv *env, jclass clss, jint space_id) { herr_t retVal = -1; retVal = H5Scopy (space_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sselect_elements * Signature: (III[J)I */ #ifdef notdef // 10/28/99 -- added code to copy the array -- this is not used, // but serves as a reminder in case we try to implement this in // the future.... /* * Note: the argument coord is actually long coord[][], which has been * flattened by the caller. */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Sselect_1elements (JNIEnv *env, jclass clss, jint space_id, jint op, jint num_elemn, jlongArray coord) { herr_t status; jint i; jlong *P; jboolean isCopy; hssize_t *sa; int rank; if (coord == NULL) { h5nullArgument( env, "H5Sselect_elements: coord is NULL"); return -1; } P = (*env)->GetLongArrayElements(env,coord,&isCopy); if (P == NULL) { h5JNIFatalError(env, "H5Sselect_elements: coord not pinned"); return -1; } sa = (hssize_t *)malloc( num_elems * 2 * sizeof(hssize_t)); if (sa == NULL) { (*env)->ReleaseLongArrayElements(env,coord,P,JNI_ABORT); h5outOfMemory(env, "H5Sselect_elements: coord array not converted to hssize_t"); return -1; } for (i= 0; i < (num_elsms * 2); i++) { sa[i] = P[i]; } status = H5Sselect_elements (space_id, (H5S_seloper_t)op, num_elemn, (const hssize_t **)&sa); (*env)->ReleaseLongArrayElements(env, coord, P, JNI_ABORT); free(sa); if (status < 0) { h5libraryError(env); } return (jint)status; } #endif JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Sselect_1elements (JNIEnv *env, jclass clss, jint space_id, jint op, jint num_elemn, jbyteArray coord) { int ii; hsize_t *lp; hsize_t *llp; jlong *jlp; herr_t status; jbyte *P; jboolean isCopy; jsize size; int nlongs; if (coord == NULL) { h5nullArgument( env, "H5Sselect_elements: coord is NULL"); return -1; } #ifdef __cplusplus P = env->GetByteArrayElements(coord,&isCopy); #else P = (*env)->GetByteArrayElements(env,coord,&isCopy); #endif if (P == NULL) { h5JNIFatalError(env, "H5Sselect_elements: coord not pinned"); return -1; } #ifdef __cplusplus size = (int) env->GetArrayLength(coord); #else size = (int) (*env)->GetArrayLength(env,coord); #endif nlongs = size / sizeof(jlong); lp = (hsize_t *) malloc(nlongs * sizeof(hssize_t)); jlp = (jlong *)P; llp = lp; for (ii = 0; ii < nlongs; ii++) { *lp = (hssize_t)*jlp; lp++; jlp++; } status = H5Sselect_elements (space_id, (H5S_seloper_t)op, num_elemn, llp); #ifdef __cplusplus env->ReleaseByteArrayElements(coord, P, JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env, coord, P, JNI_ABORT); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sselect_all * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Sselect_1all (JNIEnv *env, jclass clss, jint space_id) { herr_t retVal = -1; retVal = H5Sselect_all(space_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sselect_none * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Sselect_1none (JNIEnv *env, jclass clss, jint space_id) { herr_t retVal = -1; retVal = H5Sselect_none(space_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sselect_valid * Signature: (I)B */ JNIEXPORT jboolean JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Sselect_1valid (JNIEnv *env, jclass clss, jint space_id) { htri_t bval; bval = H5Sselect_valid(space_id); if (bval > 0) { return JNI_TRUE; } else if (bval == 0) { return JNI_FALSE; } else { h5libraryError(env); return JNI_FALSE; } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sget_simple_extent_npoints * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Sget_1simple_1extent_1npoints (JNIEnv *env, jclass clss, jint space_id) { hssize_t retVal = -1; retVal = H5Sget_simple_extent_npoints(space_id); if (retVal < 0) { h5libraryError(env); } return (jlong)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sget_select_npoints * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Sget_1select_1npoints (JNIEnv *env, jclass clss, jint space_id) { hssize_t retVal = -1; retVal = H5Sget_select_npoints(space_id); if (retVal < 0) { h5libraryError(env); } return (jlong)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sget_simple_extent_ndims * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Sget_1simple_1extent_1ndims (JNIEnv *env, jclass clss, jint space_id) { int retVal = -1; retVal = H5Sget_simple_extent_ndims(space_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sget_simple_extent_dims * Signature: (I[J[J)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Sget_1simple_1extent_1dims (JNIEnv *env, jclass clss, jint space_id, jlongArray dims, jlongArray maxdims) { int status; jlong *dimsP, *maxdimsP; jboolean isCopy; hsize_t *sa; hsize_t *msa; int i; int rank; if (dims == NULL) { dimsP = NULL; sa = (hsize_t *)dimsP; } else { #ifdef __cplusplus dimsP = env->GetLongArrayElements(dims,&isCopy); #else dimsP = (*env)->GetLongArrayElements(env,dims,&isCopy); #endif if (dimsP == NULL) { h5JNIFatalError(env, "H5Pget_simple_extent: dims not pinned"); return -1; } #ifdef __cplusplus rank = (int) env->GetArrayLength(dims); #else rank = (int) (*env)->GetArrayLength(env,dims); #endif sa = (hsize_t *)malloc( rank * sizeof(hsize_t)); if (sa == NULL) { #ifdef __cplusplus env->ReleaseLongArrayElements(dims,dimsP,JNI_ABORT); #else (*env)->ReleaseLongArrayElements(env,dims,dimsP,JNI_ABORT); #endif h5outOfMemory(env, "H5Sget_simple_extent: dims not converted to hsize_t"); return -1; } } if (maxdims == NULL) { maxdimsP = NULL; msa = (hsize_t *)maxdimsP; } else { #ifdef __cplusplus maxdimsP = env->GetLongArrayElements(maxdims,&isCopy); #else maxdimsP = (*env)->GetLongArrayElements(env,maxdims,&isCopy); #endif if (maxdimsP == NULL) { if (dimsP != NULL) { #ifdef __cplusplus env->ReleaseLongArrayElements(dims,dimsP,JNI_ABORT); #else (*env)->ReleaseLongArrayElements(env,dims,dimsP,JNI_ABORT); #endif } h5JNIFatalError(env, "H5Pget_simple_extent: maxdims not pinned"); return -1; } if (dimsP == NULL) { #ifdef __cplusplus rank = (int) env->GetArrayLength(maxdims); #else rank = (int) (*env)->GetArrayLength(env,maxdims); #endif } msa = (hsize_t *)malloc( rank * sizeof(hsize_t)); if (msa == NULL) { #ifdef __cplusplus if (dimsP != NULL) { env->ReleaseLongArrayElements(dims,dimsP,JNI_ABORT); } env->ReleaseLongArrayElements(maxdims,maxdimsP,JNI_ABORT); #else if (dimsP != NULL) { (*env)->ReleaseLongArrayElements(env,dims,dimsP,JNI_ABORT); } (*env)->ReleaseLongArrayElements(env,maxdims,maxdimsP,JNI_ABORT); #endif if (sa != NULL) { free(sa); } h5outOfMemory(env, "H5Sget_simple_extent: maxdims not converted to hsize_t"); return -1; } } status = H5Sget_simple_extent_dims(space_id, (hsize_t *)sa, (hsize_t *)msa); if (status < 0) { if (dimsP != NULL) { #ifdef __cplusplus env->ReleaseLongArrayElements(dims,dimsP,JNI_ABORT); #else (*env)->ReleaseLongArrayElements(env,dims,dimsP,JNI_ABORT); #endif free(sa); } if (maxdimsP != NULL) { #ifdef __cplusplus env->ReleaseLongArrayElements(maxdims,maxdimsP,JNI_ABORT); #else (*env)->ReleaseLongArrayElements(env,maxdims,maxdimsP,JNI_ABORT); #endif free(msa); } h5libraryError(env); } else { if (dimsP != NULL) { for (i = 0; i < rank; i++) { dimsP[i] = sa[i]; } free(sa); #ifdef __cplusplus env->ReleaseLongArrayElements(dims,dimsP,0); #else (*env)->ReleaseLongArrayElements(env,dims,dimsP,0); #endif } if (maxdimsP != NULL) { for (i = 0; i < rank; i++) { maxdimsP[i] = msa[i]; } free(msa); #ifdef __cplusplus env->ReleaseLongArrayElements(maxdims,maxdimsP,0); #else (*env)->ReleaseLongArrayElements(env,maxdims,maxdimsP,0); #endif } } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sget_simple_extent_type * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Sget_1simple_1extent_1type (JNIEnv *env, jclass clss, jint space_id) { H5S_class_t retVal = H5S_NO_CLASS; retVal = H5Sget_simple_extent_type(space_id); if (retVal == H5S_NO_CLASS) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sset_extent_simple * Signature: (II[B[B)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Sset_1extent_1simple (JNIEnv *env, jclass clss, jint space_id, jint rank, jbyteArray dims, jbyteArray maxdims) { herr_t status; jbyte *dimsP, *maxdimsP; jboolean isCopy; hsize_t *sa; hsize_t *msa; int i; hsize_t *lp; jlong *jlp; if (dims == NULL) { h5nullArgument( env, "H5Sset_simple_extent: dims is NULL"); return -1; } #ifdef __cplusplus dimsP = env->GetByteArrayElements(dims,&isCopy); #else dimsP = (*env)->GetByteArrayElements(env,dims,&isCopy); #endif if (dimsP == NULL) { h5JNIFatalError(env, "H5Pset_simple_extent: dims not pinned"); return -1; } sa = lp = (hsize_t *)malloc(rank * sizeof(hsize_t)); if (sa == NULL) { #ifdef __cplusplus env->ReleaseByteArrayElements(dims,dimsP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,dims,dimsP,JNI_ABORT); #endif h5outOfMemory(env, "H5Sset_simple_extent: dims not converted to hsize_t"); return -1; } jlp = (jlong *)dimsP; for (i = 0; i < rank; i++) { *lp = (hsize_t)*jlp; lp++; jlp++; } if (maxdims == NULL) { maxdimsP = NULL; msa = (hsize_t *)maxdimsP; } else { #ifdef __cplusplus maxdimsP = env->GetByteArrayElements(maxdims,&isCopy); #else maxdimsP = (*env)->GetByteArrayElements(env,maxdims,&isCopy); #endif if (maxdimsP == NULL) { #ifdef __cplusplus env->ReleaseByteArrayElements(dims,dimsP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,dims,dimsP,JNI_ABORT); #endif h5JNIFatalError(env, "H5Pset_simple_extent: maxdims not pinned"); return -1; } msa = lp = (hsize_t *)malloc(rank * sizeof(hsize_t)); if (msa == NULL) { #ifdef __cplusplus env->ReleaseByteArrayElements(dims,dimsP,JNI_ABORT); env->ReleaseByteArrayElements(maxdims,maxdimsP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,dims,dimsP,JNI_ABORT); (*env)->ReleaseByteArrayElements(env,maxdims,maxdimsP,JNI_ABORT); #endif free (sa); h5outOfMemory(env, "H5Sset_simple_extent: maxdims not converted to hsize_t"); return -1; } jlp = (jlong *)maxdimsP; for (i = 0; i < rank; i++) { *lp = (hsize_t)*jlp; lp++; jlp++; } } status = H5Sset_extent_simple(space_id, rank, (hsize_t *)sa, (hsize_t *)msa); #ifdef __cplusplus env->ReleaseByteArrayElements(dims,dimsP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,dims,dimsP,JNI_ABORT); #endif free (sa); if (maxdimsP != NULL) { #ifdef __cplusplus env->ReleaseByteArrayElements(maxdims,maxdimsP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,maxdims,maxdimsP,JNI_ABORT); #endif free (msa); } if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sis_simple * Signature: (I)J */ JNIEXPORT jboolean JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Sis_1simple (JNIEnv *env, jclass clss, jint space_id) { htri_t bval; bval = H5Sis_simple(space_id); if (bval > 0) { return JNI_TRUE; } else if (bval == 0) { return JNI_FALSE; } else { h5libraryError(env); return JNI_FALSE; } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Soffset_simple * Signature: (I[B)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Soffset_1simple (JNIEnv *env, jclass clss, jint space_id, jbyteArray offset) { herr_t status; jbyte *P = NULL; jboolean isCopy; hssize_t *sa; int rank; int i; hssize_t *lp; jlong *jlp; if (offset != NULL) { #ifdef __cplusplus P = env->GetByteArrayElements(offset,&isCopy); #else P = (*env)->GetByteArrayElements(env,offset,&isCopy); #endif if (P == NULL) { h5JNIFatalError(env, "H5Soffset_simple: offset not pinned"); return -1; } #ifdef __cplusplus i = (int) env->GetArrayLength(offset); #else i = (int) (*env)->GetArrayLength(env,offset); #endif rank = i / sizeof(jlong); sa = lp = (hssize_t *)malloc(rank * sizeof(hssize_t)); if (sa == NULL) { #ifdef __cplusplus env->ReleaseByteArrayElements(offset,P,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,offset,P,JNI_ABORT); #endif h5outOfMemory(env, "H5Soffset_simple: offset not converted to hssize_t"); return -1; } jlp = (jlong *)P; for (i = 0; i < rank; i++) { *lp = (hssize_t)*jlp; lp++; jlp++; } } else { P = NULL; sa = (hssize_t *)P; } status = H5Soffset_simple(space_id, sa); if (P != NULL) { #ifdef __cplusplus env->ReleaseByteArrayElements(offset,P,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,offset,P,JNI_ABORT); #endif free(sa); } if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sextent_copy * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Sextent_1copy (JNIEnv *env, jclass clss, jint space_id, jint src_id) { herr_t retVal = -1; retVal = H5Sextent_copy(space_id, src_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sset_extent_none * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Sset_1extent_1none (JNIEnv *env, jclass clss, jint space_id) { herr_t retVal = -1; retVal = H5Sset_extent_none(space_id); if (retVal < 0) { /* throw exception */ h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sselect_hyperslab * Signature: (II[B[B[B[B)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Sselect_1hyperslab (JNIEnv *env, jclass clss, jint space_id, jint op, jbyteArray start, jbyteArray stride, jbyteArray count, jbyteArray block) { herr_t status; jbyte *startP, *strideP, *countP, *blockP; jboolean isCopy; hsize_t *strt; hsize_t *strd; hsize_t *cnt; hsize_t *blk; int rank; int i; hsize_t *lp; jlong *jlp; if (start == NULL) { h5nullArgument( env, "H5Sselect_hyperslab: start is NULL"); return -1; } if (count == NULL) { h5nullArgument( env, "H5Sselect_hyperslab: count is NULL"); return -1; } #ifdef __cplusplus i = (int)env->GetArrayLength(start); if (i != env->GetArrayLength(count)) { h5badArgument( env, "H5Sselect_hyperslab: count and start have different rank!"); } #else i = (int)(*env)->GetArrayLength(env,start); if (i != (*env)->GetArrayLength(env,count)) { h5badArgument( env, "H5Sselect_hyperslab: count and start have different rank!"); } #endif rank = i / sizeof(jlong); #ifdef __cplusplus startP = env->GetByteArrayElements(start,&isCopy); #else startP = (*env)->GetByteArrayElements(env,start,&isCopy); #endif if (startP == NULL) { h5JNIFatalError(env, "H5Sselect_hyperslab: start not pinned"); return -1; } strt = lp = (hsize_t *)malloc(rank * sizeof(hsize_t)); if (strt == NULL) { #ifdef __cplusplus env->ReleaseByteArrayElements(start,startP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,start,startP,JNI_ABORT); #endif h5outOfMemory(env, "H5Sselect_hyperslab: start not converted to hsize_t"); return -1; } jlp = (jlong *)startP; for (i = 0; i < rank; i++) { *lp = (hsize_t)*jlp; lp++; jlp++; } #ifdef __cplusplus countP = env->GetByteArrayElements(count,&isCopy); #else countP = (*env)->GetByteArrayElements(env,count,&isCopy); #endif if (countP == NULL) { #ifdef __cplusplus env->ReleaseByteArrayElements(start, startP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,start, startP,JNI_ABORT); #endif free(strt); h5JNIFatalError(env, "H5Sselect_hyperslab: count not pinned"); return -1; } cnt = lp = (hsize_t *)malloc(rank * sizeof(hsize_t)); if (cnt == NULL) { #ifdef __cplusplus env->ReleaseByteArrayElements(start, startP,JNI_ABORT); env->ReleaseByteArrayElements(count, countP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,start, startP,JNI_ABORT); (*env)->ReleaseByteArrayElements(env,count, countP,JNI_ABORT); #endif free(strt); h5outOfMemory(env, "H5Sselect_hyperslab: count not converted to hsize_t"); return -1; } jlp = (jlong *)countP; for (i = 0; i < rank; i++) { *lp = (hsize_t)*jlp; lp++; jlp++; } if (stride == NULL) { strideP = NULL; strd = (hsize_t *)strideP; } else { #ifdef __cplusplus strideP = env->GetByteArrayElements(stride,&isCopy); #else strideP = (*env)->GetByteArrayElements(env,stride,&isCopy); #endif if (strideP == NULL) { #ifdef __cplusplus env->ReleaseByteArrayElements(count, countP,JNI_ABORT); env->ReleaseByteArrayElements(start, startP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,count, countP,JNI_ABORT); (*env)->ReleaseByteArrayElements(env,start, startP,JNI_ABORT); #endif free(cnt); free(strt); h5badArgument( env, "H5Sselect_hyperslab: stride not pinned"); return -1; } strd = lp = (hsize_t *)malloc(rank * sizeof(hsize_t)); if (strd == NULL) { #ifdef __cplusplus env->ReleaseByteArrayElements(count, countP,JNI_ABORT); env->ReleaseByteArrayElements(start, startP,JNI_ABORT); env->ReleaseByteArrayElements(stride, strideP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,count, countP,JNI_ABORT); (*env)->ReleaseByteArrayElements(env,start, startP,JNI_ABORT); (*env)->ReleaseByteArrayElements(env,stride, strideP,JNI_ABORT); #endif free(cnt); free(strt); h5outOfMemory(env, "H5Sselect_hyperslab: stride not converted to hsize_t"); return -1; } jlp = (jlong *)strideP; for (i = 0; i < rank; i++) { *lp = (hsize_t)*jlp; lp++; jlp++; } } if (block == NULL) { blockP = NULL; blk = (hsize_t *)blockP; } else { #ifdef __cplusplus blockP = env->GetByteArrayElements(block,&isCopy); #else blockP = (*env)->GetByteArrayElements(env,block,&isCopy); #endif if (blockP == NULL) { #ifdef __cplusplus env->ReleaseByteArrayElements(stride, strideP,JNI_ABORT); env->ReleaseByteArrayElements(count, countP,JNI_ABORT); env->ReleaseByteArrayElements(start, startP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,stride, strideP,JNI_ABORT); (*env)->ReleaseByteArrayElements(env,count, countP,JNI_ABORT); (*env)->ReleaseByteArrayElements(env,start, startP,JNI_ABORT); #endif free(cnt); free(strt); if (strd != NULL) { free(strd); } h5JNIFatalError(env, "H5Sselect_hyperslab: block not pinned"); return -1; } blk = lp = (hsize_t *)malloc(rank * sizeof(hsize_t)); if (blk == NULL) { #ifdef __cplusplus env->ReleaseByteArrayElements(stride, strideP,JNI_ABORT); env->ReleaseByteArrayElements(count, countP,JNI_ABORT); env->ReleaseByteArrayElements(start, startP,JNI_ABORT); env->ReleaseByteArrayElements(block, blockP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,stride, strideP,JNI_ABORT); (*env)->ReleaseByteArrayElements(env,count, countP,JNI_ABORT); (*env)->ReleaseByteArrayElements(env,start, startP,JNI_ABORT); (*env)->ReleaseByteArrayElements(env,block, blockP,JNI_ABORT); #endif free(cnt); free(strt); if (strd != NULL) { free(strd); } h5outOfMemory(env, "H5Sget_simple_extent: block not converted to hsize_t"); return -1; } jlp = (jlong *)blockP; for (i = 0; i < rank; i++) { *lp = (hsize_t)*jlp; lp++; jlp++; } } status = H5Sselect_hyperslab (space_id, (H5S_seloper_t)op, (const hsize_t *)strt, (const hsize_t *)strd, (const hsize_t *)cnt, (const hsize_t *)blk); #ifdef __cplusplus env->ReleaseByteArrayElements(start, startP,JNI_ABORT); env->ReleaseByteArrayElements(count, countP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,start, startP,JNI_ABORT); (*env)->ReleaseByteArrayElements(env,count, countP,JNI_ABORT); #endif free(strt); free(cnt); if (strideP != NULL) { #ifdef __cplusplus env->ReleaseByteArrayElements(stride, strideP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,stride, strideP,JNI_ABORT); #endif free(strd); } if (blockP != NULL) { #ifdef __cplusplus env->ReleaseByteArrayElements(block, blockP,JNI_ABORT); #else (*env)->ReleaseByteArrayElements(env,block, blockP,JNI_ABORT); #endif free(blk); } if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sclose * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Sclose (JNIEnv *env, jclass clss, jint space_id) { herr_t retVal = 0; if (space_id > 0) retVal = H5Sclose(space_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sget_select_hyper_nblocks * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Sget_1select_1hyper_1nblocks (JNIEnv *env, jclass clss, jint spaceid) { hssize_t status; status = H5Sget_select_hyper_nblocks((hid_t)spaceid); if (status < 0) h5libraryError(env); return (jlong)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sget_select_elem_npoints * Signature: (I)J */ JNIEXPORT jlong JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Sget_1select_1elem_1npoints (JNIEnv *env, jclass clss, jint spaceid) { hssize_t status; status = H5Sget_select_elem_npoints((hid_t)spaceid); if (status < 0) h5libraryError(env); return (jlong)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sget_select_hyper_blocklist * Signature: (IJJ[J)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Sget_1select_1hyper_1blocklist (JNIEnv *env, jclass clss, jint spaceid, jlong startblock, jlong numblocks, jlongArray buf) { herr_t status; jlong *bufP; jboolean isCopy; hsize_t *ba; int i; long st; long nb; st = (long)startblock; nb = (long)numblocks; if ( buf == NULL ) { h5nullArgument( env, "H5Sget_select_hyper_blocklist: buf is NULL"); return -1; } #ifdef __cplusplus bufP = env->GetLongArrayElements(buf,&isCopy); #else bufP = (*env)->GetLongArrayElements(env,buf,&isCopy); #endif if (bufP == NULL) { h5JNIFatalError( env, "H5Sget_select_hyper_blocklist: buf not pinned"); return -1; } ba = (hsize_t *)malloc( nb * 2 * sizeof(hsize_t)); if (ba == NULL) { #ifdef __cplusplus env->ReleaseLongArrayElements(buf, bufP,JNI_ABORT); #else (*env)->ReleaseLongArrayElements(env,buf,bufP,JNI_ABORT); #endif h5outOfMemory(env, "H5Screate-simple: buffer not converted to hsize_t"); return -1; } status = H5Sget_select_hyper_blocklist((hid_t)spaceid, (hsize_t)st, (hsize_t)nb, (hsize_t *)ba); if (status < 0) { #ifdef __cplusplus env->ReleaseLongArrayElements(buf,bufP,JNI_ABORT); #else (*env)->ReleaseLongArrayElements(env,buf,bufP,JNI_ABORT); #endif free (ba); h5libraryError(env); } else { for (i = 0; i < (numblocks*2); i++) { bufP[i] = ba[i]; } free (ba); #ifdef __cplusplus env->ReleaseLongArrayElements(buf,bufP,0); #else (*env)->ReleaseLongArrayElements(env,buf,bufP,0); #endif } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sget_select_elem_pointlist * Signature: (IJJ[J)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Sget_1select_1elem_1pointlist (JNIEnv *env, jclass clss, jint spaceid, jlong startpoint, jlong numpoints, jlongArray buf) { herr_t status; jlong *bufP; jboolean isCopy; hsize_t *ba; int i; if ( buf == NULL ) { h5nullArgument( env, "H5Sget_select_elem_pointlist: buf is NULL"); return -1; } #ifdef __cplusplus bufP = env->GetLongArrayElements(buf,&isCopy); #else bufP = (*env)->GetLongArrayElements(env,buf,&isCopy); #endif if (bufP == NULL) { h5JNIFatalError( env, "H5Sget_select_elem_pointlist: buf not pinned"); return -1; } ba = (hsize_t *)malloc( ((long)numpoints) * sizeof(hsize_t)); if (ba == NULL) { #ifdef __cplusplus env->ReleaseLongArrayElements(buf,bufP,JNI_ABORT); #else (*env)->ReleaseLongArrayElements(env,buf,bufP,JNI_ABORT); #endif h5outOfMemory(env, "H5Sget_select_elem_pointlist: buf not converted to hsize_t"); return -1; } status = H5Sget_select_elem_pointlist((hid_t)spaceid, (hsize_t)startpoint, (hsize_t)numpoints, (hsize_t *)ba); if (status < 0) { free (ba); #ifdef __cplusplus env->ReleaseLongArrayElements(buf,bufP,JNI_ABORT); #else (*env)->ReleaseLongArrayElements(env,buf,bufP,JNI_ABORT); #endif h5libraryError(env); } else { for (i = 0; i < numpoints; i++) { bufP[i] = ba[i]; } free (ba) ; #ifdef __cplusplus env->ReleaseLongArrayElements(buf,bufP,0); #else (*env)->ReleaseLongArrayElements(env,buf,bufP,0); #endif } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Sget_select_bounds * Signature: (I[J[J)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Sget_1select_1bounds (JNIEnv *env, jclass clss, jint spaceid, jlongArray start, jlongArray end) { herr_t status; jlong *startP, *endP; jboolean isCopy; hsize_t *strt; hsize_t *en; int rank; int i; if ( start == NULL ) { h5nullArgument( env, "H5Sget_select_bounds: start is NULL"); return -1; } if ( end == NULL ) { h5nullArgument( env, "H5Sget_select_bounds: end is NULL"); return -1; } #ifdef __cplusplus startP = env->GetLongArrayElements(start,&isCopy); #else startP = (*env)->GetLongArrayElements(env,start,&isCopy); #endif if (startP == NULL) { h5JNIFatalError( env, "H5Sget_select_bounds: start not pinned"); return -1; } #ifdef __cplusplus rank = (int)env->GetArrayLength(start); #else rank = (int)(*env)->GetArrayLength(env,start); #endif strt = (hsize_t *)malloc( rank * sizeof(hsize_t)); if (strt == NULL) { #ifdef __cplusplus env->ReleaseLongArrayElements(start,startP,JNI_ABORT); #else (*env)->ReleaseLongArrayElements(env,start,startP,JNI_ABORT); #endif h5outOfMemory(env, "H5Sget_select_bounds: start not converted to hsize_t"); return -1; } #ifdef __cplusplus endP = env->GetLongArrayElements(end,&isCopy); #else endP = (*env)->GetLongArrayElements(env,end,&isCopy); #endif if (endP == NULL) { #ifdef __cplusplus env->ReleaseLongArrayElements(start,startP,JNI_ABORT); #else (*env)->ReleaseLongArrayElements(env,start,startP,JNI_ABORT); #endif free(strt); h5JNIFatalError( env, "H5Sget_select_bounds: end not pinned"); return -1; } en = (hsize_t *)malloc( rank * sizeof(hsize_t)); if (en == NULL) { #ifdef __cplusplus env->ReleaseLongArrayElements(end,endP,JNI_ABORT); env->ReleaseLongArrayElements(start,startP,JNI_ABORT); #else (*env)->ReleaseLongArrayElements(env,end,endP,JNI_ABORT); (*env)->ReleaseLongArrayElements(env,start,startP,JNI_ABORT); #endif free(strt); h5outOfMemory(env, "H5Sget_simple_extent: dims not converted to hsize_t"); return -1; } status = H5Sget_select_bounds((hid_t) spaceid, (hsize_t *)strt, (hsize_t *)en); if (status < 0) { #ifdef __cplusplus env->ReleaseLongArrayElements(start,startP,JNI_ABORT); env->ReleaseLongArrayElements(end,endP,JNI_ABORT); #else (*env)->ReleaseLongArrayElements(env,start,startP,JNI_ABORT); (*env)->ReleaseLongArrayElements(env,end,endP,JNI_ABORT); #endif free(strt); free(en); h5libraryError(env); } else { for (i = 0; i < rank; i++) { startP[i] = strt[i]; endP[i] = en[i]; } free(strt); free(en); #ifdef __cplusplus env->ReleaseLongArrayElements(start,startP,0); env->ReleaseLongArrayElements(end,endP,0); #else (*env)->ReleaseLongArrayElements(env,start,startP,0); (*env)->ReleaseLongArrayElements(env,end,endP,0); #endif } return (jint)status; } #ifdef __cplusplus } #endif libsis-jhdf5-java-14.12.1/source/c/jhdf5/h5tImpJHDF5.c000077500000000000000000001155321256564762100216670ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ /* * This code is the C-interface called by Java programs to access the * Datatype Object API Functions of the HDF5 library. * * Each routine wraps a single HDF entry point, generally with the * analogous arguments and return codes. * * For details of the HDF libraries, see the HDF Documentation at: * http://hdf.ncsa.uiuc.edu/HDF5/doc/ * */ #ifdef __cplusplus extern "C" { #endif #include "hdf5.h" #include #include extern jboolean h5outOfMemory( JNIEnv *env, char *functName); extern jboolean h5JNIFatalError( JNIEnv *env, char *functName); extern jboolean h5nullArgument( JNIEnv *env, char *functName); extern jboolean h5badArgument( JNIEnv *env, char *functName); extern jboolean h5libraryError( JNIEnv *env ); extern jboolean h5raiseException( JNIEnv *env, char *exception, char *message); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Topen * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Topen (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint access_plist_id) { herr_t status; char* tname; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Topen: name is NULL"); return -1; } #ifdef __cplusplus tname = (char *)env->GetStringUTFChars(name,&isCopy); #else tname = (char *)(*env)->GetStringUTFChars(env,name,&isCopy); #endif if (tname == NULL) { h5JNIFatalError(env, "H5Topen: name not pinned"); return -1; } status = H5Topen((hid_t)loc_id, tname, (hid_t) access_plist_id); #ifdef __cplusplus env->ReleaseStringUTFChars(name,tname); #else (*env)->ReleaseStringUTFChars(env,name,tname); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tcommit * Signature: (ILjava/lang/String;I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tcommit (JNIEnv *env, jclass clss, jint loc_id, jstring name, jint type_id, jint link_create_plist_id, jint dtype_create_plist_id, jint dtype_access_plist_id) { herr_t status; char* tname; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Tcommit: name is NULL"); return -1; } #ifdef __cplusplus tname = (char *)env->GetStringUTFChars(name,&isCopy); #else tname = (char *)(*env)->GetStringUTFChars(env,name,&isCopy); #endif if (tname == NULL) { h5JNIFatalError(env, "H5Tcommit: name not pinned"); return -1; } status = H5Tcommit((hid_t)loc_id, tname, (hid_t)type_id, (hid_t)link_create_plist_id, (hid_t)dtype_create_plist_id, (hid_t)dtype_access_plist_id); #ifdef __cplusplus env->ReleaseStringUTFChars(name,tname); #else (*env)->ReleaseStringUTFChars(env,name,tname); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tcommitted * Signature: (I)B */ JNIEXPORT jboolean JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tcommitted (JNIEnv *env, jclass clss, jint type) { htri_t bval; bval = H5Tcommitted(type); if (bval > 0) { return JNI_TRUE; } else if (bval == 0) { return JNI_FALSE; } else { /* raise exception -- return value is irrelevant */ h5libraryError(env); return JNI_FALSE; } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tcreate * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tcreate (JNIEnv *env, jclass clss, jint dclass, jint size) { hid_t retVal = -1; retVal = H5Tcreate((H5T_class_t )dclass, size ); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tcopy * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tcopy (JNIEnv *env, jclass clss, jint type_id) { hid_t retVal = -1; retVal = H5Tcopy(type_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tequal * Signature: (II)B */ JNIEXPORT jboolean JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tequal (JNIEnv *env, jclass clss, jint type_id1, jint type_id2) { htri_t bval; bval = H5Tequal(type_id1, type_id2 ); if (bval > 0) { return JNI_TRUE; } else if (bval == 0) { return JNI_FALSE; } else { /* raise exception -- return value is irrelevant */ h5libraryError(env); return JNI_FALSE; } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tlock * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tlock (JNIEnv *env, jclass clss, jint type_id) { herr_t retVal = -1; retVal = H5Tlock(type_id ); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_class * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tget_1class (JNIEnv *env, jclass clss, jint type_id) { H5T_class_t retVal = H5T_NO_CLASS; retVal = H5Tget_class(type_id ); if (retVal == H5T_NO_CLASS) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_size * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tget_1size (JNIEnv *env, jclass clss, jint type_id) { size_t retVal; jint size; retVal = H5Tget_size(type_id); if (retVal == 0) { h5libraryError(env); } size = retVal; if (size != retVal) { h5raiseException( env, "ncsa/hdf/hdf5lib/exceptions/HDF5LibraryException", "H5Tget_size() overflows jint"); } return size; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_size_long * Signature: (J)I */ JNIEXPORT jlong JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tget_1size_1long (JNIEnv *env, jclass clss, jint type_id) { size_t retVal; retVal = H5Tget_size(type_id); if (retVal == 0) { h5libraryError(env); } return (jlong)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_size * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tset_1size (JNIEnv *env, jclass clss, jint type_id, jint size) { herr_t retVal = -1; retVal = H5Tset_size(type_id, size ); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_order * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tget_1order (JNIEnv *env, jclass clss, jint type_id) { H5T_order_t retVal = H5T_ORDER_ERROR; retVal = H5Tget_order(type_id ); if (retVal == H5T_ORDER_ERROR) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_order * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tset_1order (JNIEnv *env, jclass clss, jint type_id, jint order) { herr_t retVal = -1; retVal = H5Tset_order(type_id, (H5T_order_t)order); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_precision * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tget_1precision (JNIEnv *env, jclass clss, jint type_id) { size_t retVal = 0; retVal = H5Tget_precision(type_id); if (retVal == 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_precision * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tset_1precision (JNIEnv *env, jclass clss, jint type_id, jint precision) { herr_t retVal = -1; retVal = H5Tset_precision(type_id, precision); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_offset * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tget_1offset (JNIEnv *env, jclass clss, jint type_id) { size_t retVal = 0; retVal = H5Tget_offset(type_id); return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_offset * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tset_1offset (JNIEnv *env, jclass clss, jint type_id, jint offset) { herr_t retVal = -1; retVal = H5Tset_offset(type_id, offset); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_pad * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tget_1pad (JNIEnv *env, jclass clss, jint type_id, jintArray pad) { herr_t status; jboolean isCopy; jint *P; if (pad == NULL) { h5nullArgument( env, "H5Tget_pad: pad is NULL"); return -1; } #ifdef __cplusplus P = env->GetIntArrayElements(pad,&isCopy); #else P = (*env)->GetIntArrayElements(env,pad,&isCopy); #endif if (P == NULL) { h5JNIFatalError(env, "H5Tget_pad: pad not pinned"); return -1; } status = H5Tget_pad(type_id, (H5T_pad_t *)&(P[0]), (H5T_pad_t *)&(P[1])); if (status < 0) { #ifdef __cplusplus env->ReleaseIntArrayElements(pad,P,JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env,pad,P,JNI_ABORT); #endif h5libraryError(env); } else { #ifdef __cplusplus env->ReleaseIntArrayElements(pad,P,0); #else (*env)->ReleaseIntArrayElements(env,pad,P,0); #endif } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_pad * Signature: (III)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tset_1pad (JNIEnv *env, jclass clss, jint type_id, jint lsb, jint msb) { herr_t retVal = -1; retVal = H5Tset_pad(type_id, (H5T_pad_t)lsb, (H5T_pad_t)msb); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_sign * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tget_1sign (JNIEnv *env, jclass clss, jint type_id) { H5T_sign_t retVal = H5T_SGN_ERROR; retVal = H5Tget_sign(type_id); if (retVal == H5T_SGN_ERROR) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_sign * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tset_1sign (JNIEnv *env, jclass clss, jint type_id, jint sign) { herr_t retVal = -1; retVal = H5Tset_sign(type_id, (H5T_sign_t)sign); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_fields * Signature: (I[I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tget_1fields (JNIEnv *env, jclass clss, jint type_id, jintArray fields) { herr_t status; jboolean isCopy; jint *P; if (fields == NULL) { h5nullArgument( env, "H5Tget_fields: fields is NULL"); return -1; } #ifdef __cplusplus if (env->GetArrayLength(fields) < 5) { h5badArgument( env, "H5Tget_fields: fields input array < order 5"); } P = env->GetIntArrayElements(fields,&isCopy); #else if ((*env)->GetArrayLength(env, fields) < 5) { h5badArgument( env, "H5Tget_fields: fields input array < order 5"); } P = (*env)->GetIntArrayElements(env,fields,&isCopy); #endif if (P == NULL) { h5JNIFatalError(env, "H5Tget_fields: fields not pinned"); return -1; } status = H5Tget_fields(type_id, (size_t *)&(P[0]), (size_t *)&(P[1]), (size_t *)&(P[2]), (size_t *)&(P[3]), (size_t *)&(P[4])); if (status < 0) { #ifdef __cplusplus env->ReleaseIntArrayElements(fields,P,JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env,fields,P,JNI_ABORT); #endif h5libraryError(env); } else { #ifdef __cplusplus env->ReleaseIntArrayElements(fields,P,0); #else (*env)->ReleaseIntArrayElements(env,fields,P,0); #endif } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_fields * Signature: (IIIII)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tset_1fields (JNIEnv *env, jclass clss, jint type_id, jint spos, jint epos, jint esize, jint mpos, jint msiz) { herr_t retVal = -1; retVal = H5Tset_fields(type_id, spos, epos, esize, mpos, msiz); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_ebias * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tget_1ebias (JNIEnv *env, jclass clss, jint type_id) { size_t retVal = 0; retVal = H5Tget_ebias(type_id ); if (retVal == 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_ebias * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tset_1ebias (JNIEnv *env, jclass clss, jint type_id, jint ebias) { herr_t retVal = -1; retVal = H5Tset_ebias(type_id, ebias); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_norm * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tget_1norm (JNIEnv *env, jclass clss, jint type_id) { H5T_norm_t retVal = H5T_NORM_ERROR; retVal = H5Tget_norm(type_id); if (retVal == H5T_NORM_ERROR) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_norm * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tset_1norm (JNIEnv *env, jclass clss, jint type_id, jint norm) { herr_t retVal = -1; retVal = H5Tset_norm(type_id, (H5T_norm_t )norm); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_inpad * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tget_1inpad (JNIEnv *env, jclass clss, jint type_id) { H5T_pad_t retVal = H5T_PAD_ERROR; retVal = H5Tget_inpad(type_id ); if (retVal == H5T_PAD_ERROR) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_inpad * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tset_1inpad (JNIEnv *env, jclass clss, jint type_id, jint inpad) { herr_t retVal = -1; retVal = H5Tset_inpad(type_id, (H5T_pad_t) inpad); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_cset * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tget_1cset (JNIEnv *env, jclass clss, jint type_id) { H5T_cset_t retVal = H5T_CSET_ERROR; retVal = H5Tget_cset(type_id); if (retVal == H5T_CSET_ERROR) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_cset * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tset_1cset (JNIEnv *env, jclass clss, jint type_id, jint cset) { herr_t retVal = -1; retVal = H5Tset_cset(type_id, (H5T_cset_t)cset); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_strpad * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tget_1strpad (JNIEnv *env, jclass clss, jint type_id) { H5T_str_t retVal = H5T_STR_ERROR; retVal = H5Tget_strpad(type_id); if (retVal == H5T_STR_ERROR) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_strpad * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tset_1strpad (JNIEnv *env, jclass clss, jint type_id, jint strpad) { herr_t retVal = -1; retVal = H5Tset_strpad(type_id, (H5T_str_t)strpad); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_nmembers * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tget_1nmembers (JNIEnv *env, jclass clss, jint type_id) { int retVal = -1; retVal = H5Tget_nmembers(type_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_member_name * Signature: (II)Ljava/lang/String */ JNIEXPORT jstring JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tget_1member_1name (JNIEnv *env, jclass clss, jint type_id, jint field_idx) { char *name; jstring str; name = H5Tget_member_name(type_id, (unsigned) field_idx); if (name == NULL) { return NULL; } else { /* may throw OutOfMemoryError */ #ifdef __cplusplus str = env->NewStringUTF(name); #else str = (*env)->NewStringUTF(env,name); #endif if (str == NULL) { free(name); h5outOfMemory(env, "H5Tget_member_name: returned string not created"); return NULL; } free(name); return str; } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_member_index * Signature: (ILjava/lang/String)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tget_1member_1index (JNIEnv *env, jclass clss, jint type_id, jstring field_name) { char *tname; int index; jboolean isCopy; if (field_name == NULL) { h5nullArgument( env, "H5Tget_member_index: field_name is NULL"); return -1; } #ifdef __cplusplus tname = (char *)env->GetStringUTFChars(field_name,&isCopy); #else tname = (char *)(*env)->GetStringUTFChars(env,field_name,&isCopy); #endif if (tname == NULL) { h5JNIFatalError(env, "H5Tget_member_index: field_name not pinned"); return -1; } index = H5Tget_member_index(type_id, tname); #ifdef __cplusplus env->ReleaseStringUTFChars(field_name,tname); #else (*env)->ReleaseStringUTFChars(env,field_name,tname); #endif return index; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_member_type * Signature: (II)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tget_1member_1type (JNIEnv *env, jclass clss, jint type_id, jint field_idx) { hid_t retVal = -1; retVal = H5Tget_member_type(type_id, field_idx); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_member_offset * Signature: (II)I */ JNIEXPORT jlong JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tget_1member_1offset (JNIEnv *env, jclass clss, jint type_id, jint memno) { size_t retVal = 0; retVal = H5Tget_member_offset((hid_t)type_id, memno); return (jlong)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tinsert * Signature: (ILjava/lang/String;JI)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tinsert (JNIEnv *env, jclass clss, jint type_id, jstring name, jlong offset, jint field_id) { herr_t status; char* tname; jboolean isCopy; long off; off = (long)offset; if (name == NULL) { h5nullArgument( env, "H5Tinsert: name is NULL"); return -1; } #ifdef __cplusplus tname =(char *)env->GetStringUTFChars(name,&isCopy); #else tname =(char *)(*env)->GetStringUTFChars(env,name,&isCopy); #endif if (tname == NULL) { h5JNIFatalError(env, "H5Tinsert: name not pinned"); return -1; } status = H5Tinsert(type_id, tname, (size_t)off, field_id); #ifdef __cplusplus env->ReleaseStringUTFChars(name,tname); #else (*env)->ReleaseStringUTFChars(env,name,tname); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tpack * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tpack (JNIEnv *env, jclass clss, jint type_id) { herr_t retVal = -1; retVal = H5Tpack(type_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tclose * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tclose (JNIEnv *env, jclass clss, jint type_id) { herr_t retVal = 0; if (type_id > 0) retVal = H5Tclose(type_id); if (retVal < 0) { h5libraryError(env); } return (jint)retVal; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tenum_create * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tenum_1create (JNIEnv *env, jclass clss, jint base_id) { hid_t status; status = H5Tenum_create((hid_t)base_id); if (status < 0) h5libraryError(env); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tenum_insert * Signature: (ILjava/lang/String;B)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tenum_1insert__ILjava_lang_String_2B (JNIEnv *env, jclass clss, jint type, jstring name, jbyte value) { herr_t status; char *nameP; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Tenum_insert: name is NULL"); return -1; } #ifdef __cplusplus nameP = (char *)env->GetStringUTFChars(name,&isCopy); #else nameP = (char *)(*env)->GetStringUTFChars(env,name,&isCopy); #endif if (nameP == NULL) { h5JNIFatalError( env, "H5Tenum_insert: name not pinned"); return -1; } status = H5Tenum_insert((hid_t)type, nameP, &value); #ifdef __cplusplus env->ReleaseStringUTFChars(name,nameP); #else (*env)->ReleaseStringUTFChars(env,name,nameP); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tenum_insert * Signature: (ILjava/lang/String;S)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tenum_1insert__ILjava_lang_String_2S (JNIEnv *env, jclass clss, jint type, jstring name, jshort value) { herr_t status; char *nameP; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Tenum_insert: name is NULL"); return -1; } #ifdef __cplusplus nameP = (char *)env->GetStringUTFChars(name,&isCopy); #else nameP = (char *)(*env)->GetStringUTFChars(env,name,&isCopy); #endif if (nameP == NULL) { h5JNIFatalError( env, "H5Tenum_insert: name not pinned"); return -1; } status = H5Tenum_insert((hid_t)type, nameP, &value); #ifdef __cplusplus env->ReleaseStringUTFChars(name,nameP); #else (*env)->ReleaseStringUTFChars(env,name,nameP); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tenum_insert * Signature: (ILjava/lang/String;I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tenum_1insert__ILjava_lang_String_2I (JNIEnv *env, jclass clss, jint type, jstring name, jint value) { herr_t status; char *nameP; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Tenum_insert: name is NULL"); return -1; } #ifdef __cplusplus nameP = (char *)env->GetStringUTFChars(name,&isCopy); #else nameP = (char *)(*env)->GetStringUTFChars(env,name,&isCopy); #endif if (nameP == NULL) { h5JNIFatalError( env, "H5Tenum_insert: name not pinned"); return -1; } status = H5Tenum_insert((hid_t)type, nameP, &value); #ifdef __cplusplus env->ReleaseStringUTFChars(name,nameP); #else (*env)->ReleaseStringUTFChars(env,name,nameP); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tconvert_to_little_endian * Signature: ([S)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tconvert_1to_1little_1endian___3S (JNIEnv *env, jclass clss, jshortArray value) { jshort *byteP; jboolean isCopy; size_t nelem; herr_t status; int i; #ifdef __cplusplus nelem = env->GetArrayLength(value); byteP = env->GetShortArrayElements(value,&isCopy); #else nelem = (*env)->GetArrayLength(env, value); byteP = (*env)->GetShortArrayElements(env,value,&isCopy); #endif if (byteP == NULL) { h5JNIFatalError( env, "H5Tconvert_to_little_endian: value not pinned"); return -1; } status = H5Tconvert(H5T_NATIVE_INT16, H5T_STD_I16LE, nelem, byteP, NULL, H5P_DEFAULT); #ifdef __cplusplus env->ReleaseShortArrayElements(value,byteP,0); #else (*env)->ReleaseShortArrayElements(env,value,byteP,0); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tconvert_to_little_endian * Signature: ([I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tconvert_1to_1little_1endian___3I (JNIEnv *env, jclass clss, jintArray value) { jint *byteP; jboolean isCopy; size_t nelem; herr_t status; #ifdef __cplusplus nelem = env->GetArrayLength(value); byteP = env->GetIntArrayElements(value,&isCopy); #else nelem = (*env)->GetArrayLength(env, value); byteP = (*env)->GetIntArrayElements(env,value,&isCopy); #endif if (byteP == NULL) { h5JNIFatalError( env, "H5Tconvert_to_little_endian: value not pinned"); return -1; } status = H5Tconvert(H5T_NATIVE_INT32, H5T_STD_I32LE, nelem, byteP, NULL, H5P_DEFAULT); #ifdef __cplusplus env->ReleaseIntArrayElements(value,byteP,0); #else (*env)->ReleaseIntArrayElements(env,value,byteP,0); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tenum_nameof * Signature: (I[B[Ljava/lang/String;I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tenum_1nameof (JNIEnv *env, jclass clss, jint type, jintArray value, jobjectArray name, jint size) { hid_t status; jint *byteP; char *nameP; jboolean isCopy; jstring str; if (size <= 0) { h5badArgument( env, "H5Tenum_nameof: name size < 0"); return -1; } nameP = (char *)malloc(sizeof(char)*size); if (nameP == NULL) { /* exception -- out of memory */ h5outOfMemory( env, "H5Tenum_nameof: malloc name size"); return -1; } if ( value == NULL ) { free(nameP); h5nullArgument( env, "H5Tenum_nameof: value is NULL"); return -1; } #ifdef __cplusplus byteP = env->GetIntArrayElements(value,&isCopy); #else byteP = (*env)->GetIntArrayElements(env,value,&isCopy); #endif if (byteP == NULL) { free(nameP); h5JNIFatalError( env, "H5Tenum_nameof: value not pinned"); return -1; } status = H5Tenum_nameof((hid_t)type, byteP, nameP, (size_t)size); #ifdef __cplusplus env->ReleaseIntArrayElements(value,byteP,JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env,value,byteP,JNI_ABORT); #endif if (status < 0) { free(nameP); h5libraryError(env); } else { #ifdef __cplusplus str = env->NewStringUTF(nameP); #else str = (*env)->NewStringUTF(env,nameP); #endif if (str == NULL) { free(nameP); h5outOfMemory( env, "H5Tenum_nameof: return array not created"); return -1; } /* SetObjectArrayElement may raise exceptions */ #ifdef __cplusplus env->SetObjectArrayElement(name,0,(jobject)str); #else (*env)->SetObjectArrayElement(env,name,0,(jobject)str); #endif } free(nameP); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tenum_valueof * Signature: (ILjava/lang/String;[B)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tenum_1valueof (JNIEnv *env, jclass clss, jint type, jstring name, jintArray value) { hid_t status; jint *byteP; char *nameP; jboolean isCopy; if (name == NULL) { h5nullArgument( env, "H5Tenum_valueof: name is NULL"); return -1; } #ifdef __cplusplus nameP = (char *)env->GetStringUTFChars(name,&isCopy); #else nameP = (char *)(*env)->GetStringUTFChars(env,name,&isCopy); #endif if (nameP == NULL) { h5JNIFatalError( env, "H5Tenum_valueof: name not pinned"); return -1; } if ( value == NULL ) { #ifdef __cplusplus env->ReleaseStringUTFChars(name,nameP); #else (*env)->ReleaseStringUTFChars(env,name,nameP); #endif h5nullArgument( env, "H5Tenum_valueof: value is NULL"); return -1; } #ifdef __cplusplus byteP = env->GetIntArrayElements(value,&isCopy); #else byteP = (*env)->GetIntArrayElements(env,value,&isCopy); #endif if (byteP == NULL) { #ifdef __cplusplus env->ReleaseStringUTFChars(name,nameP); #else (*env)->ReleaseStringUTFChars(env,name,nameP); #endif h5JNIFatalError( env, "H5Tenum_valueof: value not pinned"); return -1; } status = H5Tenum_valueof((hid_t)type, nameP, byteP); #ifdef __cplusplus env->ReleaseStringUTFChars(name,nameP); #else (*env)->ReleaseStringUTFChars(env,name,nameP); #endif if (status < 0) { #ifdef __cplusplus env->ReleaseIntArrayElements(value,byteP,JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env,value,byteP,JNI_ABORT); #endif h5libraryError(env); } else { #ifdef __cplusplus env->ReleaseIntArrayElements(value,byteP,0); #else (*env)->ReleaseIntArrayElements(env,value,byteP,0); #endif } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tvlen_create * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tvlen_1create (JNIEnv *env, jclass clss, jint base_id) { hid_t status; status = H5Tvlen_create((hid_t)base_id); if (status < 0) h5libraryError(env); return status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tset_tag * Signature: (ILjava/lang/String;)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tset_1tag (JNIEnv *env, jclass clss, jint type, jstring tag) { herr_t status; char *tagP; jboolean isCopy; if (tag == NULL) { h5nullArgument( env, "H5Tset_tag: tag is NULL"); return -1; } #ifdef __cplusplus tagP = (char *)env->GetStringUTFChars(tag,&isCopy); #else tagP = (char *)(*env)->GetStringUTFChars(env,tag,&isCopy); #endif if (tagP == NULL) { h5JNIFatalError( env, "H5Tset_tag: tag not pinned"); return -1; } status = H5Tset_tag((hid_t)type, tagP); #ifdef __cplusplus env->ReleaseStringUTFChars(tag,tagP); #else (*env)->ReleaseStringUTFChars(env,tag,tagP); #endif if (status < 0) h5libraryError(env); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_tag * Signature: (I)Ljava/lang/String; */ JNIEXPORT jstring JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tget_1tag (JNIEnv *env, jclass clss, jint type) { jstring str; char *tag; tag = H5Tget_tag((hid_t)type); if (tag == NULL) return NULL; /* may throw OutOfMemoryError */ #ifdef __cplusplus str = env->NewStringUTF(tag); #else str = (*env)->NewStringUTF(env,tag); #endif if (str == NULL) { free(tag); h5outOfMemory(env, "H5Tget_tag: returned string not created"); return NULL; } free(tag); return str; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_super * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tget_1super (JNIEnv *env, jclass clss, jint type) { hid_t status; status = H5Tget_super((hid_t)type); if (status < 0) h5libraryError(env); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_member_value * Signature: (II[B)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tget_1member_1value (JNIEnv *env, jclass clss, jint type, jint membno, jintArray value) { hid_t status; jint *byteP; jboolean isCopy; if ( value == NULL ) { h5nullArgument( env, "H5Tget_member_value: value is NULL"); return -1; } #ifdef __cplusplus byteP = env->GetIntArrayElements(value,&isCopy); #else byteP = (*env)->GetIntArrayElements(env,value,&isCopy); #endif if (byteP == NULL) { h5JNIFatalError( env, "H5Tget_member_value: value not pinned"); return -1; } status = H5Tget_member_value((hid_t)type, (int)membno, byteP); if (status < 0) { #ifdef __cplusplus env->ReleaseIntArrayElements(value,byteP,JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env,value,byteP,JNI_ABORT); #endif h5libraryError(env); } else { #ifdef __cplusplus env->ReleaseIntArrayElements(value,byteP,0); #else (*env)->ReleaseIntArrayElements(env,value,byteP,0); #endif } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tarray_create * Signature: (II[B[B)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tarray_1create (JNIEnv *env, jclass clss, jint base, jint rank, jintArray dims) { hid_t status; jint *dimsP; int dlen; hsize_t *cdims; jboolean isCopy; int i; if (rank <= 0) { h5nullArgument( env, "H5Tarray_create: rank is < 1"); return -1; } if ( dims == NULL ) { h5nullArgument( env, "H5Tarray_create: dims is NULL"); return -1; } #ifdef __cplusplus dimsP = env->GetIntArrayElements(dims,&isCopy); #else dimsP = (*env)->GetIntArrayElements(env,dims,&isCopy); #endif if (dimsP == NULL) { h5JNIFatalError( env, "H5Tarray_create: dimsP not pinned"); return -1; } #ifdef __cplusplus dlen = env->GetArrayLength(dims); #else dlen = (*env)->GetArrayLength(env,dims); #endif if (dlen != rank) { #ifdef __cplusplus env->ReleaseIntArrayElements(dims,dimsP,JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env,dims,dimsP,JNI_ABORT); #endif return -1; } cdims = (hsize_t *)malloc(dlen * sizeof(hsize_t)); for (i = 0; i < dlen; i++) { cdims[i] = (hsize_t)dimsP[i]; } status = H5Tarray_create((hid_t)base, (int)rank, (const hsize_t *)cdims); #ifdef __cplusplus env->ReleaseIntArrayElements(dims,dimsP,JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env,dims,dimsP,JNI_ABORT); #endif if (status < 0) { h5libraryError(env); } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_array_dims * Signature: (I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tget_1array_1ndims (JNIEnv *env, jclass clss, jint dt) { hid_t status; status = H5Tget_array_ndims((hid_t)dt); if (status < 0) h5libraryError(env); return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tarray_get_dims * Signature: (I[I[I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tget_1array_1dims (JNIEnv *env, jclass clss, jint dt, jintArray dims) { hid_t status; jint *dimsP; int dlen; int i; hsize_t *cdims; jboolean isCopy; if ( dims == NULL ) { h5nullArgument( env, "H5Tget_array_dims: value is NULL"); return -1; } #ifdef __cplusplus dimsP = env->GetIntArrayElements(dims,&isCopy); #else dimsP = (*env)->GetIntArrayElements(env,dims,&isCopy); #endif if (dimsP == NULL) { h5JNIFatalError( env, "H5Tget_array_dims: dimsP not pinned"); return -1; } #ifdef __cplusplus dlen = env->GetArrayLength(dims); #else dlen = (*env)->GetArrayLength(env,dims); #endif cdims = (hsize_t *)malloc(dlen * sizeof(hsize_t)); status = H5Tget_array_dims((hid_t)dt, (hsize_t *)cdims); if (status < 0) { #ifdef __cplusplus env->ReleaseIntArrayElements(dims,dimsP,JNI_ABORT); #else (*env)->ReleaseIntArrayElements(env,dims,dimsP,JNI_ABORT); #endif h5libraryError(env); } else { for (i = 0; i < dlen; i++) { dimsP[i] = (jint) cdims[i]; } #ifdef __cplusplus env->ReleaseIntArrayElements(dims,dimsP,0); #else (*env)->ReleaseIntArrayElements(env,dims,dimsP,0); #endif } return (jint)status; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tis_variable_str(hid_t dtype_id ) * Signature: (I)J */ JNIEXPORT jboolean JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tis_1variable_1str (JNIEnv *env, jclass clss, jint dtype_id) { htri_t bval; bval = H5Tis_variable_str((hid_t)dtype_id); if (bval > 0) { return JNI_TRUE; } else if (bval == 0) { return JNI_FALSE; } else { h5libraryError(env); return JNI_FALSE; } } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tget_native_type(hid_t type_id, H5T_direction_t direction ) * Signature: (I)J */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tget_1native_1type (JNIEnv *env, jclass clss, jint dtype_id, jint direction) { hid_t native_tid; native_tid = H5Tget_native_type((hid_t)dtype_id, (H5T_direction_t)direction); if (native_tid < 0){ h5libraryError(env); return -1; } return (jint)native_tid; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Tdetect_class(hid_t dtype_id, H5T_class_t dtype_class ) * Signature: (I)J */ JNIEXPORT jboolean JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tdetect_1class (JNIEnv *env, jclass clss, jint dtype_id, jint dtype_class) { htri_t bval; bval = H5Tdetect_class((hid_t)dtype_id, (H5T_class_t)dtype_class); if (bval > 0) { return JNI_TRUE; } else if (bval == 0) { return JNI_FALSE; } else { h5libraryError(env); return JNI_FALSE; } } #ifdef __cplusplus } #endif libsis-jhdf5-java-14.12.1/source/c/jhdf5/h5utilJHDF5.c000077500000000000000000000265141256564762100217340ustar00rootroot00000000000000/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the files COPYING and Copyright.html. COPYING can be found at the root * * of the source code distribution tree; Copyright.html can be found at the * * root level of an installed copy of the electronic HDF5 document set and * * is linked from the top-level documents page. It can also be found at * * http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have * * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #include #include #include #include "hdf5.h" #include "h5utilJHDF5.h" int h5str_dump_region_jhdf5(h5str_t *str, hid_t region); static hbool_t h5tools_is_zero_jhdf5(const void *_mem, size_t size); /** frees memory held by aray of strings */ void h5str_array_free_jhdf5(char **strs, size_t len) { size_t i; if (!strs || len <=0) return; for (i=0; i 0) { str->s = (char *) malloc(len); str->max = len; str->s[0] = '\0'; } } /** free string memory */ void h5str_free_jhdf5(h5str_t *str) { if (str && str->max>0) { free(str->s); memset(str, 0, sizeof(h5str_t)); } } /** reset the max size of the string */ void h5str_resize_jhdf5 (h5str_t *str, size_t new_len) { char *new_str; if (!str || new_len<=0 || str->max == new_len) return; new_str = (char *)malloc(new_len); if (new_len > str->max) /* increase memory */ strcpy(new_str, str->s); else strncpy(new_str, str->s, new_len-1); free(str->s); str->s = new_str; str->max = new_len; } /* appends a copy of the string pointed to by cstr to the h5str. Return Value: the char string point to str->s */ char* h5str_append_jhdf5 (h5str_t *str, const char* cstr) { size_t len; if (!str) return NULL; else if (!cstr) return str->s; len = strlen(str->s) + strlen(cstr); while (len >= str->max) /* not enough to hold the new string, double the space */ { h5str_resize_jhdf5(str, str->max*2); } return strcat(str->s, cstr); } /** print value of a data point into string. Return Value: On success, the total number of characters printed is returned. On error, a negative number is returned. */ int h5str_sprintf_jhdf5(h5str_t *str, hid_t container, hid_t tid, void *ptr) { unsigned char tmp_uchar = 0; char tmp_char = 0; unsigned short tmp_ushort = 0; short tmp_short = 0; unsigned int tmp_uint = 0; int tmp_int = 0; unsigned long tmp_ulong = 0; long tmp_long = 0; float tmp_float = 0; double tmp_double = 0.0; size_t offset, size; char *cptr = (char*)ptr; unsigned char *ucptr = (unsigned char*)ptr; char *this_str; int this_strlen, i, n; hid_t mtid = -1; H5T_class_t tclass = H5Tget_class(tid); hvl_t *vlptr; if (!str || !ptr) return -1; this_str = NULL; this_strlen = 0; if (H5Tequal(tid, H5T_NATIVE_SCHAR)) { this_str = (char*)malloc(7); memcpy(&tmp_char, ptr, 1); sprintf(this_str, "%d", tmp_char); } else if (H5Tequal(tid, H5T_NATIVE_UCHAR)) { this_str = (char*)malloc(7); memcpy(&tmp_uchar, ptr, 1); sprintf(this_str, "%u", tmp_uchar); } else if (H5Tequal(tid, H5T_NATIVE_SHORT)) { this_str = (char*)malloc(9); memcpy(&tmp_short, ptr, 2); sprintf(this_str, "%d", tmp_short); } else if (H5Tequal(tid, H5T_NATIVE_USHORT)) { this_str = (char*)malloc(9); memcpy(&tmp_ushort, ptr, 2); sprintf(this_str, "%u", tmp_ushort); } else if (H5Tequal(tid, H5T_NATIVE_INT)) { this_str = (char*)malloc(14); memcpy(&tmp_int, ptr, 4); sprintf(this_str, "%d", tmp_int); } else if (H5Tequal(tid, H5T_NATIVE_UINT)) { this_str = (char*)malloc(14); memcpy(&tmp_uint, ptr, 4); sprintf(this_str, "%u", tmp_uint); } else if (H5Tequal(tid, H5T_NATIVE_LONG)) { this_str = (char*)malloc(23); memcpy(&tmp_long, ptr, sizeof(long)); sprintf(this_str, "%ld", tmp_long); } else if (H5Tequal(tid, H5T_NATIVE_ULONG)) { this_str = (char*)malloc(23); memcpy(&tmp_ulong, ptr, sizeof(unsigned long)); sprintf(this_str, "%lu", tmp_ulong); } else if (H5Tequal(tid, H5T_STD_REF_OBJ)) { this_str = (char*)malloc(23); memcpy(&tmp_ulong, ptr, sizeof(void *)); sprintf(this_str, "%lu", tmp_ulong); } else if (H5Tequal(tid, H5T_NATIVE_FLOAT)) { this_str = (char*)malloc(25); memcpy(&tmp_float, ptr, sizeof(float)); sprintf(this_str, "%f", tmp_float); } else if (H5Tequal(tid, H5T_NATIVE_DOUBLE)) { this_str = (char*)malloc(25); memcpy(&tmp_double, ptr, sizeof(double)); sprintf(this_str, "%f", tmp_double); } else if (tclass == H5T_STRING) { char *tmp_str; size = 0; if(H5Tis_variable_str(tid)) { tmp_str = *(char**)ptr; if(tmp_str) size = strlen(tmp_str); } else { tmp_str = cptr; size = H5Tget_size(tid); } if (size > 0) { this_str = (char *)malloc(size); strcpy(this_str, tmp_str); } } else if (tclass == H5T_COMPOUND) { n = H5Tget_nmembers(tid); h5str_append_jhdf5(str, " {"); for (i = 0; i < n; i++) { offset = H5Tget_member_offset(tid, i); mtid = H5Tget_member_type(tid ,i); h5str_sprintf_jhdf5(str, container, mtid, cptr+offset); if (is, ", "); H5Tclose(mtid); } h5str_append_jhdf5(str, "} "); } else if (tclass == H5T_ARRAY) { int rank=0; hsize_t dims[H5S_MAX_RANK], total_elmts; h5str_append_jhdf5(str, "[ "); mtid = H5Tget_super(tid); size = H5Tget_size(mtid); rank = H5Tget_array_ndims(tid); H5Tget_array_dims(tid, dims); total_elmts = 1; for (i=0; is, ", "); } H5Tclose(mtid); h5str_append_jhdf5(str, "] "); } else if (tclass == H5T_VLEN) { mtid = H5Tget_super(tid); size = H5Tget_size(mtid); vlptr = (hvl_t *)cptr; n = vlptr->len; for (i = 0; i < n; i++) { h5str_sprintf_jhdf5(str, container, mtid, ((char *)(vlptr->p)) + i * size); if (is, ", "); } H5Tclose(mtid); } else if (H5Tequal(tid, H5T_STD_REF_DSETREG)) { /* * Dataset region reference -- show the type and OID of the referenced * object, but we are unable to show the region yet because there * isn't enough support in the data space layer. - rpm 19990604 */ if (h5tools_is_zero_jhdf5(ptr, H5Tget_size(tid))) { h5str_append_jhdf5(str, "NULL"); } else { char obj_info[128]; hid_t obj, region; H5G_stat_t sb; /* get name of the dataset the region reference points to using H5Rget_name */ obj = H5Rdereference(container, H5R_DATASET_REGION, ptr); H5Gget_objinfo(obj, ".", 0, &sb); sprintf(obj_info, "%lu:%lu ", sb.objno[1], sb.objno[0]); h5str_append_jhdf5(str, obj_info); region = H5Rget_region(container, H5R_DATASET_REGION, ptr); h5str_dump_region_jhdf5(str, region); H5Sclose(region); H5Dclose(obj); } } else /* All other types get printed as hexadecimal */ { n = H5Tget_size(tid); this_str = (char*)malloc(4*(n+1)); if (1==n) { sprintf(this_str, "0x%02x", ucptr[0]); } else { for (i = 0; i < n; i++) sprintf(this_str, "%s%02x", i?":":"", ucptr[i]); } } if (this_str) { h5str_append_jhdf5(str, this_str); this_strlen = strlen(this_str); free (this_str); } return this_strlen; } /* dumps region reference information into a string */ int h5str_dump_region_jhdf5(h5str_t *str, hid_t region) { hssize_t nblocks, npoints; hsize_t alloc_size; hsize_t *ptdata; int ndims = H5Sget_simple_extent_ndims(region); char tmp_str[256]; /* * These two functions fail if the region does not have blocks or points, * respectively. They do not currently know how to translate from one to * the other. */ H5E_BEGIN_TRY { nblocks = H5Sget_select_hyper_nblocks(region); npoints = H5Sget_select_elem_npoints(region); } H5E_END_TRY; h5str_append_jhdf5(str, "{"); /* Print block information */ if (nblocks > 0) { int i; alloc_size = nblocks * ndims * 2 * sizeof(ptdata[0]); if (alloc_size == (hsize_t)((size_t)alloc_size)) { ptdata = malloc((size_t)alloc_size); H5Sget_select_hyper_blocklist(region, (hsize_t)0, (hsize_t)nblocks, ptdata); for (i = 0; i < nblocks; i++) { int j; h5str_append_jhdf5(str, " "); /* Start coordinates and opposite corner */ for (j = 0; j < ndims; j++) { tmp_str[0] = '\0'; sprintf(tmp_str, "%s%lu", j ? "," : "(", (unsigned long)ptdata[i * 2 * ndims + j]); h5str_append_jhdf5(str, tmp_str); } for (j = 0; j < ndims; j++) { tmp_str[0] = '\0'; sprintf(tmp_str, "%s%lu", j ? "," : ")-(", (unsigned long)ptdata[i * 2 * ndims + j + ndims]); h5str_append_jhdf5(str, tmp_str); } h5str_append_jhdf5(str, ") "); tmp_str[0] = '\0'; } free(ptdata); } /* if (alloc_size == (hsize_t)((size_t)alloc_size)) */ } /* if (nblocks > 0) */ /* Print point information */ if (npoints > 0) { int i; alloc_size = npoints * ndims * sizeof(ptdata[0]); if (alloc_size == (hsize_t)((size_t)alloc_size)) { ptdata = malloc((size_t)alloc_size); H5Sget_select_elem_pointlist(region, (hsize_t)0, (hsize_t)npoints, ptdata); for (i = 0; i < npoints; i++) { int j; h5str_append_jhdf5(str, " "); for (j = 0; j < ndims; j++) { tmp_str[0] = '\0'; sprintf(tmp_str, "%s%lu", j ? "," : "(", (unsigned long)(ptdata[i * ndims + j])); h5str_append_jhdf5(str, tmp_str); } h5str_append_jhdf5(str, ") "); } free(ptdata); } } h5str_append_jhdf5(str, "}"); return 0; } static hbool_t h5tools_is_zero_jhdf5(const void *_mem, size_t size) { const unsigned char *mem = (const unsigned char *)_mem; while (size-- > 0) if (mem[size]) return 0; return 1; } libsis-jhdf5-java-14.12.1/source/c/jhdf5/h5utilJHDF5.h000077500000000000000000000030011256564762100217230ustar00rootroot00000000000000/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the files COPYING and Copyright.html. COPYING can be found at the root * * of the source code distribution tree; Copyright.html can be found at the * * root level of an installed copy of the electronic HDF5 document set and * * is linked from the top-level documents page. It can also be found at * * http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have * * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #ifndef H5UTIL_H__ #define H5UTIL_H__ typedef struct h5str_t { char *s; size_t max; /* the allocated size of the string */ } h5str_t; void h5str_new_jhdf5 (h5str_t *str, size_t len); void h5str_free_jhdf5 (h5str_t *str); void h5str_resize_jhdf5 (h5str_t *str, size_t new_len); char* h5str_append_jhdf5 (h5str_t *str, const char* cstr); int h5str_sprintf_jhdf5(h5str_t *str, hid_t container, hid_t tid, void *buf); void h5str_array_free_jhdf5(char **strs, size_t len); #endif /* H5UTIL_H__ */ libsis-jhdf5-java-14.12.1/source/c/jhdf5/h5zImpJHDF5.c000077500000000000000000000062661256564762100217000ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ /* * This code is the C-interface called by Java programs to access the * Reference API Functions of the HDF5 library. * * Each routine wraps a single HDF entry point, generally with the * analogous arguments and return codes. * * For details of the HDF libraries, see the HDF Documentation at: * http://hdf.ncsa.uiuc.edu/HDF5/doc/ * */ #ifdef __cplusplus extern "C" { #endif #include "hdf5.h" #include #include extern jboolean h5JNIFatalError( JNIEnv *env, char *functName); extern jboolean h5nullArgument( JNIEnv *env, char *functName); extern jboolean h5badArgument( JNIEnv *env, char *functName); extern jboolean h5libraryError( JNIEnv *env ); /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Zunregister(H5Z_filter_t filter) * Signature: ([BILjava/lang/String;II)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Zunregister (JNIEnv *env, jclass clss, jbyteArray ref, jint loc_id, jstring name, jint filter) { herr_t retValue; retValue = H5Zunregister((H5Z_filter_t)filter); if (retValue < 0) { h5libraryError(env); } return (jint)retValue; } /* * Class: ncsa_hdf_hdf5lib_H5 * Method: H5Zfilter_avail(H5Z_filter_t filter) * Signature: ([BILjava/lang/String;II)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Zfilter_1avail (JNIEnv *env, jclass clss, jbyteArray ref, jint loc_id, jstring name, jint filter) { herr_t retValue; retValue = H5Zfilter_avail((H5Z_filter_t)filter); if (retValue < 0) { h5libraryError(env); } return (jint)retValue; } /********************************************************************** * * * New functions release 1.6.3 versus release 1.6.2 * * * **********************************************************************/ /* * Class: ncsa_hdf_hdf5lib_H5 * Signature: herr_t H5Zget_filter_info (H5Z_filter_t filter, unsigned * flags) * Purpose: */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Zget_1filter_1info (JNIEnv *env, jclass clss, jint filter) { herr_t status; unsigned int flags = 0; status = H5Zget_filter_info ((H5Z_filter_t) filter, (unsigned *) &flags); if (status < 0) { h5libraryError(env); } return flags; } #ifdef __cplusplus } #endif libsis-jhdf5-java-14.12.1/source/c/jhdf5/strcpyJHDF5.c000066400000000000000000000106051256564762100220350ustar00rootroot00000000000000#include "hdf5.h" #include "h5utilJHDF5.h" #include #include #include extern jboolean h5outOfMemory( JNIEnv *env, char *functName); extern jboolean h5JNIFatalError( JNIEnv *env, char *functName); extern jboolean h5nullArgument( JNIEnv *env, char *functName); extern jboolean h5libraryError( JNIEnv *env ); /* * Class: ch_systemsx_cisd_hdf5_hdf5lib_H5 * Method: getPointerSize * Signature: ()I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_getPointerSize (JNIEnv *env, jclass clss) { return sizeof(void *); } /* * Class: ch_systemsx_cisd_hdf5_hdf5lib_H5 * Method: compoundCpyVLStr * Signature: (Ljava/lang/String;[B)I)I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_compoundCpyVLStr (JNIEnv *env, jclass clss, jstring str, /* IN: the string to copy */ jbyteArray buf, /* OUT: array of byte */ jint bufOfs /* The offset to copy the pointer to the string to. */ ) { jbyte *byteP; char *strPCpy; int numberOfBytes, numberOfCharacters; if ( str == NULL ) { h5nullArgument( env, "compoundCpyVLStr: str is NULL"); return -1; } if ( buf == NULL ) { h5nullArgument( env, "compoundCpyVLStr: buf is NULL"); return -1; } numberOfBytes = (*env)->GetStringUTFLength(env, str); strPCpy = calloc(1, numberOfBytes); numberOfCharacters = (*env)->GetStringLength(env, str); (*env)->GetStringUTFRegion(env, str, 0, numberOfCharacters, strPCpy); byteP = (*env)->GetPrimitiveArrayCritical(env, buf, NULL); if (byteP == NULL) { h5JNIFatalError( env, "compoundCpyVLStr: buf not pinned"); return -1; } *((char**)(byteP + bufOfs)) = strPCpy; (*env)->ReleasePrimitiveArrayCritical(env, buf, byteP, 0); return 0; } /* * Class: ch_systemsx_cisd_hdf5_hdf5lib_H5 * Method: createVLStrFromCompound * Signature: ([B)I)Ljava/lang/String; */ JNIEXPORT jstring JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_createVLStrFromCompound (JNIEnv *env, jclass clss, jbyteArray buf, /* IN: array of byte containing the compound or compound array. */ jint offset /* IN: The offset in the compound or compound array where the pointer to the string is located. */ ) { char *byteP; char **strP; jstring str; if ( buf == NULL ) { h5nullArgument( env, "createVLStrFromCompound: buf is NULL"); return NULL; } byteP = (*env)->GetPrimitiveArrayCritical(env, buf, NULL); if (byteP == NULL) { h5JNIFatalError( env, "createVLStrFromCompound: buf not pinned"); return NULL; } strP = (char**) (byteP + offset); str = (*env)->NewStringUTF(env, *strP); (*env)->ReleasePrimitiveArrayCritical(env, buf, byteP, 0); return str; } /* * Class: ch_systemsx_cisd_hdf5_hdf5lib_H5 * Method: freeCompoundVLStr * Signature: ([B)I[I))I */ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_freeCompoundVLStr (JNIEnv *env, jclass clss, jbyteArray buf, /* IN: array of byte containing the compound or compound array. */ jint recordSize, /* IN: The size of one compound record. */ jintArray vlIndices /* IN: The indices of the variable-length compound members in the record. */ ) { char *byteP, *ptr; char **strP; jsize bufLen, idxLen; int *idxP, i; if ( buf == NULL ) { h5nullArgument( env, "freeCompoundVLStr: buf is NULL"); return -1; } if ( vlIndices == NULL ) { h5nullArgument( env, "freeCompoundVLStr: vlIndices is NULL"); return -1; } idxLen = (*env)->GetArrayLength(env, vlIndices); bufLen = (*env)->GetArrayLength(env, buf); idxP = (*env)->GetPrimitiveArrayCritical(env, vlIndices, NULL); if (idxP == NULL) { h5JNIFatalError( env, "freeCompoundVLStr: vlIndices not pinned"); return -1; } byteP = (*env)->GetPrimitiveArrayCritical(env, buf, NULL); if (byteP == NULL) { (*env)->ReleasePrimitiveArrayCritical(env, vlIndices, idxP, 0); h5JNIFatalError( env, "freeCompoundVLStr: buf not pinned"); return -1; } ptr = byteP; while (ptr - byteP < bufLen) { for (i = 0; i < idxLen; ++i) { strP = (char**) (ptr + idxP[i]); free(*strP); } ptr += recordSize; } (*env)->ReleasePrimitiveArrayCritical(env, vlIndices, idxP, 0); (*env)->ReleasePrimitiveArrayCritical(env, buf, byteP, 0); return 0; } libsis-jhdf5-java-14.12.1/source/c/version.sh000077500000000000000000000000171256564762100206440ustar00rootroot00000000000000VERSION=1.8.14 libsis-jhdf5-java-14.12.1/source/java/000077500000000000000000000000001256564762100173215ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ch/000077500000000000000000000000001256564762100177135ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/000077500000000000000000000000001256564762100216125ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/000077500000000000000000000000001256564762100225345ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/000077500000000000000000000000001256564762100233625ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/BitSetConversionUtils.java000066400000000000000000000214431256564762100305120ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.lang.reflect.Field; import java.util.BitSet; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import org.apache.commons.lang.SystemUtils; import ch.rinn.restrictions.Private; import ch.systemsx.cisd.base.mdarray.MDLongArray; /** * Methods for converting {@link BitSet}s to a storage form suitable for storing in an HDF5 file. *

* This is an internal API that should not be expected to be stable between releases! * * @author Bernd Rinn */ public final class BitSetConversionUtils { private final static int ADDRESS_BITS_PER_WORD = 6; private final static int BITS_PER_WORD = 1 << ADDRESS_BITS_PER_WORD; private final static int BIT_INDEX_MASK = BITS_PER_WORD - 1; private static final Field BIT_SET_WORDS = getBitSetWords(); private static final Field BIT_SET_WORDS_IN_USE = getBitSetWordsInUse(); private static Field getBitSetWords() { try { final Field bitsField = BitSet.class.getDeclaredField(SystemUtils.IS_JAVA_1_5 ? "bits" : "words"); bitsField.setAccessible(true); return bitsField; } catch (final NoSuchFieldException ex) { return null; } } private static Field getBitSetWordsInUse() { try { final Field unitsInUseField = BitSet.class.getDeclaredField(SystemUtils.IS_JAVA_1_5 ? "unitsInUse" : "wordsInUse"); unitsInUseField.setAccessible(true); return unitsInUseField; } catch (final NoSuchFieldException ex) { return null; } } public static BitSet fromStorageForm(final long[] serializedWordArray) { return fromStorageForm(serializedWordArray, 0, serializedWordArray.length); } public static BitSet fromStorageForm(final long[] serializedWordArray, int start, int length) { if (BIT_SET_WORDS != null) { return fromStorageFormFast(serializedWordArray, start, length); } else { return fromStorageFormGeneric(serializedWordArray, start, length); } } public static BitSet[] fromStorageForm2D(final MDLongArray serializedWordArray) { if (serializedWordArray.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + serializedWordArray.rank()); } final int dimX = serializedWordArray.dimensions()[0]; final int dimY = serializedWordArray.dimensions()[1]; final BitSet[] result = new BitSet[dimY]; for (int i = 0; i < result.length; ++i) { result[i] = fromStorageForm(serializedWordArray.getAsFlatArray(), i * dimX, dimX); } return result; } private static BitSet fromStorageFormFast(final long[] serializedWordArray, int start, int length) { try { final BitSet result = new BitSet(); int inUse = calcInUse(serializedWordArray, start, length); BIT_SET_WORDS_IN_USE.set(result, inUse); BIT_SET_WORDS.set(result, trim(serializedWordArray, start, inUse)); return result; } catch (final IllegalAccessException ex) { throw new IllegalAccessError(ex.getMessage()); } } @Private static BitSet fromStorageFormGeneric(final long[] serializedWordArray, int start, int length) { final BitSet result = new BitSet(); for (int wordIndex = 0; wordIndex < length; ++wordIndex) { final long word = serializedWordArray[start + wordIndex]; for (int bitInWord = 0; bitInWord < BITS_PER_WORD; ++bitInWord) { if ((word & 1L << bitInWord) != 0) { result.set(wordIndex << ADDRESS_BITS_PER_WORD | bitInWord); } } } return result; } public static long[] toStorageForm(final BitSet[] data, int numberOfWords) { final long[] result = new long[data.length * numberOfWords]; int idx = 0; for (BitSet bs : data) { System.arraycopy(toStorageForm(bs, numberOfWords), 0, result, idx, numberOfWords); idx += numberOfWords; } return result; } public static long[] toStorageForm(final BitSet data) { if (BIT_SET_WORDS != null) { return toStorageFormFast(data); } else { return toStorageFormGeneric(data); } } public static long[] toStorageForm(final BitSet data, int numberOfWords) { if (BIT_SET_WORDS != null) { return toStorageFormFast(data, numberOfWords); } else { return toStorageFormGeneric(data, numberOfWords); } } private static long[] toStorageFormFast(final BitSet data) { try { long[] storageForm = (long[]) BIT_SET_WORDS.get(data); int inUse = BIT_SET_WORDS_IN_USE.getInt(data); return trim(storageForm, 0, inUse); } catch (final IllegalAccessException ex) { throw new IllegalAccessError(ex.getMessage()); } } private static long[] toStorageFormFast(final BitSet data, int numberOfWords) { try { long[] storageForm = (long[]) BIT_SET_WORDS.get(data); return trimEnforceLen(storageForm, 0, numberOfWords); } catch (final IllegalAccessException ex) { throw new IllegalAccessError(ex.getMessage()); } } private static long[] trim(final long[] array, int start, int len) { final int inUse = calcInUse(array, start, len); if (inUse < array.length) { final long[] trimmedArray = new long[inUse]; System.arraycopy(array, start, trimmedArray, 0, inUse); return trimmedArray; } return array; } private static long[] trimEnforceLen(final long[] array, int start, int len) { if (len != array.length) { final long[] trimmedArray = new long[len]; final int inUse = calcInUse(array, start, len); System.arraycopy(array, start, trimmedArray, 0, inUse); return trimmedArray; } return array; } private static int calcInUse(final long[] array, int start, int len) { int result = Math.min(len, array.length); while (result > 0 && array[start + result - 1] == 0) { --result; } return result; } /** * Given a bit index return the word index containing it. */ public static int getWordIndex(final int bitIndex) { return bitIndex >> ADDRESS_BITS_PER_WORD; } /** * Given a bit index, return a unit that masks that bit in its unit. */ public static long getBitMaskInWord(final int bitIndex) { return 1L << (bitIndex & BIT_INDEX_MASK); } // @Private static long[] toStorageFormGeneric(final BitSet data) { final long[] words = new long[data.size() >> ADDRESS_BITS_PER_WORD]; for (int bitIndex = data.nextSetBit(0); bitIndex >= 0; bitIndex = data.nextSetBit(bitIndex + 1)) { final int wordIndex = getWordIndex(bitIndex); words[wordIndex] |= getBitMaskInWord(bitIndex); } return words; } // @Private static long[] toStorageFormGeneric(final BitSet data, final int numberOfWords) { final long[] words = new long[numberOfWords]; for (int bitIndex = data.nextSetBit(0); bitIndex >= 0; bitIndex = data.nextSetBit(bitIndex + 1)) { final int wordIndex = getWordIndex(bitIndex); if (wordIndex >= words.length) { break; } words[wordIndex] |= getBitMaskInWord(bitIndex); } return words; } static int getMaxLength(BitSet[] data) { int length = 0; for (BitSet bs : data) { length = Math.max(length, bs.length()); } return length; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/BuildAndEnvironmentInfo.java000066400000000000000000000024131256564762100307500ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ch.systemsx.cisd.base.utilities.AbstractBuildAndEnvironmentInfo; /** * The build and environment information for JHDF5. * * @author Franz-Josef Elmer */ public class BuildAndEnvironmentInfo extends AbstractBuildAndEnvironmentInfo { private final static String BASE = "jhdf5"; public final static BuildAndEnvironmentInfo INSTANCE = new BuildAndEnvironmentInfo(); private BuildAndEnvironmentInfo() { super(BASE); } /** * Shows build and environment information on the console. */ public static void main(String[] args) { System.out.println(INSTANCE); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/CharacterEncoding.java000066400000000000000000000037261256564762100276000ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_CSET_ASCII; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_CSET_UTF8; /** * An enum for character encodings of path names and strings in JHDF5. * * @author Bernd Rinn */ public enum CharacterEncoding { ASCII("ASCII", H5T_CSET_ASCII, 1), UTF8("UTF8", H5T_CSET_UTF8, 4); private final String charSetName; private final int cValue; private final int maxBytesPerChar; private CharacterEncoding(String charSetName, int cValue, int maxBytesPerChar) { this.charSetName = charSetName; this.cValue = cValue; this.maxBytesPerChar = maxBytesPerChar; } int getCValue() { return cValue; } String getCharSetName() { return charSetName; } /** * Returns the maximum number of bytes per character. */ int getMaxBytesPerChar() { return maxBytesPerChar; } static CharacterEncoding fromCValue(int cValue) throws IllegalArgumentException { if (cValue == H5T_CSET_ASCII) { return ASCII; } else if (cValue == H5T_CSET_UTF8) { return UTF8; } else { throw new IllegalArgumentException("Illegal character encoding id " + cValue); } } }libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/CompoundElement.java000066400000000000000000000047111256564762100273260ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static java.lang.annotation.ElementType.FIELD; import static java.lang.annotation.RetentionPolicy.RUNTIME; import java.lang.annotation.Retention; import java.lang.annotation.Target; /** * A marker annotation for fields intended to be mapped to an HDF5 compound data type member. This * marker interface is optional for many fields as otherwise the fields properties are inferred. * However, for arrays, Strings and BitSets the maximum length needs to be * given in {@link #dimensions()}. * * @author Bernd Rinn */ @Retention(RUNTIME) @Target(FIELD) public @interface CompoundElement { /** * The name of the member in the compound type. Leave empty to use the field name as member * name. */ String memberName() default ""; /** * The name of the type (for Java enumeration types only). Leave empty to use the simple class * name as the type name. */ String typeName() default ""; /** * The length / dimensions of the compound member. Is required for compound members that have a * variable length, e.g. strings or primitive arrays. Ignored for compound members that have a * fixed length, e.g. a float field. */ int[] dimensions() default 0; /** * If true, map this integer field to an unsigned integer type. */ boolean unsigned() default false; /** * If true, map this string field to a variable-length string type. */ boolean variableLength() default false; /** * If true, map this string field to an HDF5 reference type. */ boolean reference() default false; /** * The {@link HDF5DataTypeVariant} of this compound element, if any. */ HDF5DataTypeVariant typeVariant() default HDF5DataTypeVariant.NONE; } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/CompoundType.java000066400000000000000000000032641256564762100266600ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static java.lang.annotation.ElementType.TYPE; import static java.lang.annotation.RetentionPolicy.RUNTIME; import java.lang.annotation.Retention; import java.lang.annotation.Target; /** * A marker annotation for classes intended to be mapped to an HDF5 compound data type. This marker * interface is optional as inferring the field to member mapping works also when this annotation is * not present. However, this annotation is the only way to specify that not all fields should be * mapped to members but only those annotated with {@link CompoundElement}. * * @author Bernd Rinn */ @Retention(RUNTIME) @Target(TYPE) public @interface CompoundType { /** * The name this compound type should have in the HDF5 file. If left blank, the simple class * name will be used. */ String name() default ""; /** * Whether all fields should be mapped to members of the compound type or only the fields * annotated with {@link CompoundElement} (default: true). */ boolean mapAllFields() default true; } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/CompoundTypeInformation.java000066400000000000000000000051241256564762100310630ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; /** * A class with basic information about the types of compound members in an HDF5 file. * * @author Bernd Rinn */ final class CompoundTypeInformation { final String name; final int compoundDataTypeId; final int nativeCompoundDataTypeId; private final HDF5CompoundMemberInformation[] members; final int[] dataTypeIds; final HDF5EnumerationType[] enumTypes; final int recordSizeOnDisk; final int recordSizeInMemory; private int numberOfVLMembers; CompoundTypeInformation(String name, int compoundDataTypeId, int nativeCompoundDataTypeId, int numberOfElements, int recordSizeOnDisk, int recordSizeInMemory) { this.name = name; this.compoundDataTypeId = compoundDataTypeId; this.nativeCompoundDataTypeId = nativeCompoundDataTypeId; this.members = new HDF5CompoundMemberInformation[numberOfElements]; this.dataTypeIds = new int[numberOfElements]; this.enumTypes = new HDF5EnumerationType[numberOfElements]; this.recordSizeOnDisk = recordSizeOnDisk; this.recordSizeInMemory = recordSizeInMemory; } private void calcNumberOfVLMembers() { int countOfVLMembers = 0; for (HDF5CompoundMemberInformation m : members) { if (m != null && m.getType().isVariableLengthString()) { ++countOfVLMembers; } } this.numberOfVLMembers = countOfVLMembers; } int getNumberOfMembers() { return members.length; } HDF5CompoundMemberInformation getMember(int i) { return members[i]; } HDF5CompoundMemberInformation[] getCopyOfMembers() { return members.clone(); } void setMember(int i, HDF5CompoundMemberInformation member) { members[i] = member; calcNumberOfVLMembers(); } int getNumberOfVLMembers() { return numberOfVLMembers; } }libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/EnumerationType.java000066400000000000000000000242671256564762100273700ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.util.Arrays; import java.util.Collections; import java.util.HashMap; import java.util.Iterator; import java.util.List; import java.util.Map; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.base.convert.NativeData; import ch.systemsx.cisd.base.convert.NativeData.ByteOrder; import ch.systemsx.cisd.base.mdarray.MDAbstractArray; import ch.systemsx.cisd.base.mdarray.MDByteArray; import ch.systemsx.cisd.base.mdarray.MDIntArray; import ch.systemsx.cisd.base.mdarray.MDShortArray; import ch.systemsx.cisd.hdf5.HDF5EnumerationType.EnumStorageForm; import ch.systemsx.cisd.hdf5.hdf5lib.HDFNativeData; /** * An enumeration type, consisting of name and the list of names of the enumeration terms. * * @author Bernd Rinn */ public class EnumerationType implements Iterable { private final String nameOrNull; private final String[] values; private final List unmodifiableValues; private Map nameToIndexMap; public EnumerationType(String nameOrNull, String[] values) { assert values != null; this.nameOrNull = nameOrNull; this.values = values; this.unmodifiableValues = Collections.unmodifiableList(Arrays.asList(values)); } public EnumerationType(Class> enumClass) { this(enumClass.getName(), enumClass); } public EnumerationType(String nameOrNull, Class> enumClass) { this(nameOrNull, ReflectionUtils.getEnumOptions(enumClass)); } private Map getMap() { if (nameToIndexMap == null) { nameToIndexMap = new HashMap(values.length); for (int i = 0; i < values.length; ++i) { nameToIndexMap.put(values[i], i); } } return nameToIndexMap; } String[] getValueArray() { return values; } Object createArray(int length) { if (values.length < Byte.MAX_VALUE) { return new byte[length]; } else if (values.length < Short.MAX_VALUE) { return new short[length]; } else { return new int[length]; } } /** * Returns the ordinal value for the given string value, if value is a * member of the enumeration, and null otherwise. */ public Integer tryGetIndexForValue(String value) { return getMap().get(value); } /** * Returns the name of this type, if it exists, or NONAME otherwise. */ public String getName() { if (nameOrNull == null) { return "NONAME"; } else { return nameOrNull; } } /** * Returns the name of this type, if it exists, or null otherwise. */ public String tryGetName() { return nameOrNull; } /** * Returns the allowed values of this enumeration type. */ public List getValues() { return unmodifiableValues; } /** * Returns the {@link EnumStorageForm} of this enumeration type. */ public EnumStorageForm getStorageForm() { final int len = values.length; if (len < Byte.MAX_VALUE) { return EnumStorageForm.BYTE; } else if (len < Short.MAX_VALUE) { return EnumStorageForm.SHORT; } else { return EnumStorageForm.INT; } } byte getNumberOfBits() { final int n = (values.length > 0) ? values.length - 1 : 0; // Binary search - decision tree (5 tests, rarely 6) return (byte) (n < 1 << 15 ? (n < 1 << 7 ? (n < 1 << 3 ? (n < 1 << 1 ? (n < 1 << 0 ? (n < 0 ? 32 : 0) : 1) : (n < 1 << 2 ? 2 : 3)) : (n < 1 << 5 ? (n < 1 << 4 ? 4 : 5) : (n < 1 << 6 ? 6 : 7))) : (n < 1 << 11 ? (n < 1 << 9 ? (n < 1 << 8 ? 8 : 9) : (n < 1 << 10 ? 10 : 11)) : (n < 1 << 13 ? (n < 1 << 12 ? 12 : 13) : (n < 1 << 14 ? 14 : 15)))) : (n < 1 << 23 ? (n < 1 << 19 ? (n < 1 << 17 ? (n < 1 << 16 ? 16 : 17) : (n < 1 << 18 ? 18 : 19)) : (n < 1 << 21 ? (n < 1 << 20 ? 20 : 21) : (n < 1 << 22 ? 22 : 23))) : (n < 1 << 27 ? (n < 1 << 25 ? (n < 1 << 24 ? 24 : 25) : (n < 1 << 26 ? 26 : 27)) : (n < 1 << 29 ? (n < 1 << 28 ? 28 : 29) : (n < 1 << 30 ? 30 : 31))))); } byte[] toStorageForm(int ordinal) { switch (getStorageForm()) { case BYTE: return HDFNativeData.byteToByte((byte) ordinal); case SHORT: return HDFNativeData.shortToByte((short) ordinal); case INT: return HDFNativeData.intToByte(ordinal); } throw new Error("Illegal storage size."); } static int fromStorageForm(byte[] data) { if (data.length == 1) { return data[0]; } else if (data.length == 2) { return NativeData.byteToShort(data, ByteOrder.NATIVE)[0]; } else if (data.length == 4) { return NativeData.byteToInt(data, ByteOrder.NATIVE)[0]; } throw new HDF5JavaException("Unexpected size for Enum data type (" + data.length + ")"); } static int fromStorageForm(byte[] data, int index, int size) { if (size == 1) { return data[index]; } else if (size == 2) { return NativeData.byteToShort(data, ByteOrder.NATIVE, size * index, 1)[0]; } else if (size == 4) { return NativeData.byteToInt(data, ByteOrder.NATIVE, index, 1)[0]; } throw new HDF5JavaException("Unexpected size for Enum data type (" + size + ")"); } static Object fromStorageForm(byte[] data, EnumStorageForm storageForm) { switch (storageForm) { case BYTE: return data; case SHORT: return NativeData.byteToShort(data, ByteOrder.NATIVE); case INT: return NativeData.byteToInt(data, ByteOrder.NATIVE); } throw new Error("Illegal storage size."); } static MDAbstractArray fromStorageForm(byte[] data, long[] dimensions, EnumStorageForm storageForm) { switch (storageForm) { case BYTE: return new MDByteArray(data, dimensions); case SHORT: return new MDShortArray(NativeData.byteToShort(data, ByteOrder.NATIVE), dimensions); case INT: return new MDIntArray(NativeData.byteToInt(data, ByteOrder.NATIVE), dimensions); } throw new Error("Illegal storage size."); } static MDAbstractArray fromStorageForm(byte[] data, int[] dimensions, EnumStorageForm storageForm) { switch (storageForm) { case BYTE: return new MDByteArray(data, dimensions); case SHORT: return new MDShortArray(NativeData.byteToShort(data, ByteOrder.NATIVE), dimensions); case INT: return new MDIntArray(NativeData.byteToInt(data, ByteOrder.NATIVE), dimensions); } throw new Error("Illegal storage size."); } String createStringFromStorageForm(byte[] data, int offset) { return values[getOrdinalFromStorageForm(data, offset)]; } int getOrdinalFromStorageForm(byte[] data, int offset) { switch (getStorageForm()) { case BYTE: return data[offset]; case SHORT: return HDFNativeData.byteToShort(data, offset); case INT: return HDFNativeData.byteToInt(data, offset); } throw new Error("Illegal storage form (" + getStorageForm() + ".)"); } // // Iterable // /** * Returns an {@link Iterator} over all values of this enumeration type. * {@link Iterator#remove()} is not allowed and will throw an * {@link UnsupportedOperationException}. */ @Override public Iterator iterator() { return new Iterator() { private int index = 0; @Override public boolean hasNext() { return index < values.length; } @Override public String next() { return values[index++]; } /** * @throws UnsupportedOperationException As this iterator doesn't support removal. */ @Override public void remove() throws UnsupportedOperationException { throw new UnsupportedOperationException(); } }; } @Override public int hashCode() { final int prime = 31; int result = super.hashCode(); result = prime * result + Arrays.hashCode(values); return result; } @Override public boolean equals(Object obj) { if (this == obj) { return true; } if (getClass() != obj.getClass()) { return false; } final EnumerationType other = (EnumerationType) obj; return Arrays.equals(values, other.values); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5.java000066400000000000000000002136361256564762100247260ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.hdf5lib.H5F.*; import static ch.systemsx.cisd.hdf5.hdf5lib.H5A.*; import static ch.systemsx.cisd.hdf5.hdf5lib.H5D.*; import static ch.systemsx.cisd.hdf5.hdf5lib.H5GLO.*; import static ch.systemsx.cisd.hdf5.hdf5lib.H5P.*; import static ch.systemsx.cisd.hdf5.hdf5lib.H5RI.*; import static ch.systemsx.cisd.hdf5.hdf5lib.H5S.*; import static ch.systemsx.cisd.hdf5.hdf5lib.H5T.*; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5D_CHUNKED; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5D_COMPACT; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5D_FILL_TIME_ALLOC; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5F_ACC_RDONLY; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5F_ACC_RDWR; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5F_ACC_TRUNC; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5F_LIBVER_LATEST; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5F_SCOPE_GLOBAL; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5O_TYPE_GROUP; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_ATTRIBUTE_CREATE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DATASET_CREATE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_FILE_ACCESS; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_GROUP_CREATE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_LINK_CREATE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5R_OBJECT; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_ALL; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_MAX_RANK; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_SCALAR; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_SELECT_SET; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_UNLIMITED; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_ARRAY; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_COMPOUND; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_C_S1; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_ENUM; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_FLOAT; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_INTEGER; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_OPAQUE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_OPAQUE_TAG_MAX; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_SGN_NONE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_I16LE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_I32LE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_I8LE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STR_NULLPAD; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_VARIABLE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5Z_SO_FLOAT_DSCALE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5Z_SO_INT; import java.io.File; import java.util.Arrays; import java.util.LinkedList; import java.util.List; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.base.mdarray.MDAbstractArray; import ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator.FileFormat; import ch.systemsx.cisd.hdf5.cleanup.CleanUpCallable; import ch.systemsx.cisd.hdf5.cleanup.CleanUpRegistry; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; import ch.systemsx.cisd.hdf5.hdf5lib.HDFNativeData; /** * A wrapper around {@link ch.systemsx.cisd.hdf5.hdf5lib.H5General} that handles closing of * resources automatically by means of registering clean-up {@link Runnable}s. * * @author Bernd Rinn */ class HDF5 { private final static int MAX_PATH_LENGTH = 16384; private final CleanUpCallable runner; private final int dataSetCreationPropertyListCompactStorageLayoutFileTimeAlloc; private final int dataSetCreationPropertyListFillTimeAlloc; private final int numericConversionXferPropertyListID; private final int lcplCreateIntermediateGroups; private final boolean useUTF8CharEncoding; private final boolean autoDereference; public HDF5(final CleanUpRegistry fileRegistry, final CleanUpCallable runner, final boolean performNumericConversions, final boolean useUTF8CharEncoding, final boolean autoDereference) { this.runner = runner; this.useUTF8CharEncoding = useUTF8CharEncoding; this.autoDereference = autoDereference; this.dataSetCreationPropertyListCompactStorageLayoutFileTimeAlloc = createDataSetCreationPropertyList(fileRegistry); H5Pset_layout(dataSetCreationPropertyListCompactStorageLayoutFileTimeAlloc, H5D_COMPACT); this.dataSetCreationPropertyListFillTimeAlloc = createDataSetCreationPropertyList(fileRegistry); if (performNumericConversions) { this.numericConversionXferPropertyListID = createDataSetXferPropertyListAbortOverflow(fileRegistry); } else { this.numericConversionXferPropertyListID = createDataSetXferPropertyListAbort(fileRegistry); } this.lcplCreateIntermediateGroups = createLinkCreationPropertyList(true, fileRegistry); } private static void checkMaxLength(String path) throws HDF5JavaException { if (path.length() > MAX_PATH_LENGTH) { throw new HDF5JavaException("Path too long (length=" + path.length() + ")"); } } // // File // public int createFile(String fileName, boolean useLatestFormat, ICleanUpRegistry registry) { final int fileAccessPropertyListId = createFileAccessPropertyListId(useLatestFormat, registry); final int fileId = H5Fcreate(fileName, H5F_ACC_TRUNC, H5P_DEFAULT, fileAccessPropertyListId); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Fclose(fileId); } }); return fileId; } private int createFileAccessPropertyListId(boolean enforce_1_8, ICleanUpRegistry registry) { int fileAccessPropertyListId = H5P_DEFAULT; if (enforce_1_8) { final int fapl = H5Pcreate(H5P_FILE_ACCESS); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Pclose(fapl); } }); H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST); fileAccessPropertyListId = fapl; } return fileAccessPropertyListId; } public int openFileReadOnly(String fileName, ICleanUpRegistry registry) { final int fileId = H5Fopen(fileName, H5F_ACC_RDONLY, H5P_DEFAULT); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Fclose(fileId); } }); return fileId; } public int openFileReadWrite(String fileName, boolean enforce_1_8, ICleanUpRegistry registry) { final int fileAccessPropertyListId = createFileAccessPropertyListId(enforce_1_8, registry); final File f = new File(fileName); if (f.exists() && f.isFile() == false) { throw new HDF5Exception("An entry with name '" + fileName + "' exists but is not a file."); } final int fileId = H5Fopen(fileName, H5F_ACC_RDWR, fileAccessPropertyListId); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Fclose(fileId); } }); return fileId; } public void flushFile(int fileId) { H5Fflush(fileId, H5F_SCOPE_GLOBAL); } // // Object // public int openObject(int fileId, String path, ICleanUpRegistry registry) { checkMaxLength(path); final int objectId = isReference(path) ? H5Rdereference(fileId, Long.parseLong(path.substring(1))) : H5Oopen(fileId, path, H5P_DEFAULT); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Oclose(objectId); } }); return objectId; } public int deleteObject(int fileId, String path) { checkMaxLength(path); final int success = H5Gunlink(fileId, path); return success; } public int copyObject(int srcFileId, String srcPath, int dstFileId, String dstPath) { checkMaxLength(srcPath); checkMaxLength(dstPath); final int success = H5Ocopy(srcFileId, srcPath, dstFileId, dstPath, H5P_DEFAULT, H5P_DEFAULT); return success; } public int moveLink(int fileId, String srcLinkPath, String dstLinkPath) { checkMaxLength(srcLinkPath); checkMaxLength(dstLinkPath); final int success = H5Lmove(fileId, srcLinkPath, fileId, dstLinkPath, lcplCreateIntermediateGroups, H5P_DEFAULT); return success; } // // Group // public void createGroup(int fileId, String groupName) { checkMaxLength(groupName); final int groupId = H5Gcreate(fileId, groupName, lcplCreateIntermediateGroups, H5P_DEFAULT, H5P_DEFAULT); H5Gclose(groupId); } public void createOldStyleGroup(int fileId, String groupName, int sizeHint, ICleanUpRegistry registry) { checkMaxLength(groupName); final int gcplId = H5Pcreate(H5P_GROUP_CREATE); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Pclose(gcplId); } }); H5Pset_local_heap_size_hint(gcplId, sizeHint); final int groupId = H5Gcreate(fileId, groupName, lcplCreateIntermediateGroups, gcplId, H5P_DEFAULT); H5Gclose(groupId); } public void createNewStyleGroup(int fileId, String groupName, int maxCompact, int minDense, ICleanUpRegistry registry) { checkMaxLength(groupName); final int gcplId = H5Pcreate(H5P_GROUP_CREATE); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Pclose(gcplId); } }); H5Pset_link_phase_change(gcplId, maxCompact, minDense); final int groupId = H5Gcreate(fileId, groupName, lcplCreateIntermediateGroups, gcplId, H5P_DEFAULT); H5Gclose(groupId); } public int openGroup(int fileId, String path, ICleanUpRegistry registry) { checkMaxLength(path); final int groupId = isReference(path) ? H5Rdereference(fileId, Long.parseLong(path.substring(1))) : H5Gopen(fileId, path, H5P_DEFAULT); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Gclose(groupId); } }); return groupId; } public long getNumberOfGroupMembers(int fileId, String path, ICleanUpRegistry registry) { checkMaxLength(path); final int groupId = H5Gopen(fileId, path, H5P_DEFAULT); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Gclose(groupId); } }); return H5Gget_nlinks(groupId); } public boolean existsAttribute(final int objectId, final String attributeName) { checkMaxLength(attributeName); return H5Aexists(objectId, attributeName); } public boolean exists(final int fileId, final String linkName) { checkMaxLength(linkName); return H5Lexists(fileId, linkName); } public HDF5LinkInformation getLinkInfo(final int fileId, final String objectName, boolean exceptionIfNonExistent) { checkMaxLength(objectName); if ("/".equals(objectName)) { return HDF5LinkInformation.ROOT_LINK_INFO; } final String[] lname = new String[1]; final int typeId = H5Lget_link_info(fileId, objectName, lname, exceptionIfNonExistent); return HDF5LinkInformation.create(objectName, typeId, lname[0]); } public HDF5ObjectType getLinkTypeInfo(final int fileId, final String objectName, boolean exceptionWhenNonExistent) { checkMaxLength(objectName); if ("/".equals(objectName)) { return HDF5ObjectType.GROUP; } final int typeId = H5Lget_link_info(fileId, objectName, null, exceptionWhenNonExistent); return HDF5CommonInformation.objectTypeIdToObjectType(typeId); } public HDF5ObjectInformation getObjectInfo(final int fileId, final String objectName, boolean exceptionWhenNonExistent) { checkMaxLength(objectName); final long[] info = new long[5]; final int typeId = H5Oget_info_by_name(fileId, objectName, info, exceptionWhenNonExistent); return new HDF5ObjectInformation(objectName, HDF5CommonInformation.objectTypeIdToObjectType(typeId), info); } public int getObjectTypeId(final int fileId, final String objectName, boolean exceptionWhenNonExistent) { checkMaxLength(objectName); if ("/".equals(objectName)) { return H5O_TYPE_GROUP; } return H5Oget_info_by_name(fileId, objectName, null, exceptionWhenNonExistent); } public HDF5ObjectType getObjectTypeInfo(final int fileId, final String objectName, boolean exceptionWhenNonExistent) { return HDF5CommonInformation.objectTypeIdToObjectType(getObjectTypeId(fileId, objectName, exceptionWhenNonExistent)); } public String[] getGroupMembers(final int fileId, final String groupName) { checkMaxLength(groupName); final ICallableWithCleanUp dataDimensionRunnable = new ICallableWithCleanUp() { @Override public String[] call(ICleanUpRegistry registry) { final int groupId = openGroup(fileId, groupName, registry); final long nLong = H5Gget_nlinks(groupId); final int n = (int) nLong; if (n != nLong) { throw new HDF5JavaException( "Number of group members is too large (n=" + nLong + ")"); } final String[] names = new String[n]; H5Lget_link_names_all(groupId, ".", names); return names; } }; return runner.call(dataDimensionRunnable); } public List getGroupMemberLinkInfo(final int fileId, final String groupName, final boolean includeInternal, final String houseKeepingNameSuffix) { checkMaxLength(groupName); final ICallableWithCleanUp> dataDimensionRunnable = new ICallableWithCleanUp>() { @Override public List call(ICleanUpRegistry registry) { final int groupId = openGroup(fileId, groupName, registry); final long nLong = H5Gget_nlinks(groupId); final int n = (int) nLong; if (n != nLong) { throw new HDF5JavaException( "Number of group members is too large (n=" + nLong + ")"); } final String[] names = new String[n]; final String[] linkNames = new String[n]; final int[] types = new int[n]; H5Lget_link_info_all(groupId, ".", names, types, linkNames); final String superGroupName = (groupName.equals("/") ? "/" : groupName + "/"); final List info = new LinkedList(); for (int i = 0; i < n; ++i) { if (includeInternal || HDF5Utils.isInternalName(names[i], houseKeepingNameSuffix) == false) { info.add(HDF5LinkInformation.create(superGroupName + names[i], types[i], linkNames[i])); } } return info; } }; return runner.call(dataDimensionRunnable); } public List getGroupMemberTypeInfo(final int fileId, final String groupName, final boolean includeInternal, final String houseKeepingNameSuffix) { checkMaxLength(groupName); final ICallableWithCleanUp> dataDimensionRunnable = new ICallableWithCleanUp>() { @Override public List call(ICleanUpRegistry registry) { final int groupId = openGroup(fileId, groupName, registry); final long nLong = H5Gget_nlinks(groupId); final int n = (int) nLong; if (n != nLong) { throw new HDF5JavaException( "Number of group members is too large (n=" + nLong + ")"); } final String[] names = new String[n]; final int[] types = new int[n]; H5Lget_link_info_all(groupId, ".", names, types, null); final String superGroupName = (groupName.equals("/") ? "/" : groupName + "/"); final List info = new LinkedList(); for (int i = 0; i < n; ++i) { if (includeInternal || HDF5Utils.isInternalName(names[i], houseKeepingNameSuffix) == false) { info.add(HDF5LinkInformation.create(superGroupName + names[i], types[i], null)); } } return info; } }; return runner.call(dataDimensionRunnable); } // // Link // public void createHardLink(int fileId, String objectName, String linkName) { checkMaxLength(objectName); checkMaxLength(linkName); H5Lcreate_hard(fileId, objectName, fileId, linkName, lcplCreateIntermediateGroups, H5P_DEFAULT); } public void createSoftLink(int fileId, String linkName, String targetPath) { checkMaxLength(linkName); checkMaxLength(targetPath); H5Lcreate_soft(targetPath, fileId, linkName, lcplCreateIntermediateGroups, H5P_DEFAULT); } public void createExternalLink(int fileId, String linkName, String targetFileName, String targetPath) { checkMaxLength(linkName); checkMaxLength(targetFileName); checkMaxLength(targetPath); H5Lcreate_external(targetFileName, targetPath, fileId, linkName, lcplCreateIntermediateGroups, H5P_DEFAULT); } // // Data Set // public void writeStringVL(int dataSetId, int dataTypeId, String[] value) { H5DwriteString(dataSetId, dataTypeId, H5S_ALL, H5S_ALL, H5P_DEFAULT, value); } public void writeStringVL(int dataSetId, int dataTypeId, int memorySpaceId, int fileSpaceId, String[] value) { H5DwriteString(dataSetId, dataTypeId, memorySpaceId, fileSpaceId, H5P_DEFAULT, value); } public int createDataSet(int fileId, long[] dimensions, long[] chunkSizeOrNull, int dataTypeId, HDF5AbstractStorageFeatures compression, String dataSetName, HDF5StorageLayout layout, FileFormat fileFormat, ICleanUpRegistry registry) { checkMaxLength(dataSetName); final int dataSpaceId = H5Screate_simple(dimensions.length, dimensions, createMaxDimensions(dimensions, (layout == HDF5StorageLayout.CHUNKED))); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Sclose(dataSpaceId); } }); final int dataSetCreationPropertyListId; if (layout == HDF5StorageLayout.CHUNKED && chunkSizeOrNull != null) { dataSetCreationPropertyListId = createDataSetCreationPropertyList(registry); setChunkedLayout(dataSetCreationPropertyListId, chunkSizeOrNull); if (compression.isScaling()) { compression.checkScalingOK(fileFormat); final int classTypeId = getClassType(dataTypeId); assert compression.isCompatibleWithDataClass(classTypeId); if (classTypeId == H5T_INTEGER) { H5Pset_scaleoffset(dataSetCreationPropertyListId, H5Z_SO_INT, compression.getScalingFactor()); } else if (classTypeId == H5T_FLOAT) { H5Pset_scaleoffset(dataSetCreationPropertyListId, H5Z_SO_FLOAT_DSCALE, compression.getScalingFactor()); } } if (compression.isShuffleBeforeDeflate()) { setShuffle(dataSetCreationPropertyListId); } if (compression.isDeflating()) { setDeflate(dataSetCreationPropertyListId, compression.getDeflateLevel()); } } else if (layout == HDF5StorageLayout.COMPACT) { dataSetCreationPropertyListId = dataSetCreationPropertyListCompactStorageLayoutFileTimeAlloc; } else { dataSetCreationPropertyListId = dataSetCreationPropertyListFillTimeAlloc; } final int dataSetId = H5Dcreate(fileId, dataSetName, dataTypeId, dataSpaceId, lcplCreateIntermediateGroups, dataSetCreationPropertyListId, H5P_DEFAULT); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Dclose(dataSetId); } }); return dataSetId; } private int createDataSetCreationPropertyList(ICleanUpRegistry registry) { final int dataSetCreationPropertyListId = H5Pcreate(H5P_DATASET_CREATE); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Pclose(dataSetCreationPropertyListId); } }); H5Pset_fill_time(dataSetCreationPropertyListId, H5D_FILL_TIME_ALLOC); return dataSetCreationPropertyListId; } /** * Returns one of: COMPACT, CHUNKED, CONTIGUOUS. */ public HDF5StorageLayout getLayout(int dataSetId, ICleanUpRegistry registry) { final int dataSetCreationPropertyListId = getCreationPropertyList(dataSetId, registry); final int layoutId = H5Pget_layout(dataSetCreationPropertyListId); if (layoutId == H5D_COMPACT) { return HDF5StorageLayout.COMPACT; } else if (layoutId == H5D_CHUNKED) { return HDF5StorageLayout.CHUNKED; } else { return HDF5StorageLayout.CONTIGUOUS; } } private int getCreationPropertyList(int dataSetId, ICleanUpRegistry registry) { final int dataSetCreationPropertyListId = H5Dget_create_plist(dataSetId); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Pclose(dataSetCreationPropertyListId); } }); return dataSetCreationPropertyListId; } private static final long[] createMaxDimensions(long[] dimensions, boolean unlimited) { if (unlimited == false) { return dimensions; } final long[] maxDimensions = new long[dimensions.length]; Arrays.fill(maxDimensions, H5S_UNLIMITED); return maxDimensions; } private void setChunkedLayout(int dscpId, long[] chunkSize) { assert dscpId >= 0; H5Pset_layout(dscpId, H5D_CHUNKED); H5Pset_chunk(dscpId, chunkSize.length, chunkSize); } private void setShuffle(int dscpId) { assert dscpId >= 0; H5Pset_shuffle(dscpId); } private void setDeflate(int dscpId, int deflateLevel) { assert dscpId >= 0; assert deflateLevel >= 0; H5Pset_deflate(dscpId, deflateLevel); } public int createScalarDataSet(int fileId, int dataTypeId, String dataSetName, boolean compactLayout, ICleanUpRegistry registry) { checkMaxLength(dataSetName); final int dataSpaceId = H5Screate(H5S_SCALAR); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Sclose(dataSpaceId); } }); final int dataSetId = H5Dcreate( fileId, dataSetName, dataTypeId, dataSpaceId, lcplCreateIntermediateGroups, compactLayout ? dataSetCreationPropertyListCompactStorageLayoutFileTimeAlloc : dataSetCreationPropertyListFillTimeAlloc, H5P_DEFAULT); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Dclose(dataSetId); } }); return dataSetId; } public int openDataSet(int fileId, String path, ICleanUpRegistry registry) { checkMaxLength(path); final int dataSetId = isReference(path) ? H5Rdereference(fileId, Long.parseLong(path.substring(1))) : H5Dopen(fileId, path, H5P_DEFAULT); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Dclose(dataSetId); } }); return dataSetId; } boolean isReference(String path) { return autoDereference && (path.charAt(0) == '\0'); } /** * @param storageDataTypeId The storage type id, if in overwrite mode, or else -1. */ public int openAndExtendDataSet(int fileId, String path, FileFormat fileFormat, long[] dimensions, int storageDataTypeId, ICleanUpRegistry registry) throws HDF5JavaException { checkMaxLength(path); final boolean overwriteMode = (storageDataTypeId > -1); final int dataSetId = isReference(path) ? H5Rdereference(fileId, Long.parseLong(path.substring(1))) : H5Dopen(fileId, path, H5P_DEFAULT); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Dclose(dataSetId); } }); final long[] oldDimensions = getDataDimensions(dataSetId, registry); if (Arrays.equals(oldDimensions, dimensions) == false) { final HDF5StorageLayout layout = getLayout(dataSetId, registry); if (layout == HDF5StorageLayout.CHUNKED) { // Safety check. JHDF5 creates CHUNKED data sets always with unlimited max // dimensions but we may have to work on a file we haven't created. if (areDimensionsInBounds(dataSetId, dimensions, registry)) { final long[] newDimensions = computeNewDimensions(oldDimensions, dimensions, overwriteMode); setDataSetExtentChunked(dataSetId, newDimensions); } else { throw new HDF5JavaException("New data set dimensions are out of bounds."); } } else if (overwriteMode) { throw new HDF5JavaException("Cannot change dimensions on non-extendable data set."); } else { int dataTypeId = getDataTypeForDataSet(dataSetId, registry); if (getClassType(dataTypeId) == H5T_ARRAY) { throw new HDF5JavaException("Cannot partially overwrite array type."); } if (HDF5Utils.isInBounds(oldDimensions, dimensions) == false) { throw new HDF5JavaException("New data set dimensions are out of bounds."); } } } return dataSetId; } private long[] computeNewDimensions(long[] oldDimensions, long[] newDimensions, boolean cutDownExtendIfNecessary) { if (cutDownExtendIfNecessary) { return newDimensions; } else { final long[] newUncutDimensions = new long[oldDimensions.length]; for (int i = 0; i < newUncutDimensions.length; ++i) { newUncutDimensions[i] = Math.max(oldDimensions[i], newDimensions[i]); } return newUncutDimensions; } } /** * Checks whether the given dimensions are in bounds for dataSetId. */ private boolean areDimensionsInBounds(final int dataSetId, final long[] dimensions, ICleanUpRegistry registry) { final long[] maxDimensions = getDataMaxDimensions(dataSetId, registry); if (dimensions.length != maxDimensions.length) // Actually an error condition { return false; } for (int i = 0; i < dimensions.length; ++i) { if (maxDimensions[i] != H5S_UNLIMITED && dimensions[i] > maxDimensions[i]) { return false; } } return true; } public void setDataSetExtentChunked(int dataSetId, long[] dimensions) { assert dataSetId >= 0; assert dimensions != null; H5Dset_extent(dataSetId, dimensions); } public void readDataSetNonNumeric(int dataSetId, int nativeDataTypeId, byte[] data) { H5Dread(dataSetId, nativeDataTypeId, H5S_ALL, H5S_ALL, H5P_DEFAULT, data); } public void readDataSetNonNumeric(int dataSetId, int nativeDataTypeId, int memorySpaceId, int fileSpaceId, byte[] data) { H5Dread(dataSetId, nativeDataTypeId, memorySpaceId, fileSpaceId, H5P_DEFAULT, data); } public void readDataSetString(int dataSetId, int nativeDataTypeId, String[] data) { H5Dread_string(dataSetId, nativeDataTypeId, H5S_ALL, H5S_ALL, H5P_DEFAULT, data); } public void readDataSetString(int dataSetId, int nativeDataTypeId, int memorySpaceId, int fileSpaceId, String[] data) { H5Dread_string(dataSetId, nativeDataTypeId, memorySpaceId, fileSpaceId, H5P_DEFAULT, data); } public void readDataSet(int dataSetId, int nativeDataTypeId, byte[] data) { H5Dread(dataSetId, nativeDataTypeId, H5S_ALL, H5S_ALL, numericConversionXferPropertyListID, data); } public void readDataSet(int dataSetId, int nativeDataTypeId, short[] data) { H5Dread(dataSetId, nativeDataTypeId, H5S_ALL, H5S_ALL, numericConversionXferPropertyListID, data); } public void readDataSet(int dataSetId, int nativeDataTypeId, int[] data) { H5Dread(dataSetId, nativeDataTypeId, H5S_ALL, H5S_ALL, numericConversionXferPropertyListID, data); } public void readDataSet(int dataSetId, int nativeDataTypeId, long[] data) { H5Dread(dataSetId, nativeDataTypeId, H5S_ALL, H5S_ALL, numericConversionXferPropertyListID, data); } public void readDataSet(int dataSetId, int nativeDataTypeId, float[] data) { H5Dread(dataSetId, nativeDataTypeId, H5S_ALL, H5S_ALL, numericConversionXferPropertyListID, data); } public void readDataSet(int dataSetId, int nativeDataTypeId, double[] data) { H5Dread(dataSetId, nativeDataTypeId, H5S_ALL, H5S_ALL, numericConversionXferPropertyListID, data); } public void readDataSet(int dataSetId, int nativeDataTypeId, int memorySpaceId, int fileSpaceId, byte[] data) { H5Dread(dataSetId, nativeDataTypeId, memorySpaceId, fileSpaceId, numericConversionXferPropertyListID, data); } public void readDataSet(int dataSetId, int nativeDataTypeId, int memorySpaceId, int fileSpaceId, short[] data) { H5Dread(dataSetId, nativeDataTypeId, memorySpaceId, fileSpaceId, numericConversionXferPropertyListID, data); } public void readDataSet(int dataSetId, int nativeDataTypeId, int memorySpaceId, int fileSpaceId, int[] data) { H5Dread(dataSetId, nativeDataTypeId, memorySpaceId, fileSpaceId, numericConversionXferPropertyListID, data); } public void readDataSet(int dataSetId, int nativeDataTypeId, int memorySpaceId, int fileSpaceId, long[] data) { H5Dread(dataSetId, nativeDataTypeId, memorySpaceId, fileSpaceId, numericConversionXferPropertyListID, data); } public void readDataSet(int dataSetId, int nativeDataTypeId, int memorySpaceId, int fileSpaceId, float[] data) { H5Dread(dataSetId, nativeDataTypeId, memorySpaceId, fileSpaceId, numericConversionXferPropertyListID, data); } public void readDataSet(int dataSetId, int nativeDataTypeId, int memorySpaceId, int fileSpaceId, double[] data) { H5Dread(dataSetId, nativeDataTypeId, memorySpaceId, fileSpaceId, numericConversionXferPropertyListID, data); } public void readDataSetVL(int dataSetId, int dataTypeId, String[] data) { H5DreadVL(dataSetId, dataTypeId, H5S_ALL, H5S_ALL, H5P_DEFAULT, data); replaceNullWithEmptyString(data); } public void readDataSetVL(int dataSetId, int dataTypeId, int memorySpaceId, int fileSpaceId, String[] data) { H5DreadVL(dataSetId, dataTypeId, memorySpaceId, fileSpaceId, H5P_DEFAULT, data); replaceNullWithEmptyString(data); } // A fixed-length string array returns uninitialized strings as "", a variable-length string as // null. We don't want the application programmer to have to be aware of this difference, // thus we replace null with "" here. private void replaceNullWithEmptyString(String[] data) { for (int i = 0; i < data.length; ++i) { if (data[i] == null) { data[i] = ""; } } } // // Attribute // public int createAttribute(int locationId, String attributeName, int dataTypeId, int dataSpaceIdOrMinusOne, ICleanUpRegistry registry) { checkMaxLength(attributeName); final int dataSpaceId = (dataSpaceIdOrMinusOne == -1) ? H5Screate(H5S_SCALAR) : dataSpaceIdOrMinusOne; if (dataSpaceIdOrMinusOne == -1) { registry.registerCleanUp(new Runnable() { @Override public void run() { H5Sclose(dataSpaceId); } }); } final int attCreationPlistId; if (useUTF8CharEncoding) { attCreationPlistId = H5Pcreate(H5P_ATTRIBUTE_CREATE); setCharacterEncodingCreationPropertyList(attCreationPlistId, CharacterEncoding.UTF8); } else { attCreationPlistId = H5P_DEFAULT; } final int attributeId = H5Acreate(locationId, attributeName, dataTypeId, dataSpaceId, attCreationPlistId, H5P_DEFAULT); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Aclose(attributeId); } }); return attributeId; } public int deleteAttribute(int locationId, String attributeName) { checkMaxLength(attributeName); final int success = H5Adelete(locationId, attributeName); return success; } public int openAttribute(int locationId, String attributeName, ICleanUpRegistry registry) { checkMaxLength(attributeName); final int attributeId = H5Aopen_name(locationId, attributeName); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Aclose(attributeId); } }); return attributeId; } public List getAttributeNames(int locationId, ICleanUpRegistry registry) { final int numberOfAttributes = H5Aget_num_attrs(locationId); final List attributeNames = new LinkedList(); for (int i = 0; i < numberOfAttributes; ++i) { final int attributeId = H5Aopen_idx(locationId, i); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Aclose(attributeId); } }); final String[] nameContainer = new String[1]; // Find out length of attribute name. final long nameLength = H5Aget_name(attributeId, 0L, null); // Read attribute name final long nameLengthRead = H5Aget_name(attributeId, nameLength + 1, nameContainer); if (nameLengthRead != nameLength) { throw new HDF5JavaException(String.format( "Error reading attribute name [wrong name length " + "when reading attribute %d, expected: %d, found: %d]", i, nameLength, nameLengthRead)); } attributeNames.add(nameContainer[0]); } return attributeNames; } public byte[] readAttributeAsByteArray(int attributeId, int dataTypeId, int length) { final byte[] data = new byte[length]; H5Aread(attributeId, dataTypeId, data); return data; } public short[] readAttributeAsShortArray(int attributeId, int dataTypeId, int length) { final short[] data = new short[length]; H5Aread(attributeId, dataTypeId, data); return data; } public int[] readAttributeAsIntArray(int attributeId, int dataTypeId, int length) { final int[] data = new int[length]; H5Aread(attributeId, dataTypeId, data); return data; } public long[] readAttributeAsLongArray(int attributeId, int dataTypeId, int length) { final long[] data = new long[length]; H5Aread(attributeId, dataTypeId, data); return data; } public float[] readAttributeAsFloatArray(int attributeId, int dataTypeId, int length) { final float[] data = new float[length]; H5Aread(attributeId, dataTypeId, data); return data; } public double[] readAttributeAsDoubleArray(int attributeId, int dataTypeId, int length) { final double[] data = new double[length]; H5Aread(attributeId, dataTypeId, data); return data; } public void readAttributeVL(int attributeId, int dataTypeId, String[] data) { H5AreadVL(attributeId, dataTypeId, data); } public void writeAttribute(int attributeId, int dataTypeId, byte[] value) { H5Awrite(attributeId, dataTypeId, value); } public void writeAttribute(int attributeId, int dataTypeId, short[] value) { H5Awrite(attributeId, dataTypeId, value); } public void writeAttribute(int attributeId, int dataTypeId, int[] value) { H5Awrite(attributeId, dataTypeId, value); } public void writeAttribute(int attributeId, int dataTypeId, long[] value) { H5Awrite(attributeId, dataTypeId, value); } public void writeAttribute(int attributeId, int dataTypeId, float[] value) { H5Awrite(attributeId, dataTypeId, value); } public void writeAttribute(int attributeId, int dataTypeId, double[] value) { H5Awrite(attributeId, dataTypeId, value); } public void writeAttributeStringVL(int attributeId, int dataTypeId, String[] value) { H5AwriteString(attributeId, dataTypeId, value); } // // Data Type // public int copyDataType(int dataTypeId, ICleanUpRegistry registry) { final int copiedDataTypeId = H5Tcopy(dataTypeId); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Tclose(copiedDataTypeId); } }); return copiedDataTypeId; } public int createDataTypeVariableString(ICleanUpRegistry registry) { final int dataTypeId = createDataTypeStringVariableLength(); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Tclose(dataTypeId); } }); if (useUTF8CharEncoding) { setCharacterEncodingDataType(dataTypeId, CharacterEncoding.UTF8); } return dataTypeId; } private int createDataTypeStringVariableLength() { int dataTypeId = H5Tcopy(H5T_C_S1); H5Tset_size(dataTypeId, H5T_VARIABLE); return dataTypeId; } public int createDataTypeString(int length, ICleanUpRegistry registry) { assert length > 0; final int dataTypeId = H5Tcopy(H5T_C_S1); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Tclose(dataTypeId); } }); H5Tset_size(dataTypeId, length); H5Tset_strpad(dataTypeId, H5T_STR_NULLPAD); if (useUTF8CharEncoding) { setCharacterEncodingDataType(dataTypeId, CharacterEncoding.UTF8); } return dataTypeId; } private void setCharacterEncodingDataType(int dataTypeId, CharacterEncoding encoding) { H5Tset_cset(dataTypeId, encoding.getCValue()); } public int createArrayType(int baseTypeId, int length, ICleanUpRegistry registry) { final int dataTypeId = H5Tarray_create(baseTypeId, 1, new int[] { length }); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Tclose(dataTypeId); } }); return dataTypeId; } public int createArrayType(int baseTypeId, int[] dimensions, ICleanUpRegistry registry) { final int dataTypeId = H5Tarray_create(baseTypeId, dimensions.length, dimensions); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Tclose(dataTypeId); } }); return dataTypeId; } private enum EnumSize { BYTE8, SHORT16, INT32 } public int createDataTypeEnum(String[] names, ICleanUpRegistry registry) { for (String name : names) { checkMaxLength(name); } final EnumSize size = (names.length < Byte.MAX_VALUE) ? EnumSize.BYTE8 : (names.length < Short.MAX_VALUE) ? EnumSize.SHORT16 : EnumSize.INT32; final int baseDataTypeId; switch (size) { case BYTE8: baseDataTypeId = H5T_STD_I8LE; break; case SHORT16: baseDataTypeId = H5T_STD_I16LE; break; case INT32: baseDataTypeId = H5T_STD_I32LE; break; default: throw new InternalError(); } final int dataTypeId = H5Tenum_create(baseDataTypeId); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Tclose(dataTypeId); } }); switch (size) { case BYTE8: for (byte i = 0; i < names.length; ++i) { insertMemberEnum(dataTypeId, names[i], i); } break; case SHORT16: { final short[] values = getLittleEndianSuccessiveShortValues(names); for (short i = 0; i < names.length; ++i) { insertMemberEnum(dataTypeId, names[i], values[i]); } break; } case INT32: { final int[] values = getLittleEndianSuccessiveIntValues(names); for (int i = 0; i < names.length; ++i) { insertMemberEnum(dataTypeId, names[i], values[i]); } break; } } return dataTypeId; } private short[] getLittleEndianSuccessiveShortValues(String[] names) { final short[] values = new short[names.length]; for (short i = 0; i < names.length; ++i) { values[i] = i; } H5Tconvert_to_little_endian(values); return values; } private int[] getLittleEndianSuccessiveIntValues(String[] names) { final int[] values = new int[names.length]; for (int i = 0; i < names.length; ++i) { values[i] = i; } H5Tconvert_to_little_endian(values); return values; } private void insertMemberEnum(int dataTypeId, String name, byte value) { assert dataTypeId >= 0; assert name != null; H5Tenum_insert(dataTypeId, name, value); } private void insertMemberEnum(int dataTypeId, String name, short value) { assert dataTypeId >= 0; assert name != null; H5Tenum_insert(dataTypeId, name, value); } private void insertMemberEnum(int dataTypeId, String name, int value) { assert dataTypeId >= 0; assert name != null; H5Tenum_insert(dataTypeId, name, value); } /** Returns the number of members of an enum type or a compound type. */ public int getNumberOfMembers(int dataTypeId) { return H5Tget_nmembers(dataTypeId); } /** * Returns the name of an enum value or compound member for the given index. *

* Must not be called on a dateTypeId that is not an enum or compound type. */ public String getNameForEnumOrCompoundMemberIndex(int dataTypeId, int index) { return H5Tget_member_name(dataTypeId, index); } /** * Returns the offset of a compound member for the given index. *

* Must not be called on a dateTypeId that is not a compound type. */ public int getOffsetForCompoundMemberIndex(int dataTypeId, int index) { return (int) H5Tget_member_offset(dataTypeId, index); } /** * Returns the names of an enum value or compound members. *

* Must not be called on a dateTypeId that is not an enum or compound type. */ public String[] getNamesForEnumOrCompoundMembers(int dataTypeId) { final int len = getNumberOfMembers(dataTypeId); final String[] values = new String[len]; for (int i = 0; i < len; ++i) { values[i] = H5Tget_member_name(dataTypeId, i); } return values; } /** * Returns the index of an enum value or compound member for the given name. Works on * enum and compound data types. */ public int getIndexForMemberName(int dataTypeId, String name) { checkMaxLength(name); return H5Tget_member_index(dataTypeId, name); } /** * Returns the data type id for a member of a compound data type, specified by index. */ public int getDataTypeForIndex(int compoundDataTypeId, int index, ICleanUpRegistry registry) { final int memberTypeId = H5Tget_member_type(compoundDataTypeId, index); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Tclose(memberTypeId); } }); return memberTypeId; } /** * Returns the data type id for a member of a compound data type, specified by name. */ public int getDataTypeForMemberName(int compoundDataTypeId, String memberName) { checkMaxLength(memberName); final int index = H5Tget_member_index(compoundDataTypeId, memberName); return H5Tget_member_type(compoundDataTypeId, index); } public Boolean tryGetBooleanValue(final int dataTypeId, final int intValue) { if (getClassType(dataTypeId) != H5T_ENUM) { return null; } final String value = getNameForEnumOrCompoundMemberIndex(dataTypeId, intValue); if ("TRUE".equalsIgnoreCase(value)) { return true; } else if ("FALSE".equalsIgnoreCase(value)) { return false; } else { return null; } } public int createDataTypeCompound(int lengthInBytes, ICleanUpRegistry registry) { final int dataTypeId = H5Tcreate(H5T_COMPOUND, lengthInBytes); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Tclose(dataTypeId); } }); return dataTypeId; } public int createDataTypeOpaque(int lengthInBytes, String tag, ICleanUpRegistry registry) { checkMaxLength(tag); final int dataTypeId = H5Tcreate(H5T_OPAQUE, lengthInBytes); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Tclose(dataTypeId); } }); H5Tset_tag(dataTypeId, tag.length() > H5T_OPAQUE_TAG_MAX ? tag.substring(0, H5T_OPAQUE_TAG_MAX) : tag); return dataTypeId; } public void commitDataType(int fileId, String name, int dataTypeId) { checkMaxLength(name); H5Tcommit(fileId, name, dataTypeId, lcplCreateIntermediateGroups, H5P_DEFAULT, H5P_DEFAULT); } public int openDataType(int fileId, String name, ICleanUpRegistry registry) { checkMaxLength(name); final int dataTypeId = isReference(name) ? H5Rdereference(fileId, Long.parseLong(name.substring(1))) : H5Topen(fileId, name, H5P_DEFAULT); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Tclose(dataTypeId); } }); return dataTypeId; } public boolean dataTypesAreEqual(int dataTypeId1, int dataTypeId2) { return H5Tequal(dataTypeId1, dataTypeId2); } public int getDataTypeForDataSet(int dataSetId, ICleanUpRegistry registry) { final int dataTypeId = H5Dget_type(dataSetId); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Tclose(dataTypeId); } }); return dataTypeId; } public int getDataTypeForAttribute(int attributeId, ICleanUpRegistry registry) { final int dataTypeId = H5Aget_type(attributeId); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Tclose(dataTypeId); } }); return dataTypeId; } public String tryGetOpaqueTag(int dataTypeId) { return H5Tget_tag(dataTypeId); } public int getNativeDataType(int dataTypeId, ICleanUpRegistry registry) { final int nativeDataTypeId = H5Tget_native_type(dataTypeId); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Tclose(nativeDataTypeId); } }); return nativeDataTypeId; } public int getNativeDataTypeForDataSet(int dataSetId, ICleanUpRegistry registry) { final int dataTypeId = H5Dget_type(dataSetId); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Tclose(dataTypeId); } }); return getNativeDataType(dataTypeId, registry); } public int getNativeDataTypeForAttribute(int attributeId, ICleanUpRegistry registry) { final int dataTypeId = H5Aget_type(attributeId); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Tclose(dataTypeId); } }); return getNativeDataType(dataTypeId, registry); } public int getDataTypeSize(int dataTypeId) { return H5Tget_size(dataTypeId); } public long getDataTypeSizeLong(int dataTypeId) throws HDF5JavaException { return H5Tget_size_long(dataTypeId); } public boolean isVariableLengthString(int dataTypeId) { return H5Tis_variable_str(dataTypeId); } public int getClassType(int dataTypeId) { return H5Tget_class(dataTypeId); } public CharacterEncoding getCharacterEncoding(int dataTypeId) { final int cValue = H5Tget_cset(dataTypeId); if (cValue == CharacterEncoding.ASCII.getCValue()) { return CharacterEncoding.ASCII; } else if (cValue == CharacterEncoding.UTF8.getCValue()) { return CharacterEncoding.UTF8; } else { throw new HDF5JavaException("Unknown character encoding cValue " + cValue); } } public boolean hasClassType(int dataTypeId, int classTypeId) { return H5Tdetect_class(dataTypeId, classTypeId); } public int getBaseDataType(int dataTypeId, ICleanUpRegistry registry) { final int baseDataTypeId = H5Tget_super(dataTypeId); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Tclose(baseDataTypeId); } }); return baseDataTypeId; } public boolean getSigned(int dataTypeId) { return H5Tget_sign(dataTypeId) != H5T_SGN_NONE; } public String tryGetDataTypePath(int dataTypeId) { if (dataTypeId < 0 || H5Tcommitted(dataTypeId) == false) { return null; } final String[] result = new String[1]; final long len = H5Iget_name(dataTypeId, result, 64); if (len >= result[0].length()) { H5Iget_name(dataTypeId, result, len + 1); } return result[0]; } /** * Reclaims the variable-length data structures from a compound buffer, if any. */ public void reclaimCompoundVL(HDF5CompoundType type, byte[] buf) { int[] vlMemberIndices = type.getObjectByteifyer().getVLMemberIndices(); if (vlMemberIndices.length > 0) // This type has variable-length data members { HDFNativeData.freeCompoundVLStr(buf, type.getRecordSizeInMemory(), vlMemberIndices); } } // // Data Space // public int getDataSpaceForDataSet(int dataSetId, ICleanUpRegistry registry) { final int dataTypeId = H5Dget_space(dataSetId); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Sclose(dataTypeId); } }); return dataTypeId; } public long[] getDataDimensionsForAttribute(final int attributeId, ICleanUpRegistry registry) { final int dataSpaceId = H5Aget_space(attributeId); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Sclose(dataSpaceId); } }); final long[] dimensions = getDataSpaceDimensions(dataSpaceId); return dimensions; } public long[] getDataDimensions(final int dataSetId, ICleanUpRegistry registry) { final int dataSpaceId = H5Dget_space(dataSetId); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Sclose(dataSpaceId); } }); long[] dimensions = getDataSpaceDimensions(dataSpaceId); // Ensure backward compatibility with 8.10 if (HDF5Utils.mightBeEmptyInStorage(dimensions) && existsAttribute(dataSetId, HDF5Utils.DATASET_IS_EMPTY_LEGACY_ATTRIBUTE)) { dimensions = new long[dimensions.length]; } return dimensions; } public long[] getDataMaxDimensions(final int dataSetId) { ICallableWithCleanUp dataDimensionRunnable = new ICallableWithCleanUp() { @Override public long[] call(ICleanUpRegistry registry) { return getDataMaxDimensions(dataSetId, registry); } }; return runner.call(dataDimensionRunnable); } private long[] getDataMaxDimensions(final int dataSetId, ICleanUpRegistry registry) { final int dataSpaceId = H5Dget_space(dataSetId); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Sclose(dataSpaceId); } }); final long[] dimensions = getDataSpaceMaxDimensions(dataSpaceId); return dimensions; } public int getDataSpaceRank(int dataSpaceId) { return H5Sget_simple_extent_ndims(dataSpaceId); } public long[] getDataSpaceDimensions(int dataSpaceId) { final int rank = H5Sget_simple_extent_ndims(dataSpaceId); return getDataSpaceDimensions(dataSpaceId, rank); } public long[] getDataSpaceDimensions(int dataSpaceId, int rank) { assert dataSpaceId >= 0; assert rank >= 0; final long[] dimensions = new long[rank]; H5Sget_simple_extent_dims(dataSpaceId, dimensions, null); return dimensions; } public long[] getDataSpaceMaxDimensions(int dataSpaceId) { final int rank = H5Sget_simple_extent_ndims(dataSpaceId); return getDataSpaceMaxDimensions(dataSpaceId, rank); } public long[] getDataSpaceMaxDimensions(int dataSpaceId, int rank) { assert dataSpaceId >= 0; assert rank >= 0; final long[] maxDimensions = new long[rank]; H5Sget_simple_extent_dims(dataSpaceId, null, maxDimensions); return maxDimensions; } /** * @param dataSetOrAttributeId The id of either the data set or the attribute to get the rank * for. * @param isAttribute If true, dataSetOrAttributeId will be interpreted * as an attribute, otherwise as a data set. */ public int getRank(final int dataSetOrAttributeId, final boolean isAttribute, ICleanUpRegistry registry) { final int dataSpaceId = isAttribute ? H5Aget_space(dataSetOrAttributeId) : H5Dget_space(dataSetOrAttributeId); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Sclose(dataSpaceId); } }); return H5Sget_simple_extent_ndims(dataSpaceId); } /** * @param dataSetOrAttributeId The id of either the data set or the attribute to get the rank * for. * @param isAttribute If true, dataSetOrAttributeId will be interpreted * as an attribute, otherwise as a data set. */ public long[] getDimensions(final int dataSetOrAttributeId, final boolean isAttribute, ICleanUpRegistry registry) { final int dataSpaceId = isAttribute ? H5Aget_space(dataSetOrAttributeId) : H5Dget_space(dataSetOrAttributeId); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Sclose(dataSpaceId); } }); final long[] dimensions = new long[H5S_MAX_RANK]; final int rank = H5Sget_simple_extent_dims(dataSpaceId, dimensions, null); final long[] realDimensions = new long[rank]; System.arraycopy(dimensions, 0, realDimensions, 0, rank); return realDimensions; } /** * @param dataSetOrAttributeId The id of either the data set or the attribute to get the * dimensions for. * @param isAttribute If true, dataSetOrAttributeId will be interpreted * as an attribute, otherwise as a data set. * @param dataSetInfo The info object to fill. */ public void fillDataDimensions(final int dataSetOrAttributeId, final boolean isAttribute, final HDF5DataSetInformation dataSetInfo, ICleanUpRegistry registry) { final int dataSpaceId = isAttribute ? H5Aget_space(dataSetOrAttributeId) : H5Dget_space(dataSetOrAttributeId); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Sclose(dataSpaceId); } }); final long[] dimensions = new long[H5S_MAX_RANK]; final long[] maxDimensions = new long[H5S_MAX_RANK]; final int rank = H5Sget_simple_extent_dims(dataSpaceId, dimensions, maxDimensions); final long[] realDimensions = new long[rank]; System.arraycopy(dimensions, 0, realDimensions, 0, rank); final long[] realMaxDimensions = new long[rank]; System.arraycopy(maxDimensions, 0, realMaxDimensions, 0, rank); dataSetInfo.setDimensions(realDimensions); dataSetInfo.setMaxDimensions(realMaxDimensions); if (isAttribute == false) { final long[] chunkSizes = new long[rank]; final int creationPropertyList = getCreationPropertyList(dataSetOrAttributeId, registry); final HDF5StorageLayout layout = HDF5StorageLayout.fromId(H5Pget_layout(creationPropertyList)); dataSetInfo.setStorageLayout(layout); if (layout == HDF5StorageLayout.CHUNKED) { H5Pget_chunk(creationPropertyList, rank, chunkSizes); dataSetInfo.setChunkSizes(MDAbstractArray.toInt(chunkSizes)); } } } public int[] getArrayDimensions(int arrayTypeId) { final int rank = H5Tget_array_ndims(arrayTypeId); final int[] dims = new int[rank]; H5Tget_array_dims(arrayTypeId, dims); return dims; } public int createScalarDataSpace() { return H5Screate(H5S_SCALAR); } public int createSimpleDataSpace(long[] dimensions, ICleanUpRegistry registry) { final int dataSpaceId = H5Screate_simple(dimensions.length, dimensions, null); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Sclose(dataSpaceId); } }); return dataSpaceId; } public void setHyperslabBlock(int dataSpaceId, long[] start, long[] count) { assert dataSpaceId >= 0; assert start != null; assert count != null; H5Sselect_hyperslab(dataSpaceId, H5S_SELECT_SET, start, null, count, null); } // // Properties // private int createLinkCreationPropertyList(boolean createIntermediateGroups, ICleanUpRegistry registry) { final int linkCreationPropertyList = H5Pcreate(H5P_LINK_CREATE); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Pclose(linkCreationPropertyList); } }); if (createIntermediateGroups) { H5Pset_create_intermediate_group(linkCreationPropertyList, true); } if (useUTF8CharEncoding) { setCharacterEncodingCreationPropertyList(linkCreationPropertyList, CharacterEncoding.UTF8); } return linkCreationPropertyList; } // Only use with H5P_LINK_CREATE, H5P_ATTRIBUTE_CREATE and H5P_STRING_CREATE property list ids private void setCharacterEncodingCreationPropertyList(int creationPropertyList, CharacterEncoding encoding) { H5Pset_char_encoding(creationPropertyList, encoding.getCValue()); } private int createDataSetXferPropertyListAbortOverflow(ICleanUpRegistry registry) { final int datasetXferPropertyList = H5Pcreate_xfer_abort_overflow(); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Pclose(datasetXferPropertyList); } }); return datasetXferPropertyList; } private int createDataSetXferPropertyListAbort(ICleanUpRegistry registry) { final int datasetXferPropertyList = H5Pcreate_xfer_abort(); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Pclose(datasetXferPropertyList); } }); return datasetXferPropertyList; } // // References // String getReferencedObjectName(int objectId, byte[] reference) { return H5Rget_name(objectId, H5R_OBJECT, reference); } String getReferencedObjectName(int objectId, long reference) { return H5Rget_name(objectId, reference); } String[] getReferencedObjectNames(int objectId, long[] reference) { return H5Rget_name(objectId, reference); } String getReferencedObjectName(int objectId, byte[] references, int ofs) { final byte[] reference = new byte[HDF5BaseReader.REFERENCE_SIZE_IN_BYTES]; System.arraycopy(references, ofs, reference, 0, HDF5BaseReader.REFERENCE_SIZE_IN_BYTES); return H5Rget_name(objectId, H5R_OBJECT, reference); } byte[] createObjectReference(int fileId, String objectPath) { return H5Rcreate(fileId, objectPath, H5R_OBJECT, -1); } long[] createObjectReferences(int fileId, String[] objectPaths) { return H5Rcreate(fileId, objectPaths); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5AbstractStorageFeatures.java000066400000000000000000000300551256564762100314260ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator.FileFormat; /** * An object representing the storage features that are to be used for a data set. *

* The available storage layouts are {@link HDF5StorageLayout#COMPACT}, * {@link HDF5StorageLayout#CONTIGUOUS} or {@link HDF5StorageLayout#CHUNKED} can be chosen. Only * {@link HDF5StorageLayout#CHUNKED} is extendable and can be compressed. *

* Two types of compressions are supported: deflation (the method used by gzip) * and scaling, which can be used if the accuracy of the values are smaller than what the * atomic data type can store. Note that scaling in general can be a lossy compression while * deflation is always lossless. Scaling compression is only available with HDF5 1.8 * and newer. Trying to use scaling in strict HDF5 1.6 compatibility mode will throw an * {@link IllegalStateException}. *

* For deflation the deflation level can be chosen to get the right balance between speed of * compression and compression ratio. Often the {@link #DEFAULT_DEFLATION_LEVEL} will be the right * choice. *

* For scaling, the scaling factor can be chosen that determines the accuracy of the values * saved. What exactly the scaling factor means, differs between float and integer values. * * @author Bernd Rinn */ abstract class HDF5AbstractStorageFeatures { /** * A constant that specifies that no deflation should be used. */ public final static byte NO_DEFLATION_LEVEL = 0; /** * A constant that specifies the default deflation level (gzip compression). */ public final static byte DEFAULT_DEFLATION_LEVEL = 6; /** * A constant that specifies the maximal deflation level (gzip compression). */ public final static byte MAX_DEFLATION_LEVEL = 9; /** * The policy on how to deal with write access to existing datasets. "Keeping the dataset" means * to overwrite the content of the dataset, while "replacing the dataset" refers to deleting the * existing dataset and create a new one. */ public enum DataSetReplacementPolicy { /** Use the default behavior as specified when the writer was created. */ USE_WRITER_DEFAULT, /** Enforce to keep the existing dataset, overwriting the writer's default. */ ENFORCE_KEEP_EXISTING, /** Enforce to replace the existing dataset, overwriting the writer's default. */ ENFORCE_REPLACE_WITH_NEW } /** * Do not perform any scaling on the data. */ final static byte NO_SCALING_FACTOR = -1; static byte toByte(int i) { final byte b = (byte) i; if (b != i) { throw new HDF5JavaException("Value " + i + " cannot be casted to type byte"); } return b; } private final byte deflateLevel; private final byte scalingFactor; private final DataSetReplacementPolicy datasetReplacementPolicy; private final HDF5StorageLayout proposedLayoutOrNull; private final boolean shuffleBeforeDeflate; public abstract static class HDF5AbstractStorageFeatureBuilder { private byte deflateLevel; private byte scalingFactor; private HDF5StorageLayout storageLayout; private DataSetReplacementPolicy datasetReplacementPolicy = DataSetReplacementPolicy.USE_WRITER_DEFAULT; private boolean shuffleBeforeDeflate; HDF5AbstractStorageFeatureBuilder() { } public HDF5AbstractStorageFeatureBuilder(HDF5AbstractStorageFeatures template) { deflateLevel(template.getDeflateLevel()); scalingFactor(template.getScalingFactor()); storageLayout(template.tryGetProposedLayout()); datasetReplacementPolicy(template.getDatasetReplacementPolicy()); shuffleBeforeDeflate(template.isShuffleBeforeDeflate()); } byte getDeflateLevel() { return deflateLevel; } byte getScalingFactor() { return scalingFactor; } HDF5StorageLayout getStorageLayout() { return storageLayout; } DataSetReplacementPolicy getDatasetReplacementPolicy() { return datasetReplacementPolicy; } boolean isShuffleBeforeDeflate() { return shuffleBeforeDeflate; } public HDF5AbstractStorageFeatureBuilder compress(boolean compress) { this.deflateLevel = compress ? DEFAULT_DEFLATION_LEVEL : NO_DEFLATION_LEVEL; return this; } public HDF5AbstractStorageFeatureBuilder compress() { this.deflateLevel = DEFAULT_DEFLATION_LEVEL; return this; } public HDF5AbstractStorageFeatureBuilder deflateLevel(@SuppressWarnings("hiding") byte deflateLevel) { this.deflateLevel = deflateLevel; return this; } public HDF5AbstractStorageFeatureBuilder scalingFactor(@SuppressWarnings("hiding") byte scalingFactor) { this.scalingFactor = scalingFactor; return this; } public HDF5AbstractStorageFeatureBuilder noScaling() { this.scalingFactor = (byte) -1; return this; } public HDF5AbstractStorageFeatureBuilder shuffleBeforeDeflate(@SuppressWarnings("hiding") boolean shuffleBeforeDeflate) { this.shuffleBeforeDeflate = shuffleBeforeDeflate; return this; } public HDF5AbstractStorageFeatureBuilder shuffleBeforeDeflate() { this.shuffleBeforeDeflate = true; return this; } public HDF5AbstractStorageFeatureBuilder noShuffleBeforeDeflate() { this.shuffleBeforeDeflate = true; return this; } public HDF5AbstractStorageFeatureBuilder storageLayout(@SuppressWarnings("hiding") HDF5StorageLayout storageLayout) { this.storageLayout = storageLayout; return this; } public HDF5AbstractStorageFeatureBuilder compactStorageLayout() { this.storageLayout = HDF5StorageLayout.COMPACT; return this; } public HDF5AbstractStorageFeatureBuilder contiguousStorageLayout() { this.storageLayout = HDF5StorageLayout.CONTIGUOUS; return this; } public HDF5AbstractStorageFeatureBuilder chunkedStorageLayout() { this.storageLayout = HDF5StorageLayout.CHUNKED; return this; } public HDF5AbstractStorageFeatureBuilder defaultStorageLayout() { this.storageLayout = null; return this; } public HDF5AbstractStorageFeatureBuilder datasetReplacementPolicy( @SuppressWarnings("hiding") DataSetReplacementPolicy datasetReplacementPolicy) { this.datasetReplacementPolicy = datasetReplacementPolicy; return this; } public HDF5AbstractStorageFeatureBuilder datasetReplacementUseWriterDefault() { this.datasetReplacementPolicy = DataSetReplacementPolicy.USE_WRITER_DEFAULT; return this; } public HDF5AbstractStorageFeatureBuilder datasetReplacementEnforceKeepExisting() { this.datasetReplacementPolicy = DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING; return this; } public HDF5AbstractStorageFeatureBuilder datasetReplacementEnforceReplaceWithNew() { this.datasetReplacementPolicy = DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW; return this; } abstract public HDF5AbstractStorageFeatures features(); } HDF5AbstractStorageFeatures(final HDF5StorageLayout proposedLayoutOrNull, final DataSetReplacementPolicy datasetReplacementPolicy, final byte deflateLevel, final byte scalingFactor) { this(proposedLayoutOrNull, datasetReplacementPolicy, false, deflateLevel, scalingFactor); } HDF5AbstractStorageFeatures(final HDF5StorageLayout proposedLayoutOrNull, final DataSetReplacementPolicy datasetReplacementPolicy, final boolean shuffleBeforeDeflate, final byte deflateLevel, final byte scalingFactor) { if (deflateLevel < 0) { throw new IllegalArgumentException("Invalid deflateLevel " + deflateLevel); } this.proposedLayoutOrNull = proposedLayoutOrNull; this.datasetReplacementPolicy = datasetReplacementPolicy; this.shuffleBeforeDeflate = shuffleBeforeDeflate; this.deflateLevel = deflateLevel; this.scalingFactor = scalingFactor; } /** * Returns true, if this compression setting can be applied on the given dataClassId. */ abstract boolean isCompatibleWithDataClass(int dataClassId); /** * Returns the proposed storage layout, or null, if no particular storage layout * should be proposed. */ public HDF5StorageLayout tryGetProposedLayout() { return proposedLayoutOrNull; } /** * Returns the policy of this storage feature object regarding replacing or keeping already * existing datasets. */ public DataSetReplacementPolicy getDatasetReplacementPolicy() { return datasetReplacementPolicy; } boolean requiresChunking() { return isDeflating() || isScaling() || proposedLayoutOrNull == HDF5StorageLayout.CHUNKED; } boolean allowsCompact() { return proposedLayoutOrNull == null || proposedLayoutOrNull == HDF5StorageLayout.COMPACT; } /** * Returns true, if this storage feature object deflates data. */ public boolean isDeflating() { return (deflateLevel != NO_DEFLATION_LEVEL); } /** * Returns true, if this storage feature object scales data. */ public boolean isScaling() { return scalingFactor >= 0; } void checkScalingOK(FileFormat fileFormat) throws IllegalStateException { if (fileFormat.isHDF5_1_8_OK() == false) { throw new IllegalStateException( "Scaling compression is not allowed in strict HDF5 1.6.x compatibility mode."); } } /** * Returns true, if this storage feature object performs shuffling before deflating * the data. */ public boolean isShuffleBeforeDeflate() { return shuffleBeforeDeflate; } /** * Returns the deflate level of this storage feature object. 0 means no deflate. */ public byte getDeflateLevel() { return deflateLevel; } /** * Returns the scaling factor of this storage feature object. -1 means no scaling, 0 means * auto-scaling. */ public byte getScalingFactor() { return scalingFactor; } static DataSetReplacementPolicy getDataSetReplacementPolicy(boolean keepDataSetIfExists, boolean deleteDataSetIfExists) { return keepDataSetIfExists ? DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING : (deleteDataSetIfExists ? DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW : DataSetReplacementPolicy.USE_WRITER_DEFAULT); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5BaseReader.java000066400000000000000000002130071256564762100266340ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.HDF5Utils.HOUSEKEEPING_NAME_SUFFIX_STRINGLENGTH_ATTRIBUTE_NAME; import static ch.systemsx.cisd.hdf5.HDF5Utils.createAttributeTypeVariantAttributeName; import static ch.systemsx.cisd.hdf5.HDF5Utils.createObjectTypeVariantAttributeName; import static ch.systemsx.cisd.hdf5.HDF5Utils.getBooleanDataTypePath; import static ch.systemsx.cisd.hdf5.HDF5Utils.getDataTypeGroup; import static ch.systemsx.cisd.hdf5.HDF5Utils.getOneDimensionalArraySize; import static ch.systemsx.cisd.hdf5.HDF5Utils.getTypeVariantDataTypePath; import static ch.systemsx.cisd.hdf5.HDF5Utils.getTypeVariantMembersAttributeName; import static ch.systemsx.cisd.hdf5.HDF5Utils.getVariableLengthStringDataTypePath; import static ch.systemsx.cisd.hdf5.HDF5Utils.removeInternalNames; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_ALL; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_ARRAY; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_ENUM; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_INT32; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STRING; import java.io.File; import java.util.ArrayList; import java.util.Arrays; import java.util.HashMap; import java.util.LinkedList; import java.util.List; import java.util.Map; import ncsa.hdf.hdf5lib.exceptions.HDF5FileNotFoundException; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ncsa.hdf.hdf5lib.exceptions.HDF5SpaceRankMismatch; import ch.systemsx.cisd.base.mdarray.MDAbstractArray; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.hdf5.HDF5DataTypeInformation.DataTypeInfoOptions; import ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator.FileFormat; import ch.systemsx.cisd.hdf5.cleanup.CleanUpCallable; import ch.systemsx.cisd.hdf5.cleanup.CleanUpRegistry; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; import ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants; /** * Class that provides base methods for reading HDF5 files. * * @author Bernd Rinn */ class HDF5BaseReader { /** State that this reader / writer is currently in. */ protected enum State { CONFIG, OPEN, CLOSED } /** The size of a reference in bytes. */ static final int REFERENCE_SIZE_IN_BYTES = 8; protected final File hdf5File; protected final CleanUpCallable runner; protected final CleanUpRegistry fileRegistry; protected final boolean performNumericConversions; /** Map from named data types to ids. */ private final Map namedDataTypeMap; private class DataTypeContainer { final int typeId; final String typePath; DataTypeContainer(int typeId, String typePath) { this.typeId = typeId; this.typePath = typePath; } } private final List namedDataTypeList; protected final HDF5 h5; protected final int fileId; protected final int booleanDataTypeId; protected final int variableLengthStringDataTypeId; protected final HDF5EnumerationType typeVariantDataType; protected State state; final String houseKeepingNameSuffix; final CharacterEncoding encodingForNewDataSets; HDF5BaseReader(File hdf5File, boolean performNumericConversions, boolean autoDereference, FileFormat fileFormat, boolean overwrite, String preferredHouseKeepingNameSuffix) { this(hdf5File, performNumericConversions, false, autoDereference, fileFormat, overwrite, preferredHouseKeepingNameSuffix); } HDF5BaseReader(File hdf5File, boolean performNumericConversions, boolean useUTF8CharEncoding, boolean autoDereference, FileFormat fileFormat, boolean overwrite, String preferredHouseKeepingNameSuffix) { assert hdf5File != null; assert preferredHouseKeepingNameSuffix != null; this.performNumericConversions = performNumericConversions; this.hdf5File = hdf5File.getAbsoluteFile(); this.runner = new CleanUpCallable(); this.fileRegistry = CleanUpRegistry.createSynchonized(); this.namedDataTypeMap = new HashMap(); this.namedDataTypeList = new ArrayList(); this.encodingForNewDataSets = useUTF8CharEncoding ? CharacterEncoding.UTF8 : CharacterEncoding.ASCII; this.h5 = new HDF5(fileRegistry, runner, performNumericConversions, useUTF8CharEncoding, autoDereference); this.fileId = openFile(fileFormat, overwrite); this.state = State.OPEN; final String houseKeepingNameSuffixFromFileOrNull = tryGetHouseKeepingNameSuffix(); this.houseKeepingNameSuffix = (houseKeepingNameSuffixFromFileOrNull == null) ? preferredHouseKeepingNameSuffix : houseKeepingNameSuffixFromFileOrNull; readNamedDataTypes(); variableLengthStringDataTypeId = openOrCreateVLStringType(); booleanDataTypeId = openOrCreateBooleanDataType(); typeVariantDataType = openOrCreateTypeVariantDataType(); } void copyObject(String srcPath, int dstFileId, String dstPath) { final boolean dstIsDir = dstPath.endsWith("/"); if (dstIsDir && h5.exists(dstFileId, dstPath) == false) { h5.createGroup(dstFileId, dstPath); } if ("/".equals(srcPath)) { final String dstDir = dstIsDir ? dstPath : dstPath + "/"; for (String object : getGroupMembers("/")) { h5.copyObject(fileId, object, dstFileId, dstDir + object); } } else if (dstIsDir) { final int idx = srcPath.lastIndexOf('/'); final String sourceObjectName = srcPath.substring(idx < 0 ? 0 : idx); h5.copyObject(fileId, srcPath, dstFileId, dstPath + sourceObjectName); } else { h5.copyObject(fileId, srcPath, dstFileId, dstPath); } } int openFile(FileFormat fileFormat, boolean overwrite) { if (hdf5File.exists() == false) { throw new HDF5FileNotFoundException(hdf5File, "Path does not exit."); } if (hdf5File.canRead() == false) { throw new HDF5FileNotFoundException(hdf5File, "Path is not readable."); } if (hdf5File.isFile() == false) { throw new HDF5FileNotFoundException(hdf5File, "Path is not a file."); } if (HDF5Factory.isHDF5File(hdf5File) == false) { throw new HDF5FileNotFoundException(hdf5File, "Path is not a valid HDF5 file."); } return h5.openFileReadOnly(hdf5File.getPath(), fileRegistry); } void checkOpen() throws HDF5JavaException { if (state != State.OPEN) { final String msg = "HDF5 file '" + hdf5File.getPath() + "' is " + (state == State.CLOSED ? "closed." : "not opened yet."); throw new HDF5JavaException(msg); } } /** * Closes this object and the file referenced by this object. This object must not be used after * being closed. */ void close() { synchronized (fileRegistry) { if (state == State.OPEN) { fileRegistry.cleanUp(false); } state = State.CLOSED; } } boolean isClosed() { return state == State.CLOSED; } String tryGetHouseKeepingNameSuffix() { final ICallableWithCleanUp readRunnable = new ICallableWithCleanUp() { @Override public String call(ICleanUpRegistry registry) { final int objectId = h5.openObject(fileId, "/", registry); if (h5.existsAttribute(objectId, HDF5Utils.HOUSEKEEPING_NAME_SUFFIX_ATTRIBUTE_NAME)) { final int suffixLen = getHousekeepingAttributeExplicitStringLength(objectId, registry); final boolean explicitLengthStored = (suffixLen >= 0); final String rawSuffix = getStringAttribute(objectId, "/", HDF5Utils.HOUSEKEEPING_NAME_SUFFIX_ATTRIBUTE_NAME, explicitLengthStored, registry); return explicitLengthStored ? rawSuffix.substring(0, suffixLen) : rawSuffix; } else { return null; } } }; return runner.call(readRunnable); } byte[] getAttributeAsByteArray(final int objectId, final String attributeName, ICleanUpRegistry registry) { final int attributeId = h5.openAttribute(objectId, attributeName, registry); final int nativeDataTypeId = h5.getNativeDataTypeForAttribute(attributeId, registry); final int dataClass = h5.getClassType(nativeDataTypeId); final int size; if (dataClass == H5T_ARRAY) { final int numberOfElements = MDAbstractArray.getLength(h5.getArrayDimensions(nativeDataTypeId)); final int baseDataType = h5.getBaseDataType(nativeDataTypeId, registry); final int elementSize = h5.getDataTypeSize(baseDataType); size = numberOfElements * elementSize; } else if (dataClass == H5T_STRING) { final int stringDataTypeId = h5.getDataTypeForAttribute(attributeId, registry); size = h5.getDataTypeSize(stringDataTypeId); if (h5.isVariableLengthString(stringDataTypeId)) { String[] data = new String[1]; h5.readAttributeVL(attributeId, stringDataTypeId, data); return data[0].getBytes(); } } else { final int numberOfElements = MDAbstractArray.getLength(h5.getDataDimensionsForAttribute(attributeId, registry)); final int elementSize = h5.getDataTypeSize(nativeDataTypeId); size = numberOfElements * elementSize; } return h5.readAttributeAsByteArray(attributeId, nativeDataTypeId, size); } int openOrCreateBooleanDataType() { final String booleanDataTypePath = getBooleanDataTypePath(houseKeepingNameSuffix); int dataTypeId = getDataTypeId(booleanDataTypePath); if (dataTypeId < 0) { dataTypeId = createBooleanDataType(); commitDataType(booleanDataTypePath, dataTypeId); } return dataTypeId; } String tryGetDataTypePath(int dataTypeId) { for (DataTypeContainer namedDataType : namedDataTypeList) { if (h5.dataTypesAreEqual(dataTypeId, namedDataType.typeId)) { return namedDataType.typePath; } } return h5.tryGetDataTypePath(dataTypeId); } void renameNamedDataType(String oldPath, String newPath) { final Integer typeIdOrNull = namedDataTypeMap.remove(oldPath); if (typeIdOrNull != null) { namedDataTypeMap.put(newPath, typeIdOrNull); } for (int i = 0; i < namedDataTypeList.size(); ++i) { final DataTypeContainer c = namedDataTypeList.get(i); if (c.typePath.equals(oldPath)) { namedDataTypeList.set(i, new DataTypeContainer(c.typeId, newPath)); } } } String tryGetDataTypeName(int dataTypeId, HDF5DataClass dataClass) { final String dataTypePathOrNull = tryGetDataTypePath(dataTypeId); return HDF5Utils.tryGetDataTypeNameFromPath(dataTypePathOrNull, houseKeepingNameSuffix, dataClass); } int getDataTypeId(final String dataTypePath) { final Integer dataTypeIdOrNull = namedDataTypeMap.get(dataTypePath); if (dataTypeIdOrNull == null) { // Just in case of data types added to other groups than HDF5Utils.DATATYPE_GROUP if (h5.exists(fileId, dataTypePath)) { final int dataTypeId = h5.openDataType(fileId, dataTypePath, fileRegistry); namedDataTypeMap.put(dataTypePath, dataTypeId); return dataTypeId; } else { return -1; } } else { return dataTypeIdOrNull; } } int createBooleanDataType() { return h5.createDataTypeEnum(new String[] { "FALSE", "TRUE" }, fileRegistry); } HDF5EnumerationType openOrCreateTypeVariantDataType() { final String typeVariantTypePath = getTypeVariantDataTypePath(houseKeepingNameSuffix); int dataTypeId = getDataTypeId(typeVariantTypePath); if (dataTypeId < 0) { return createTypeVariantDataType(); } final int nativeDataTypeId = h5.getNativeDataType(dataTypeId, fileRegistry); final String[] typeVariantNames = h5.getNamesForEnumOrCompoundMembers(dataTypeId); return new HDF5EnumerationType(fileId, dataTypeId, nativeDataTypeId, typeVariantTypePath, typeVariantNames, this); } HDF5EnumerationType createTypeVariantDataType() { final HDF5DataTypeVariant[] typeVariants = HDF5DataTypeVariant.values(); final String[] typeVariantNames = new String[typeVariants.length]; for (int i = 0; i < typeVariants.length; ++i) { typeVariantNames[i] = typeVariants[i].name(); } final int dataTypeId = h5.createDataTypeEnum(typeVariantNames, fileRegistry); final int nativeDataTypeId = h5.getNativeDataType(dataTypeId, fileRegistry); return new HDF5EnumerationType(fileId, dataTypeId, nativeDataTypeId, getTypeVariantDataTypePath(houseKeepingNameSuffix), typeVariantNames, this); } void readNamedDataTypes() { final String typeGroup = getDataTypeGroup(houseKeepingNameSuffix); if (h5.exists(fileId, typeGroup) == false) { return; } readNamedDataTypes(typeGroup); } private void readNamedDataTypes(String dataTypePath) { for (String dataTypeSubPath : getGroupMemberPaths(dataTypePath)) { final HDF5ObjectType type = h5.getObjectTypeInfo(fileId, dataTypeSubPath, false); if (HDF5ObjectType.isGroup(type)) { readNamedDataTypes(dataTypeSubPath); } else if (HDF5ObjectType.isDataType(type)) { final int dataTypeId = h5.openDataType(fileId, dataTypeSubPath, fileRegistry); namedDataTypeMap.put(dataTypeSubPath, dataTypeId); namedDataTypeList.add(new DataTypeContainer(dataTypeId, dataTypeSubPath)); } } } void commitDataType(final String dataTypePath, final int dataTypeId) { // Overwrite this method in writer. } /** * Class to store the parameters of a 1d data space. */ static class DataSpaceParameters { final int memorySpaceId; final int dataSpaceId; final int blockSize; final long[] dimensions; DataSpaceParameters(int memorySpaceId, int dataSpaceId, int blockSize, long[] dimensions) { this.memorySpaceId = memorySpaceId; this.dataSpaceId = dataSpaceId; this.blockSize = blockSize; this.dimensions = dimensions; } } /** * Returns the {@link DataSpaceParameters} for the given dataSetId. */ DataSpaceParameters getSpaceParameters(final int dataSetId, ICleanUpRegistry registry) { long[] dimensions = h5.getDataDimensions(dataSetId, registry); return new DataSpaceParameters(H5S_ALL, H5S_ALL, MDAbstractArray.getLength(dimensions), dimensions); } /** * Returns the {@link DataSpaceParameters} for a 1d block of the given dataSetId, or * null, if the offset is outside of the dataset and * nullWhenOutside == true. */ DataSpaceParameters tryGetSpaceParameters(final int dataSetId, final long offset, final int blockSize, boolean nullWhenOutside, ICleanUpRegistry registry) { return tryGetSpaceParameters(dataSetId, 0, offset, blockSize, nullWhenOutside, registry); } /** * Returns the {@link DataSpaceParameters} for a 1d block of the given dataSetId. */ DataSpaceParameters getSpaceParameters(final int dataSetId, final long offset, final int blockSize, ICleanUpRegistry registry) { return tryGetSpaceParameters(dataSetId, 0, offset, blockSize, false, registry); } /** * Returns the {@link DataSpaceParameters} for a 1d block of the given dataSetId. */ DataSpaceParameters getSpaceParameters(final int dataSetId, final long memoryOffset, final long offset, final int blockSize, ICleanUpRegistry registry) { return tryGetSpaceParameters(dataSetId, memoryOffset, offset, blockSize, false, registry); } /** * Returns the {@link DataSpaceParameters} for a 1d block of the given dataSetId. */ DataSpaceParameters tryGetSpaceParameters(final int dataSetId, final long memoryOffset, final long offset, final int blockSize, boolean nullWhenOutside, ICleanUpRegistry registry) { final int memorySpaceId; final int dataSpaceId; final int effectiveBlockSize; final long[] dimensions; if (blockSize > 0) { dataSpaceId = h5.getDataSpaceForDataSet(dataSetId, registry); dimensions = h5.getDataSpaceDimensions(dataSpaceId); if (dimensions.length != 1) { throw new HDF5JavaException("Data Set is expected to be of rank 1 (rank=" + dimensions.length + ")"); } final long size = dimensions[0]; final long maxFileBlockSize = size - offset; if (maxFileBlockSize <= 0) { if (nullWhenOutside) { return null; } throw new HDF5JavaException("Offset " + offset + " >= Size " + size); } final long maxMemoryBlockSize = size - memoryOffset; if (maxMemoryBlockSize <= 0) { if (nullWhenOutside) { return null; } throw new HDF5JavaException("Memory offset " + memoryOffset + " >= Size " + size); } effectiveBlockSize = (int) Math.min(blockSize, Math.min(maxMemoryBlockSize, maxFileBlockSize)); final long[] blockShape = new long[] { effectiveBlockSize }; h5.setHyperslabBlock(dataSpaceId, new long[] { offset }, blockShape); memorySpaceId = h5.createSimpleDataSpace(blockShape, registry); h5.setHyperslabBlock(memorySpaceId, new long[] { memoryOffset }, blockShape); } else { memorySpaceId = HDF5Constants.H5S_ALL; dataSpaceId = HDF5Constants.H5S_ALL; dimensions = h5.getDataDimensions(dataSetId, registry); effectiveBlockSize = getOneDimensionalArraySize(dimensions); } return new DataSpaceParameters(memorySpaceId, dataSpaceId, effectiveBlockSize, dimensions); } /** * Returns the {@link DataSpaceParameters} for a multi-dimensional block of the given * dataSetId. */ DataSpaceParameters getSpaceParameters(final int dataSetId, final long[] offset, final int[] blockDimensionsOrNull, ICleanUpRegistry registry) { return tryGetSpaceParameters(dataSetId, offset, blockDimensionsOrNull, false, registry); } /** * Returns the {@link DataSpaceParameters} for a multi-dimensional block of the given * dataSetId. */ DataSpaceParameters tryGetSpaceParameters(final int dataSetId, final long[] offset, final int[] blockDimensionsOrNull, boolean nullWhenOutside, ICleanUpRegistry registry) { final int memorySpaceId; final int dataSpaceId; final long[] effectiveBlockDimensions; if (blockDimensionsOrNull != null) { assert offset != null; assert blockDimensionsOrNull.length == offset.length; dataSpaceId = h5.getDataSpaceForDataSet(dataSetId, registry); final long[] dimensions = h5.getDataSpaceDimensions(dataSpaceId); if (dimensions.length != blockDimensionsOrNull.length) { throw new HDF5SpaceRankMismatch(blockDimensionsOrNull.length, dimensions.length); } effectiveBlockDimensions = new long[blockDimensionsOrNull.length]; for (int i = 0; i < offset.length; ++i) { final long maxBlockSize = dimensions[i] - offset[i]; if (maxBlockSize <= 0) { if (nullWhenOutside) { return null; } throw new HDF5JavaException("Offset " + offset[i] + " >= Size " + dimensions[i]); } effectiveBlockDimensions[i] = (blockDimensionsOrNull[i] < 0) ? (int) maxBlockSize : Math.min( blockDimensionsOrNull[i], maxBlockSize); } h5.setHyperslabBlock(dataSpaceId, offset, effectiveBlockDimensions); memorySpaceId = h5.createSimpleDataSpace(effectiveBlockDimensions, registry); } else { memorySpaceId = H5S_ALL; dataSpaceId = H5S_ALL; effectiveBlockDimensions = h5.getDataDimensions(dataSetId, registry); } return new DataSpaceParameters(memorySpaceId, dataSpaceId, MDAbstractArray.getLength(effectiveBlockDimensions), effectiveBlockDimensions); } /** * Returns the {@link DataSpaceParameters} for the given dataSetId when they are * mapped to a block in memory. */ DataSpaceParameters getBlockSpaceParameters(final int dataSetId, final int[] memoryOffset, final int[] memoryDimensions, ICleanUpRegistry registry) { return tryGetBlockSpaceParameters(dataSetId, memoryOffset, memoryDimensions, false, registry); } /** * Returns the {@link DataSpaceParameters} for the given dataSetId when they are * mapped to a block in memory. */ DataSpaceParameters tryGetBlockSpaceParameters(final int dataSetId, final int[] memoryOffset, final int[] memoryDimensions, final boolean nullWhenOutside, ICleanUpRegistry registry) { assert memoryOffset != null; assert memoryDimensions != null; assert memoryDimensions.length == memoryOffset.length; final long[] dimensions = h5.getDataDimensions(dataSetId, registry); final int memorySpaceId = h5.createSimpleDataSpace(MDAbstractArray.toLong(memoryDimensions), registry); for (int i = 0; i < dimensions.length; ++i) { if (dimensions[i] + memoryOffset[i] > memoryDimensions[i]) { if (nullWhenOutside) { return null; } throw new HDF5JavaException("Dimensions " + dimensions[i] + " + memory offset " + memoryOffset[i] + " >= memory buffer " + memoryDimensions[i]); } } h5.setHyperslabBlock(memorySpaceId, MDAbstractArray.toLong(memoryOffset), dimensions); return new DataSpaceParameters(memorySpaceId, H5S_ALL, MDAbstractArray.getLength(dimensions), dimensions); } /** * Returns the {@link DataSpaceParameters} for a block of the given dataSetId when * they are mapped to a block in memory. */ DataSpaceParameters getBlockSpaceParameters(final int dataSetId, final int[] memoryOffset, final int[] memoryDimensions, final long[] offset, final int[] blockDimensions, ICleanUpRegistry registry) { return tryGetBlockSpaceParameters(dataSetId, memoryOffset, memoryDimensions, offset, blockDimensions, false, registry); } /** * Returns the {@link DataSpaceParameters} for a block of the given dataSetId when * they are mapped to a block in memory. */ DataSpaceParameters tryGetBlockSpaceParameters(final int dataSetId, final int[] memoryOffset, final int[] memoryDimensions, final long[] offset, final int[] blockDimensions, final boolean nullWhenOutside, ICleanUpRegistry registry) { assert memoryOffset != null; assert memoryDimensions != null; assert offset != null; assert blockDimensions != null; assert memoryOffset.length == offset.length; assert memoryDimensions.length == memoryOffset.length; assert blockDimensions.length == offset.length; final int memorySpaceId; final int dataSpaceId; final long[] effectiveBlockDimensions; dataSpaceId = h5.getDataSpaceForDataSet(dataSetId, registry); final long[] dimensions = h5.getDataSpaceDimensions(dataSpaceId); if (dimensions.length != blockDimensions.length) { throw new HDF5JavaException("Data Set is expected to be of rank " + blockDimensions.length + " (rank=" + dimensions.length + ")"); } effectiveBlockDimensions = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { final long maxFileBlockSize = dimensions[i] - offset[i]; if (maxFileBlockSize <= 0) { if (nullWhenOutside) { return null; } throw new HDF5JavaException("Offset " + offset[i] + " >= Size " + dimensions[i]); } final long maxMemoryBlockSize = memoryDimensions[i] - memoryOffset[i]; if (maxMemoryBlockSize <= 0) { if (nullWhenOutside) { return null; } throw new HDF5JavaException("Memory offset " + memoryOffset[i] + " >= Size " + memoryDimensions[i]); } effectiveBlockDimensions[i] = Math.min(blockDimensions[i], Math.min(maxMemoryBlockSize, maxFileBlockSize)); } h5.setHyperslabBlock(dataSpaceId, offset, effectiveBlockDimensions); memorySpaceId = h5.createSimpleDataSpace(MDAbstractArray.toLong(memoryDimensions), registry); h5.setHyperslabBlock(memorySpaceId, MDAbstractArray.toLong(memoryOffset), effectiveBlockDimensions); return new DataSpaceParameters(memorySpaceId, dataSpaceId, MDAbstractArray.getLength(effectiveBlockDimensions), effectiveBlockDimensions); } /** * Returns the native data type for the given dataSetId, or * overrideDataTypeId, if it is not negative. */ int getNativeDataTypeId(final int dataSetId, final int overrideDataTypeId, ICleanUpRegistry registry) { final int nativeDataTypeId; if (overrideDataTypeId < 0) { nativeDataTypeId = h5.getNativeDataTypeForDataSet(dataSetId, registry); } else { nativeDataTypeId = overrideDataTypeId; } return nativeDataTypeId; } /** * Returns the members of groupPath. The order is not well defined. * * @param groupPath The path of the group to get the members for. * @throws IllegalArgumentException If groupPath is not a group. */ List getGroupMembers(final String groupPath) { assert groupPath != null; return removeInternalNames(getAllGroupMembers(groupPath), houseKeepingNameSuffix, false); } /** * Returns all members of groupPath, including internal groups that may be used by * the library to do house-keeping. The order is not well defined. * * @param groupPath The path of the group to get the members for. * @throws IllegalArgumentException If groupPath is not a group. */ List getAllGroupMembers(final String groupPath) { final String[] groupMemberArray = h5.getGroupMembers(fileId, groupPath); return new LinkedList(Arrays.asList(groupMemberArray)); } /** * Returns the paths of the members of groupPath (including the parent). The order is * not well defined. * * @param groupPath The path of the group to get the member paths for. * @throws IllegalArgumentException If groupPath is not a group. */ List getGroupMemberPaths(final String groupPath) { final String superGroupName = (groupPath.equals("/") ? "/" : groupPath + "/"); final List memberNames = getGroupMembers(groupPath); for (int i = 0; i < memberNames.size(); ++i) { memberNames.set(i, superGroupName + memberNames.get(i)); } return memberNames; } /** * Returns the information about a data set as a {@link HDF5DataTypeInformation} object. It is a * failure condition if the dataSetPath does not exist or does not identify a data * set.
* Does not read the data type path of a committed data type. * * @param dataSetPath The name (including path information) of the data set to return * information about. */ HDF5DataSetInformation getDataSetInformation(final String dataSetPath) { return getDataSetInformation(dataSetPath, DataTypeInfoOptions.DEFAULT, true); } /** * Returns the information about a data set as a {@link HDF5DataTypeInformation} object. It is a * failure condition if the dataSetPath does not exist or does not identify a data * set. * * @param dataSetPath The name (including path information) of the data set to return * information about. * @param options What information to obtain about the data type. * @param fillDimensions If true, fill in the dimensions of the dataset */ HDF5DataSetInformation getDataSetInformation(final String dataSetPath, final DataTypeInfoOptions options, final boolean fillDimensions) { assert dataSetPath != null; final ICallableWithCleanUp informationDeterminationRunnable = new ICallableWithCleanUp() { @Override public HDF5DataSetInformation call(ICleanUpRegistry registry) { final int dataSetId = h5.openDataSet(fileId, dataSetPath, registry); final int dataTypeId = h5.getDataTypeForDataSet(dataSetId, registry); final HDF5DataTypeInformation dataTypeInfo = getDataTypeInformation(dataTypeId, options, registry); final HDF5DataTypeVariant variantOrNull = options.knowsDataTypeVariant() ? tryGetTypeVariant(dataSetId, registry) : null; final HDF5DataSetInformation dataSetInfo = new HDF5DataSetInformation(dataTypeInfo, variantOrNull); // Is it a variable-length string? final boolean vlString = (dataTypeInfo.getDataClass() == HDF5DataClass.STRING && h5 .isVariableLengthString(dataTypeId)); if (vlString) { dataTypeInfo.setElementSize(-1); } if (fillDimensions) { h5.fillDataDimensions(dataSetId, false, dataSetInfo, registry); } return dataSetInfo; } }; return runner.call(informationDeterminationRunnable); } /** * Returns the dimensions of the data set. It is a failure condition if the * dataSetPath does not exist or does not identify a data set. * * @param dataSetPath The name (including path information) of the data set to return * information about. */ long[] getSpaceDimensions(final String dataSetPath) { assert dataSetPath != null; final ICallableWithCleanUp informationDeterminationRunnable = new ICallableWithCleanUp() { @Override public long[] call(ICleanUpRegistry registry) { final int dataSetId = h5.openDataSet(fileId, dataSetPath, registry); return h5.getDimensions(dataSetId, false, registry); } }; return runner.call(informationDeterminationRunnable); } /** * Returns the rank of this data set of objectPath. This combines the space rank and * the array rank into one rank. It is a failure condition if the objectPath does not * exist or does not identify a data set. This method follows symbolic links. */ int getRank(String dataSetPath) { final HDF5DataSetInformation info = getDataSetInformation(dataSetPath, DataTypeInfoOptions.MINIMAL, true); return info.getRank() + info.getTypeInformation().getRank(); } /** * Returns the dimensions of the space of objectPath (empty if this is a scalar * space). It is a failure condition if the objectPath does not exist or does not * identify a data set. This method follows symbolic links. */ long[] getDimensions(String dataSetPath) { assert dataSetPath != null; final HDF5DataSetInformation info = getDataSetInformation(dataSetPath, DataTypeInfoOptions.MINIMAL, true); return MatrixUtils.concat(info.getDimensions(), info.getTypeInformation().getDimensions()); } /** * Returns the rank of the data set. It is a failure condition if the dataSetPath * does not exist or does not identify a data set. * * @param dataSetPath The name (including path information) of the data set to return * information about. */ int getSpaceRank(final String dataSetPath) { assert dataSetPath != null; final ICallableWithCleanUp informationDeterminationRunnable = new ICallableWithCleanUp() { @Override public Integer call(ICleanUpRegistry registry) { final int dataSetId = h5.openDataSet(fileId, dataSetPath, registry); return h5.getRank(dataSetId, false, registry); } }; return runner.call(informationDeterminationRunnable); } HDF5DataTypeVariant tryGetTypeVariant(final String objectPath) { assert objectPath != null; final ICallableWithCleanUp readRunnable = new ICallableWithCleanUp() { @Override public HDF5DataTypeVariant call(ICleanUpRegistry registry) { final int objectId = h5.openObject(fileId, objectPath, registry); return tryGetTypeVariant(objectId, registry); } }; return runner.call(readRunnable); } HDF5DataTypeVariant tryGetTypeVariant(final String objectPath, final String attributeName) { assert objectPath != null; final ICallableWithCleanUp readRunnable = new ICallableWithCleanUp() { @Override public HDF5DataTypeVariant call(ICleanUpRegistry registry) { final int objectId = h5.openObject(fileId, objectPath, registry); return tryGetTypeVariant(objectId, attributeName, registry); } }; return runner.call(readRunnable); } HDF5EnumerationValueArray getEnumValueArray(final int attributeId, final String objectPath, final String attributeName, ICleanUpRegistry registry) { final int storageDataTypeId = h5.getDataTypeForAttribute(attributeId, registry); final int nativeDataTypeId = h5.getNativeDataType(storageDataTypeId, registry); final int len; final int enumTypeId; if (h5.getClassType(storageDataTypeId) == H5T_ARRAY) { final int[] arrayDimensions = h5.getArrayDimensions(storageDataTypeId); if (arrayDimensions.length != 1) { throw new HDF5JavaException("Attribute '" + attributeName + "' of object '" + objectPath + "' is not an array of rank 1, but is of rank " + arrayDimensions.length); } len = arrayDimensions[0]; enumTypeId = h5.getBaseDataType(storageDataTypeId, registry); if (h5.getClassType(enumTypeId) != H5T_ENUM) { throw new HDF5JavaException("Attribute '" + attributeName + "' of object '" + objectPath + "' is not of type enumeration array."); } } else { if (h5.getClassType(storageDataTypeId) != H5T_ENUM) { throw new HDF5JavaException("Attribute '" + attributeName + "' of object '" + objectPath + "' is not of type enumeration array."); } enumTypeId = storageDataTypeId; final long[] arrayDimensions = h5.getDataDimensionsForAttribute(attributeId, registry); len = HDF5Utils.getOneDimensionalArraySize(arrayDimensions); } final HDF5EnumerationType enumType = getEnumTypeForEnumDataType(null, enumTypeId, true, fileRegistry); final byte[] data = h5.readAttributeAsByteArray(attributeId, nativeDataTypeId, len * enumType.getStorageForm().getStorageSize()); final HDF5EnumerationValueArray value = new HDF5EnumerationValueArray(enumType, EnumerationType.fromStorageForm(data, enumType.getStorageForm())); return value; } HDF5EnumerationValueMDArray getEnumValueMDArray(final int attributeId, final String objectPath, final String attributeName, ICleanUpRegistry registry) { final int storageDataTypeId = h5.getDataTypeForAttribute(attributeId, registry); final int nativeDataTypeId = h5.getNativeDataType(storageDataTypeId, registry); final int len; final int enumTypeId; final int[] arrayDimensions; if (h5.getClassType(storageDataTypeId) == H5T_ARRAY) { arrayDimensions = h5.getArrayDimensions(storageDataTypeId); len = MDAbstractArray.getLength(arrayDimensions); enumTypeId = h5.getBaseDataType(storageDataTypeId, registry); if (h5.getClassType(enumTypeId) != H5T_ENUM) { throw new HDF5JavaException("Attribute '" + attributeName + "' of object '" + objectPath + "' is not of type enumeration array."); } } else { if (h5.getClassType(storageDataTypeId) != H5T_ENUM) { throw new HDF5JavaException("Attribute '" + attributeName + "' of object '" + objectPath + "' is not of type enumeration array."); } enumTypeId = storageDataTypeId; arrayDimensions = MDAbstractArray.toInt(h5.getDataDimensionsForAttribute(attributeId, registry)); len = MDAbstractArray.getLength(arrayDimensions); } final HDF5EnumerationType enumType = getEnumTypeForEnumDataType(null, enumTypeId, true, fileRegistry); final byte[] data = h5.readAttributeAsByteArray(attributeId, nativeDataTypeId, len * enumType.getStorageForm().getStorageSize()); final HDF5EnumerationValueMDArray value = new HDF5EnumerationValueMDArray(enumType, EnumerationType.fromStorageForm(data, arrayDimensions, enumType.getStorageForm())); return value; } int getEnumDataTypeId(final int storageDataTypeId, ICleanUpRegistry registry) { final int enumDataTypeId; if (h5.getClassType(storageDataTypeId) == H5T_ARRAY) { enumDataTypeId = h5.getBaseDataType(storageDataTypeId, registry); } else { enumDataTypeId = storageDataTypeId; } return enumDataTypeId; } HDF5DataTypeVariant[] tryGetTypeVariantForCompoundMembers(String dataTypePathOrNull, ICleanUpRegistry registry) { if (dataTypePathOrNull == null) { return null; } checkOpen(); final int objectId = h5.openObject(fileId, dataTypePathOrNull, registry); final String typeVariantMembersAttributeName = getTypeVariantMembersAttributeName(houseKeepingNameSuffix); if (h5.existsAttribute(objectId, typeVariantMembersAttributeName) == false) { return null; } final int attributeId = h5.openAttribute(objectId, typeVariantMembersAttributeName, registry); final HDF5EnumerationValueArray valueArray = getEnumValueArray(attributeId, dataTypePathOrNull, typeVariantMembersAttributeName, registry); final HDF5DataTypeVariant[] variants = new HDF5DataTypeVariant[valueArray.getLength()]; boolean hasVariants = false; for (int i = 0; i < variants.length; ++i) { variants[i] = HDF5DataTypeVariant.values()[valueArray.getOrdinal(i)]; hasVariants |= variants[i].isTypeVariant(); } if (hasVariants) { return variants; } else { return null; } } HDF5DataTypeVariant tryGetTypeVariant(final int objectId, ICleanUpRegistry registry) { final int typeVariantOrdinal = getAttributeTypeVariant(objectId, registry); return typeVariantOrdinal < 0 ? null : HDF5DataTypeVariant.values()[typeVariantOrdinal]; } HDF5DataTypeVariant tryGetTypeVariant(final int objectId, String attributeName, ICleanUpRegistry registry) { final int typeVariantOrdinal = getAttributeTypeVariant(objectId, attributeName, registry); return typeVariantOrdinal < 0 ? null : HDF5DataTypeVariant.values()[typeVariantOrdinal]; } /** * Returns the ordinal for the type variant of objectPath, or -1, if no * type variant is defined for this objectPath. * * @param objectId The id of the data set object in the file. * @return The ordinal of the type variant or null. */ int getAttributeTypeVariant(final int objectId, ICleanUpRegistry registry) { checkOpen(); final String dataTypeVariantAttributeName = createObjectTypeVariantAttributeName(houseKeepingNameSuffix); if (h5.existsAttribute(objectId, dataTypeVariantAttributeName) == false) { return -1; } final int attributeId = h5.openAttribute(objectId, dataTypeVariantAttributeName, registry); return getEnumOrdinal(attributeId, -1, typeVariantDataType); } /** * Returns the ordinal for the type variant of objectPath, or -1, if no * type variant is defined for this objectPath. * * @param objectId The id of the data set object in the file. * @param attributeName The name of the attribute to get the type variant for. * @return The ordinal of the type variant or null. */ int getAttributeTypeVariant(final int objectId, String attributeName, ICleanUpRegistry registry) { checkOpen(); final String typeVariantAttrName = createAttributeTypeVariantAttributeName(attributeName, houseKeepingNameSuffix); if (h5.existsAttribute(objectId, typeVariantAttrName) == false) { return -1; } final int attributeId = h5.openAttribute(objectId, typeVariantAttrName, registry); return getEnumOrdinal(attributeId, -1, typeVariantDataType); } int getEnumOrdinal(final int attributeId, int nativeDataTypeId, final HDF5EnumerationType enumType) { final byte[] data = h5.readAttributeAsByteArray(attributeId, (nativeDataTypeId < 0) ? enumType.getNativeTypeId() : nativeDataTypeId, enumType.getStorageForm().getStorageSize()); return EnumerationType.fromStorageForm(data); } /** * Returns the explicitly saved string length for attribute * HOUSEKEEPING_NAME_SUFFIX_ATTRIBUTE_NAME of objectId, or -1 * , if no explicit string length is defined for this attribute. * * @param objectId The id of the data set object in the file. * @return The length of the string attribute or -1. */ private int getHousekeepingAttributeExplicitStringLength(final int objectId, ICleanUpRegistry registry) { if (h5.existsAttribute(objectId, HOUSEKEEPING_NAME_SUFFIX_STRINGLENGTH_ATTRIBUTE_NAME) == false) { return -1; } final int attributeId = h5.openAttribute(objectId, HOUSEKEEPING_NAME_SUFFIX_STRINGLENGTH_ATTRIBUTE_NAME, registry); final int[] data = h5.readAttributeAsIntArray(attributeId, H5T_NATIVE_INT32, 1); return data[0]; } HDF5DataTypeInformation getDataTypeInformation(final int dataTypeId, final DataTypeInfoOptions options) { final ICallableWithCleanUp informationDeterminationRunnable = new ICallableWithCleanUp() { @Override public HDF5DataTypeInformation call(ICleanUpRegistry registry) { final HDF5DataTypeInformation dataTypeInfo = getDataTypeInformation(dataTypeId, options, registry); // Is it a variable-length string? final boolean vlString = (dataTypeInfo.getDataClass() == HDF5DataClass.STRING && h5 .isVariableLengthString(dataTypeId)); if (vlString) { dataTypeInfo.setElementSize(-1); } return dataTypeInfo; } }; return runner.call(informationDeterminationRunnable); } HDF5DataTypeInformation getDataTypeInformation(final int dataTypeId, final DataTypeInfoOptions options, final ICleanUpRegistry registry) { final int classTypeId = h5.getClassType(dataTypeId); final HDF5DataClass dataClass; final int totalSize = h5.getDataTypeSize(dataTypeId); if (classTypeId == H5T_ARRAY) { dataClass = getElementClassForArrayDataType(dataTypeId); final int[] arrayDimensions = h5.getArrayDimensions(dataTypeId); final int numberOfElements = MDAbstractArray.getLength(arrayDimensions); final int size = totalSize / numberOfElements; final int baseTypeId = h5.getBaseDataType(dataTypeId, registry); final boolean signed = (dataClass == HDF5DataClass.INTEGER) ? h5.getSigned(baseTypeId) : (dataClass == HDF5DataClass.FLOAT); final String dataTypePathOrNull = options.knowsDataTypePath() ? tryGetDataTypePath(baseTypeId) : null; final CharacterEncoding dataSetEncoding = (dataClass == HDF5DataClass.STRING) ? h5.getCharacterEncoding(baseTypeId) : CharacterEncoding.ASCII; final boolean variableLengthString = (dataClass == HDF5DataClass.STRING) ? h5.isVariableLengthString(baseTypeId) : false; return new HDF5DataTypeInformation(dataTypePathOrNull, options, dataClass, dataSetEncoding, houseKeepingNameSuffix, size, arrayDimensions, true, signed, variableLengthString); } else { dataClass = getDataClassForClassType(classTypeId, dataTypeId); final String opaqueTagOrNull; if (dataClass == HDF5DataClass.OPAQUE) { opaqueTagOrNull = h5.tryGetOpaqueTag(dataTypeId); } else { opaqueTagOrNull = null; } final String dataTypePathOrNull = options.knowsDataTypePath() ? tryGetDataTypePath(dataTypeId) : null; final boolean signed = (dataClass == HDF5DataClass.INTEGER) ? h5.getSigned(dataTypeId) : (dataClass == HDF5DataClass.FLOAT); final CharacterEncoding dataSetEncoding = (dataClass == HDF5DataClass.STRING) ? h5.getCharacterEncoding(dataTypeId) : CharacterEncoding.ASCII; final boolean variableLengthString = (dataClass == HDF5DataClass.STRING) ? h5.isVariableLengthString(dataTypeId) : false; return new HDF5DataTypeInformation(dataTypePathOrNull, options, dataClass, dataSetEncoding, houseKeepingNameSuffix, totalSize, signed, variableLengthString, opaqueTagOrNull); } } private HDF5DataClass getDataClassForClassType(final int classTypeId, final int dataTypeId) { HDF5DataClass dataClass = HDF5DataClass.classIdToDataClass(classTypeId); // Is it a boolean? if (dataClass == HDF5DataClass.ENUM && h5.dataTypesAreEqual(dataTypeId, booleanDataTypeId)) { dataClass = HDF5DataClass.BOOLEAN; } return dataClass; } private HDF5DataClass getElementClassForArrayDataType(final int arrayDataTypeId) { for (HDF5DataClass eClass : HDF5DataClass.values()) { if (h5.hasClassType(arrayDataTypeId, eClass.getId())) { return eClass; } } return HDF5DataClass.OTHER; } // // Compound // String getCompoundDataTypeName(final String nameOrNull, final int dataTypeId) { return getDataTypeName(nameOrNull, HDF5DataClass.COMPOUND, dataTypeId); } HDF5ValueObjectByteifyer createCompoundByteifyers(final Class compoundClazz, final HDF5CompoundMemberMapping[] compoundMembers, final CompoundTypeInformation compoundTypeInfoOrNull) { final HDF5ValueObjectByteifyer objectByteifyer = new HDF5ValueObjectByteifyer(compoundClazz, new HDF5ValueObjectByteifyer.IFileAccessProvider() { @Override public int getBooleanDataTypeId() { return booleanDataTypeId; } @Override public int getStringDataTypeId(int maxLength) { final int typeId = h5.createDataTypeString(maxLength, fileRegistry); return typeId; } @Override public int getArrayTypeId(int baseTypeId, int length) { final int typeId = h5.createArrayType(baseTypeId, length, fileRegistry); return typeId; } @Override public int getArrayTypeId(int baseTypeId, int[] dimensions) { final int typeId = h5.createArrayType(baseTypeId, dimensions, fileRegistry); return typeId; } @Override public CharacterEncoding getCharacterEncoding(int dataTypeId) { return (dataTypeId < 0) ? encodingForNewDataSets : h5 .getCharacterEncoding(dataTypeId); } @Override public HDF5EnumerationType getEnumType(String[] options) { final int storageDataTypeId = h5.createDataTypeEnum(options, fileRegistry); final int nativeDataTypeId = h5.getNativeDataType(storageDataTypeId, fileRegistry); return new HDF5EnumerationType(fileId, storageDataTypeId, nativeDataTypeId, null, options, HDF5BaseReader.this); } @Override public int getVariableLengthStringDataTypeId() { return variableLengthStringDataTypeId; } @Override public byte[] createObjectReference(String referencedObjectPath) { return h5.createObjectReference(fileId, referencedObjectPath); } }, compoundTypeInfoOrNull, compoundMembers); return objectByteifyer; } int createStorageCompoundDataType(HDF5ValueObjectByteifyer objectArrayifyer) { final int storageDataTypeId = h5.createDataTypeCompound(objectArrayifyer.getRecordSizeOnDisk(), fileRegistry); objectArrayifyer.insertMemberTypes(storageDataTypeId); return storageDataTypeId; } int createNativeCompoundDataType(HDF5ValueObjectByteifyer objectArrayifyer) { final int nativeDataTypeId = h5.createDataTypeCompound(objectArrayifyer.getRecordSizeInMemory(), fileRegistry); objectArrayifyer.insertNativeMemberTypes(nativeDataTypeId, h5, fileRegistry); return nativeDataTypeId; } // // Enum // HDF5EnumerationType getEnumTypeForStorageDataType(final String nameOrNull, final int storageDataTypeId, final boolean resolveName, final String objectPathOrNull, final String attributeNameOrNull, final ICleanUpRegistry registry) { int classType = h5.getClassType(storageDataTypeId); final boolean isArray = (classType == H5T_ARRAY); final int enumStoreDataTypeId; if (isArray) { enumStoreDataTypeId = h5.getBaseDataType(storageDataTypeId, registry); classType = h5.getClassType(enumStoreDataTypeId); } else { enumStoreDataTypeId = storageDataTypeId; } if (classType != H5T_ENUM) { if (attributeNameOrNull != null) { throw new HDF5JavaException("Attribute '" + attributeNameOrNull + "' of object '" + objectPathOrNull + "' is not of enum type."); } else if (objectPathOrNull != null) { throw new HDF5JavaException("Object '" + objectPathOrNull + "' is not of enum type."); } else { throw new HDF5JavaException("Type '" + (nameOrNull != null ? nameOrNull : "???") + "' is not of enum type."); } } return getEnumTypeForEnumDataType(nameOrNull, enumStoreDataTypeId, resolveName, registry); } HDF5EnumerationType getEnumTypeForEnumDataType(final String nameOrNull, final int enumStoreDataTypeId, final boolean resolveName, final ICleanUpRegistry registry) { final int nativeDataTypeId = h5.getNativeDataType(enumStoreDataTypeId, registry); final String[] values = h5.getNamesForEnumOrCompoundMembers(enumStoreDataTypeId); return new HDF5EnumerationType(fileId, enumStoreDataTypeId, nativeDataTypeId, resolveName ? getEnumDataTypeName(nameOrNull, enumStoreDataTypeId) : nameOrNull, values, this); } void checkEnumValues(int dataTypeId, final String[] values, final String nameOrNull) { final String[] valuesStored = h5.getNamesForEnumOrCompoundMembers(dataTypeId); if (valuesStored.length != values.length) { throw new IllegalStateException("Enum " + getEnumDataTypeName(nameOrNull, dataTypeId) + " has " + valuesStored.length + " members, but should have " + values.length); } for (int i = 0; i < values.length; ++i) { if (values[i].equals(valuesStored[i]) == false) { throw new HDF5JavaException("Enum member index " + i + " of enum " + getEnumDataTypeName(nameOrNull, dataTypeId) + " is '" + valuesStored[i] + "', but should be '" + values[i] + "'"); } } } String getEnumDataTypeName(final String nameOrNull, final int dataTypeId) { return getDataTypeName(nameOrNull, HDF5DataClass.ENUM, dataTypeId); } private String getDataTypeName(final String nameOrNull, final HDF5DataClass dataClass, final int dataTypeId) { if (nameOrNull != null) { return nameOrNull; } else { final String nameFromPathOrNull = HDF5Utils.tryGetDataTypeNameFromPath(tryGetDataTypePath(dataTypeId), houseKeepingNameSuffix, dataClass); return (nameFromPathOrNull == null) ? "UNKNOWN" : nameFromPathOrNull; } } boolean isScaledEnum(final int objectId, final ICleanUpRegistry registry) { final HDF5DataTypeVariant typeVariantOrNull = tryGetTypeVariant(objectId, registry); return (HDF5DataTypeVariant.ENUM == typeVariantOrNull); } boolean isScaledBitField(final int objectId, final ICleanUpRegistry registry) { final HDF5DataTypeVariant typeVariantOrNull = tryGetTypeVariant(objectId, registry); return (HDF5DataTypeVariant.BITFIELD == typeVariantOrNull); } // // String // private int openOrCreateVLStringType() { final String variableLengthStringTypePath = getVariableLengthStringDataTypePath(houseKeepingNameSuffix); int dataTypeId = getDataTypeId(variableLengthStringTypePath); if (dataTypeId < 0) { dataTypeId = h5.createDataTypeVariableString(fileRegistry); commitDataType(variableLengthStringTypePath, dataTypeId); } return dataTypeId; } String getStringAttribute(final int objectId, final String objectPath, final String attributeName, final boolean readRaw, final ICleanUpRegistry registry) { final int attributeId = h5.openAttribute(objectId, attributeName, registry); final int stringDataTypeId = h5.getDataTypeForAttribute(attributeId, registry); final boolean isString = (h5.getClassType(stringDataTypeId) == H5T_STRING); if (isString == false) { throw new IllegalArgumentException("Attribute " + attributeName + " of object " + objectPath + " needs to be a String."); } final int size = h5.getDataTypeSize(stringDataTypeId); if (h5.isVariableLengthString(stringDataTypeId)) { String[] data = new String[1]; h5.readAttributeVL(attributeId, stringDataTypeId, data); return data[0]; } else { final CharacterEncoding dataSetEncoding = h5.getCharacterEncoding(stringDataTypeId); final byte[] data = h5.readAttributeAsByteArray(attributeId, stringDataTypeId, size); return (readRaw ? StringUtils.fromBytes(data, dataSetEncoding) : StringUtils .fromBytes0Term(data, dataSetEncoding)); } } String[] getStringArrayAttribute(final int objectId, final String objectPath, final String attributeName, final boolean readRaw, final ICleanUpRegistry registry) { final int attributeId = h5.openAttribute(objectId, attributeName, registry); final int stringArrayDataTypeId = h5.getDataTypeForAttribute(attributeId, registry); final boolean isArray = (h5.getClassType(stringArrayDataTypeId) == H5T_ARRAY); if (isArray == false) { throw new HDF5JavaException("Attribute " + attributeName + " of object " + objectPath + " needs to be a String array of rank 1."); } final int stringDataTypeId = h5.getBaseDataType(stringArrayDataTypeId, registry); final boolean isStringArray = (h5.getClassType(stringDataTypeId) == H5T_STRING); if (isStringArray == false) { throw new HDF5JavaException("Attribute " + attributeName + " of object " + objectPath + " needs to be a String array of rank 1."); } final int size = h5.getDataTypeSize(stringArrayDataTypeId); if (h5.isVariableLengthString(stringDataTypeId)) { String[] data = new String[1]; h5.readAttributeVL(attributeId, stringDataTypeId, data); return data; } else { final CharacterEncoding dataSetEncoding = h5.getCharacterEncoding(stringArrayDataTypeId); byte[] data = h5.readAttributeAsByteArray(attributeId, stringArrayDataTypeId, size); final int[] arrayDimensions = h5.getArrayDimensions(stringArrayDataTypeId); if (arrayDimensions.length != 1) { throw new HDF5JavaException("Attribute " + attributeName + " of object " + objectPath + " needs to be a String array of rank 1."); } final int lengthPerElement = h5.getDataTypeSize(stringDataTypeId); final int numberOfElements = arrayDimensions[0]; final String[] result = new String[numberOfElements]; for (int i = 0, startIdx = 0, endIdx = lengthPerElement; i < numberOfElements; ++i, startIdx += lengthPerElement, endIdx += lengthPerElement) { result[i] = readRaw ? StringUtils.fromBytes(data, startIdx, endIdx, dataSetEncoding) : StringUtils.fromBytes0Term(data, startIdx, endIdx, dataSetEncoding); } return result; } } MDArray getStringMDArrayAttribute(final int objectId, final String objectPath, final String attributeName, final boolean readRaw, final ICleanUpRegistry registry) { final int attributeId = h5.openAttribute(objectId, attributeName, registry); final int stringArrayDataTypeId = h5.getDataTypeForAttribute(attributeId, registry); final boolean isArray = (h5.getClassType(stringArrayDataTypeId) == H5T_ARRAY); if (isArray == false) { throw new HDF5JavaException("Attribute " + attributeName + " of object " + objectPath + " needs to be a String array."); } final int stringDataTypeId = h5.getBaseDataType(stringArrayDataTypeId, registry); final boolean isStringArray = (h5.getClassType(stringDataTypeId) == H5T_STRING); if (isStringArray == false) { throw new HDF5JavaException("Attribute " + attributeName + " of object " + objectPath + " needs to be a String array."); } final int size = h5.getDataTypeSize(stringArrayDataTypeId); if (h5.isVariableLengthString(stringDataTypeId)) { String[] data = new String[1]; h5.readAttributeVL(attributeId, stringDataTypeId, data); return new MDArray(data, new int[] { 1 }); } else { final byte[] data = h5.readAttributeAsByteArray(attributeId, stringArrayDataTypeId, size); final CharacterEncoding dataSetEncoding = h5.getCharacterEncoding(stringArrayDataTypeId); final int[] arrayDimensions = h5.getArrayDimensions(stringArrayDataTypeId); final int lengthPerElement = h5.getDataTypeSize(stringDataTypeId); final int numberOfElements = MDAbstractArray.getLength(arrayDimensions); final String[] result = new String[numberOfElements]; for (int i = 0, startIdx = 0, endIdx = lengthPerElement; i < numberOfElements; ++i, startIdx += lengthPerElement, endIdx += lengthPerElement) { result[i] = readRaw ? StringUtils.fromBytes(data, startIdx, endIdx, dataSetEncoding) : StringUtils.fromBytes0Term(data, startIdx, endIdx, dataSetEncoding); } return new MDArray(result, arrayDimensions); } } // Date & Time void checkIsTimeStamp(final String objectPath, final int dataSetId, ICleanUpRegistry registry) throws HDF5JavaException { final int typeVariantOrdinal = getAttributeTypeVariant(dataSetId, registry); if (typeVariantOrdinal != HDF5DataTypeVariant.TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH .ordinal()) { throw new HDF5JavaException("Data set '" + objectPath + "' is not a time stamp."); } } void checkIsTimeStamp(final String objectPath, final String attributeName, final int dataSetId, ICleanUpRegistry registry) throws HDF5JavaException { final int typeVariantOrdinal = getAttributeTypeVariant(dataSetId, attributeName, registry); if (typeVariantOrdinal != HDF5DataTypeVariant.TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH .ordinal()) { throw new HDF5JavaException("Attribute '" + attributeName + "' of data set '" + objectPath + "' is not a time stamp."); } } HDF5TimeUnit checkIsTimeDuration(final String objectPath, final int dataSetId, ICleanUpRegistry registry) throws HDF5JavaException { final int typeVariantOrdinal = getAttributeTypeVariant(dataSetId, registry); if (HDF5DataTypeVariant.isTimeDuration(typeVariantOrdinal) == false) { throw new HDF5JavaException("Data set '" + objectPath + "' is not a time duration."); } return HDF5DataTypeVariant.getTimeUnit(typeVariantOrdinal); } HDF5TimeUnit checkIsTimeDuration(final String objectPath, final String attributeName, final int dataSetId, ICleanUpRegistry registry) throws HDF5JavaException { final int typeVariantOrdinal = getAttributeTypeVariant(dataSetId, attributeName, registry); if (HDF5DataTypeVariant.isTimeDuration(typeVariantOrdinal) == false) { throw new HDF5JavaException("Attribute '" + attributeName + "' of data set '" + objectPath + "' is not a time duration."); } return HDF5DataTypeVariant.getTimeUnit(typeVariantOrdinal); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5BaseWriter.java000066400000000000000000002026471256564762100267160ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.HDF5Utils.HOUSEKEEPING_NAME_SUFFIX_STRINGLENGTH_ATTRIBUTE_NAME; import static ch.systemsx.cisd.hdf5.HDF5Utils.createAttributeTypeVariantAttributeName; import static ch.systemsx.cisd.hdf5.HDF5Utils.createObjectTypeVariantAttributeName; import static ch.systemsx.cisd.hdf5.HDF5Utils.getDataTypeGroup; import static ch.systemsx.cisd.hdf5.HDF5Utils.getTypeVariantDataTypePath; import static ch.systemsx.cisd.hdf5.HDF5Utils.isEmpty; import static ch.systemsx.cisd.hdf5.HDF5Utils.isNonPositive; import static ch.systemsx.cisd.hdf5.hdf5lib.H5D.H5Dwrite; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_SCALAR; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_UNLIMITED; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_INT16; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_INT32; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_INT8; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_I16LE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_I32LE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_I8LE; import java.io.File; import java.io.FileNotFoundException; import java.io.Flushable; import java.io.IOException; import java.io.RandomAccessFile; import java.util.EnumSet; import java.util.LinkedHashSet; import java.util.Set; import java.util.concurrent.BlockingQueue; import java.util.concurrent.ExecutorService; import java.util.concurrent.LinkedBlockingQueue; import java.util.concurrent.TimeUnit; import ncsa.hdf.hdf5lib.exceptions.HDF5DatasetInterfaceException; import ncsa.hdf.hdf5lib.exceptions.HDF5FileNotFoundException; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel; import ch.systemsx.cisd.base.exceptions.IErrorStrategy; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.namedthread.NamingThreadPoolExecutor; import ch.systemsx.cisd.hdf5.IHDF5CompoundInformationRetriever.IByteArrayInspector; import ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator.FileFormat; import ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator.SyncMode; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; /** * Class that provides base methods for reading and writing HDF5 files. * * @author Bernd Rinn */ final class HDF5BaseWriter extends HDF5BaseReader { private static final int SHUTDOWN_TIMEOUT_SECONDS = 60; private static final int MAX_TYPE_VARIANT_TYPES = 1024; private final static EnumSet BLOCKING_SYNC_MODES = EnumSet.of(SyncMode.SYNC_BLOCK, SyncMode.SYNC_ON_FLUSH_BLOCK); private final static EnumSet NON_BLOCKING_SYNC_MODES = EnumSet.of(SyncMode.SYNC, SyncMode.SYNC_ON_FLUSH); private final static EnumSet SYNC_ON_CLOSE_MODES = EnumSet.of(SyncMode.SYNC_BLOCK, SyncMode.SYNC); /** * The size threshold for the COMPACT storage layout. */ final static int COMPACT_LAYOUT_THRESHOLD = 256; /** * ExecutorService for calling fsync(2) in a non-blocking way. */ private final static ExecutorService syncExecutor = new NamingThreadPoolExecutor("HDF5 Sync") .corePoolSize(3).daemonize(); static { // Ensure all sync() calls are finished. Runtime.getRuntime().addShutdownHook(new Thread() { @Override public void run() { syncExecutor.shutdownNow(); try { syncExecutor.awaitTermination(SHUTDOWN_TIMEOUT_SECONDS, TimeUnit.SECONDS); } catch (InterruptedException ex) { // Unexpected ex.printStackTrace(); } } }); } private final RandomAccessFile fileForSyncing; private enum Command { SYNC, CLOSE_ON_EXIT, CLOSE_SYNC, EXIT } private final BlockingQueue commandQueue; private final Set flushables = new LinkedHashSet(); final boolean useExtentableDataTypes; final boolean overwriteFile; final boolean keepDataSetIfExists; final boolean useSimpleDataSpaceForAttributes; final SyncMode syncMode; final FileFormat fileFormat; HDF5BaseWriter(File hdf5File, boolean performNumericConversions, boolean useUTF8CharEncoding, boolean autoDereference, FileFormat fileFormat, boolean useExtentableDataTypes, boolean overwriteFile, boolean keepDataSetIfExists, boolean useSimpleDataSpaceForAttributes, String preferredHouseKeepingNameSuffix, SyncMode syncMode) { super(hdf5File, performNumericConversions, useUTF8CharEncoding, autoDereference, fileFormat, overwriteFile, preferredHouseKeepingNameSuffix); try { this.fileForSyncing = new RandomAccessFile(hdf5File, "rw"); } catch (FileNotFoundException ex) { // Should not be happening as openFile() was called in super() throw new HDF5JavaException("Cannot open RandomAccessFile: " + ex.getMessage()); } this.fileFormat = fileFormat; this.useExtentableDataTypes = useExtentableDataTypes; this.overwriteFile = overwriteFile; this.keepDataSetIfExists = keepDataSetIfExists; this.useSimpleDataSpaceForAttributes = useSimpleDataSpaceForAttributes; this.syncMode = syncMode; readNamedDataTypes(); saveNonDefaultHouseKeepingNameSuffix(); commandQueue = new LinkedBlockingQueue(); setupSyncThread(); } private void setupSyncThread() { syncExecutor.execute(new Runnable() { @Override public void run() { while (true) { try { switch (commandQueue.take()) { case SYNC: syncNow(); break; case CLOSE_ON_EXIT: closeNow(); return; case CLOSE_SYNC: closeSync(); return; case EXIT: return; } } catch (InterruptedException ex) { // Shutdown has been triggered by showdownNow(), add // CLOSEHDF to queue. // (Note that a close() on a closed RandomAccessFile is harmless.) commandQueue.add(Command.CLOSE_ON_EXIT); } } } }); } @Override int openFile(FileFormat fileFormatInit, boolean overwriteInit) { final boolean enforce_1_8 = (fileFormatInit == FileFormat.STRICTLY_1_8); if (hdf5File.exists() && overwriteInit == false) { if (hdf5File.canWrite() == false) { throw new HDF5FileNotFoundException(hdf5File, "File is not writable."); } return h5.openFileReadWrite(hdf5File.getPath(), enforce_1_8, fileRegistry); } else { final File directory = hdf5File.getParentFile(); if (directory.exists() == false) { throw new HDF5FileNotFoundException(directory, "Directory does not exist."); } if (directory.canWrite() == false) { throw new HDF5FileNotFoundException(directory, "Directory is not writable."); } return h5.createFile(hdf5File.getPath(), enforce_1_8, fileRegistry); } } /** * Calls fsync(2) in the current thread. */ private void syncNow() { try { // Implementation note 1: Unix will call fsync(), , Windows: FlushFileBuffers() // Implementation note 2: We do not call fileForSyncing.getChannel().force(false) which // might be better in terms of performance as if shutdownNow() already has been // triggered on the syncExecutor and thus this thread has already been interrupted, // channel methods would throw a ClosedByInterruptException at us no matter what we do. fileForSyncing.getFD().sync(); } catch (IOException ex) { final String msg = (ex.getMessage() == null) ? ex.getClass().getSimpleName() : ex.getMessage(); throw new HDF5JavaException("Error syncing file: " + msg); } } /** * Closes and, depending on the sync mode, syncs the HDF5 file in the current thread. *

* To be called from the syncer thread only. */ private void closeNow() { synchronized (fileRegistry) { if (state == State.OPEN) { flushExternals(); flushables.clear(); super.close(); if (SYNC_ON_CLOSE_MODES.contains(syncMode)) { syncNow(); } closeSync(); } } } private void closeSync() { try { fileForSyncing.close(); } catch (IOException ex) { throw new HDF5JavaException("Error closing file: " + ex.getMessage()); } } boolean addFlushable(Flushable flushable) { return flushables.add(flushable); } boolean removeFlushable(Flushable flushable) { return flushables.remove(flushable); } void flushExternals() { for (Flushable f : flushables) { try { f.flush(); } catch (Throwable ex) { if (f instanceof IErrorStrategy) { ((IErrorStrategy) f).dealWithError(ex); } else { throw CheckedExceptionTunnel.wrapIfNecessary(ex); } } } } void flush() { synchronized (fileRegistry) { flushExternals(); h5.flushFile(fileId); if (NON_BLOCKING_SYNC_MODES.contains(syncMode)) { commandQueue.add(Command.SYNC); } else if (BLOCKING_SYNC_MODES.contains(syncMode)) { syncNow(); } } } void flushSyncBlocking() { synchronized (fileRegistry) { flushExternals(); h5.flushFile(fileId); syncNow(); } } @Override void close() { synchronized (fileRegistry) { if (state == State.OPEN) { flushExternals(); flushables.clear(); super.close(); if (SyncMode.SYNC == syncMode) { commandQueue.add(Command.SYNC); } else if (SyncMode.SYNC_BLOCK == syncMode) { syncNow(); } if (EnumSet.complementOf(NON_BLOCKING_SYNC_MODES).contains(syncMode)) { closeSync(); commandQueue.add(Command.EXIT); } else { // End syncer thread and avoid a race condition for non-blocking sync modes as // the // syncer thread still may want to use the fileForSynching commandQueue.add(Command.CLOSE_SYNC); } } } } void saveNonDefaultHouseKeepingNameSuffix() { // If it is empty, then there is nothing to save. if ("".equals(houseKeepingNameSuffix)) { return; } final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { final int objectId = h5.openObject(fileId, "/", registry); setStringAttribute(objectId, HDF5Utils.HOUSEKEEPING_NAME_SUFFIX_ATTRIBUTE_NAME, houseKeepingNameSuffix, houseKeepingNameSuffix.length(), false, registry); setIntAttributeAutoSize(objectId, HOUSEKEEPING_NAME_SUFFIX_STRINGLENGTH_ATTRIBUTE_NAME, houseKeepingNameSuffix.length(), registry); return null; // Nothing to return. } }; runner.call(addAttributeRunnable); } /** * Saves the value as integer attribute attributeName of * objectId, choosing the size of the integer type automatically based on the * value. * * @param objectId The id of the data set object in the file. */ private void setIntAttributeAutoSize(final int objectId, final String attributeName, final int value, ICleanUpRegistry registry) { if (value > Short.MAX_VALUE) { setAttribute(objectId, attributeName, H5T_STD_I32LE, H5T_NATIVE_INT32, -1, new int[] { value }, registry); } else if (value > Byte.MAX_VALUE) { setAttribute(objectId, attributeName, H5T_STD_I16LE, H5T_NATIVE_INT16, -1, new int[] { value }, registry); } else { setAttribute(objectId, attributeName, H5T_STD_I8LE, H5T_NATIVE_INT8, -1, new byte[] { (byte) value }, registry); } } @Override void commitDataType(final String dataTypePath, final int dataTypeId) { h5.commitDataType(fileId, dataTypePath, dataTypeId); } HDF5EnumerationType openOrCreateTypeVariantDataType(final HDF5Writer writer) { final String typeVariantTypePath = getTypeVariantDataTypePath(houseKeepingNameSuffix); final HDF5EnumerationType dataType; int dataTypeId = getDataTypeId(typeVariantTypePath); if (dataTypeId < 0 || h5.getNumberOfMembers(dataTypeId) < HDF5DataTypeVariant.values().length) { final String typeVariantPath = findFirstUnusedTypeVariantPath(writer); dataType = createTypeVariantDataType(); commitDataType(typeVariantPath, dataType.getStorageTypeId()); writer.createOrUpdateSoftLink(typeVariantPath.substring(getDataTypeGroup( houseKeepingNameSuffix).length() + 1), typeVariantTypePath); } else { final int nativeDataTypeId = h5.getNativeDataType(dataTypeId, fileRegistry); final String[] typeVariantNames = h5.getNamesForEnumOrCompoundMembers(dataTypeId); dataType = new HDF5EnumerationType(fileId, dataTypeId, nativeDataTypeId, typeVariantTypePath, typeVariantNames, this); } return dataType; } void setEnumArrayAttribute(final String objectPath, final String name, final HDF5EnumerationValueArray value) { assert objectPath != null; assert name != null; assert value != null; checkOpen(); final ICallableWithCleanUp setAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int baseMemoryTypeId = value.getType().getNativeTypeId(); final int memoryTypeId = h5.createArrayType(baseMemoryTypeId, value.getLength(), registry); final int baseStorageTypeId = value.getType().getStorageTypeId(); final int storageTypeId = h5.createArrayType(baseStorageTypeId, value.getLength(), registry); setAttribute(objectPath, name, storageTypeId, memoryTypeId, -1, value.toStorageForm(), registry); return null; // Nothing to return. } }; runner.call(setAttributeRunnable); } void setEnumMDArrayAttribute(final String objectPath, final String name, final HDF5EnumerationValueMDArray value) { assert objectPath != null; assert name != null; assert value != null; checkOpen(); final ICallableWithCleanUp setAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int baseMemoryTypeId = value.getType().getNativeTypeId(); final int memoryTypeId = h5.createArrayType(baseMemoryTypeId, value.dimensions(), registry); final int baseStorageTypeId = value.getType().getStorageTypeId(); final int storageTypeId = h5.createArrayType(baseStorageTypeId, value.dimensions(), registry); setAttribute(objectPath, name, storageTypeId, memoryTypeId, -1, value.toStorageForm(), registry); return null; // Nothing to return. } }; runner.call(setAttributeRunnable); } void setCompoundArrayAttribute(final String objectPath, final String attributeName, final HDF5CompoundType type, final T[] data, final IByteArrayInspector inspectorOrNull) { assert objectPath != null; assert attributeName != null; assert data != null; checkOpen(); type.check(fileId); final ICallableWithCleanUp setAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final byte[] byteArray = type.getObjectByteifyer().byteify(type.getStorageTypeId(), data); if (inspectorOrNull != null) { inspectorOrNull.inspect(byteArray); } final int baseMemoryTypeId = type.getNativeTypeId(); final int memoryTypeId = h5.createArrayType(baseMemoryTypeId, data.length, registry); final int baseStorageTypeId = type.getStorageTypeId(); final int storageTypeId = h5.createArrayType(baseStorageTypeId, data.length, registry); setAttribute(objectPath, attributeName, storageTypeId, memoryTypeId, -1, byteArray, registry); h5.reclaimCompoundVL(type, byteArray); return null; // Nothing to return. } }; runner.call(setAttributeRunnable); } void setCompoundMDArrayAttribute(final String objectPath, final String attributeName, final HDF5CompoundType type, final MDArray data, final IByteArrayInspector inspectorOrNull) { assert objectPath != null; assert attributeName != null; assert data != null; checkOpen(); type.check(fileId); final ICallableWithCleanUp setAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final byte[] byteArray = type.getObjectByteifyer().byteify(type.getStorageTypeId(), data.getAsFlatArray()); if (inspectorOrNull != null) { inspectorOrNull.inspect(byteArray); } final int baseMemoryTypeId = type.getNativeTypeId(); final int memoryTypeId = h5.createArrayType(baseMemoryTypeId, data.dimensions(), registry); final int baseStorageTypeId = type.getStorageTypeId(); final int storageTypeId = h5.createArrayType(baseStorageTypeId, data.dimensions(), registry); setAttribute(objectPath, attributeName, storageTypeId, memoryTypeId, -1, byteArray, registry); h5.reclaimCompoundVL(type, byteArray); return null; // Nothing to return. } }; runner.call(setAttributeRunnable); } private String findFirstUnusedTypeVariantPath(final HDF5Reader reader) { int number = 0; String path; do { path = getTypeVariantDataTypePath(houseKeepingNameSuffix) + "." + (number++); } while (reader.exists(path, false) && number < MAX_TYPE_VARIANT_TYPES); return path; } /** * Write a scalar value provided as byte[]. */ void writeScalar(final String dataSetPath, final int storageDataTypeId, final int nativeDataTypeId, final byte[] value) { assert dataSetPath != null; assert storageDataTypeId >= 0; assert nativeDataTypeId >= 0; assert value != null; final ICallableWithCleanUp writeScalarRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { writeScalar(dataSetPath, storageDataTypeId, nativeDataTypeId, value, true, keepDataSetIfExists, registry); return null; // Nothing to return. } }; runner.call(writeScalarRunnable); } /** * Internal method for writing a scalar value provided as byte[]. */ int writeScalar(final String dataSetPath, final int storageDataTypeId, final int nativeDataTypeId, final byte[] value, final boolean compactLayout, final boolean keepDatasetIfExists, ICleanUpRegistry registry) { final int dataSetId; boolean exists = h5.exists(fileId, dataSetPath); if (exists && keepDatasetIfExists == false) { h5.deleteObject(fileId, dataSetPath); exists = false; } if (exists) { dataSetId = h5.openObject(fileId, dataSetPath, registry); } else { dataSetId = h5.createScalarDataSet(fileId, storageDataTypeId, dataSetPath, compactLayout, registry); } H5Dwrite(dataSetId, nativeDataTypeId, H5S_SCALAR, H5S_SCALAR, H5P_DEFAULT, value); return dataSetId; } /** * Write a scalar value provided as byte. */ void writeScalar(final String dataSetPath, final int storageDataTypeId, final int nativeDataTypeId, final byte value) { assert dataSetPath != null; assert storageDataTypeId >= 0; assert nativeDataTypeId >= 0; final ICallableWithCleanUp writeScalarRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { writeScalar(dataSetPath, storageDataTypeId, nativeDataTypeId, value, true, true, registry); return null; // Nothing to return. } }; runner.call(writeScalarRunnable); } /** * Internal method for writing a scalar value provided as byte. */ int writeScalar(final String dataSetPath, final int storageDataTypeId, final int nativeDataTypeId, final byte value, final boolean compactLayout, final boolean keepDatasetIfExists, ICleanUpRegistry registry) { final int dataSetId; boolean exists = h5.exists(fileId, dataSetPath); if (exists && keepDatasetIfExists == false) { h5.deleteObject(fileId, dataSetPath); exists = false; } if (exists) { dataSetId = h5.openObject(fileId, dataSetPath, registry); } else { dataSetId = h5.createScalarDataSet(fileId, storageDataTypeId, dataSetPath, compactLayout, registry); } H5Dwrite(dataSetId, nativeDataTypeId, H5S_SCALAR, H5S_SCALAR, H5P_DEFAULT, new byte[] { value }); return dataSetId; } /** * Write a scalar value provided as short. */ void writeScalar(final String dataSetPath, final int storageDataTypeId, final int nativeDataTypeId, final short value) { assert dataSetPath != null; assert storageDataTypeId >= 0; assert nativeDataTypeId >= 0; final ICallableWithCleanUp writeScalarRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { writeScalar(dataSetPath, storageDataTypeId, nativeDataTypeId, value, true, true, registry); return null; // Nothing to return. } }; runner.call(writeScalarRunnable); } /** * Internal method for writing a scalar value provided as short. */ int writeScalar(final String dataSetPath, final int storageDataTypeId, final int nativeDataTypeId, final short value, final boolean compactLayout, final boolean keepDatasetIfExists, ICleanUpRegistry registry) { final int dataSetId; boolean exists = h5.exists(fileId, dataSetPath); if (exists && keepDatasetIfExists == false) { h5.deleteObject(fileId, dataSetPath); exists = false; } if (exists) { dataSetId = h5.openObject(fileId, dataSetPath, registry); } else { dataSetId = h5.createScalarDataSet(fileId, storageDataTypeId, dataSetPath, compactLayout, registry); } H5Dwrite(dataSetId, nativeDataTypeId, H5S_SCALAR, H5S_SCALAR, H5P_DEFAULT, new short[] { value }); return dataSetId; } /** * Write a scalar value provided as int. */ void writeScalar(final String dataSetPath, final int storageDataTypeId, final int nativeDataTypeId, final int value) { assert dataSetPath != null; assert storageDataTypeId >= 0; assert nativeDataTypeId >= 0; final ICallableWithCleanUp writeScalarRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { writeScalar(dataSetPath, storageDataTypeId, nativeDataTypeId, value, true, true, registry); return null; // Nothing to return. } }; runner.call(writeScalarRunnable); } /** * Internal method for writing a scalar value provided as int. */ int writeScalar(final String dataSetPath, final int storageDataTypeId, final int nativeDataTypeId, final int value, final boolean compactLayout, final boolean keepDatasetIfExists, ICleanUpRegistry registry) { final int dataSetId; boolean exists = h5.exists(fileId, dataSetPath); if (exists && keepDatasetIfExists == false) { h5.deleteObject(fileId, dataSetPath); exists = false; } if (exists) { dataSetId = h5.openObject(fileId, dataSetPath, registry); } else { dataSetId = h5.createScalarDataSet(fileId, storageDataTypeId, dataSetPath, compactLayout, registry); } H5Dwrite(dataSetId, nativeDataTypeId, H5S_SCALAR, H5S_SCALAR, H5P_DEFAULT, new int[] { value }); return dataSetId; } /** * Write a scalar value provided as long. */ void writeScalar(final String dataSetPath, final int storageDataTypeId, final int nativeDataTypeId, final long value) { assert dataSetPath != null; assert storageDataTypeId >= 0; assert nativeDataTypeId >= 0; final ICallableWithCleanUp writeScalarRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { writeScalar(dataSetPath, storageDataTypeId, nativeDataTypeId, value, true, true, registry); return null; // Nothing to return. } }; runner.call(writeScalarRunnable); } /** * Internal method for writing a scalar value provided as long. */ int writeScalar(final String dataSetPath, final int storageDataTypeId, final int nativeDataTypeId, final long value, final boolean compactLayout, final boolean keepDatasetIfExists, ICleanUpRegistry registry) { final int dataSetId; boolean exists = h5.exists(fileId, dataSetPath); if (exists && keepDatasetIfExists == false) { h5.deleteObject(fileId, dataSetPath); exists = false; } if (exists) { dataSetId = h5.openObject(fileId, dataSetPath, registry); } else { dataSetId = h5.createScalarDataSet(fileId, storageDataTypeId, dataSetPath, compactLayout, registry); } H5Dwrite(dataSetId, nativeDataTypeId, H5S_SCALAR, H5S_SCALAR, H5P_DEFAULT, new long[] { value }); return dataSetId; } /** * Write a scalar value provided as float. */ void writeScalar(final String dataSetPath, final int storageDataTypeId, final int nativeDataTypeId, final float value) { assert dataSetPath != null; assert storageDataTypeId >= 0; assert nativeDataTypeId >= 0; final ICallableWithCleanUp writeScalarRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { writeScalar(dataSetPath, storageDataTypeId, nativeDataTypeId, value, true, keepDataSetIfExists, registry); return null; // Nothing to return. } }; runner.call(writeScalarRunnable); } /** * Internal method for writing a scalar value provided as float. */ int writeScalar(final String dataSetPath, final int storageDataTypeId, final int nativeDataTypeId, final float value, final boolean compactLayout, final boolean keepDatasetIfExists, ICleanUpRegistry registry) { final int dataSetId; boolean exists = h5.exists(fileId, dataSetPath); if (exists && keepDatasetIfExists == false) { h5.deleteObject(fileId, dataSetPath); exists = false; } if (exists) { dataSetId = h5.openObject(fileId, dataSetPath, registry); } else { dataSetId = h5.createScalarDataSet(fileId, storageDataTypeId, dataSetPath, compactLayout, registry); } H5Dwrite(dataSetId, nativeDataTypeId, H5S_SCALAR, H5S_SCALAR, H5P_DEFAULT, new float[] { value }); return dataSetId; } /** * Write a scalar value provided as double. */ void writeScalar(final String dataSetPath, final int storageDataTypeId, final int nativeDataTypeId, final double value) { assert dataSetPath != null; assert storageDataTypeId >= 0; assert nativeDataTypeId >= 0; final ICallableWithCleanUp writeScalarRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { writeScalar(dataSetPath, storageDataTypeId, nativeDataTypeId, value, true, true, registry); return null; // Nothing to return. } }; runner.call(writeScalarRunnable); } /** * Internal method for writing a scalar value provided as double. */ int writeScalar(final String dataSetPath, final int storageDataTypeId, final int nativeDataTypeId, final double value, final boolean compactLayout, final boolean keepDatasetIfExists, ICleanUpRegistry registry) { final int dataSetId; boolean exists = h5.exists(fileId, dataSetPath); if (exists && keepDatasetIfExists == false) { h5.deleteObject(fileId, dataSetPath); exists = false; } if (exists) { dataSetId = h5.openObject(fileId, dataSetPath, registry); } else { dataSetId = h5.createScalarDataSet(fileId, storageDataTypeId, dataSetPath, compactLayout, registry); } H5Dwrite(dataSetId, nativeDataTypeId, H5S_SCALAR, H5S_SCALAR, H5P_DEFAULT, new double[] { value }); return dataSetId; } /** * Writes a variable-length string array data set. */ void writeStringVL(int dataSetId, int memorySpaceId, int fileSpaceId, String[] value) { h5.writeStringVL(dataSetId, variableLengthStringDataTypeId, memorySpaceId, fileSpaceId, value); } /** * Writes a variable-length string array data set. */ void writeStringVL(int dataSetId, String[] value) { h5.writeStringVL(dataSetId, variableLengthStringDataTypeId, value); } /** * Writes a variable-length string array attribute. */ void writeAttributeStringVL(int attributeId, String[] value) { h5.writeAttributeStringVL(attributeId, variableLengthStringDataTypeId, value); } /** * Creates a data set. */ int createDataSet(final String objectPath, final int storageDataTypeId, final HDF5AbstractStorageFeatures features, final long[] dimensions, final long[] chunkSizeOrNull, int elementLength, final ICleanUpRegistry registry) { final int dataSetId; final boolean empty = isEmpty(dimensions); final boolean chunkSizeProvided = (chunkSizeOrNull != null && isNonPositive(chunkSizeOrNull) == false); final long[] definitiveChunkSizeOrNull; if (h5.exists(fileId, objectPath)) { if (keepDataIfExists(features)) { return h5.openDataSet(fileId, objectPath, registry); } h5.deleteObject(fileId, objectPath); } if (empty) { definitiveChunkSizeOrNull = chunkSizeProvided ? chunkSizeOrNull : HDF5Utils.tryGetChunkSize(dimensions, elementLength, features.requiresChunking(), true); } else if (features.tryGetProposedLayout() == HDF5StorageLayout.COMPACT || features.tryGetProposedLayout() == HDF5StorageLayout.CONTIGUOUS || (useExtentableDataTypes == false) && features.requiresChunking() == false) { definitiveChunkSizeOrNull = null; } else if (chunkSizeProvided) { definitiveChunkSizeOrNull = chunkSizeOrNull; } else { definitiveChunkSizeOrNull = HDF5Utils .tryGetChunkSize( dimensions, elementLength, features.requiresChunking(), useExtentableDataTypes || features.tryGetProposedLayout() == HDF5StorageLayout.CHUNKED); } final HDF5StorageLayout layout = determineLayout(storageDataTypeId, dimensions, definitiveChunkSizeOrNull, features.tryGetProposedLayout()); dataSetId = h5.createDataSet(fileId, dimensions, definitiveChunkSizeOrNull, storageDataTypeId, features, objectPath, layout, fileFormat, registry); return dataSetId; } boolean keepDataIfExists(final HDF5AbstractStorageFeatures features) { switch (features.getDatasetReplacementPolicy()) { case ENFORCE_KEEP_EXISTING: return true; case ENFORCE_REPLACE_WITH_NEW: return false; case USE_WRITER_DEFAULT: default: return keepDataSetIfExists; } } /** * Determine which {@link HDF5StorageLayout} to use for the given storageDataTypeId. */ HDF5StorageLayout determineLayout(final int storageDataTypeId, final long[] dimensions, final long[] chunkSizeOrNull, final HDF5StorageLayout proposedLayoutOrNull) { if (chunkSizeOrNull != null) { return HDF5StorageLayout.CHUNKED; } if (proposedLayoutOrNull != null) { return proposedLayoutOrNull; } if (computeSizeForDimensions(storageDataTypeId, dimensions) < HDF5BaseWriter.COMPACT_LAYOUT_THRESHOLD) { return HDF5StorageLayout.COMPACT; } return HDF5StorageLayout.CONTIGUOUS; } private int computeSizeForDimensions(int dataTypeId, long[] dimensions) { int size = h5.getDataTypeSize(dataTypeId); for (long d : dimensions) { size *= d; } return size; } /** * Checks whether the given dimensions are in bounds for dataSetId. */ boolean areDimensionsInBounds(final int dataSetId, final long[] dimensions) { final long[] maxDimensions = h5.getDataMaxDimensions(dataSetId); if (dimensions.length != maxDimensions.length) // Actually an error condition { return false; } for (int i = 0; i < dimensions.length; ++i) { if (maxDimensions[i] != H5S_UNLIMITED && dimensions[i] > maxDimensions[i]) { return false; } } return true; } /** * Returns the data set id for the given objectPath. If the data sets exists, it * depends on the features and on the status of keepDataSetIfExists * whether the existing data set will be opened or whether the data set will be deleted and * re-created. */ int getOrCreateDataSetId(final String objectPath, final int storageDataTypeId, final long[] dimensions, int elementLength, final HDF5AbstractStorageFeatures features, ICleanUpRegistry registry) { final int dataSetId; boolean exists = h5.exists(fileId, objectPath); if (exists && keepDataIfExists(features) == false) { h5.deleteObject(fileId, objectPath); exists = false; } if (exists) { dataSetId = h5.openAndExtendDataSet(fileId, objectPath, fileFormat, dimensions, storageDataTypeId, registry); } else { dataSetId = createDataSet(objectPath, storageDataTypeId, features, dimensions, null, elementLength, registry); } return dataSetId; } void setDataSetDimensions(final String objectPath, final long[] newDimensions, ICleanUpRegistry registry) { assert newDimensions != null; final int dataSetId = h5.openDataSet(fileId, objectPath, registry); try { h5.setDataSetExtentChunked(dataSetId, newDimensions); } catch (HDF5DatasetInterfaceException ex) { if (HDF5StorageLayout.CHUNKED != h5.getLayout(dataSetId, registry)) { throw new HDF5JavaException("Cannot change dimensions of non-extendable data set."); } else { throw ex; } } } // // Attributes // void setAttribute(final String objectPath, final String name, final int storageDataTypeId, final int nativeDataTypeId, final int dataSpaceId, final byte[] value, ICleanUpRegistry registry) { assert objectPath != null; assert name != null; assert storageDataTypeId >= 0; assert nativeDataTypeId >= 0; assert value != null; final int objectId = h5.openObject(fileId, objectPath, registry); setAttribute(objectId, name, storageDataTypeId, nativeDataTypeId, dataSpaceId, value, registry); } void setAttribute(final int objectId, final String name, final int storageDataTypeId, final int nativeDataTypeId, final int dataSpaceId, final byte[] value, ICleanUpRegistry registry) { int attributeId; if (h5.existsAttribute(objectId, name)) { attributeId = h5.openAttribute(objectId, name, registry); final int oldStorageDataTypeId = h5.getDataTypeForAttribute(attributeId, registry); if (h5.dataTypesAreEqual(oldStorageDataTypeId, storageDataTypeId) == false) { h5.deleteAttribute(objectId, name); attributeId = h5.createAttribute(objectId, name, storageDataTypeId, dataSpaceId, registry); } } else { attributeId = h5.createAttribute(objectId, name, storageDataTypeId, dataSpaceId, registry); } h5.writeAttribute(attributeId, nativeDataTypeId, value); } void setAttribute(final String objectPath, final String name, final int storageDataTypeId, final int nativeDataTypeId, final int dataSpaceId, final short[] value) { assert objectPath != null; assert name != null; assert storageDataTypeId >= 0; assert nativeDataTypeId >= 0; assert value != null; final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { setAttribute(objectPath, name, storageDataTypeId, nativeDataTypeId, dataSpaceId, value, registry); return null; // Nothing to return. } }; runner.call(addAttributeRunnable); } void setAttribute(final String objectPath, final String name, final int storageDataTypeId, final int nativeDataTypeId, final int dataSpaceId, final short[] value, ICleanUpRegistry registry) { final int objectId = h5.openObject(fileId, objectPath, registry); setAttribute(objectId, name, storageDataTypeId, nativeDataTypeId, dataSpaceId, value, registry); } void setAttribute(final int objectId, final String name, final int storageDataTypeId, final int nativeDataTypeId, final int dataSpaceId, final short[] value, ICleanUpRegistry registry) { int attributeId; if (h5.existsAttribute(objectId, name)) { attributeId = h5.openAttribute(objectId, name, registry); final int oldStorageDataTypeId = h5.getDataTypeForAttribute(attributeId, registry); if (h5.dataTypesAreEqual(oldStorageDataTypeId, storageDataTypeId) == false) { h5.deleteAttribute(objectId, name); attributeId = h5.createAttribute(objectId, name, storageDataTypeId, dataSpaceId, registry); } } else { attributeId = h5.createAttribute(objectId, name, storageDataTypeId, dataSpaceId, registry); } h5.writeAttribute(attributeId, nativeDataTypeId, value); } void setAttribute(final String objectPath, final String name, final int storageDataTypeId, final int nativeDataTypeId, final int dataSpaceId, final int[] value) { assert objectPath != null; assert name != null; assert storageDataTypeId >= 0; assert nativeDataTypeId >= 0; assert value != null; final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { setAttribute(objectPath, name, storageDataTypeId, nativeDataTypeId, dataSpaceId, value, registry); return null; // Nothing to return. } }; runner.call(addAttributeRunnable); } void setAttribute(final String objectPath, final String name, final int storageDataTypeId, final int nativeDataTypeId, final int dataSpaceId, final int[] value, ICleanUpRegistry registry) { final int objectId = h5.openObject(fileId, objectPath, registry); setAttribute(objectId, name, storageDataTypeId, nativeDataTypeId, dataSpaceId, value, registry); } void setAttribute(final int objectId, final String name, final int storageDataTypeId, final int nativeDataTypeId, final int dataSpaceId, final int[] value, ICleanUpRegistry registry) { int attributeId; if (h5.existsAttribute(objectId, name)) { attributeId = h5.openAttribute(objectId, name, registry); final int oldStorageDataTypeId = h5.getDataTypeForAttribute(attributeId, registry); if (h5.dataTypesAreEqual(oldStorageDataTypeId, storageDataTypeId) == false) { h5.deleteAttribute(objectId, name); attributeId = h5.createAttribute(objectId, name, storageDataTypeId, dataSpaceId, registry); } } else { attributeId = h5.createAttribute(objectId, name, storageDataTypeId, dataSpaceId, registry); } h5.writeAttribute(attributeId, nativeDataTypeId, value); } void setAttribute(final String objectPath, final String name, final int storageDataTypeId, final int nativeDataTypeId, final int dataSpaceId, final long[] value) { assert objectPath != null; assert name != null; assert storageDataTypeId >= 0; assert nativeDataTypeId >= 0; assert value != null; final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { setAttribute(objectPath, name, storageDataTypeId, nativeDataTypeId, dataSpaceId, value, registry); return null; // Nothing to return. } }; runner.call(addAttributeRunnable); } void setAttribute(final String objectPath, final String name, final int storageDataTypeId, final int nativeDataTypeId, final int dataSpaceId, final long[] value, ICleanUpRegistry registry) { final int objectId = h5.openObject(fileId, objectPath, registry); setAttribute(objectId, name, storageDataTypeId, nativeDataTypeId, dataSpaceId, value, registry); } void setAttribute(final String objectPath, final String name, final HDF5DataTypeVariant typeVariant, final int storageDataTypeId, final int nativeDataTypeId, final int dataSpaceId, final long[] value, ICleanUpRegistry registry) { assert objectPath != null; assert name != null; assert storageDataTypeId >= 0; assert nativeDataTypeId >= 0; assert value != null; final int objectId = h5.openObject(fileId, objectPath, registry); setAttribute(objectPath, name, storageDataTypeId, nativeDataTypeId, dataSpaceId, value, registry); setTypeVariant(objectId, name, (dataSpaceId != -1), typeVariant, registry); } void setAttribute(final int objectId, final String name, final int storageDataTypeId, final int nativeDataTypeId, final int dataSpaceId, final long[] value, ICleanUpRegistry registry) { int attributeId; if (h5.existsAttribute(objectId, name)) { attributeId = h5.openAttribute(objectId, name, registry); final int oldStorageDataTypeId = h5.getDataTypeForAttribute(attributeId, registry); if (h5.dataTypesAreEqual(oldStorageDataTypeId, storageDataTypeId) == false) { h5.deleteAttribute(objectId, name); attributeId = h5.createAttribute(objectId, name, storageDataTypeId, dataSpaceId, registry); } } else { attributeId = h5.createAttribute(objectId, name, storageDataTypeId, dataSpaceId, registry); } h5.writeAttribute(attributeId, nativeDataTypeId, value); } void setAttribute(final String objectPath, final String name, final int storageDataTypeId, final int nativeDataTypeId, final int dataSpaceId, final float[] value) { assert objectPath != null; assert name != null; assert storageDataTypeId >= 0; assert nativeDataTypeId >= 0; assert value != null; final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { setAttribute(objectPath, name, storageDataTypeId, nativeDataTypeId, dataSpaceId, value, registry); return null; // Nothing to return. } }; runner.call(addAttributeRunnable); } void setAttribute(final String objectPath, final String name, final int storageDataTypeId, final int nativeDataTypeId, final int dataSpaceId, final float[] value, ICleanUpRegistry registry) { final int objectId = h5.openObject(fileId, objectPath, registry); setAttribute(objectId, name, storageDataTypeId, nativeDataTypeId, dataSpaceId, value, registry); } void setAttribute(final int objectId, final String name, final int storageDataTypeId, final int nativeDataTypeId, final int dataSpaceId, final float[] value, ICleanUpRegistry registry) { int attributeId; if (h5.existsAttribute(objectId, name)) { attributeId = h5.openAttribute(objectId, name, registry); final int oldStorageDataTypeId = h5.getDataTypeForAttribute(attributeId, registry); if (h5.dataTypesAreEqual(oldStorageDataTypeId, storageDataTypeId) == false) { h5.deleteAttribute(objectId, name); attributeId = h5.createAttribute(objectId, name, storageDataTypeId, dataSpaceId, registry); } } else { attributeId = h5.createAttribute(objectId, name, storageDataTypeId, dataSpaceId, registry); } h5.writeAttribute(attributeId, nativeDataTypeId, value); } void setAttribute(final String objectPath, final String name, final int storageDataTypeId, final int nativeDataTypeId, final int dataSpaceId, final double[] value) { assert objectPath != null; assert name != null; assert storageDataTypeId >= 0; assert nativeDataTypeId >= 0; assert value != null; final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { setAttribute(objectPath, name, storageDataTypeId, nativeDataTypeId, dataSpaceId, value, registry); return null; // Nothing to return. } }; runner.call(addAttributeRunnable); } void setAttribute(final String objectPath, final String name, final int storageDataTypeId, final int nativeDataTypeId, final int dataSpaceId, final double[] value, ICleanUpRegistry registry) { final int objectId = h5.openObject(fileId, objectPath, registry); setAttribute(objectId, name, storageDataTypeId, nativeDataTypeId, dataSpaceId, value, registry); } void setAttribute(final int objectId, final String name, final int storageDataTypeId, final int nativeDataTypeId, final int dataSpaceId, final double[] value, ICleanUpRegistry registry) { int attributeId; if (h5.existsAttribute(objectId, name)) { attributeId = h5.openAttribute(objectId, name, registry); final int oldStorageDataTypeId = h5.getDataTypeForAttribute(attributeId, registry); if (h5.dataTypesAreEqual(oldStorageDataTypeId, storageDataTypeId) == false) { h5.deleteAttribute(objectId, name); attributeId = h5.createAttribute(objectId, name, storageDataTypeId, dataSpaceId, registry); } } else { attributeId = h5.createAttribute(objectId, name, storageDataTypeId, dataSpaceId, registry); } h5.writeAttribute(attributeId, nativeDataTypeId, value); } void setTypeVariant(final int objectId, final HDF5DataTypeVariant typeVariant, ICleanUpRegistry registry) { setAttribute(objectId, createObjectTypeVariantAttributeName(houseKeepingNameSuffix), typeVariantDataType.getStorageTypeId(), typeVariantDataType.getNativeTypeId(), -1, typeVariantDataType.getEnumType().toStorageForm(typeVariant.ordinal()), registry); } void setTypeVariant(final int objectId, final String attributeName, final boolean enforceSimpleDataSpace, final HDF5DataTypeVariant typeVariant, ICleanUpRegistry registry) { final int dataSpaceId = enforceSimpleDataSpace ? h5.createSimpleDataSpace(new long[] { 1 }, registry) : -1; setAttribute(objectId, createAttributeTypeVariantAttributeName(attributeName, houseKeepingNameSuffix), typeVariantDataType.getStorageTypeId(), typeVariantDataType.getNativeTypeId(), dataSpaceId, typeVariantDataType.getEnumType().toStorageForm(typeVariant.ordinal()), registry); } void setStringAttribute(final int objectId, final String name, final String value, final int maxLength, final boolean lengthFitsValue, ICleanUpRegistry registry) { final byte[] bytes; final int realMaxLengthInBytes; if (lengthFitsValue) { bytes = StringUtils.toBytes(value, encodingForNewDataSets); realMaxLengthInBytes = (bytes.length == 0) ? 1 : bytes.length; } else { bytes = StringUtils.toBytes(value, maxLength, encodingForNewDataSets); realMaxLengthInBytes = encodingForNewDataSets.getMaxBytesPerChar() * ((maxLength == 0) ? 1 : maxLength); } final int storageDataTypeId = h5.createDataTypeString(realMaxLengthInBytes, registry); int attributeId; if (h5.existsAttribute(objectId, name)) { attributeId = h5.openAttribute(objectId, name, registry); final int oldStorageDataTypeId = h5.getDataTypeForAttribute(attributeId, registry); if (h5.dataTypesAreEqual(oldStorageDataTypeId, storageDataTypeId) == false) { h5.deleteAttribute(objectId, name); attributeId = h5.createAttribute(objectId, name, storageDataTypeId, -1, registry); } } else { attributeId = h5.createAttribute(objectId, name, storageDataTypeId, -1, registry); } h5.writeAttribute(attributeId, storageDataTypeId, StringUtils.cutOrPadBytes(bytes, realMaxLengthInBytes)); } class StringArrayBuffer { private byte[] buf; private int len; private int realMaxLengthPerString; private boolean valueContainsChar0; private int[] lengths; private final int maxLengthPerString; private final boolean lengthFitsValue; StringArrayBuffer(int maxLengthPerString, boolean lengthFitsValue) { this.maxLengthPerString = maxLengthPerString; this.lengthFitsValue = lengthFitsValue; } void addAll(String[] array) { if (lengthFitsValue) { addAllLengthFitsValue(array); } else { addAllLengthFixedLength(array); } } private void addAllLengthFixedLength(String[] array) { this.realMaxLengthPerString = encodingForNewDataSets.getMaxBytesPerChar() * maxLengthPerString; this.buf = new byte[realMaxLengthPerString * array.length]; this.lengths = new int[array.length]; int idx = 0; for (String s : array) { final byte[] data = StringUtils.toBytes(s, maxLengthPerString, encodingForNewDataSets); final int dataLen = Math.min(data.length, realMaxLengthPerString); final int newLen = len + realMaxLengthPerString; System.arraycopy(data, 0, buf, len, dataLen); len = newLen; if (valueContainsChar0 == false) { valueContainsChar0 |= s.contains("\0"); } lengths[idx++] = dataLen; } } private void addAllLengthFitsValue(String[] array) { final byte[][] data = new byte[array.length][]; this.lengths = new int[array.length]; int idx = 0; for (String s : array) { final byte[] bytes = StringUtils.toBytes(s, encodingForNewDataSets); realMaxLengthPerString = Math.max(realMaxLengthPerString, bytes.length); data[idx] = bytes; lengths[idx] = bytes.length; if (valueContainsChar0 == false) { valueContainsChar0 |= s.contains("\0"); } ++idx; } this.buf = new byte[realMaxLengthPerString * array.length]; for (byte[] bytes : data) { System.arraycopy(bytes, 0, buf, len, bytes.length); len = len + realMaxLengthPerString; } } byte[] toArray() { return StringUtils.cutOrPadBytes(buf, len); } int getMaxLengthInByte() { return (realMaxLengthPerString == 0) ? 1 : realMaxLengthPerString; } boolean shouldSaveExplicitLength() { return valueContainsChar0 || (realMaxLengthPerString == 0); } int[] getLengths() { return lengths; } } void setStringArrayAttribute(final int objectId, final String name, final String[] value, final int maxLength, final boolean lengthFitsValue, ICleanUpRegistry registry) { final StringArrayBuffer array = new StringArrayBuffer(maxLength, lengthFitsValue); array.addAll(value); final byte[] arrData = array.toArray(); final int stringDataTypeId = h5.createDataTypeString(array.getMaxLengthInByte(), registry); final int storageDataTypeId = h5.createArrayType(stringDataTypeId, value.length, registry); int attributeId; if (h5.existsAttribute(objectId, name)) { attributeId = h5.openAttribute(objectId, name, registry); final int oldStorageDataTypeId = h5.getDataTypeForAttribute(attributeId, registry); if (h5.dataTypesAreEqual(oldStorageDataTypeId, storageDataTypeId) == false) { h5.deleteAttribute(objectId, name); attributeId = h5.createAttribute(objectId, name, storageDataTypeId, -1, registry); } } else { attributeId = h5.createAttribute(objectId, name, storageDataTypeId, -1, registry); } h5.writeAttribute(attributeId, storageDataTypeId, arrData); } void setStringArrayAttribute(final int objectId, final String name, final MDArray value, final int maxLength, final boolean lengthFitsValue, ICleanUpRegistry registry) { final StringArrayBuffer array = new StringArrayBuffer(maxLength, lengthFitsValue); array.addAll(value.getAsFlatArray()); final byte[] arrData = array.toArray(); final int stringDataTypeId = h5.createDataTypeString(array.getMaxLengthInByte(), registry); final int storageDataTypeId = h5.createArrayType(stringDataTypeId, value.dimensions(), registry); int attributeId; if (h5.existsAttribute(objectId, name)) { attributeId = h5.openAttribute(objectId, name, registry); final int oldStorageDataTypeId = h5.getDataTypeForAttribute(attributeId, registry); if (h5.dataTypesAreEqual(oldStorageDataTypeId, storageDataTypeId) == false) { h5.deleteAttribute(objectId, name); attributeId = h5.createAttribute(objectId, name, storageDataTypeId, -1, registry); } } else { attributeId = h5.createAttribute(objectId, name, storageDataTypeId, -1, registry); } h5.writeAttribute(attributeId, storageDataTypeId, arrData); } void setStringAttributeVariableLength(final int objectId, final String name, final String value, ICleanUpRegistry registry) { int attributeId; if (h5.existsAttribute(objectId, name)) { attributeId = h5.openAttribute(objectId, name, registry); final int oldStorageDataTypeId = h5.getDataTypeForAttribute(attributeId, registry); if (h5.dataTypesAreEqual(oldStorageDataTypeId, variableLengthStringDataTypeId) == false) { h5.deleteAttribute(objectId, name); attributeId = h5.createAttribute(objectId, name, variableLengthStringDataTypeId, -1, registry); } } else { attributeId = h5.createAttribute(objectId, name, variableLengthStringDataTypeId, -1, registry); } writeAttributeStringVL(attributeId, new String[] { value }); } String moveLinkOutOfTheWay(String linkPath) { final String newLinkPath = createNonExistentReplacementLinkPath(linkPath); h5.moveLink(fileId, linkPath, newLinkPath); return newLinkPath; } private String createNonExistentReplacementLinkPath(final String dataTypePath) { final String dstLinkPath = dataTypePath + "__REPLACED_"; int idx = 1; while (h5.exists(fileId, dstLinkPath + idx)) { ++idx; } return dstLinkPath + idx; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5BooleanReader.java000066400000000000000000000314141256564762100273410ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_B64; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_UINT64; import java.util.BitSet; import ncsa.hdf.hdf5lib.exceptions.HDF5DatatypeInterfaceException; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.base.mdarray.MDLongArray; import ch.systemsx.cisd.hdf5.HDF5BaseReader.DataSpaceParameters; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; /** * Implementation of {@link IHDF5BooleanReader}. * * @author Bernd Rinn */ public class HDF5BooleanReader implements IHDF5BooleanReader { private final HDF5BaseReader baseReader; HDF5BooleanReader(HDF5BaseReader baseReader) { assert baseReader != null; this.baseReader = baseReader; } // ///////////////////// // Attributes // ///////////////////// @Override public boolean getAttr(final String objectPath, final String attributeName) throws HDF5JavaException { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Boolean call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int nativeDataTypeId = baseReader.h5.getNativeDataTypeForAttribute(attributeId, registry); byte[] data = baseReader.h5 .readAttributeAsByteArray(attributeId, nativeDataTypeId, 1); final Boolean value = baseReader.h5.tryGetBooleanValue(nativeDataTypeId, data[0]); if (value == null) { throw new HDF5JavaException("Attribute " + attributeName + " of path " + objectPath + " needs to be a Boolean."); } return value; } }; return baseReader.runner.call(writeRunnable); } // ///////////////////// // Data Sets // ///////////////////// @Override public boolean read(final String objectPath) throws HDF5JavaException { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Boolean call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final int nativeDataTypeId = baseReader.h5.getNativeDataTypeForDataSet(dataSetId, registry); final byte[] data = new byte[1]; baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, data); final Boolean value = baseReader.h5.tryGetBooleanValue(nativeDataTypeId, data[0]); if (value == null) { throw new HDF5JavaException(objectPath + " needs to be a Boolean."); } return value; } }; return baseReader.runner.call(writeRunnable); } @Override public BitSet readBitField(final String objectPath) throws HDF5DatatypeInterfaceException { baseReader.checkOpen(); return BitSetConversionUtils.fromStorageForm(readBitFieldStorageForm(objectPath)); } private long[] readBitFieldStorageForm(final String objectPath) { assert objectPath != null; final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public long[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); final long[] data = new long[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_B64, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return data; } }; return baseReader.runner.call(readCallable); } @Override public BitSet readBitFieldBlock(String objectPath, int blockSize, long blockNumber) { return readBitFieldBlockWithOffset(objectPath, blockSize, blockSize * blockNumber); } private long[] readBitFieldStorageForm(final String objectPath, final int blockSize, final long offset, final boolean nullWhenOutside) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public long[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParamsOrNull = baseReader.tryGetSpaceParameters(dataSetId, offset, blockSize, nullWhenOutside, registry); if (spaceParamsOrNull == null) { return null; } final long[] data = new long[spaceParamsOrNull.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_B64, spaceParamsOrNull.memorySpaceId, spaceParamsOrNull.dataSpaceId, data); return data; } }; return baseReader.runner.call(readCallable); } @Override public BitSet readBitFieldBlockWithOffset(String objectPath, int blockSize, long offset) { baseReader.checkOpen(); return BitSetConversionUtils.fromStorageForm(readBitFieldStorageForm(objectPath, blockSize, offset, false)); } @Override public boolean isBitSet(String objectPath, int bitIndex) { final int wordIndex = BitSetConversionUtils.getWordIndex(bitIndex); final long[] storageFormOrNull = readBitFieldStorageForm(objectPath, 1, wordIndex, true); // If the bitIndex is outside of the bit field, we return false if (storageFormOrNull == null) { return false; } final long word = storageFormOrNull[0]; return (word & BitSetConversionUtils.getBitMaskInWord(bitIndex)) != 0; } @Override public BitSet[] readBitFieldArray(String objectPath) { baseReader.checkOpen(); return BitSetConversionUtils.fromStorageForm2D(readBitFieldArrayStorageForm(objectPath)); } private MDLongArray readBitFieldArrayStorageForm(final String objectPath) { assert objectPath != null; final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public MDLongArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); checkDimensions2D(spaceParams.dimensions); final long[] data = new long[spaceParams.blockSize]; if (baseReader.isScaledBitField(dataSetId, registry)) { baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_UINT64, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); } else { baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_B64, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); } return new MDLongArray(data, spaceParams.dimensions); } }; return baseReader.runner.call(readCallable); } @Override public BitSet[] readBitFieldArrayBlockWithOffset(String objectPath, int blockSize, long offset) { baseReader.checkOpen(); return BitSetConversionUtils.fromStorageForm2D(readBitFieldBlockStorageForm2D(objectPath, blockSize, offset, true)); } private MDLongArray readBitFieldBlockStorageForm2D(final String objectPath, final int blockSize, final long offset, final boolean nullWhenOutside) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public MDLongArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final long[] dimensions = baseReader.h5.getDataDimensions(dataSetId, registry); checkDimensions2D(dimensions); final int numberOfWords = dimToInt(dimensions[0]); final int[] blockDimensions = new int[] { numberOfWords, blockSize }; final DataSpaceParameters spaceParamsOrNull = baseReader.tryGetSpaceParameters(dataSetId, new long[] { 0, offset }, blockDimensions, nullWhenOutside, registry); if (spaceParamsOrNull == null) { return null; } final long[] data = new long[spaceParamsOrNull.blockSize]; if (baseReader.isScaledBitField(dataSetId, registry)) { baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_UINT64, spaceParamsOrNull.memorySpaceId, spaceParamsOrNull.dataSpaceId, data); } else { baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_B64, spaceParamsOrNull.memorySpaceId, spaceParamsOrNull.dataSpaceId, data); } return new MDLongArray(data, blockDimensions); } }; return baseReader.runner.call(readCallable); } private static void checkDimensions2D(final long[] dimensions) { if (dimensions.length != 2) { throw new HDF5JavaException( "Array is supposed to be of rank 2, but is of rank " + dimensions.length); } } static int dimToInt(long longNumber) { final int intNumber = (int) longNumber; if (intNumber != longNumber) { throw new HDF5JavaException("Dimension " + longNumber + " out of bounds."); } return intNumber; } @Override public BitSet[] readBitFieldArrayBlock(String objectPath, int blockSize, long blockNumber) { return readBitFieldArrayBlockWithOffset(objectPath, blockSize, blockNumber * blockSize); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5BooleanWriter.java000066400000000000000000000455741256564762100274270ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION; import static ch.systemsx.cisd.hdf5.HDF5IntStorageFeatures.INT_NO_COMPRESSION; import static ch.systemsx.cisd.hdf5.hdf5lib.H5D.H5Dwrite; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_ALL; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_B64; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_UINT64; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_B64LE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_U64LE; import java.util.BitSet; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; import ch.systemsx.cisd.hdf5.hdf5lib.HDFNativeData; /** * Implementation of {@link IHDF5BooleanWriter}. * * @author Bernd Rinn */ public class HDF5BooleanWriter extends HDF5BooleanReader implements IHDF5BooleanWriter { private final HDF5BaseWriter baseWriter; HDF5BooleanWriter(HDF5BaseWriter baseWriter) { super(baseWriter); assert baseWriter != null; this.baseWriter = baseWriter; } // ///////////////////// // Attributes // ///////////////////// @Override public void setAttr(final String objectPath, final String name, final boolean value) { baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { final byte byteValue = (byte) (value ? 1 : 0); if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { 1 }, registry); baseWriter.setAttribute(objectPath, name, baseWriter.booleanDataTypeId, baseWriter.booleanDataTypeId, dataSpaceId, new byte[] { byteValue }, registry); } else { baseWriter.setAttribute(objectPath, name, baseWriter.booleanDataTypeId, baseWriter.booleanDataTypeId, -1, new byte[] { byteValue }, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } // ///////////////////// // Data Sets // ///////////////////// @Override public void write(final String objectPath, final boolean value) { baseWriter.checkOpen(); baseWriter.writeScalar(objectPath, baseWriter.booleanDataTypeId, baseWriter.booleanDataTypeId, HDFNativeData.byteToByte((byte) (value ? 1 : 0))); } @Override public void writeBitField(final String objectPath, final BitSet data) { writeBitField(objectPath, data, HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION); } @Override public void writeBitField(final String objectPath, final BitSet data, final HDF5GenericStorageFeatures features) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int longBytes = 8; final int longBits = longBytes * 8; final int msb = data.length(); final int realLength = msb / longBits + (msb % longBits != 0 ? 1 : 0); final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, H5T_STD_B64LE, new long[] { realLength }, longBytes, features, registry); H5Dwrite(dataSetId, H5T_NATIVE_B64, H5S_ALL, H5S_ALL, H5P_DEFAULT, BitSetConversionUtils.toStorageForm(data)); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createBitField(String objectPath, int size) { createBitField(objectPath, size, GENERIC_NO_COMPRESSION); } @Override public void createBitField(String objectPath, long size, int blockSize) { createBitField(objectPath, size, blockSize, GENERIC_NO_COMPRESSION); } @Override public void createBitField(final String objectPath, final int size, final HDF5GenericStorageFeatures features) { assert objectPath != null; assert size >= 0; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (features.requiresChunking()) { baseWriter.createDataSet(objectPath, H5T_STD_B64LE, features, new long[] { 0 }, new long[] { size }, 8, registry); } else { baseWriter.createDataSet(objectPath, H5T_STD_B64LE, features, new long[] { size }, null, 8, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void createBitField(final String objectPath, final long size, final int blockSize, final HDF5GenericStorageFeatures features) { assert objectPath != null; assert size >= 0; assert blockSize >= 0 && (blockSize <= size || size == 0); baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { baseWriter.createDataSet(objectPath, H5T_STD_B64LE, features, new long[] { size }, new long[] { blockSize }, 8, registry); return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void writeBitFieldBlock(String objectPath, BitSet data, int dataSize, long blockNumber) { writeBitFieldBlockWithOffset(objectPath, data, dataSize, dataSize * blockNumber); } @Override public void writeBitFieldBlockWithOffset(final String objectPath, final BitSet data, final int dataSize, final long offset) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] blockDimensions = new long[] { dataSize }; final long[] slabStartOrNull = new long[] { offset }; final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, new long[] { offset + dataSize }, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, slabStartOrNull, blockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(blockDimensions, registry); H5Dwrite(dataSetId, H5T_NATIVE_B64, memorySpaceId, dataSpaceId, H5P_DEFAULT, BitSetConversionUtils.toStorageForm(data, dataSize)); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeBitFieldArray(final String objectPath, final BitSet[] data) { writeBitFieldArray(objectPath, data, HDF5IntStorageFeatures.INT_NO_COMPRESSION); } @Override public void writeBitFieldArray(final String objectPath, final BitSet[] data, final HDF5IntStorageFeatures features) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int longBytes = 8; final int longBits = longBytes * 8; final int msb = BitSetConversionUtils.getMaxLength(data); final int numberOfWords = msb / longBits + (msb % longBits != 0 ? 1 : 0); if (features.isScaling() && msb < longBits) { features.checkScalingOK(baseWriter.fileFormat); final HDF5IntStorageFeatures actualFeatures = HDF5IntStorageFeatures.build(features).scalingFactor((byte) msb) .features(); final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, H5T_STD_U64LE, new long[] { numberOfWords, data.length }, longBytes, actualFeatures, registry); H5Dwrite(dataSetId, H5T_NATIVE_UINT64, H5S_ALL, H5S_ALL, H5P_DEFAULT, BitSetConversionUtils.toStorageForm(data, numberOfWords)); baseWriter .setTypeVariant(dataSetId, HDF5DataTypeVariant.BITFIELD, registry); } else { final HDF5IntStorageFeatures actualFeatures = HDF5IntStorageFeatures.build(features).noScaling().features(); final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, H5T_STD_B64LE, new long[] { numberOfWords, data.length }, longBytes, actualFeatures, registry); H5Dwrite(dataSetId, H5T_NATIVE_B64, H5S_ALL, H5S_ALL, H5P_DEFAULT, BitSetConversionUtils.toStorageForm(data, numberOfWords)); } return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createBitFieldArray(final String objectPath, final int bitFieldSize, final long arraySize, final long arrayBlockSize, final HDF5IntStorageFeatures features) { assert objectPath != null; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int longBytes = 8; final int longBits = longBytes * 8; final int numberOfWords = bitFieldSize / longBits + (bitFieldSize % longBits != 0 ? 1 : 0); if (features.requiresChunking() || arraySize > 0) { create(objectPath, new long[] { numberOfWords, arraySize }, new long[] { numberOfWords, arrayBlockSize }, features, registry); } else { create(objectPath, new long[] { numberOfWords, arrayBlockSize }, null, features, registry); } return null; // Nothing to return. } @SuppressWarnings("hiding") void create(final String objectPath, final long[] dimensions, final long[] blockDimensionsOrNull, final HDF5IntStorageFeatures features, ICleanUpRegistry registry) { final int longBytes = 8; final int longBits = longBytes * 8; if (features.isScaling() && bitFieldSize < longBits) { features.checkScalingOK(baseWriter.fileFormat); final HDF5IntStorageFeatures actualFeatures = HDF5IntStorageFeatures.build(features) .scalingFactor((byte) bitFieldSize).features(); final int dataSetId = baseWriter.createDataSet(objectPath, H5T_STD_U64LE, actualFeatures, dimensions, blockDimensionsOrNull, longBytes, registry); baseWriter .setTypeVariant(dataSetId, HDF5DataTypeVariant.BITFIELD, registry); } else { final HDF5IntStorageFeatures actualFeatures = HDF5IntStorageFeatures.build(features).noScaling().features(); baseWriter.createDataSet(objectPath, H5T_STD_B64LE, actualFeatures, dimensions, blockDimensionsOrNull, longBytes, registry); } } }; baseWriter.runner.call(createRunnable); } @Override public void createBitFieldArray(String objectPath, int bitFieldSize, long arrayBlockSize, HDF5IntStorageFeatures features) { createBitFieldArray(objectPath, bitFieldSize, 0, arrayBlockSize, features); } @Override public void createBitFieldArray(String objectPath, int bitFieldSize, long arraySize, long arrayBlockSize) { createBitFieldArray(objectPath, bitFieldSize, arraySize, arrayBlockSize, INT_NO_COMPRESSION); } @Override public void createBitFieldArray(String objectPath, int bitFieldSize, long arrayBlockSize) { createBitFieldArray(objectPath, bitFieldSize, 0, arrayBlockSize, INT_NO_COMPRESSION); } @Override public void writeBitFieldArrayBlockWithOffset(final String objectPath, final BitSet[] data, final int dataSize, final long offset) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, new long[] { -1, offset + dataSize }, -1, registry); final long[] dimensions = baseWriter.h5.getDataDimensions(dataSetId, registry); if (dimensions.length != 2) { throw new HDF5JavaException( "Array is supposed to be of rank 2, but is of rank " + dimensions.length); } final int numberOfWords = dimToInt(dimensions[0]); final long[] blockDimensions = new long[] { numberOfWords, dataSize }; final long[] slabStartOrNull = new long[] { 0, offset }; final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, slabStartOrNull, blockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(blockDimensions, registry); if (baseWriter.isScaledBitField(dataSetId, registry)) { H5Dwrite(dataSetId, H5T_NATIVE_UINT64, memorySpaceId, dataSpaceId, H5P_DEFAULT, BitSetConversionUtils.toStorageForm(data, numberOfWords)); } else { H5Dwrite(dataSetId, H5T_NATIVE_B64, memorySpaceId, dataSpaceId, H5P_DEFAULT, BitSetConversionUtils.toStorageForm(data, numberOfWords)); } return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeBitFieldArrayBlockWithOffset(String objectPath, BitSet[] data, long offset) { writeBitFieldArrayBlockWithOffset(objectPath, data, data.length, offset); } @Override public void writeBitFieldArrayBlock(String objectPath, BitSet[] data, int dataSize, long blockNumber) { writeBitFieldArrayBlockWithOffset(objectPath, data, dataSize, dataSize * blockNumber); } @Override public void writeBitFieldArrayBlock(String objectPath, BitSet[] data, long blockNumber) { writeBitFieldArrayBlock(objectPath, data, data.length, blockNumber); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5ByteReader.java000066400000000000000000001020151256564762100266610ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.MatrixUtils.cardinalityBoundIndices; import static ch.systemsx.cisd.hdf5.MatrixUtils.checkBoundIndices; import static ch.systemsx.cisd.hdf5.MatrixUtils.createFullBlockDimensionsAndOffset; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_ARRAY; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_INT8; import java.util.Arrays; import java.util.Iterator; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import ncsa.hdf.hdf5lib.exceptions.HDF5SpaceRankMismatch; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDByteArray; import ch.systemsx.cisd.hdf5.HDF5BaseReader.DataSpaceParameters; import ch.systemsx.cisd.hdf5.HDF5DataTypeInformation.DataTypeInfoOptions; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; import ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants; /** * The implementation of {@link IHDF5ByteReader}. * * @author Bernd Rinn */ class HDF5ByteReader implements IHDF5ByteReader { private final HDF5BaseReader baseReader; HDF5ByteReader(HDF5BaseReader baseReader) { assert baseReader != null; this.baseReader = baseReader; } // For Unit tests only. HDF5BaseReader getBaseReader() { return baseReader; } // ///////////////////// // Attributes // ///////////////////// @Override public byte getAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public Byte call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final byte[] data = baseReader.h5.readAttributeAsByteArray(attributeId, H5T_NATIVE_INT8, 1); return data[0]; } }; return baseReader.runner.call(getAttributeRunnable); } @Override public byte[] getArrayAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public byte[] call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); return getByteArrayAttribute(objectId, attributeName, registry); } }; return baseReader.runner.call(getAttributeRunnable); } @Override public MDByteArray getMDArrayAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public MDByteArray call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); return getByteMDArrayAttribute(objectId, attributeName, registry); } }; return baseReader.runner.call(getAttributeRunnable); } @Override public byte[][] getMatrixAttr(final String objectPath, final String attributeName) throws HDF5JavaException { final MDByteArray array = getMDArrayAttr(objectPath, attributeName); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } // ///////////////////// // Data Sets // ///////////////////// @Override public byte read(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public Byte call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final byte[] data = new byte[1]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_INT8, data); return data[0]; } }; return baseReader.runner.call(readCallable); } @Override public byte[] readArray(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public byte[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); return readByteArray(dataSetId, registry); } }; return baseReader.runner.call(readCallable); } private byte[] readByteArray(int dataSetId, ICleanUpRegistry registry) { try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); final byte[] data = new byte[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_INT8, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return data; } catch (HDF5LibraryException ex) { if (ex.getMajorErrorNumber() == HDF5Constants.H5E_DATATYPE && ex.getMinorErrorNumber() == HDF5Constants.H5E_CANTINIT) { // Check whether it is an array data type. final int dataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); if (baseReader.h5.getClassType(dataTypeId) == HDF5Constants.H5T_ARRAY) { return readByteArrayFromArrayType(dataSetId, dataTypeId, registry); } } throw ex; } } private byte[] readByteArrayFromArrayType(int dataSetId, final int dataTypeId, ICleanUpRegistry registry) { final int spaceId = baseReader.h5.createScalarDataSpace(); final int[] dimensions = baseReader.h5.getArrayDimensions(dataTypeId); final byte[] data = new byte[HDF5Utils.getOneDimensionalArraySize(dimensions)]; final int memoryDataTypeId = baseReader.h5.createArrayType(H5T_NATIVE_INT8, data.length, registry); baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceId, spaceId, data); return data; } @Override public int[] readToMDArrayWithOffset(final String objectPath, final MDByteArray array, final int[] memoryOffset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getBlockSpaceParameters(dataSetId, memoryOffset, array .dimensions(), registry); final int nativeDataTypeId = baseReader.getNativeDataTypeId(dataSetId, H5T_NATIVE_INT8, registry); baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, array. getAsFlatArray()); return MDArray.toInt(spaceParams.dimensions); } }; return baseReader.runner.call(readCallable); } @Override public int[] readToMDArrayBlockWithOffset(final String objectPath, final MDByteArray array, final int[] blockDimensions, final long[] offset, final int[] memoryOffset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getBlockSpaceParameters(dataSetId, memoryOffset, array .dimensions(), offset, blockDimensions, registry); final int nativeDataTypeId = baseReader.getNativeDataTypeId(dataSetId, H5T_NATIVE_INT8, registry); baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, array .getAsFlatArray()); return MDArray.toInt(spaceParams.dimensions); } }; return baseReader.runner.call(readCallable); } @Override public byte[] readArrayBlock(final String objectPath, final int blockSize, final long blockNumber) { return readArrayBlockWithOffset(objectPath, blockSize, blockNumber * blockSize); } @Override public byte[] readArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public byte[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockSize, registry); final byte[] data = new byte[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_INT8, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return data; } }; return baseReader.runner.call(readCallable); } @Override public byte[][] readMatrix(final String objectPath) throws HDF5JavaException { final MDByteArray array = readMDArray(objectPath); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public byte[][] readMatrixBlock(final String objectPath, final int blockSizeX, final int blockSizeY, final long blockNumberX, final long blockNumberY) throws HDF5JavaException { final MDByteArray array = readMDArrayBlock(objectPath, new int[] { blockSizeX, blockSizeY }, new long[] { blockNumberX, blockNumberY }); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public byte[][] readMatrixBlockWithOffset(final String objectPath, final int blockSizeX, final int blockSizeY, final long offsetX, final long offsetY) throws HDF5JavaException { final MDByteArray array = readMDArrayBlockWithOffset(objectPath, new int[] { blockSizeX, blockSizeY }, new long[] { offsetX, offsetY }); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public MDByteArray readMDArraySlice(String objectPath, IndexMap boundIndices) { baseReader.checkOpen(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; final int cardBoundIndices = cardinalityBoundIndices(boundIndices); checkBoundIndices(objectPath, fullDimensions, cardBoundIndices); final int[] effectiveBlockDimensions = new int[fullBlockDimensions.length - cardBoundIndices]; Arrays.fill(effectiveBlockDimensions, -1); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, null, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDByteArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); if (fullBlockDimensions.length == cardBoundIndices) // no free indices { return new MDByteArray(result.getAsFlatArray(), new int[] { 1 }); } else { return new MDByteArray(result.getAsFlatArray(), effectiveBlockDimensions); } } @Override public MDByteArray readMDArraySlice(String objectPath, long[] boundIndices) { baseReader.checkOpen(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; final int cardBoundIndices = cardinalityBoundIndices(boundIndices); checkBoundIndices(objectPath, fullDimensions, boundIndices); final int[] effectiveBlockDimensions = new int[fullBlockDimensions.length - cardBoundIndices]; Arrays.fill(effectiveBlockDimensions, -1); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, null, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDByteArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); if (fullBlockDimensions.length == cardBoundIndices) // no free indices { return new MDByteArray(result.getAsFlatArray(), new int[] { 1 }); } else { return new MDByteArray(result.getAsFlatArray(), effectiveBlockDimensions); } } @Override public MDByteArray readMDArray(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public MDByteArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); return readByteMDArray(dataSetId, registry); } }; return baseReader.runner.call(readCallable); } MDByteArray readByteMDArray(int dataSetId, ICleanUpRegistry registry) { try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); final byte[] data = new byte[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_INT8, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return new MDByteArray(data, spaceParams.dimensions); } catch (HDF5LibraryException ex) { if (ex.getMajorErrorNumber() == HDF5Constants.H5E_DATATYPE && ex.getMinorErrorNumber() == HDF5Constants.H5E_CANTINIT) { // Check whether it is an array data type. final int dataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); if (baseReader.h5.getClassType(dataTypeId) == HDF5Constants.H5T_ARRAY) { return readByteMDArrayFromArrayType(dataSetId, dataTypeId, registry); } } throw ex; } } private MDByteArray readByteMDArrayFromArrayType(int dataSetId, final int dataTypeId, ICleanUpRegistry registry) { final int[] arrayDimensions = baseReader.h5.getArrayDimensions(dataTypeId); final int memoryDataTypeId = baseReader.h5.createArrayType(H5T_NATIVE_INT8, arrayDimensions, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); if (spaceParams.blockSize == 0) { final int spaceId = baseReader.h5.createScalarDataSpace(); final byte[] data = new byte[MDArray.getLength(arrayDimensions)]; baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceId, spaceId, data); return new MDByteArray(data, arrayDimensions); } else { final byte[] data = new byte[MDArray.getLength(arrayDimensions) * spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return new MDByteArray(data, MatrixUtils.concat(MDArray.toInt(spaceParams.dimensions), arrayDimensions)); } } @Override public MDByteArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, IndexMap boundIndices) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readSlicedMDArrayBlockWithOffset(objectPath, blockDimensions, offset, boundIndices); } @Override public MDByteArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, long[] boundIndices) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readSlicedMDArrayBlockWithOffset(objectPath, blockDimensions, offset, boundIndices); } @Override public MDByteArray readMDArrayBlock(final String objectPath, final int[] blockDimensions, final long[] blockNumber) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readMDArrayBlockWithOffset(objectPath, blockDimensions, offset); } @Override public MDByteArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, IndexMap boundIndices) { baseReader.checkOpen(); final int[] effectiveBlockDimensions = blockDimensions.clone(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; checkBoundIndices(objectPath, fullDimensions, blockDimensions, cardinalityBoundIndices(boundIndices)); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, offset, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDByteArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); return new MDByteArray(result.getAsFlatArray(), effectiveBlockDimensions); } @Override public MDByteArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, long[] boundIndices) { baseReader.checkOpen(); final int[] effectiveBlockDimensions = blockDimensions.clone(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; checkBoundIndices(objectPath, fullDimensions, blockDimensions, cardinalityBoundIndices(boundIndices)); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, offset, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDByteArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); return new MDByteArray(result.getAsFlatArray(), effectiveBlockDimensions); } @Override public MDByteArray readMDArrayBlockWithOffset(final String objectPath, final int[] blockDimensions, final long[] offset) { assert objectPath != null; assert blockDimensions != null; assert offset != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public MDByteArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockDimensions, registry); final byte[] dataBlock = new byte[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_INT8, spaceParams.memorySpaceId, spaceParams.dataSpaceId, dataBlock); return new MDByteArray(dataBlock, spaceParams.dimensions); } catch (HDF5SpaceRankMismatch ex) { final HDF5DataSetInformation info = baseReader.getDataSetInformation(objectPath, DataTypeInfoOptions.MINIMAL, false); if (ex.getSpaceRankExpected() - ex.getSpaceRankFound() == info .getTypeInformation().getRank()) { return readMDArrayBlockOfArrays(dataSetId, blockDimensions, offset, info, ex.getSpaceRankFound(), registry); } else { throw ex; } } } }; return baseReader.runner.call(readCallable); } private MDByteArray readMDArrayBlockOfArrays(final int dataSetId, final int[] blockDimensions, final long[] offset, final HDF5DataSetInformation info, final int spaceRank, final ICleanUpRegistry registry) { final int[] arrayDimensions = info.getTypeInformation().getDimensions(); int[] effectiveBlockDimensions = blockDimensions; // We do not support block-wise reading of array types, check // that we do not have to and bail out otherwise. for (int i = 0; i < arrayDimensions.length; ++i) { final int j = spaceRank + i; if (effectiveBlockDimensions[j] < 0) { if (effectiveBlockDimensions == blockDimensions) { effectiveBlockDimensions = blockDimensions.clone(); } effectiveBlockDimensions[j] = arrayDimensions[i]; } if (effectiveBlockDimensions[j] != arrayDimensions[i]) { throw new HDF5JavaException( "Block-wise reading of array type data sets is not supported."); } } final int[] spaceBlockDimensions = Arrays.copyOfRange(effectiveBlockDimensions, 0, spaceRank); final long[] spaceOfs = Arrays.copyOfRange(offset, 0, spaceRank); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, spaceOfs, spaceBlockDimensions, registry); final byte[] dataBlock = new byte[spaceParams.blockSize * info.getTypeInformation().getNumberOfElements()]; final int memoryDataTypeId = baseReader.h5.createArrayType(H5T_NATIVE_INT8, info.getTypeInformation() .getDimensions(), registry); baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, dataBlock); return new MDByteArray(dataBlock, effectiveBlockDimensions); } @Override public Iterable> getArrayNaturalBlocks(final String dataSetPath) throws HDF5JavaException { baseReader.checkOpen(); final HDF5NaturalBlock1DParameters params = new HDF5NaturalBlock1DParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlock1DParameters.HDF5NaturalBlock1DIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5DataBlock next() { final long offset = index.computeOffsetAndSizeGetOffset(); final byte[] block = readArrayBlockWithOffset(dataSetPath, index .getBlockSize(), offset); return new HDF5DataBlock(block, index.getAndIncIndex(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } @Override public Iterable> getMDArrayNaturalBlocks(final String dataSetPath) { baseReader.checkOpen(); final HDF5NaturalBlockMDParameters params = new HDF5NaturalBlockMDParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlockMDParameters.HDF5NaturalBlockMDIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5MDDataBlock next() { final long[] offset = index.computeOffsetAndSizeGetOffsetClone(); final MDByteArray data = readMDArrayBlockWithOffset(dataSetPath, index .getBlockSize(), offset); return new HDF5MDDataBlock(data, index .getIndexClone(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } byte[] getByteArrayAttribute(final int objectId, final String attributeName, ICleanUpRegistry registry) { final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, registry); final int memoryTypeId; final int len; if (baseReader.h5.getClassType(attributeTypeId) == H5T_ARRAY) { final int[] arrayDimensions = baseReader.h5.getArrayDimensions(attributeTypeId); if (arrayDimensions.length != 1) { throw new HDF5JavaException( "Array needs to be of rank 1, but is of rank " + arrayDimensions.length); } len = arrayDimensions[0]; memoryTypeId = baseReader.h5.createArrayType(H5T_NATIVE_INT8, len, registry); } else { final long[] arrayDimensions = baseReader.h5.getDataDimensionsForAttribute(attributeId, registry); memoryTypeId = H5T_NATIVE_INT8; len = HDF5Utils.getOneDimensionalArraySize(arrayDimensions); } final byte[] data = baseReader.h5.readAttributeAsByteArray(attributeId, memoryTypeId, len); return data; } MDByteArray getByteMDArrayAttribute(final int objectId, final String attributeName, ICleanUpRegistry registry) { try { final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, registry); final int memoryTypeId; final int[] arrayDimensions; if (baseReader.h5.getClassType(attributeTypeId) == H5T_ARRAY) { arrayDimensions = baseReader.h5.getArrayDimensions(attributeTypeId); memoryTypeId = baseReader.h5.createArrayType(H5T_NATIVE_INT8, arrayDimensions, registry); } else { arrayDimensions = MDArray.toInt(baseReader.h5.getDataDimensionsForAttribute( attributeId, registry)); memoryTypeId = H5T_NATIVE_INT8; } final int len = MDArray.getLength(arrayDimensions); final byte[] data = baseReader.h5.readAttributeAsByteArray(attributeId, memoryTypeId, len); return new MDByteArray(data, arrayDimensions); } catch (IllegalArgumentException ex) { throw new HDF5JavaException(ex.getMessage()); } } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5ByteWriter.java000066400000000000000000000665511256564762100267510ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.HDF5IntStorageFeatures.INT_NO_COMPRESSION; import static ch.systemsx.cisd.hdf5.hdf5lib.H5D.H5Dwrite; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_ALL; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_INT8; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_I8LE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_U8LE; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDByteArray; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; /** * The implementation of {@link IHDF5ByteWriter}. * * @author Bernd Rinn */ class HDF5ByteWriter extends HDF5ByteReader implements IHDF5ByteWriter { private final HDF5BaseWriter baseWriter; HDF5ByteWriter(HDF5BaseWriter baseWriter) { super(baseWriter); assert baseWriter != null; this.baseWriter = baseWriter; } // ///////////////////// // Attributes // ///////////////////// @Override public void setAttr(final String objectPath, final String name, final byte value) { assert objectPath != null; assert name != null; baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { 1 }, registry); baseWriter.setAttribute(objectPath, name, H5T_STD_I8LE, H5T_NATIVE_INT8, dataSpaceId, new byte[] { value }, registry); } else { baseWriter.setAttribute(objectPath, name, H5T_STD_I8LE, H5T_NATIVE_INT8, -1, new byte[] { value }, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void setArrayAttr(final String objectPath, final String name, final byte[] value) { assert objectPath != null; assert name != null; assert value != null; baseWriter.checkOpen(); final ICallableWithCleanUp setAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { value.length }, registry); baseWriter.setAttribute(objectPath, name, H5T_STD_I8LE, H5T_NATIVE_INT8, dataSpaceId, value, registry); } else { final int memoryTypeId = baseWriter.h5.createArrayType(H5T_NATIVE_INT8, value.length, registry); final int storageTypeId = baseWriter.h5.createArrayType(H5T_STD_I8LE, value.length, registry); baseWriter.setAttribute(objectPath, name, storageTypeId, memoryTypeId, -1, value, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(setAttributeRunnable); } @Override public void setMDArrayAttr(final String objectPath, final String name, final MDByteArray value) { assert objectPath != null; assert name != null; assert value != null; baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(value.longDimensions(), registry); baseWriter.setAttribute(objectPath, name, H5T_STD_I8LE, H5T_NATIVE_INT8, dataSpaceId, value.getAsFlatArray(), registry); } else { final int memoryTypeId = baseWriter.h5.createArrayType(H5T_NATIVE_INT8, value.dimensions(), registry); final int storageTypeId = baseWriter.h5.createArrayType(H5T_STD_I8LE, value.dimensions(), registry); baseWriter.setAttribute(objectPath, name, storageTypeId, memoryTypeId, -1, value.getAsFlatArray(), registry); } return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void setMatrixAttr(final String objectPath, final String name, final byte[][] value) { setMDArrayAttr(objectPath, name, new MDByteArray(value)); } // ///////////////////// // Data Sets // ///////////////////// @Override public void write(final String objectPath, final byte value) { assert objectPath != null; baseWriter.checkOpen(); baseWriter.writeScalar(objectPath, H5T_STD_I8LE, H5T_NATIVE_INT8, value); } @Override public void writeArray(final String objectPath, final byte[] data) { writeArray(objectPath, data, INT_NO_COMPRESSION); } @Override public void writeArray(final String objectPath, final byte[] data, final HDF5IntStorageFeatures features) { assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, features.isSigned() ? H5T_STD_I8LE : H5T_STD_U8LE, new long[] { data.length }, 1, features, registry); H5Dwrite(dataSetId, H5T_NATIVE_INT8, H5S_ALL, H5S_ALL, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createArray(final String objectPath, final int size) { createArray(objectPath, size, INT_NO_COMPRESSION); } @Override public void createArray(final String objectPath, final long size, final int blockSize) { createArray(objectPath, size, blockSize, INT_NO_COMPRESSION); } @Override public void createArray(final String objectPath, final int size, final HDF5IntStorageFeatures features) { assert objectPath != null; assert size >= 0; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (features.requiresChunking()) { baseWriter.createDataSet(objectPath, features.isSigned() ? H5T_STD_I8LE : H5T_STD_U8LE, features, new long[] { 0 }, new long[] { size }, 1, registry); } else { baseWriter.createDataSet(objectPath, features.isSigned() ? H5T_STD_I8LE : H5T_STD_U8LE, features, new long[] { size }, null, 1, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void createArray(final String objectPath, final long size, final int blockSize, final HDF5IntStorageFeatures features) { assert objectPath != null; assert size >= 0; assert blockSize >= 0 && (blockSize <= size || size == 0); baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { baseWriter.createDataSet(objectPath, features.isSigned() ? H5T_STD_I8LE : H5T_STD_U8LE, features, new long[] { size }, new long[] { blockSize }, 1, registry); return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void writeArrayBlock(final String objectPath, final byte[] data, final long blockNumber) { writeArrayBlockWithOffset(objectPath, data, data.length, data.length * blockNumber); } @Override public void writeArrayBlockWithOffset(final String objectPath, final byte[] data, final int dataSize, final long offset) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] blockDimensions = new long[] { dataSize }; final long[] slabStartOrNull = new long[] { offset }; final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, new long[] { offset + dataSize }, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, slabStartOrNull, blockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(blockDimensions, registry); H5Dwrite(dataSetId, H5T_NATIVE_INT8, memorySpaceId, dataSpaceId, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } /** * Writes out a byte matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ @Override public void writeMatrix(final String objectPath, final byte[][] data) { writeMatrix(objectPath, data, INT_NO_COMPRESSION); } @Override public void writeMatrix(final String objectPath, final byte[][] data, final HDF5IntStorageFeatures features) { assert objectPath != null; assert data != null; assert HDF5Utils.areMatrixDimensionsConsistent(data); writeMDArray(objectPath, new MDByteArray(data), features); } @Override public void createMatrix(final String objectPath, final int sizeX, final int sizeY) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; createMDArray(objectPath, new int[] { sizeX, sizeY }); } @Override public void createMatrix(final String objectPath, final int sizeX, final int sizeY, final HDF5IntStorageFeatures features) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; createMDArray(objectPath, new int[] { sizeX, sizeY }, features); } @Override public void createMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; assert blockSizeX >= 0 && (blockSizeX <= sizeX || sizeX == 0); assert blockSizeY >= 0 && (blockSizeY <= sizeY || sizeY == 0); createMDArray(objectPath, new long[] { sizeX, sizeY }, new int[] { blockSizeX, blockSizeY }); } @Override public void createMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY, final HDF5IntStorageFeatures features) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; assert blockSizeX >= 0 && (blockSizeX <= sizeX || sizeX == 0); assert blockSizeY >= 0 && (blockSizeY <= sizeY || sizeY == 0); createMDArray(objectPath, new long[] { sizeX, sizeY }, new int[] { blockSizeX, blockSizeY }, features); } @Override public void writeMatrixBlock(final String objectPath, final byte[][] data, final long blockNumberX, final long blockNumberY) { assert objectPath != null; assert data != null; writeMDArrayBlock(objectPath, new MDByteArray(data), new long[] { blockNumberX, blockNumberY }); } @Override public void writeMatrixBlockWithOffset(final String objectPath, final byte[][] data, final long offsetX, final long offsetY) { assert objectPath != null; assert data != null; writeMDArrayBlockWithOffset(objectPath, new MDByteArray(data, new int[] { data.length, data[0].length }), new long[] { offsetX, offsetY }); } @Override public void writeMatrixBlockWithOffset(final String objectPath, final byte[][] data, final int dataSizeX, final int dataSizeY, final long offsetX, final long offsetY) { assert objectPath != null; assert data != null; writeMDArrayBlockWithOffset(objectPath, new MDByteArray(data, new int[] { dataSizeX, dataSizeY }), new long[] { offsetX, offsetY }); } @Override public void writeMDArray(final String objectPath, final MDByteArray data) { writeMDArray(objectPath, data, INT_NO_COMPRESSION); } @Override public void writeMDArraySlice(String objectPath, MDByteArray data, IndexMap boundIndices) { baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), null, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDByteArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArraySlice(String objectPath, MDByteArray data, long[] boundIndices) { baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), null, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDByteArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArray(final String objectPath, final MDByteArray data, final HDF5IntStorageFeatures features) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, features.isSigned() ? H5T_STD_I8LE : H5T_STD_U8LE, data.longDimensions(), 1, features, registry); H5Dwrite(dataSetId, H5T_NATIVE_INT8, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createMDArray(final String objectPath, final int[] dimensions) { createMDArray(objectPath, dimensions, INT_NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions) { createMDArray(objectPath, dimensions, blockDimensions, INT_NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final int[] dimensions, final HDF5IntStorageFeatures features) { assert objectPath != null; assert dimensions != null; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (features.requiresChunking()) { final long[] nullDimensions = new long[dimensions.length]; baseWriter.createDataSet(objectPath, features.isSigned() ? H5T_STD_I8LE : H5T_STD_U8LE, features, nullDimensions, MDArray.toLong(dimensions), 1, registry); } else { baseWriter.createDataSet(objectPath, features.isSigned() ? H5T_STD_I8LE : H5T_STD_U8LE, features, MDArray.toLong(dimensions), null, 1, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void createMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions, final HDF5IntStorageFeatures features) { assert objectPath != null; assert dimensions != null; assert blockDimensions != null; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { baseWriter.createDataSet(objectPath, features.isSigned() ? H5T_STD_I8LE : H5T_STD_U8LE, features, dimensions, MDArray.toLong(blockDimensions), 1, registry); return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void writeMDArrayBlock(final String objectPath, final MDByteArray data, final long[] blockNumber) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeMDArrayBlockWithOffset(objectPath, data, offset); } @Override public void writeSlicedMDArrayBlock(final String objectPath, final MDByteArray data, final long[] blockNumber, IndexMap boundIndices) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeSlicedMDArrayBlockWithOffset(objectPath, data, offset, boundIndices); } @Override public void writeSlicedMDArrayBlock(String objectPath, MDByteArray data, long[] blockNumber, long[] boundIndices) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeSlicedMDArrayBlockWithOffset(objectPath, data, offset, boundIndices); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final MDByteArray data, final long[] offset) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] dimensions = data.longDimensions(); assert dimensions.length == offset.length; final long[] dataSetDimensions = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + dimensions[i]; } final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, dimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(dimensions, registry); H5Dwrite(dataSetId, H5T_NATIVE_INT8, memorySpaceId, dataSpaceId, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeSlicedMDArrayBlockWithOffset(String objectPath, MDByteArray data, long[] offset, IndexMap boundIndices) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), offset, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDByteArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeSlicedMDArrayBlockWithOffset(String objectPath, MDByteArray data, long[] offset, long[] boundIndices) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), offset, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDByteArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final MDByteArray data, final int[] blockDimensions, final long[] offset, final int[] memoryOffset) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] memoryDimensions = data.longDimensions(); assert memoryDimensions.length == offset.length; final long[] longBlockDimensions = MDArray.toLong(blockDimensions); assert longBlockDimensions.length == offset.length; final long[] dataSetDimensions = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + blockDimensions[i]; } final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, longBlockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(memoryDimensions, registry); baseWriter.h5.setHyperslabBlock(memorySpaceId, MDArray.toLong(memoryOffset), longBlockDimensions); H5Dwrite(dataSetId, H5T_NATIVE_INT8, memorySpaceId, dataSpaceId, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5CommonInformation.java000066400000000000000000000103561256564762100302770ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5L_TYPE_EXTERNAL; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5L_TYPE_SOFT; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5O_TYPE_DATASET; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5O_TYPE_GROUP; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5O_TYPE_NAMED_DATATYPE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5O_TYPE_NTYPES; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; /** * The common super class of {@link HDF5LinkInformation} and {@link HDF5ObjectInformation}. * * @author Bernd Rinn */ class HDF5CommonInformation { protected final String path; protected final HDF5ObjectType type; static HDF5ObjectType objectTypeIdToObjectType(final int objectTypeId) { if (-1 == objectTypeId) { return HDF5ObjectType.NONEXISTENT; } else if (H5O_TYPE_GROUP == objectTypeId) { return HDF5ObjectType.GROUP; } else if (H5O_TYPE_DATASET == objectTypeId) { return HDF5ObjectType.DATASET; } else if (H5O_TYPE_NAMED_DATATYPE == objectTypeId) { return HDF5ObjectType.DATATYPE; } else if (objectTypeId >= H5O_TYPE_NTYPES) { final int linkTypeId = objectTypeId - H5O_TYPE_NTYPES; if (linkTypeId == H5L_TYPE_SOFT) { return HDF5ObjectType.SOFT_LINK; } else if (linkTypeId == H5L_TYPE_EXTERNAL) { return HDF5ObjectType.EXTERNAL_LINK; } } return HDF5ObjectType.OTHER; } HDF5CommonInformation(String path, HDF5ObjectType type) { assert path != null; assert type != null; this.path = path; this.type = type; } /** * @throws HDF5JavaException If the link does not exist. */ public void checkExists() throws HDF5JavaException { if (exists() == false) { throw new HDF5JavaException("Link '" + getPath() + "' does not exist."); } } /** * Returns the path of this link in the HDF5 file. */ public String getPath() { return path; } /** * Returns the parent of the path of this link the HDF5 file. If this link corresponds to the * root, then this method will return the root ("/") itself. */ public String getParentPath() { final int lastSlashIndex = path.lastIndexOf('/'); if (lastSlashIndex <= 0) { return "/"; } else { return path.substring(0, lastSlashIndex); } } /** * Returns the name of this link in the HDF5 file (the path without the parent). */ public String getName() { return path.substring(path.lastIndexOf('/') + 1); } /** * Returns the type of this link. */ public HDF5ObjectType getType() { return type; } /** * Returns true, if the link exists. */ public boolean exists() { return HDF5ObjectType.exists(type); } /** * Returns true, if the link is a group. */ public boolean isGroup() { return HDF5ObjectType.isGroup(type); } /** * Returns true, if the link is a data set. */ public boolean isDataSet() { return HDF5ObjectType.isDataSet(type); } /** * Returns true, if the link is a data type. */ public boolean isDataType() { return HDF5ObjectType.isDataType(type); } }libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5CompoundByteifyerFactory.java000066400000000000000000000300551256564762100316360ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.lang.reflect.Field; import java.util.ArrayList; import java.util.List; import java.util.Map; import ch.systemsx.cisd.hdf5.HDF5ValueObjectByteifyer.IFileAccessProvider; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; /** * A factory for {@link HDF5MemberByteifyer}s. * * @author Bernd Rinn */ class HDF5CompoundByteifyerFactory { private static List memberFactories = new ArrayList(14); static { memberFactories.add(new HDF5CompoundMemberByteifyerBooleanFactory()); memberFactories.add(new HDF5CompoundMemberByteifyerIntFactory()); memberFactories.add(new HDF5CompoundMemberByteifyerLongFactory()); memberFactories.add(new HDF5CompoundMemberByteifyerShortFactory()); memberFactories.add(new HDF5CompoundMemberByteifyerByteFactory()); memberFactories.add(new HDF5CompoundMemberByteifyerFloatFactory()); memberFactories.add(new HDF5CompoundMemberByteifyerDoubleFactory()); memberFactories.add(new HDF5CompoundMemberByteifyerStringFactory()); memberFactories.add(new HDF5CompoundMemberByteifyerBitSetFactory()); memberFactories.add(new HDF5CompoundMemberByteifyerDateFactory()); memberFactories.add(new HDF5CompoundMemberByteifyerHDF5TimeDurationFactory()); memberFactories.add(new HDF5CompoundMemberByteifyerEnumFactory()); memberFactories.add(new HDF5CompoundMemberByteifyerEnumArrayFactory()); } /** * The type of access to the information. */ enum AccessType { FIELD, MAP, LIST, ARRAY } /** * The interface for member factories. */ interface IHDF5CompoundMemberBytifyerFactory { /** * Returns true if this factory can handle a member of type clazz. */ boolean canHandle(Class clazz, HDF5CompoundMemberInformation memberInfoOrNull); /** * Creates a byteifyer. */ HDF5MemberByteifyer createBytifyer(AccessType accessType, Field fieldOrNull, HDF5CompoundMemberMapping member, HDF5CompoundMemberInformation compoundMemberInfoOrNull, HDF5EnumerationType enumTypeOrNull, Class memberClazz, int index, int offset, int memOffset, IFileAccessProvider fileInfoProvider); /** * Returns a suitable Java type, if this factory has one, or null otherwise. */ Class tryGetOverrideJavaType(HDF5DataClass dataClass, int rank, int elementSize, HDF5DataTypeVariant typeVariantOrNull); } /** * Returns a Java type overriding the one given by {@link HDF5DataClass}, if the factories have * one, or null otherwise. */ static Class tryGetOverrideJavaType(HDF5DataClass dataClass, int rank, int elementSize, HDF5DataTypeVariant typeVariantOrNull) { for (IHDF5CompoundMemberBytifyerFactory factory : memberFactories) { final Class javaClassOrNull = factory.tryGetOverrideJavaType(dataClass, rank, elementSize, typeVariantOrNull); if (javaClassOrNull != null) { return javaClassOrNull; } } return null; } static HDF5MemberByteifyer[] createMemberByteifyers(Class clazz, IFileAccessProvider fileInfoProvider, CompoundTypeInformation compoundTypeInfoOrNull, HDF5CompoundMemberMapping[] members) { final HDF5MemberByteifyer[] result = new HDF5MemberByteifyer[members.length]; int offsetOnDisk = 0; int offsetInMemory = 0; for (int i = 0; i < result.length; ++i) { final AccessType accessType = getAccessType(clazz); final HDF5CompoundMemberInformation compoundMemberInfoOrNull = (compoundTypeInfoOrNull == null) ? null : compoundTypeInfoOrNull.getMember(i); final Field fieldOrNull = (accessType == AccessType.FIELD) ? members[i].tryGetField(clazz, (compoundMemberInfoOrNull != null)) : null; final Class memberClazzOrNull = (fieldOrNull != null) ? fieldOrNull.getType() : members[i].tryGetMemberClass(); final IHDF5CompoundMemberBytifyerFactory factory = findFactory(memberClazzOrNull, compoundMemberInfoOrNull, members[i].getMemberName()); final HDF5EnumerationType enumTypeOrNullOrNull = (compoundTypeInfoOrNull == null) ? null : compoundTypeInfoOrNull.enumTypes[i]; if (compoundMemberInfoOrNull != null) { offsetOnDisk = compoundMemberInfoOrNull.getOffsetOnDisk(); offsetInMemory = compoundMemberInfoOrNull.getOffsetInMemory(); } if (isDummy(accessType, fieldOrNull)) { result[i] = new HDF5DummyMemberByteifyer(factory.createBytifyer(accessType, fieldOrNull, members[i], compoundMemberInfoOrNull, enumTypeOrNullOrNull, memberClazzOrNull, i, offsetOnDisk, offsetInMemory, fileInfoProvider)); } else { result[i] = factory.createBytifyer(accessType, fieldOrNull, members[i], compoundMemberInfoOrNull, enumTypeOrNullOrNull, memberClazzOrNull, i, offsetOnDisk, offsetInMemory, fileInfoProvider); } if (compoundMemberInfoOrNull == null) { final int size = result[i].getSize(); final int elementSize = result[i].getElementSize(); offsetOnDisk += size; offsetInMemory = PaddingUtils.padOffset(offsetInMemory + size, elementSize); } } return result; } // // Dummy helpers // private static boolean isDummy(AccessType accessType, Field fieldOrNull) { return (accessType == AccessType.FIELD) && (fieldOrNull == null); } private static class HDF5DummyMemberByteifyer extends HDF5MemberByteifyer { private final HDF5MemberByteifyer delegate; public HDF5DummyMemberByteifyer(HDF5MemberByteifyer delegate) { super(null, null, 0, 0, 0, false, null); this.delegate = delegate; } @Override int getElementSize() { return 0; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { // Dummy implementation return new byte[delegate.getSize()]; } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { // Dummy implementation } @Override protected int getMemberStorageTypeId() { return delegate.getMemberStorageTypeId(); } @Override protected int getMemberNativeTypeId() { return delegate.getMemberNativeTypeId(); } @Override public HDF5DataTypeVariant getTypeVariant() { return delegate.getTypeVariant(); } @Override public void insertType(int dataTypeId) { delegate.insertType(dataTypeId); } @Override public void insertNativeType(int dataTypeId, HDF5 h5, ICleanUpRegistry registry) { delegate.insertNativeType(dataTypeId, h5, registry); } @Override public int getMaxCharacters() { return delegate.getMaxCharacters(); } @Override public int getSize() { return delegate.getSize(); } @Override public int getOffsetOnDisk() { return delegate.getOffsetOnDisk(); } @Override public int getOffsetInMemory() { return delegate.getOffsetInMemory(); } @Override public int getTotalSizeOnDisk() { return delegate.getTotalSizeOnDisk(); } @Override public int getTotalSizeInMemory() { return delegate.getTotalSizeInMemory(); } @Override public String getMemberName() { return delegate.getMemberName(); } @Override public String describe() { return delegate.describe(); } @Override public boolean isDummy() { return true; } @Override public String toString() { return delegate.toString(); } } // // Auxiliary getter and setter methods. // private static IHDF5CompoundMemberBytifyerFactory findFactory(Class memberClazz, HDF5CompoundMemberInformation memberInfoOrNull, String memberName) { if (memberClazz == null) { throw new IllegalArgumentException("No type given for member '" + memberName + "'."); } for (IHDF5CompoundMemberBytifyerFactory factory : memberFactories) { if (factory.canHandle(memberClazz, memberInfoOrNull)) { return factory; } } if (memberInfoOrNull == null) { throw new IllegalArgumentException("The member '" + memberName + "' is of type '" + memberClazz.getCanonicalName() + "' which cannot be handled by any HDFMemberByteifyer."); } else { throw new IllegalArgumentException("The member '" + memberName + "' is of type '" + memberClazz.getCanonicalName() + "' [memory] and '" + memberInfoOrNull.getType() + "' [disk] which cannot be handled by any HDFMemberByteifyer."); } } private static AccessType getAccessType(Class clazz) { if (Map.class.isAssignableFrom(clazz)) { return AccessType.MAP; } else if (List.class.isAssignableFrom(clazz)) { return AccessType.LIST; } else if (Object[].class == clazz) { return AccessType.ARRAY; } else { return AccessType.FIELD; } } @SuppressWarnings("unchecked") static Object getMap(Object obj, final String name) { return ((Map) obj).get(name); } @SuppressWarnings("unchecked") static Object getList(Object obj, final int index) { return ((List) obj).get(index); } static Object getArray(Object obj, final int index) { return ((Object[]) obj)[index]; } @SuppressWarnings("unchecked") static void putMap(final Object obj, final String memberName, final Object value) { ((Map) obj).put(memberName, value); } @SuppressWarnings("unchecked") static void setList(final Object obj, final int index, final Object value) { ((List) obj).set(index, value); } static void setArray(final Object obj, final int index, final Object value) { ((Object[]) obj)[index] = value; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5CompoundDataList.java000066400000000000000000000025171256564762100300530ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.util.ArrayList; import java.util.Collection; /** * A list to be used to store the members of a compound. * * @author Bernd Rinn */ public class HDF5CompoundDataList extends ArrayList { private static final long serialVersionUID = 8683452581122892189L; /** * @see ArrayList#ArrayList() */ public HDF5CompoundDataList() { super(); } /** * @see ArrayList#ArrayList(Collection) */ public HDF5CompoundDataList(Collection c) { super(c); } /** * @see ArrayList#ArrayList(int) */ public HDF5CompoundDataList(int initialCapacity) { super(initialCapacity); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5CompoundDataMap.java000066400000000000000000000027651256564762100276620ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.util.HashMap; import java.util.Map; /** * A map to be used to store the member data of a compound. * * @author Bernd Rinn */ public class HDF5CompoundDataMap extends HashMap { private static final long serialVersionUID = 362498820763181265L; /** * @see HashMap#HashMap() */ public HDF5CompoundDataMap() { super(); } /** * @see HashMap#HashMap(int, float) */ public HDF5CompoundDataMap(int initialCapacity, float loadFactor) { super(initialCapacity, loadFactor); } /** * @see HashMap#HashMap(int) */ public HDF5CompoundDataMap(int initialCapacity) { super(initialCapacity); } /** * @see HashMap#HashMap(Map) */ public HDF5CompoundDataMap(Map m) { super(m); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5CompoundInformationRetriever.java000066400000000000000000001116421256564762100325230ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_ARRAY; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_COMPOUND; import java.lang.reflect.Field; import java.util.ArrayList; import java.util.Arrays; import java.util.List; import java.util.Map; import org.apache.commons.lang.StringUtils; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.hdf5.HDF5DataTypeInformation.DataTypeInfoOptions; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; /** * The implementation of {@link IHDF5CompoundInformationRetriever}. * * @author Bernd Rinn */ abstract class HDF5CompoundInformationRetriever implements IHDF5CompoundInformationRetriever { protected final HDF5BaseReader baseReader; protected final IHDF5EnumTypeRetriever enumTypeRetriever; HDF5CompoundInformationRetriever(HDF5BaseReader baseReader, IHDF5EnumTypeRetriever enumTypeRetriever) { assert baseReader != null; assert enumTypeRetriever != null; this.baseReader = baseReader; this.enumTypeRetriever = enumTypeRetriever; } @Override public HDF5CompoundMemberInformation[] getMemberInfo(final Class compoundClass) { return getMemberInfo(compoundClass.getSimpleName()); } @Override public HDF5CompoundMemberInformation[] getMemberInfo(final String dataTypeName) { return getMemberInfo(dataTypeName, DataTypeInfoOptions.DEFAULT); } @Override public HDF5CompoundMemberInformation[] getMemberInfo(final String dataTypeName, final DataTypeInfoOptions dataTypeInfoOptions) { baseReader.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public HDF5CompoundMemberInformation[] call(final ICleanUpRegistry registry) { final String dataTypePath = HDF5Utils.createDataTypePath(HDF5Utils.COMPOUND_PREFIX, baseReader.houseKeepingNameSuffix, dataTypeName); final int compoundDataTypeId = baseReader.h5.openDataType(baseReader.fileId, dataTypePath, registry); final CompoundTypeInformation compoundInformation = getCompoundTypeInformation(compoundDataTypeId, dataTypePath, dataTypeInfoOptions, registry); return compoundInformation.getCopyOfMembers(); } }; return baseReader.runner.call(writeRunnable); } @Override public HDF5CompoundMemberInformation[] getDataSetInfo(final String dataSetPath) throws HDF5JavaException { return getDataSetInfo(dataSetPath, DataTypeInfoOptions.DEFAULT); } @Override public HDF5CompoundMemberInformation[] getDataSetInfo(final String dataSetPath, final DataTypeInfoOptions dataTypeInfoOptions) throws HDF5JavaException { final ICallableWithCleanUp infoRunnable = new ICallableWithCleanUp() { @Override public HDF5CompoundMemberInformation[] call(final ICleanUpRegistry registry) { return getFullCompoundDataSetInformation(dataSetPath, dataTypeInfoOptions, registry).getCopyOfMembers(); } }; final HDF5CompoundMemberInformation[] compoundInformation = baseReader.runner.call(infoRunnable); return compoundInformation; } private CompoundTypeInformation getFullCompoundAttributeInformation(final String objectPath, final String attributeName, final DataTypeInfoOptions dataTypeInfoOptions, final ICleanUpRegistry registry) throws HDF5JavaException { final int dataSetId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); final int attributeId = baseReader.h5.openAttribute(dataSetId, attributeName, registry); final int storageDataTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, registry); final int compoundDataTypeId; int classType = baseReader.h5.getClassType(storageDataTypeId); if (classType == H5T_ARRAY) { compoundDataTypeId = baseReader.h5.getBaseDataType(storageDataTypeId, registry); classType = baseReader.h5.getClassType(compoundDataTypeId); } else { compoundDataTypeId = storageDataTypeId; } if (classType != H5T_COMPOUND) { throw new HDF5JavaException("Attribute '" + attributeName + "' of object '" + objectPath + "' is not of compound type."); } final String dataTypePathOrNull = baseReader.tryGetDataTypePath(compoundDataTypeId); final CompoundTypeInformation compoundInformation = getCompoundTypeInformation(compoundDataTypeId, dataTypePathOrNull, dataTypeInfoOptions, registry); return compoundInformation; } private CompoundTypeInformation getFullCompoundDataSetInformation(final String dataSetPath, final DataTypeInfoOptions dataTypeInfoOptions, final ICleanUpRegistry registry) throws HDF5JavaException { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, dataSetPath, registry); final int compoundDataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); if (baseReader.h5.getClassType(compoundDataTypeId) != H5T_COMPOUND) { throw new HDF5JavaException("Data set '" + dataSetPath + "' is not of compound type."); } // Note: the type variants for the compound members are stored at the compound type. // So if we want to know the data set variant, we need to read the data type path as well. final String dataTypePathOrNull = (dataTypeInfoOptions.knowsDataTypePath() || dataTypeInfoOptions .knowsDataTypeVariant()) ? baseReader .tryGetDataTypePath(compoundDataTypeId) : null; final CompoundTypeInformation compoundInformation = getCompoundTypeInformation(compoundDataTypeId, dataTypePathOrNull, dataTypeInfoOptions, registry); return compoundInformation; } private CompoundTypeInformation getFullCompoundDataTypeInformation(final String dataTypePath, final DataTypeInfoOptions dataTypeInfoOptions, final ICleanUpRegistry registry) throws HDF5JavaException { final int compoundDataTypeId = baseReader.h5.openDataType(baseReader.fileId, dataTypePath, registry); if (baseReader.h5.getClassType(compoundDataTypeId) != H5T_COMPOUND) { throw new HDF5JavaException("Data type '" + dataTypePath + "' is not a compound type."); } final CompoundTypeInformation compoundInformation = getCompoundTypeInformation(compoundDataTypeId, dataTypePath, dataTypeInfoOptions, registry); return compoundInformation; } CompoundTypeInformation getCompoundTypeInformation(final int compoundDataTypeId, final String dataTypePathOrNull, final DataTypeInfoOptions dataTypeInfoOptions, final ICleanUpRegistry registry) { final String typeName = HDF5Utils.getDataTypeNameFromPath(dataTypePathOrNull, baseReader.houseKeepingNameSuffix, HDF5DataClass.COMPOUND); final String[] memberNames = baseReader.h5.getNamesForEnumOrCompoundMembers(compoundDataTypeId); final int nativeCompoundDataTypeId = baseReader.h5.getNativeDataType(compoundDataTypeId, registry); final int recordSizeOnDisk = baseReader.h5.getDataTypeSize(compoundDataTypeId); final int recordSizeInMemory = baseReader.h5.getDataTypeSize(nativeCompoundDataTypeId); final CompoundTypeInformation compoundInfo = new CompoundTypeInformation(typeName, compoundDataTypeId, nativeCompoundDataTypeId, memberNames.length, recordSizeOnDisk, recordSizeInMemory); final HDF5DataTypeVariant[] memberTypeVariantsOrNull = dataTypeInfoOptions.knowsDataTypeVariant() ? baseReader .tryGetTypeVariantForCompoundMembers(dataTypePathOrNull, registry) : null; if (memberTypeVariantsOrNull != null && memberTypeVariantsOrNull.length != memberNames.length) { throw new HDF5JavaException( "Invalid member data type variant information on committed data type '" + dataTypePathOrNull + "'."); } int offsetOnDisk = 0; int offsetInMemory = 0; for (int i = 0; i < memberNames.length; ++i) { final int dataTypeId = baseReader.h5.getDataTypeForIndex(compoundDataTypeId, i, registry); // This should safe us from computing the offsets ourselves, but as it turns out, the // offset for the native data type is wrong for bit fields, // Test failing: HDF5RoundtripTest.testCompoundMap() // Tested: 2014-07-28, HDF5 1.8.13 // offsetOnDisk = baseReader.h5.getOffsetForCompoundMemberIndex(compoundDataTypeId, i); // offsetInMemory = // baseReader.h5.getOffsetForCompoundMemberIndex(nativeCompoundDataTypeId, i); compoundInfo.dataTypeIds[i] = dataTypeId; final HDF5DataTypeInformation dataTypeInformation = baseReader.getDataTypeInformation(dataTypeId, dataTypeInfoOptions, registry); if (memberTypeVariantsOrNull != null && memberTypeVariantsOrNull[i].isTypeVariant()) { dataTypeInformation.setTypeVariant(memberTypeVariantsOrNull[i]); } final HDF5EnumerationType enumTypeOrNull; if (dataTypeInformation.getDataClass() == HDF5DataClass.ENUM) { if (dataTypeInformation.isArrayType()) { final int baseDataSetType = baseReader.h5.getBaseDataType(dataTypeId, registry); enumTypeOrNull = baseReader.getEnumTypeForStorageDataType(null, baseDataSetType, false, null, null, registry); } else { enumTypeOrNull = baseReader.getEnumTypeForStorageDataType(null, dataTypeId, false, null, null, registry); } } else { enumTypeOrNull = null; } compoundInfo.enumTypes[i] = enumTypeOrNull; if (enumTypeOrNull != null) { compoundInfo.setMember(i, new HDF5CompoundMemberInformation(memberNames[i], dataTypeInformation, offsetOnDisk, offsetInMemory, enumTypeOrNull .getEnumType().getValueArray())); } else { compoundInfo.setMember(i, new HDF5CompoundMemberInformation(memberNames[i], dataTypeInformation, offsetOnDisk, offsetInMemory)); } final HDF5DataTypeInformation typeInfo = compoundInfo.getMember(i).getType(); final int size = typeInfo.getSize(); offsetOnDisk += size; offsetInMemory = PaddingUtils.padOffset(offsetInMemory + size, typeInfo.getElementSizeForPadding()); } return compoundInfo; } @Override public HDF5CompoundType getType(final String name, final Class pojoClass, boolean requireTypesToBeEqual, final HDF5CompoundMemberMapping... members) { baseReader.checkOpen(); final HDF5ValueObjectByteifyer objectArrayifyer = baseReader.createCompoundByteifyers(pojoClass, members, null); return getType(name, -1, pojoClass, requireTypesToBeEqual, objectArrayifyer); } @Override public HDF5CompoundType getType(final String name, final Class pojoClass, final HDF5CompoundMemberMapping... members) { return getType(name, pojoClass, true, members); } HDF5CompoundType getType(final String name, int committedDataTypeId, final Class compoundType, final boolean requireEqualsType, final HDF5ValueObjectByteifyer objectArrayifyer) { final int storageDataTypeId = (committedDataTypeId < 0) ? baseReader .createStorageCompoundDataType(objectArrayifyer) : committedDataTypeId; final int nativeDataTypeId = baseReader.createNativeCompoundDataType(objectArrayifyer); return new HDF5CompoundType(baseReader.fileId, storageDataTypeId, nativeDataTypeId, name, compoundType, requireEqualsType, objectArrayifyer, new HDF5CompoundType.IHDF5InternalCompoundMemberInformationRetriever() { @Override public HDF5CompoundMemberInformation[] getCompoundMemberInformation( final DataTypeInfoOptions dataTypeInfoOptions) { return HDF5CompoundInformationRetriever.this .getCompoundMemberInformation(storageDataTypeId, name, dataTypeInfoOptions); } }, baseReader); } HDF5CompoundMemberInformation[] getCompoundMemberInformation(final int storageDataTypeId, final String dataTypeNameOrNull, final DataTypeInfoOptions dataTypeInfoOptions) { baseReader.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public HDF5CompoundMemberInformation[] call(final ICleanUpRegistry registry) { final String dataTypePath = (dataTypeNameOrNull == null) ? null : HDF5Utils .createDataTypePath(HDF5Utils.COMPOUND_PREFIX, baseReader.houseKeepingNameSuffix, dataTypeNameOrNull); final CompoundTypeInformation compoundInformation = getCompoundTypeInformation(storageDataTypeId, dataTypePath, dataTypeInfoOptions, registry); return compoundInformation.getCopyOfMembers(); } }; return baseReader.runner.call(writeRunnable); } @Override public HDF5CompoundType getType(final Class pojoClass, final HDF5CompoundMemberMapping... members) { return getType(null, pojoClass, members); } @Override public HDF5CompoundType getInferredType(String name, Class pojoClass, HDF5CompoundMappingHints hints) { return getInferredType(name, pojoClass, hints, true); } @Override public HDF5CompoundType getInferredType(String name, Class pojoClass, HDF5CompoundMappingHints hints, boolean requireTypesToBeEqual) { return getType( name, pojoClass, requireTypesToBeEqual, addEnumTypes(HDF5CompoundMemberMapping.addHints( HDF5CompoundMemberMapping.inferMapping(pojoClass), hints))); } @Override public HDF5CompoundType getInferredType(Class pojoClass, HDF5CompoundMappingHints hints) { return getInferredType(null, pojoClass, hints); } @Override public HDF5CompoundType getInferredType(final String name, final Class pojoClass) { return getInferredType(name, pojoClass, null); } @Override public HDF5CompoundType getInferredType(final Class pojoClass) { return getInferredType(null, pojoClass); } @Override public HDF5CompoundType getInferredType(String name, T pojo, HDF5CompoundMappingHints hints) { return getInferredType(name, pojo, hints, true); } @Override @SuppressWarnings( { "unchecked", "rawtypes" }) public HDF5CompoundType getInferredType(String name, T pojo, HDF5CompoundMappingHints hints, boolean requireTypesToBeEqual) { if (Map.class.isInstance(pojo)) { final String compoundTypeName = (name == null) ? HDF5CompoundMemberMapping.constructCompoundTypeName( ((Map) pojo).keySet(), true) : name; return (HDF5CompoundType) getType( compoundTypeName, Map.class, requireTypesToBeEqual, addEnumTypes(HDF5CompoundMemberMapping.addHints( HDF5CompoundMemberMapping.inferMapping((Map) pojo), hints))); } else { final Class pojoClass = (Class) pojo.getClass(); return getType(name, pojoClass, requireTypesToBeEqual, addEnumTypes(HDF5CompoundMemberMapping.addHints(HDF5CompoundMemberMapping .inferMapping(pojo, HDF5CompoundMemberMapping.inferEnumerationTypeMap( pojo, enumTypeRetriever), HDF5CompoundMappingHints .isUseVariableLengthStrings(hints)), hints))); } } @Override public HDF5CompoundType getInferredType(final String name, final T[] pojo) { return getInferredType(name, pojo, null); } @Override public HDF5CompoundType getInferredType(final T[] pojo) { return getInferredType((String) null, pojo, null); } @Override public HDF5CompoundType getInferredType(String name, T[] pojo, HDF5CompoundMappingHints hints) { return getInferredType(name, pojo, hints, true); } @Override @SuppressWarnings( { "unchecked", "rawtypes" }) public HDF5CompoundType getInferredType(String name, T[] pojo, HDF5CompoundMappingHints hints, boolean requireTypesToBeEqual) { final Class componentType = pojo.getClass().getComponentType(); if (pojo.length == 0) { return (HDF5CompoundType) getInferredType(name, componentType, hints); } if (Map.class.isAssignableFrom(componentType)) { final String compoundTypeName = (name == null) ? HDF5CompoundMemberMapping.constructCompoundTypeName( ((Map) pojo[0]).keySet(), true) : name; return (HDF5CompoundType) getType( compoundTypeName, Map.class, requireTypesToBeEqual, addEnumTypes(HDF5CompoundMemberMapping.addHints( HDF5CompoundMemberMapping.inferMapping((Map) pojo[0]), hints))); } else { return (HDF5CompoundType) getType(name, componentType, requireTypesToBeEqual, addEnumTypes(HDF5CompoundMemberMapping.addHints(HDF5CompoundMemberMapping .inferMapping(pojo, HDF5CompoundMemberMapping.inferEnumerationTypeMap( pojo, enumTypeRetriever), hints == null ? false : hints.isUseVariableLengthStrings()), hints))); } } HDF5CompoundMemberMapping[] addEnumTypes(HDF5CompoundMemberMapping[] mapping) { for (HDF5CompoundMemberMapping m : mapping) { final Class memberClass = m.tryGetMemberClass(); if (memberClass != null) { if (memberClass.isEnum()) { @SuppressWarnings("unchecked") final Class> enumClass = (Class>) memberClass; final String typeName = (StringUtils.isBlank(m.tryGetEnumTypeName())) ? memberClass .getSimpleName() : m.tryGetEnumTypeName(); m.setEnumerationType(enumTypeRetriever.getType(typeName, ReflectionUtils.getEnumOptions(enumClass))); } else if (memberClass == HDF5EnumerationValue.class || memberClass == HDF5EnumerationValueArray.class || memberClass == HDF5EnumerationValueMDArray.class) { final HDF5CompoundMappingHints hintsOrNull = m.tryGetHints(); final HDF5EnumerationType typeOrNull = (hintsOrNull != null) ? hintsOrNull.tryGetEnumType(m.getMemberName()) : null; if (typeOrNull != null) { m.setEnumerationType(typeOrNull); } } } } return mapping; } @Override public HDF5CompoundType getInferredType(final String name, final T pojo) { return getInferredType(name, pojo, null); } @Override public HDF5CompoundType getInferredType(final T pojo) { return getInferredType(null, pojo); } @Override public HDF5CompoundType> getInferredType(String name, List memberNames, List data, HDF5CompoundMappingHints hints) { return getInferredType(name, memberNames, data, hints, true); } @Override @SuppressWarnings("unchecked") public HDF5CompoundType> getInferredType(String name, List memberNames, List data, HDF5CompoundMappingHints hints, boolean requireTypesToBeEqual) { final String compoundTypeName = (name == null) ? HDF5CompoundMemberMapping.constructCompoundTypeName(memberNames, false) : name; final HDF5CompoundType type = getType(compoundTypeName, List.class, requireTypesToBeEqual, HDF5CompoundMemberMapping.addHints( HDF5CompoundMemberMapping.inferMapping(memberNames, data), hints)); return (HDF5CompoundType>) type; } @Override public HDF5CompoundType> getInferredType(String name, List memberNames, List data) { return getInferredType(name, memberNames, data, null); } @Override public HDF5CompoundType> getInferredType(List memberNames, List data) { return getInferredType(null, memberNames, data); } @Override public HDF5CompoundType> getInferredType(List memberNames, List data, HDF5CompoundMappingHints hints) { return getInferredType(null, memberNames, data, hints); } @Override public HDF5CompoundType getInferredType(String[] memberNames, Object[] data) { return getInferredType(null, memberNames, data); } @Override public HDF5CompoundType getInferredType(String name, String[] memberNames, Object[] data) { final String compoundTypeName = (name == null) ? HDF5CompoundMemberMapping.constructCompoundTypeName( Arrays.asList(memberNames), false) : name; return getType(compoundTypeName, Object[].class, HDF5CompoundMemberMapping.inferMapping(memberNames, data)); } @Override public HDF5CompoundType getInferredType(String name, String[] memberNames, Object[] data, HDF5CompoundMappingHints hints) { return getInferredType(name, memberNames, data, hints, true); } @Override public HDF5CompoundType getInferredType(String name, String[] memberNames, Object[] data, HDF5CompoundMappingHints hints, boolean requireTypesToBeEqual) { final String compoundTypeName = (name == null) ? HDF5CompoundMemberMapping.constructCompoundTypeName( Arrays.asList(memberNames), false) : name; return getType(compoundTypeName, Object[].class, requireTypesToBeEqual, HDF5CompoundMemberMapping.inferMapping(memberNames, data, hints)); } @Override public HDF5CompoundType getInferredType(String[] memberNames, Object[] data, HDF5CompoundMappingHints hints) { return getInferredType(null, memberNames, data, hints); } @Override public HDF5CompoundType getDataSetType(String objectPath, Class pojoClass, HDF5CompoundMemberMapping... members) { return getDataSetType(objectPath, pojoClass, true, members); } @Override public HDF5CompoundType getDataSetType(String objectPath, Class pojoClass, boolean requireTypesToBeEqual, HDF5CompoundMemberMapping... members) { baseReader.checkOpen(); final CompoundTypeInformation cpdTypeInfo = getFullCompoundDataSetInformation(objectPath, DataTypeInfoOptions.MINIMAL, baseReader.fileRegistry); final HDF5CompoundType typeForClass = getType(cpdTypeInfo.name, cpdTypeInfo.compoundDataTypeId, pojoClass, requireTypesToBeEqual, createByteifyers(pojoClass, cpdTypeInfo, members)); return typeForClass; } @Override public HDF5CompoundType getDataSetType(String objectPath, Class pojoClass, HDF5CompoundMappingHints hints) { return getDataSetType(objectPath, pojoClass, hints, true); } @Override public HDF5CompoundType getDataSetType(String objectPath, Class pojoClass, HDF5CompoundMappingHints hints, boolean requireTypesToBeEqual) { baseReader.checkOpen(); // We need to get ALL information for the type as otherwise the mapping might be wrong (due // to a missing data type variant). final CompoundTypeInformation cpdTypeInfo = getFullCompoundDataSetInformation(objectPath, DataTypeInfoOptions.ALL, baseReader.fileRegistry); final HDF5CompoundType typeForClass = getType(cpdTypeInfo.name, cpdTypeInfo.compoundDataTypeId, pojoClass, requireTypesToBeEqual, createByteifyers(pojoClass, cpdTypeInfo, hints)); return typeForClass; } @Override public HDF5CompoundType getDataSetType(String objectPath, Class pojoClass) { return getDataSetType(objectPath, pojoClass, (HDF5CompoundMappingHints) null); } @Override public HDF5CompoundType getAttributeType(String objectPath, String attributeName, Class pojoClass) { return getAttributeType(objectPath, attributeName, pojoClass, null); } @Override public HDF5CompoundType getAttributeType(String objectPath, String attributeName, Class pojoClass, HDF5CompoundMappingHints hints) { return getAttributeType(objectPath, attributeName, pojoClass, hints, DataTypeInfoOptions.DEFAULT); } @Override public HDF5CompoundType getAttributeType(String objectPath, String attributeName, Class pojoClass, HDF5CompoundMappingHints hints, DataTypeInfoOptions dataTypeInfoOptions) { return getAttributeType(objectPath, attributeName, pojoClass, hints, dataTypeInfoOptions, true); } @Override public HDF5CompoundType getAttributeType(String objectPath, String attributeName, Class pojoClass, HDF5CompoundMappingHints hints, DataTypeInfoOptions dataTypeInfoOptions, boolean requireTypesToBeEqual) { final CompoundTypeInformation cpdTypeInfo = getFullCompoundAttributeInformation(objectPath, attributeName, dataTypeInfoOptions, baseReader.fileRegistry); final HDF5CompoundType typeForClass = getType(cpdTypeInfo.name, cpdTypeInfo.compoundDataTypeId, pojoClass, requireTypesToBeEqual, createByteifyers(pojoClass, cpdTypeInfo, hints)); return typeForClass; } @Override public HDF5CompoundType getNamedType(Class pojoClass) { return getNamedType(pojoClass.getSimpleName(), pojoClass); } @Override public HDF5CompoundType getNamedType(String dataTypeName, Class pojoClass) { return getNamedType(dataTypeName, pojoClass, null, DataTypeInfoOptions.DEFAULT); } @Override public HDF5CompoundType getNamedType(String dataTypeName, Class pojoClass, HDF5CompoundMappingHints hints) { return getNamedType(dataTypeName, pojoClass, hints, DataTypeInfoOptions.DEFAULT); } @Override public HDF5CompoundType getNamedType(String dataTypeName, Class pojoClass, DataTypeInfoOptions dataTypeInfoOptions) { return getNamedType(dataTypeName, pojoClass, null, dataTypeInfoOptions); } @Override public HDF5CompoundType getNamedType(String dataTypeName, Class pojoClass, HDF5CompoundMappingHints hints, DataTypeInfoOptions dataTypeInfoOptions) { return getNamedType(dataTypeName, pojoClass, hints, dataTypeInfoOptions, true); } @Override public HDF5CompoundType getNamedType(String dataTypeName, Class pojoClass, HDF5CompoundMappingHints hints, DataTypeInfoOptions dataTypeInfoOptions, boolean requireTypesToBeEqual) { final String dataTypePath = HDF5Utils.createDataTypePath(HDF5Utils.COMPOUND_PREFIX, baseReader.houseKeepingNameSuffix, dataTypeName); final CompoundTypeInformation cpdTypeInfo = getFullCompoundDataTypeInformation(dataTypePath, dataTypeInfoOptions, baseReader.fileRegistry); final HDF5CompoundType typeForClass = getType(dataTypeName, cpdTypeInfo.compoundDataTypeId, pojoClass, requireTypesToBeEqual, createByteifyers(pojoClass, cpdTypeInfo, hints)); return typeForClass; } private HDF5ValueObjectByteifyer createByteifyers(final Class compoundClazz, final CompoundTypeInformation compoundTypeInfo, final HDF5CompoundMemberMapping[] mapping) { return baseReader.createCompoundByteifyers(compoundClazz, mapping, compoundTypeInfo); } private HDF5ValueObjectByteifyer createByteifyers(final Class compoundClazz, final CompoundTypeInformation compoundTypeInfo, final HDF5CompoundMappingHints hintsOrNull) { return baseReader.createCompoundByteifyers(compoundClazz, inferMemberMapping(compoundClazz, compoundTypeInfo, hintsOrNull), compoundTypeInfo); } private HDF5CompoundMemberMapping[] inferMemberMapping(final Class compoundClazz, final CompoundTypeInformation compoundTypeInfo, final HDF5CompoundMappingHints hintsOrNull) { final List mapping = new ArrayList(compoundTypeInfo.getNumberOfMembers()); final Map fields = ReflectionUtils.getFieldMap(compoundClazz); for (int i = 0; i < compoundTypeInfo.getNumberOfMembers(); ++i) { final HDF5CompoundMemberInformation compoundMember = compoundTypeInfo.getMember(i); final int compoundMemberTypeId = compoundTypeInfo.dataTypeIds[i]; final Field fieldOrNull = fields.get(compoundMember.getName()); final String memberName = compoundMember.getName(); final String fieldName = (fieldOrNull != null) ? fieldOrNull.getName() : memberName; final HDF5DataTypeInformation typeInfo = compoundMember.getType(); final int[] dimensions = typeInfo.getDimensions(); if (typeInfo.getDataClass() == HDF5DataClass.ENUM) { if (dimensions.length == 0 || (dimensions.length == 1 && dimensions[0] == 1)) { mapping.add(HDF5CompoundMemberMapping.mapping(memberName).fieldName(fieldName) .enumType(compoundTypeInfo.enumTypes[i]) .typeVariant(typeInfo.tryGetTypeVariant())); } else if (dimensions.length == 1) { mapping.add(HDF5CompoundMemberMapping.mappingWithStorageTypeId( fieldName, memberName, new HDF5EnumerationType(baseReader.fileId, -1, baseReader.h5 .getNativeDataType(compoundMemberTypeId, baseReader.fileRegistry), baseReader .getEnumDataTypeName(compoundMember.getType().tryGetName(), compoundMemberTypeId), compoundMember .tryGetEnumValues(), baseReader), dimensions, compoundMemberTypeId, typeInfo.tryGetTypeVariant())); } } else if (typeInfo.getDataClass() == HDF5DataClass.STRING) { if (fieldOrNull != null && (fieldOrNull.getType() != String.class) && (fieldOrNull.getType() != char[].class)) { throw new HDF5JavaException( "Field of string type does not correspond to string or char[] value"); } mapping.add(HDF5CompoundMemberMapping.mappingArrayWithStorageId(fieldName, memberName, String.class, new int[] { typeInfo.getElementSize() }, compoundMemberTypeId, false, typeInfo.isVariableLengthString(), false, typeInfo.tryGetTypeVariant())); } else if (typeInfo.getDataClass() == HDF5DataClass.REFERENCE) { if (fieldOrNull != null && (fieldOrNull.getType() != String.class) && (fieldOrNull.getType() != char[].class)) { throw new HDF5JavaException( "Field of rererence type does not correspond to string or char[] value"); } mapping.add(HDF5CompoundMemberMapping.mappingArrayWithStorageId(fieldName, memberName, String.class, new int[] { typeInfo.getElementSize() }, compoundMemberTypeId, false, false, true, typeInfo.tryGetTypeVariant())); } else { final Class memberClazz; if (fieldOrNull != null) { memberClazz = fieldOrNull.getType(); } else { memberClazz = typeInfo.tryGetJavaType(); } mapping.add(HDF5CompoundMemberMapping.mappingArrayWithStorageId(fieldName, memberName, memberClazz, dimensions, compoundMemberTypeId, false == compoundMember.getType().isSigned(), false, false, typeInfo.tryGetTypeVariant())); } } return HDF5CompoundMemberMapping.addHints( mapping.toArray(new HDF5CompoundMemberMapping[mapping.size()]), hintsOrNull); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5CompoundMappingHints.java000066400000000000000000000112071256564762100307430ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.util.HashMap; import java.util.Map; /** * A class to store general hints that can influence the compound member mapping. * * @author Bernd Rinn */ public class HDF5CompoundMappingHints { public enum EnumReturnType { ORDINAL, STRING, JAVAENUMERATION, HDF5ENUMERATIONVALUE } private EnumReturnType enumReturnType = EnumReturnType.HDF5ENUMERATIONVALUE; private boolean useVariableLengthStrings = false; private Map enumerationTypeMap; /** * Returns the desired return type for enums. */ public EnumReturnType getEnumReturnType() { return enumReturnType; } /** * Sets the desired return type for enums. */ public void setEnumReturnType(EnumReturnType enumReturnType) { this.enumReturnType = enumReturnType; } /** * Sets the return type for enums . * * @return This object (for chaining) */ public HDF5CompoundMappingHints enumReturnType(@SuppressWarnings("hiding") EnumReturnType enumReturnType) { this.enumReturnType = enumReturnType; return this; } /** * Adds an enum type mapping to this hints object. * * @return The hint object. */ public HDF5CompoundMappingHints enumTypeMapping(String memberName, HDF5EnumerationType enumType) { if (enumerationTypeMap == null) { enumerationTypeMap = new HashMap(); } enumerationTypeMap.put(memberName, enumType); return this; } /** * Replaces the enum type mapping of this hints object. * * @return The hint object. */ public HDF5CompoundMappingHints enumTypeMapping(Map enumTypeMapping) { enumerationTypeMap = enumTypeMapping; return this; } /** * Returns the {@link HDF5EnumerationType} for the given memberName, or * null, if no mapping is available for this member. */ public HDF5EnumerationType tryGetEnumType(String memberName) { if (enumerationTypeMap == null) { return null; } return enumerationTypeMap.get(memberName); } /** * Returns the desired enumeration return type. */ public static EnumReturnType getEnumReturnType(HDF5CompoundMemberMapping mapping) { return (mapping.tryGetHints() == null) ? EnumReturnType.HDF5ENUMERATIONVALUE : mapping .tryGetHints().getEnumReturnType(); } /** * Returns whether variable-length-string types should be used if the length is not set * explicitly. */ public static boolean isUseVariableLengthStrings(HDF5CompoundMappingHints hintsOrNull) { return hintsOrNull == null ? false : hintsOrNull.useVariableLengthStrings; } /** * Returns whether variable-length-string types should be used if the length is not set * explicitly. */ public boolean isUseVariableLengthStrings() { return useVariableLengthStrings; } /** * Sets whether variable-length-string types should be used if the length is not set explicitly. */ public void setUseVariableLengthStrings(boolean useVariableLengthStrings) { this.useVariableLengthStrings = useVariableLengthStrings; } /** * Sets that variable-length-string types should be used if the length is not set explicitly. * * @return The hint object. */ public HDF5CompoundMappingHints useVariableLengthStrings() { this.useVariableLengthStrings = true; return this; } /** * Sets whether variable-length-string types should be used if the length is not set explicitly. * * @return The hint object. */ public HDF5CompoundMappingHints useVariableLengthStrings(@SuppressWarnings("hiding") boolean useVariableLengthStrings) { this.useVariableLengthStrings = useVariableLengthStrings; return this; } }HDF5CompoundMemberByteifyerBitSetFactory.java000066400000000000000000000267631256564762100340350ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.base.convert.NativeData.LONG_SIZE; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getArray; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getList; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getMap; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.putMap; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.setArray; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.setList; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_B64LE; import java.lang.reflect.Field; import java.util.BitSet; import ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.AccessType; import ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.IHDF5CompoundMemberBytifyerFactory; import ch.systemsx.cisd.hdf5.HDF5ValueObjectByteifyer.IFileAccessProvider; import ch.systemsx.cisd.hdf5.hdf5lib.HDFNativeData; /** * A {@link HDF5CompoundByteifyerFactory.IHDF5CompoundMemberBytifyerFactory} for BitSet * * @author Bernd Rinn */ class HDF5CompoundMemberByteifyerBitSetFactory implements IHDF5CompoundMemberBytifyerFactory { @Override public boolean canHandle(Class clazz, HDF5CompoundMemberInformation memberInfoOrNull) { if (memberInfoOrNull != null) { return (clazz == BitSet.class) && memberInfoOrNull.getType().getDataClass() == HDF5DataClass.BITFIELD; } else { return (clazz == BitSet.class); } } @Override public Class tryGetOverrideJavaType(HDF5DataClass dataClass, int rank, int elementSize, HDF5DataTypeVariant typeVariantOrNull) { return null; } @Override public HDF5MemberByteifyer createBytifyer(final AccessType accessType, final Field fieldOrNull, final HDF5CompoundMemberMapping member, final HDF5CompoundMemberInformation compoundMemberInfoOrNull, HDF5EnumerationType enumTypeOrNull, final Class memberClazz, final int index, final int offset, int memOffset, final IFileAccessProvider fileInfoProvider) { final String memberName = member.getMemberName(); final int memberTypeLengthInLongs; if (compoundMemberInfoOrNull == null) { final int memberTypeLengthInBits = member.getMemberTypeLength(); memberTypeLengthInLongs = memberTypeLengthInBits / 64 + (memberTypeLengthInBits % 64 != 0 ? 1 : 0); } else { memberTypeLengthInLongs = compoundMemberInfoOrNull.getType().getNumberOfElements(); } if (memberTypeLengthInLongs <= 0) { throw new IllegalArgumentException( "Length of a bit field must be a positive number (len=" + memberTypeLengthInLongs + ")."); } final int storageTypeId = member.getStorageDataTypeId(); final int memberTypeId = (storageTypeId < 0) ? fileInfoProvider.getArrayTypeId(H5T_STD_B64LE, memberTypeLengthInLongs) : storageTypeId; switch (accessType) { case FIELD: return createByteifyerForField(fieldOrNull, memberName, offset, memOffset, memberTypeLengthInLongs, memberTypeId, member.tryGetTypeVariant()); case MAP: return createByteifyerForMap(memberName, offset, memOffset, memberTypeLengthInLongs, memberTypeId, member.tryGetTypeVariant()); case LIST: return createByteifyerForList(memberName, index, offset, memOffset, memberTypeLengthInLongs, memberTypeId, member.tryGetTypeVariant()); case ARRAY: return createByteifyerForArray(memberName, index, offset, memOffset, memberTypeLengthInLongs, memberTypeId, member.tryGetTypeVariant()); default: throw new Error("Unknown access type"); } } private HDF5MemberByteifyer createByteifyerForField(final Field field, final String memberName, final int offset, int memOffset, final int memberTypeLengthInLongs, final int memberTypeId, final HDF5DataTypeVariant typeVariant) { ReflectionUtils.ensureAccessible(field); return new HDF5MemberByteifyer(field, memberName, memberTypeLengthInLongs * LONG_SIZE, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 8; } @Override protected int getMemberStorageTypeId() { return memberTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { final BitSet bs = (BitSet) field.get(obj); return HDFNativeData.longToByte(BitSetConversionUtils.toStorageForm(bs)); } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { final BitSet bs = BitSetConversionUtils.fromStorageForm(HDFNativeData.byteToLong(byteArr, arrayOffset + offsetInMemory, memberTypeLengthInLongs)); field.set(obj, bs); } }; } private HDF5MemberByteifyer createByteifyerForMap(final String memberName, final int offset, int memOffset, final int memberTypeLengthInLongs, final int memberTypeId, final HDF5DataTypeVariant typeVariant) { return new HDF5MemberByteifyer(null, memberName, memberTypeLengthInLongs * LONG_SIZE, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 8; } @Override protected int getMemberStorageTypeId() { return memberTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { final BitSet bs = (BitSet) getMap(obj, memberName); return HDFNativeData.longToByte(BitSetConversionUtils.toStorageForm(bs)); } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { final BitSet bitSet = BitSetConversionUtils.fromStorageForm(HDFNativeData.byteToLong(byteArr, arrayOffset + offsetInMemory, memberTypeLengthInLongs)); putMap(obj, memberName, bitSet); } }; } private HDF5MemberByteifyer createByteifyerForList(final String memberName, final int index, final int offset, int memOffset, final int memberTypeLengthInLongs, final int memberTypeId, final HDF5DataTypeVariant typeVariant) { return new HDF5MemberByteifyer(null, memberName, memberTypeLengthInLongs * LONG_SIZE, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 8; } @Override protected int getMemberStorageTypeId() { return memberTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { final BitSet bs = (BitSet) getList(obj, index); return HDFNativeData.longToByte(BitSetConversionUtils.toStorageForm(bs)); } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { final BitSet bitSet = BitSetConversionUtils.fromStorageForm(HDFNativeData.byteToLong(byteArr, arrayOffset + offsetInMemory, memberTypeLengthInLongs)); setList(obj, index, bitSet); } }; } private HDF5MemberByteifyer createByteifyerForArray(final String memberName, final int index, final int offset, int memOffset, final int memberTypeLengthInLongs, final int memberTypeId, final HDF5DataTypeVariant typeVariant) { return new HDF5MemberByteifyer(null, memberName, memberTypeLengthInLongs * LONG_SIZE, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 8; } @Override protected int getMemberStorageTypeId() { return memberTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { final BitSet bs = (BitSet) getArray(obj, index); return HDFNativeData.longToByte(BitSetConversionUtils.toStorageForm(bs)); } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { final BitSet bitSet = BitSetConversionUtils.fromStorageForm(HDFNativeData.byteToLong(byteArr, arrayOffset + offsetInMemory, memberTypeLengthInLongs)); setArray(obj, index, bitSet); } }; } } HDF5CompoundMemberByteifyerBooleanFactory.java000066400000000000000000000234071256564762100342120ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getArray; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getList; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getMap; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.putMap; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.setArray; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.setList; import java.lang.reflect.Field; import ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.AccessType; import ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.IHDF5CompoundMemberBytifyerFactory; import ch.systemsx.cisd.hdf5.HDF5ValueObjectByteifyer.IFileAccessProvider; import ch.systemsx.cisd.hdf5.hdf5lib.HDFNativeData; /** * A {@link HDF5CompoundByteifyerFactory.IHDF5CompoundMemberBytifyerFactory} for * boolean. * * @author Bernd Rinn */ class HDF5CompoundMemberByteifyerBooleanFactory implements IHDF5CompoundMemberBytifyerFactory { @Override public boolean canHandle(Class clazz, HDF5CompoundMemberInformation memberInfoOrNull) { if (memberInfoOrNull != null) { final HDF5DataClass dataClass = memberInfoOrNull.getType().getDataClass(); return (clazz == boolean.class) && (dataClass == HDF5DataClass.BOOLEAN || dataClass == HDF5DataClass.INTEGER); } else { return (clazz == boolean.class); } } @Override public Class tryGetOverrideJavaType(HDF5DataClass dataClass, int rank, int elementSize, HDF5DataTypeVariant typeVariantOrNull) { return null; } @Override public HDF5MemberByteifyer createBytifyer(final AccessType accessType, final Field fieldOrNull, final HDF5CompoundMemberMapping member, final HDF5CompoundMemberInformation compoundMemberInfoOrNull, HDF5EnumerationType enumTypeOrNull, final Class memberClazz, final int index, final int offset, int memOffset, final IFileAccessProvider fileInfoProvider) { final String memberName = member.getMemberName(); // May be -1 if not known final int memberTypeId = member.getStorageDataTypeId(); final int booleanDataTypeId = (memberTypeId < 0) ? fileInfoProvider.getBooleanDataTypeId() : memberTypeId; switch (accessType) { case FIELD: return createByteifyerForField(fieldOrNull, memberName, offset, memOffset, booleanDataTypeId, member.tryGetTypeVariant()); case MAP: return createByteifyerForMap(memberName, offset, memOffset, booleanDataTypeId, member.tryGetTypeVariant()); case LIST: return createByteifyerForList(memberName, index, offset, memOffset, booleanDataTypeId, member.tryGetTypeVariant()); case ARRAY: return createByteifyerForArray(memberName, index, offset, memOffset, booleanDataTypeId, member.tryGetTypeVariant()); default: throw new Error("Unknown access type"); } } private HDF5MemberByteifyer createByteifyerForField(final Field field, final String memberName, final int offset, int memOffset, final int booleanDataTypeId, final HDF5DataTypeVariant typeVariant) { ReflectionUtils.ensureAccessible(field); return new HDF5MemberByteifyer(field, memberName, 1, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 1; } @Override protected int getMemberStorageTypeId() { return booleanDataTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { return HDFNativeData.byteToByte((byte) (field.getBoolean(obj) ? 1 : 0)); } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { final boolean value = (byteArr[arrayOffset + offsetInMemory] == 0) ? false : true; field.setBoolean(obj, value); } }; } private HDF5MemberByteifyer createByteifyerForMap(final String memberName, final int offset, int memOffset, final int booleanDataTypeId, final HDF5DataTypeVariant typeVariant) { return new HDF5MemberByteifyer(null, memberName, 1, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 1; } @Override protected int getMemberStorageTypeId() { return booleanDataTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { return HDFNativeData.byteToByte((byte) (((Boolean) getMap(obj, memberName)) ? 1 : 0)); } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { final boolean value = (byteArr[arrayOffset + offsetInMemory] == 0) ? false : true; putMap(obj, memberName, value); } }; } private HDF5MemberByteifyer createByteifyerForList(final String memberName, final int index, final int offset, int memOffset, final int booleanDataTypeId, final HDF5DataTypeVariant typeVariant) { return new HDF5MemberByteifyer(null, memberName, 1, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 1; } @Override protected int getMemberStorageTypeId() { return booleanDataTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { return HDFNativeData .byteToByte((byte) (((Boolean) getList(obj, index)) ? 1 : 0)); } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { final boolean value = (byteArr[arrayOffset + offsetInMemory] == 0) ? false : true; setList(obj, index, value); } }; } private HDF5MemberByteifyer createByteifyerForArray(final String memberName, final int index, final int offset, int memOffset, final int booleanDataTypeId, final HDF5DataTypeVariant typeVariant) { return new HDF5MemberByteifyer(null, memberName, 1, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 1; } @Override protected int getMemberStorageTypeId() { return booleanDataTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { return HDFNativeData.byteToByte((byte) (((Boolean) getArray(obj, index)) ? 1 : 0)); } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { final boolean value = (byteArr[arrayOffset + offsetInMemory] == 0) ? false : true; setArray(obj, index, value); } }; } } HDF5CompoundMemberByteifyerByteFactory.java000066400000000000000000000526771256564762100335510ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getArray; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getList; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getMap; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.putMap; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.setArray; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.setList; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_I8LE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_U8LE; import java.lang.reflect.Field; import java.util.IdentityHashMap; import java.util.Map; import ch.systemsx.cisd.base.mdarray.MDByteArray; import ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.AccessType; import ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.IHDF5CompoundMemberBytifyerFactory; import ch.systemsx.cisd.hdf5.HDF5ValueObjectByteifyer.IFileAccessProvider; import ch.systemsx.cisd.hdf5.hdf5lib.HDFNativeData; /** * A {@link HDF5CompoundByteifyerFactory.IHDF5CompoundMemberBytifyerFactory} for byte, * byte[], byte[][] and MDByteArray. * * @author Bernd Rinn */ class HDF5CompoundMemberByteifyerByteFactory implements IHDF5CompoundMemberBytifyerFactory { private static Map, Rank> classToRankMap = new IdentityHashMap, Rank>(); private enum Rank { SCALAR(byte.class, 0), ARRAY1D(byte[].class, 1), ARRAY2D(byte[][].class, 2), ARRAYMD( MDByteArray.class, -1); private final Class clazz; private final int rank; Rank(Class clazz, int rank) { this.clazz = clazz; this.rank = rank; } int getRank() { return rank; } boolean isScalar() { return rank == 0; } boolean anyRank() { return rank == -1; } Class getClazz() { return clazz; } } static { for (Rank r : Rank.values()) { classToRankMap.put(r.getClazz(), r); } } @Override public boolean canHandle(Class clazz, HDF5CompoundMemberInformation memberInfoOrNull) { final Rank rankOrNull = classToRankMap.get(clazz); if (memberInfoOrNull != null) { final HDF5DataTypeInformation typeInfo = memberInfoOrNull.getType(); if (rankOrNull == null || typeInfo.getDataClass() != HDF5DataClass.INTEGER || typeInfo.getElementSize() != 1) { return false; } return rankOrNull.anyRank() || (rankOrNull.getRank() == typeInfo.getDimensions().length) || (rankOrNull.isScalar() && typeInfo.getDimensions().length == 1 && typeInfo .getDimensions()[0] == 1); } else { return rankOrNull != null; } } @Override public Class tryGetOverrideJavaType(HDF5DataClass dataClass, int rank, int elementSize, HDF5DataTypeVariant typeVariantOrNull) { return null; } @Override public HDF5MemberByteifyer createBytifyer(AccessType accessType, Field fieldOrNull, HDF5CompoundMemberMapping member, HDF5CompoundMemberInformation compoundMemberInfoOrNull, HDF5EnumerationType enumTypeOrNull, Class memberClazz, int index, int offset, int memOffset, IFileAccessProvider fileInfoProvider) { final String memberName = member.getMemberName(); final Rank rank = classToRankMap.get(memberClazz); final int len = (compoundMemberInfoOrNull != null) ? compoundMemberInfoOrNull.getType() .getNumberOfElements() : rank.isScalar() ? 1 : member.getMemberTypeLength(); final int[] dimensions = rank.isScalar() ? new int[] { 1 } : member.getMemberTypeDimensions(); final int storageTypeId = member.getStorageDataTypeId(); final int memberTypeId = rank.isScalar() ? (member.isUnsigned() ? H5T_STD_U8LE : H5T_STD_I8LE) : ((storageTypeId < 0) ? fileInfoProvider.getArrayTypeId( member.isUnsigned() ? H5T_STD_U8LE : H5T_STD_I8LE, dimensions) : storageTypeId); switch (accessType) { case FIELD: return createByteifyerForField(fieldOrNull, memberName, offset, memOffset, dimensions, len, memberTypeId, rank, member.tryGetTypeVariant()); case MAP: return createByteifyerForMap(memberName, offset, memOffset, dimensions, len, memberTypeId, rank, member.tryGetTypeVariant()); case LIST: return createByteifyerForList(memberName, index, offset, memOffset, dimensions, len, memberTypeId, rank, member.tryGetTypeVariant()); case ARRAY: return createByteifyerForArray(memberName, index, offset, memOffset, dimensions, len, memberTypeId, rank, member.tryGetTypeVariant()); default: throw new Error("Unknown access type"); } } private HDF5MemberByteifyer createByteifyerForField(final Field field, final String memberName, final int offset, int memOffset, final int[] dimensions, final int len, final int memberTypeId, final Rank rank, final HDF5DataTypeVariant typeVariant) { ReflectionUtils.ensureAccessible(field); return new HDF5MemberByteifyer(field, memberName, len, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 1; } @Override protected int getMemberStorageTypeId() { return memberTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { switch (rank) { case SCALAR: return HDFNativeData.byteToByte(field.getByte(obj)); case ARRAY1D: return (byte[]) field.get(obj); case ARRAY2D: { final byte[][] array = (byte[][]) field.get(obj); MatrixUtils.checkMatrixDimensions(memberName, dimensions, array); return MatrixUtils.flatten(array); } case ARRAYMD: { final MDByteArray array = (MDByteArray) field.get(obj); MatrixUtils.checkMDArrayDimensions(memberName, dimensions, array); return array.getAsFlatArray(); } default: throw new Error("Unknown rank."); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { switch (rank) { case SCALAR: field.setByte(obj, byteArr[arrayOffset + offsetInMemory]); break; case ARRAY1D: { final byte[] array = new byte[len]; System.arraycopy(byteArr, arrayOffset + offsetInMemory, array, 0, array.length); field.set(obj, array); break; } case ARRAY2D: { final byte[] array = new byte[len]; System.arraycopy(byteArr, arrayOffset + offsetInMemory, array, 0, array.length); field.set(obj, MatrixUtils.shapen(array, dimensions)); break; } case ARRAYMD: { final byte[] array = new byte[len]; System.arraycopy(byteArr, arrayOffset + offsetInMemory, array, 0, array.length); field.set(obj, new MDByteArray(array, dimensions)); break; } default: throw new Error("Unknown rank."); } } }; } private HDF5MemberByteifyer createByteifyerForMap(final String memberName, final int offset, int memOffset, final int[] dimensions, final int len, final int memberTypeId, final Rank rank, final HDF5DataTypeVariant typeVariant) { return new HDF5MemberByteifyer(null, memberName, len, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 1; } @Override protected int getMemberStorageTypeId() { return memberTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { switch (rank) { case SCALAR: return HDFNativeData.byteToByte((((Number) getMap(obj, memberName)) .byteValue())); case ARRAY1D: return (byte[]) getMap(obj, memberName); case ARRAY2D: { final byte[][] array = (byte[][]) getMap(obj, memberName); MatrixUtils.checkMatrixDimensions(memberName, dimensions, array); return MatrixUtils.flatten(array); } case ARRAYMD: { final MDByteArray array = (MDByteArray) getMap(obj, memberName); MatrixUtils.checkMDArrayDimensions(memberName, dimensions, array); return array.getAsFlatArray(); } default: throw new Error("Unknown rank."); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { switch (rank) { case SCALAR: putMap(obj, memberName, byteArr[arrayOffset + offsetInMemory]); break; case ARRAY1D: { final byte[] array = new byte[len]; System.arraycopy(byteArr, arrayOffset + offsetInMemory, array, 0, array.length); putMap(obj, memberName, array); break; } case ARRAY2D: { final byte[] array = new byte[len]; System.arraycopy(byteArr, arrayOffset + offsetInMemory, array, 0, array.length); putMap(obj, memberName, MatrixUtils.shapen(array, dimensions)); break; } case ARRAYMD: { final byte[] array = new byte[len]; System.arraycopy(byteArr, arrayOffset + offsetInMemory, array, 0, array.length); putMap(obj, memberName, new MDByteArray(array, dimensions)); break; } default: throw new Error("Unknown rank."); } } }; } private HDF5MemberByteifyer createByteifyerForList(final String memberName, final int index, final int offset, int memOffset, final int[] dimensions, final int len, final int memberTypeId, final Rank rank, final HDF5DataTypeVariant typeVariant) { return new HDF5MemberByteifyer(null, memberName, len, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 1; } @Override protected int getMemberStorageTypeId() { return memberTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { switch (rank) { case SCALAR: return HDFNativeData.byteToByte((((Number) getList(obj, index)) .byteValue())); case ARRAY1D: return (byte[]) getList(obj, index); case ARRAY2D: { final byte[][] array = (byte[][]) getList(obj, index); MatrixUtils.checkMatrixDimensions(memberName, dimensions, array); return MatrixUtils.flatten(array); } case ARRAYMD: { final MDByteArray array = (MDByteArray) getList(obj, index); MatrixUtils.checkMDArrayDimensions(memberName, dimensions, array); return array.getAsFlatArray(); } default: throw new Error("Unknown rank."); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { switch (rank) { case SCALAR: setList(obj, index, byteArr[arrayOffset + offsetInMemory]); break; case ARRAY1D: { final byte[] array = new byte[len]; System.arraycopy(byteArr, arrayOffset + offsetInMemory, array, 0, array.length); setList(obj, index, array); break; } case ARRAY2D: { final byte[] array = new byte[len]; System.arraycopy(byteArr, arrayOffset + offsetInMemory, array, 0, array.length); setList(obj, index, MatrixUtils.shapen(array, dimensions)); break; } case ARRAYMD: { final byte[] array = new byte[len]; System.arraycopy(byteArr, arrayOffset + offsetInMemory, array, 0, array.length); setList(obj, index, new MDByteArray(array, dimensions)); break; } default: throw new Error("Unknown rank."); } } }; } private HDF5MemberByteifyer createByteifyerForArray(final String memberName, final int index, final int offset, int memOffset, final int[] dimensions, final int len, final int memberTypeId, final Rank rank, final HDF5DataTypeVariant typeVariant) { return new HDF5MemberByteifyer(null, memberName, len, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 1; } @Override protected int getMemberStorageTypeId() { return memberTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { switch (rank) { case SCALAR: return HDFNativeData.byteToByte((((Number) getArray(obj, index)) .byteValue())); case ARRAY1D: return (byte[]) getArray(obj, index); case ARRAY2D: { final byte[][] array = (byte[][]) getArray(obj, index); MatrixUtils.checkMatrixDimensions(memberName, dimensions, array); return MatrixUtils.flatten(array); } case ARRAYMD: { final MDByteArray array = (MDByteArray) getArray(obj, index); MatrixUtils.checkMDArrayDimensions(memberName, dimensions, array); return array.getAsFlatArray(); } default: throw new Error("Unknown rank."); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { switch (rank) { case SCALAR: setArray(obj, index, byteArr[arrayOffset + offsetInMemory]); break; case ARRAY1D: { final byte[] array = new byte[len]; System.arraycopy(byteArr, arrayOffset + offsetInMemory, array, 0, array.length); setArray(obj, index, array); break; } case ARRAY2D: { final byte[] array = new byte[len]; System.arraycopy(byteArr, arrayOffset + offsetInMemory, array, 0, array.length); setArray(obj, index, MatrixUtils.shapen(array, dimensions)); break; } case ARRAYMD: { final byte[] array = new byte[len]; System.arraycopy(byteArr, arrayOffset + offsetInMemory, array, 0, array.length); setArray(obj, index, new MDByteArray(array, dimensions)); break; } default: throw new Error("Unknown rank."); } } }; } } HDF5CompoundMemberByteifyerDateFactory.java000066400000000000000000000255401256564762100335100ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.base.convert.NativeData.LONG_SIZE; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getArray; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getList; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getMap; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.putMap; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.setArray; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.setList; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_I64LE; import java.lang.reflect.Field; import java.util.Date; import ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.AccessType; import ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.IHDF5CompoundMemberBytifyerFactory; import ch.systemsx.cisd.hdf5.HDF5ValueObjectByteifyer.IFileAccessProvider; import ch.systemsx.cisd.hdf5.hdf5lib.HDFNativeData; /** * A {@link HDF5CompoundByteifyerFactory.IHDF5CompoundMemberBytifyerFactory} for Date. * * @author Bernd Rinn */ class HDF5CompoundMemberByteifyerDateFactory implements IHDF5CompoundMemberBytifyerFactory { @Override public boolean canHandle(Class clazz, HDF5CompoundMemberInformation memberInfoOrNull) { if (memberInfoOrNull != null) { return (clazz == Date.class || Long.class.isAssignableFrom(clazz)) && memberInfoOrNull.getType().isTimeStamp(); } else { return (clazz == Date.class); } } @Override public Class tryGetOverrideJavaType(HDF5DataClass dataClass, int rank, int elementSize, HDF5DataTypeVariant typeVariantOrNull) { if (dataClass == HDF5DataClass.INTEGER && rank == 0 && elementSize == 8 && typeVariantOrNull == HDF5DataTypeVariant.TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH) { return java.util.Date.class; } else { return null; } } @Override public HDF5MemberByteifyer createBytifyer(AccessType accessType, Field fieldOrNull, HDF5CompoundMemberMapping member, HDF5CompoundMemberInformation compoundMemberInfoOrNull, HDF5EnumerationType enumTypeOrNull, Class memberClazz, int index, int offset, int memOffset, IFileAccessProvider fileInfoProvider) { final String memberName = member.getMemberName(); final HDF5DataTypeVariant typeVariant = HDF5DataTypeVariant.isTypeVariant(member.tryGetTypeVariant()) ? member .tryGetTypeVariant() : HDF5DataTypeVariant.TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH; switch (accessType) { case FIELD: return createByteifyerForField(fieldOrNull, memberName, offset, memOffset, typeVariant); case MAP: return createByteifyerForMap(memberName, offset, memOffset, typeVariant); case LIST: return createByteifyerForList(memberName, index, offset, memOffset, typeVariant); case ARRAY: return createByteifyerForArray(memberName, index, offset, memOffset, typeVariant); default: throw new Error("Unknown access type"); } } private HDF5MemberByteifyer createByteifyerForField(final Field field, final String memberName, final int offset, int memOffset, final HDF5DataTypeVariant typeVariant) { ReflectionUtils.ensureAccessible(field); return new HDF5MemberByteifyer(field, memberName, LONG_SIZE, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 8; } @Override protected int getMemberStorageTypeId() { return H5T_STD_I64LE; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { return HDFNativeData.longToByte(((java.util.Date) field.get(obj)).getTime()); } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { field.set( obj, new java.util.Date(HDFNativeData.byteToLong(byteArr, arrayOffset + offsetInMemory))); } }; } private HDF5MemberByteifyer createByteifyerForMap(final String memberName, final int offset, int memOffset, final HDF5DataTypeVariant typeVariant) { return new HDF5MemberByteifyer(null, memberName, LONG_SIZE, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 8; } @Override protected int getMemberStorageTypeId() { return H5T_STD_I64LE; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { final Object dateObj = getMap(obj, memberName); if (dateObj instanceof java.util.Date) { return HDFNativeData.longToByte(((java.util.Date) dateObj).getTime()); } else { return HDFNativeData.longToByte(((Long) dateObj)); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { putMap(obj, memberName, new java.util.Date(HDFNativeData.byteToLong(byteArr, arrayOffset + offsetInMemory))); } }; } private HDF5MemberByteifyer createByteifyerForList(final String memberName, final int index, final int offset, int memOffset, final HDF5DataTypeVariant typeVariant) { return new HDF5MemberByteifyer(null, memberName, LONG_SIZE, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 8; } @Override protected int getMemberStorageTypeId() { return H5T_STD_I64LE; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { final Object dateObj = getList(obj, index); if (dateObj instanceof java.util.Date) { return HDFNativeData.longToByte(((java.util.Date) dateObj).getTime()); } else { return HDFNativeData.longToByte(((Long) dateObj)); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { setList(obj, index, new java.util.Date(HDFNativeData.byteToLong(byteArr, arrayOffset + offsetInMemory))); } }; } private HDF5MemberByteifyer createByteifyerForArray(final String memberName, final int index, final int offset, int memOffset, final HDF5DataTypeVariant typeVariant) { return new HDF5MemberByteifyer(null, memberName, LONG_SIZE, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 8; } @Override protected int getMemberStorageTypeId() { return H5T_STD_I64LE; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { final Object dateObj = getArray(obj, index); if (dateObj instanceof java.util.Date) { return HDFNativeData.longToByte(((java.util.Date) dateObj).getTime()); } else { return HDFNativeData.longToByte(((Long) dateObj)); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { setArray( obj, index, new java.util.Date(HDFNativeData.byteToLong(byteArr, arrayOffset + offsetInMemory))); } }; } } HDF5CompoundMemberByteifyerDoubleFactory.java000066400000000000000000000525521256564762100340500ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.base.convert.NativeData.DOUBLE_SIZE; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getArray; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getList; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getMap; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.putMap; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.setArray; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.setList; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_IEEE_F64LE; import java.lang.reflect.Field; import java.util.IdentityHashMap; import java.util.Map; import ch.systemsx.cisd.base.mdarray.MDDoubleArray; import ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.AccessType; import ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.IHDF5CompoundMemberBytifyerFactory; import ch.systemsx.cisd.hdf5.HDF5ValueObjectByteifyer.IFileAccessProvider; import ch.systemsx.cisd.hdf5.hdf5lib.HDFNativeData; /** * A {@link HDF5CompoundByteifyerFactory.IHDF5CompoundMemberBytifyerFactory} for double * , double[], double[][] and MDDoubleArray. * * @author Bernd Rinn */ class HDF5CompoundMemberByteifyerDoubleFactory implements IHDF5CompoundMemberBytifyerFactory { private static Map, Rank> classToRankMap = new IdentityHashMap, Rank>(); private enum Rank { SCALAR(double.class, 0), ARRAY1D(double[].class, 1), ARRAY2D(double[][].class, 2), ARRAYMD( MDDoubleArray.class, -1); private final Class clazz; private final int rank; Rank(Class clazz, int rank) { this.clazz = clazz; this.rank = rank; } int getRank() { return rank; } boolean isScalar() { return rank == 0; } boolean anyRank() { return rank == -1; } Class getClazz() { return clazz; } } static { for (Rank r : Rank.values()) { classToRankMap.put(r.getClazz(), r); } } @Override public boolean canHandle(Class clazz, HDF5CompoundMemberInformation memberInfoOrNull) { final Rank rankOrNull = classToRankMap.get(clazz); if (memberInfoOrNull != null) { final HDF5DataTypeInformation typeInfo = memberInfoOrNull.getType(); if (rankOrNull == null || typeInfo.getDataClass() != HDF5DataClass.FLOAT || typeInfo.getElementSize() != DOUBLE_SIZE) { return false; } return rankOrNull.anyRank() || (rankOrNull.getRank() == typeInfo.getDimensions().length) || (rankOrNull.isScalar() && typeInfo.getDimensions().length == 1 && typeInfo .getDimensions()[0] == 1); } else { return rankOrNull != null; } } @Override public Class tryGetOverrideJavaType(HDF5DataClass dataClass, int rank, int elementSize, HDF5DataTypeVariant typeVariantOrNull) { return null; } @Override public HDF5MemberByteifyer createBytifyer(AccessType accessType, Field fieldOrNull, HDF5CompoundMemberMapping member, HDF5CompoundMemberInformation compoundMemberInfoOrNull, HDF5EnumerationType enumTypeOrNull, Class memberClazz, int index, int offset, int memOffset, IFileAccessProvider fileInfoProvider) { final String memberName = member.getMemberName(); final Rank rank = classToRankMap.get(memberClazz); final int len = (compoundMemberInfoOrNull != null) ? compoundMemberInfoOrNull.getType() .getNumberOfElements() : rank.isScalar() ? 1 : member.getMemberTypeLength(); final int[] dimensions = rank.isScalar() ? new int[] { 1 } : member.getMemberTypeDimensions(); final int storageTypeId = member.getStorageDataTypeId(); final int memberTypeId = rank.isScalar() ? H5T_IEEE_F64LE : ((storageTypeId < 0) ? fileInfoProvider .getArrayTypeId(H5T_IEEE_F64LE, dimensions) : storageTypeId); switch (accessType) { case FIELD: return createByteifyerForField(fieldOrNull, memberName, offset, memOffset, dimensions, len, memberTypeId, rank, member.tryGetTypeVariant()); case MAP: return createByteifyerForMap(memberName, offset, memOffset, dimensions, len, memberTypeId, rank, member.tryGetTypeVariant()); case LIST: return createByteifyerForList(memberName, index, offset, memOffset, dimensions, len, memberTypeId, rank, member.tryGetTypeVariant()); case ARRAY: return createByteifyerForArray(memberName, index, offset, memOffset, dimensions, len, memberTypeId, rank, member.tryGetTypeVariant()); default: throw new Error("Unknown access type"); } } private HDF5MemberByteifyer createByteifyerForField(final Field field, final String memberName, final int offset, int memOffset, final int[] dimensions, final int len, final int memberTypeId, final Rank rank, final HDF5DataTypeVariant typeVariant) { ReflectionUtils.ensureAccessible(field); return new HDF5MemberByteifyer(field, memberName, DOUBLE_SIZE * len, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 8; } @Override protected int getMemberStorageTypeId() { return memberTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { switch (rank) { case SCALAR: return HDFNativeData.doubleToByte(field.getDouble(obj)); case ARRAY1D: return HDFNativeData.doubleToByte((double[]) field.get(obj)); case ARRAY2D: { final double[][] array = (double[][]) field.get(obj); MatrixUtils.checkMatrixDimensions(memberName, dimensions, array); return HDFNativeData.doubleToByte(MatrixUtils.flatten(array)); } case ARRAYMD: { final MDDoubleArray array = (MDDoubleArray) field.get(obj); MatrixUtils.checkMDArrayDimensions(memberName, dimensions, array); return HDFNativeData.doubleToByte(array.getAsFlatArray()); } default: throw new Error("Unknown rank."); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { switch (rank) { case SCALAR: field.setDouble(obj, HDFNativeData.byteToDouble(byteArr, arrayOffset + offsetInMemory)); break; case ARRAY1D: field.set(obj, HDFNativeData.byteToDouble(byteArr, arrayOffset + offsetInMemory, len)); break; case ARRAY2D: { final double[] array = HDFNativeData.byteToDouble(byteArr, arrayOffset + offsetInMemory, len); field.set(obj, MatrixUtils.shapen(array, dimensions)); break; } case ARRAYMD: { final double[] array = HDFNativeData.byteToDouble(byteArr, arrayOffset + offsetInMemory, len); field.set(obj, new MDDoubleArray(array, dimensions)); break; } default: throw new Error("Unknown rank."); } } }; } private HDF5MemberByteifyer createByteifyerForMap(final String memberName, final int offset, int memOffset, final int[] dimensions, final int len, final int memberTypeId, final Rank rank, final HDF5DataTypeVariant typeVariant) { return new HDF5MemberByteifyer(null, memberName, DOUBLE_SIZE * len, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 8; } @Override protected int getMemberStorageTypeId() { return memberTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { switch (rank) { case SCALAR: return HDFNativeData.doubleToByte(((Number) getMap(obj, memberName)) .doubleValue()); case ARRAY1D: return HDFNativeData.doubleToByte((double[]) getMap(obj, memberName)); case ARRAY2D: { final double[][] array = (double[][]) getMap(obj, memberName); MatrixUtils.checkMatrixDimensions(memberName, dimensions, array); return HDFNativeData.doubleToByte(MatrixUtils.flatten(array)); } case ARRAYMD: { final MDDoubleArray array = (MDDoubleArray) getMap(obj, memberName); MatrixUtils.checkMDArrayDimensions(memberName, dimensions, array); return HDFNativeData.doubleToByte(array.getAsFlatArray()); } default: throw new Error("Unknown rank."); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { switch (rank) { case SCALAR: putMap(obj, memberName, HDFNativeData.byteToDouble(byteArr, arrayOffset + offsetInMemory)); break; case ARRAY1D: putMap(obj, memberName, HDFNativeData.byteToDouble(byteArr, arrayOffset + offsetInMemory, len)); break; case ARRAY2D: { final double[] array = HDFNativeData.byteToDouble(byteArr, arrayOffset + offsetInMemory, len); putMap(obj, memberName, MatrixUtils.shapen(array, dimensions)); break; } case ARRAYMD: { final double[] array = HDFNativeData.byteToDouble(byteArr, arrayOffset + offsetInMemory, len); putMap(obj, memberName, new MDDoubleArray(array, dimensions)); break; } default: throw new Error("Unknown rank."); } } }; } private HDF5MemberByteifyer createByteifyerForList(final String memberName, final int index, final int offset, int memOffset, final int[] dimensions, final int len, final int memberTypeId, final Rank rank, final HDF5DataTypeVariant typeVariant) { return new HDF5MemberByteifyer(null, memberName, DOUBLE_SIZE * len, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 8; } @Override protected int getMemberStorageTypeId() { return memberTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { switch (rank) { case SCALAR: return HDFNativeData.doubleToByte(((Number) getList(obj, index)) .doubleValue()); case ARRAY1D: return HDFNativeData.doubleToByte((double[]) getList(obj, index)); case ARRAY2D: { final double[][] array = (double[][]) getList(obj, index); MatrixUtils.checkMatrixDimensions(memberName, dimensions, array); return HDFNativeData.doubleToByte(MatrixUtils.flatten(array)); } case ARRAYMD: { final MDDoubleArray array = (MDDoubleArray) getList(obj, index); MatrixUtils.checkMDArrayDimensions(memberName, dimensions, array); return HDFNativeData.doubleToByte(array.getAsFlatArray()); } default: throw new Error("Unknown rank."); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { switch (rank) { case SCALAR: setList(obj, index, HDFNativeData.byteToDouble(byteArr, arrayOffset + offsetInMemory)); break; case ARRAY1D: putMap(obj, memberName, HDFNativeData.byteToDouble(byteArr, arrayOffset + offsetInMemory, len)); break; case ARRAY2D: { final double[] array = HDFNativeData.byteToDouble(byteArr, arrayOffset + offsetInMemory, len); setList(obj, index, MatrixUtils.shapen(array, dimensions)); break; } case ARRAYMD: { final double[] array = HDFNativeData.byteToDouble(byteArr, arrayOffset + offsetInMemory, len); setList(obj, index, new MDDoubleArray(array, dimensions)); break; } default: throw new Error("Unknown rank."); } } }; } private HDF5MemberByteifyer createByteifyerForArray(final String memberName, final int index, final int offset, int memOffset, final int[] dimensions, final int len, final int memberTypeId, final Rank rank, final HDF5DataTypeVariant typeVariant) { return new HDF5MemberByteifyer(null, memberName, DOUBLE_SIZE * len, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 8; } @Override protected int getMemberStorageTypeId() { return memberTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { switch (rank) { case SCALAR: return HDFNativeData.doubleToByte(((Number) getArray(obj, index)) .doubleValue()); case ARRAY1D: return HDFNativeData.doubleToByte((double[]) getArray(obj, index)); case ARRAY2D: { final double[][] array = (double[][]) getArray(obj, index); MatrixUtils.checkMatrixDimensions(memberName, dimensions, array); return HDFNativeData.doubleToByte(MatrixUtils.flatten(array)); } case ARRAYMD: { final MDDoubleArray array = (MDDoubleArray) getArray(obj, index); MatrixUtils.checkMDArrayDimensions(memberName, dimensions, array); return HDFNativeData.doubleToByte(array.getAsFlatArray()); } default: throw new Error("Unknown rank."); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { switch (rank) { case SCALAR: setArray(obj, index, HDFNativeData.byteToDouble(byteArr, arrayOffset + offsetInMemory)); break; case ARRAY1D: setArray(obj, index, HDFNativeData.byteToDouble(byteArr, arrayOffset + offsetInMemory, len)); break; case ARRAY2D: { final double[] array = HDFNativeData.byteToDouble(byteArr, arrayOffset + offsetInMemory, len); setArray(obj, index, MatrixUtils.shapen(array, dimensions)); break; } case ARRAYMD: { final double[] array = HDFNativeData.byteToDouble(byteArr, arrayOffset + offsetInMemory, len); setArray(obj, index, new MDDoubleArray(array, dimensions)); break; } default: throw new Error("Unknown rank."); } } }; } } HDF5CompoundMemberByteifyerEnumArrayFactory.java000066400000000000000000000452451256564762100345420ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getArray; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getList; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getMap; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.putMap; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.setArray; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.setList; import static ch.systemsx.cisd.hdf5.HDF5CompoundMappingHints.getEnumReturnType; import static ch.systemsx.cisd.hdf5.HDF5CompoundMemberByteifyerEnumFactory.getEnumReturnTypeFromField; import java.lang.reflect.Array; import java.lang.reflect.Field; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.AccessType; import ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.IHDF5CompoundMemberBytifyerFactory; import ch.systemsx.cisd.hdf5.HDF5CompoundMappingHints.EnumReturnType; import ch.systemsx.cisd.hdf5.HDF5ValueObjectByteifyer.IFileAccessProvider; /** * A {@link HDF5CompoundByteifyerFactory.IHDF5CompoundMemberBytifyerFactory} for * HDF5EnumerationValueArray. * * @author Bernd Rinn */ class HDF5CompoundMemberByteifyerEnumArrayFactory implements IHDF5CompoundMemberBytifyerFactory { @Override public boolean canHandle(Class clazz, HDF5CompoundMemberInformation memberInfoOrNull) { if (memberInfoOrNull != null) { return ((clazz == HDF5EnumerationValueArray.class) || (clazz.isArray() && clazz.getComponentType().isEnum()) || clazz == String[].class || (clazz.isArray() && (Number.class .isAssignableFrom(clazz.getComponentType()) || (clazz.getComponentType() .isPrimitive() && clazz.getComponentType() != boolean.class)))) && memberInfoOrNull.getType().getDataClass() == HDF5DataClass.ENUM; } else { return (clazz == HDF5EnumerationValueArray.class) || (clazz.isArray() && clazz.getComponentType().isEnum()); } } @Override public Class tryGetOverrideJavaType(HDF5DataClass dataClass, int rank, int elementSize, HDF5DataTypeVariant typeVariantOrNull) { return null; } @Override public HDF5MemberByteifyer createBytifyer(final AccessType accessType, final Field fieldOrNull, final HDF5CompoundMemberMapping member, HDF5CompoundMemberInformation compoundMemberInfoOrNull, HDF5EnumerationType compoundMemberInfoEnumTypeOrNull, Class memberClazz, final int index, final int offset, int memOffset, final IFileAccessProvider fileInfoProvider) { final String memberName = member.getMemberName(); HDF5EnumerationType enumTypeOrNull = member.tryGetEnumerationType() != null ? member.tryGetEnumerationType() : compoundMemberInfoEnumTypeOrNull; if (enumTypeOrNull == null) { if (fieldOrNull.getType().isArray() && fieldOrNull.getType().getComponentType().isEnum()) { @SuppressWarnings("unchecked") Class> enumClass = (Class>) fieldOrNull.getType().getComponentType(); enumTypeOrNull = fileInfoProvider.getEnumType(ReflectionUtils.getEnumOptions(enumClass)); } else { throw new HDF5JavaException("Enumeration type not known for member byteifyer."); } } final int memberTypeLength = (compoundMemberInfoOrNull != null) ? compoundMemberInfoOrNull.getType() .getNumberOfElements() : member.getMemberTypeLength(); final int storageTypeId = member.getStorageDataTypeId(); final int memberStorageTypeId = (storageTypeId < 0) ? fileInfoProvider.getArrayTypeId( enumTypeOrNull.getStorageTypeId(), memberTypeLength) : storageTypeId; switch (accessType) { case FIELD: { if (fieldOrNull == null) { throw new HDF5JavaException("No field for member " + memberName + "."); } return createByteifyerForField(fieldOrNull, memberName, offset, memOffset, enumTypeOrNull, memberTypeLength, memberStorageTypeId, member.tryGetTypeVariant(), getEnumReturnTypeFromField(fieldOrNull.getType())); } case MAP: return createByteifyerForMap(memberName, offset, memOffset, enumTypeOrNull, memberTypeLength, memberStorageTypeId, member.tryGetTypeVariant(), getEnumReturnType(member)); case LIST: return createByteifyerForList(memberName, index, offset, memOffset, enumTypeOrNull, memberTypeLength, memberStorageTypeId, member.tryGetTypeVariant(), getEnumReturnType(member)); case ARRAY: return createByteifyerForArray(memberName, index, offset, memOffset, enumTypeOrNull, memberTypeLength, memberStorageTypeId, member.tryGetTypeVariant(), getEnumReturnType(member)); } throw new Error("Unknown access type"); } private HDF5MemberByteifyer createByteifyerForField(final Field field, final String memberName, final int offset, int memOffset, final HDF5EnumerationType enumType, final int memberTypeLength, final int memberStorageTypeId, final HDF5DataTypeVariant typeVariant, final EnumReturnType enumReturnType) { ReflectionUtils.ensureAccessible(field); return new HDF5MemberByteifyer(field, memberName, enumType.getStorageForm() .getStorageSize() * memberTypeLength, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return enumType.getStorageForm().getStorageSize(); } @Override protected int getMemberStorageTypeId() { return memberStorageTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { return getEnumArray(obj).toStorageForm(); } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { final Object enumValueArray = getEnumValue(enumType, byteArr, arrayOffset + offsetInMemory, memberTypeLength, enumReturnType, field); field.set(obj, enumValueArray); } private HDF5EnumerationValueArray getEnumArray(Object obj) throws IllegalAccessException, IllegalArgumentException { assert obj != null; final Object enumArrayObj = field.get(obj); return getEnumArrayFromField(enumArrayObj, enumType, enumReturnType); } }; } private HDF5MemberByteifyer createByteifyerForMap(final String memberName, final int offset, int memOffset, final HDF5EnumerationType enumType, final int memberTypeLength, final int memberStorageTypeId, final HDF5DataTypeVariant typeVariant, final HDF5CompoundMappingHints.EnumReturnType enumReturnType) { return new HDF5MemberByteifyer(null, memberName, enumType.getStorageForm().getStorageSize() * memberTypeLength, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return enumType.getStorageForm().getStorageSize(); } @Override protected int getMemberStorageTypeId() { return memberStorageTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { return getEnumArray(obj).toStorageForm(); } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { final Object enumValueArray = getEnumValue(enumType, byteArr, arrayOffset + offsetInMemory, memberTypeLength, enumReturnType, null); putMap(obj, memberName, enumValueArray); } private HDF5EnumerationValueArray getEnumArray(Object obj) throws IllegalAccessException, IllegalArgumentException { assert obj != null; final Object enumArrayObj = getMap(obj, memberName); return guessEnumArray(enumArrayObj, enumType); } }; } private HDF5MemberByteifyer createByteifyerForList(final String memberName, final int index, final int offset, int memOffset, final HDF5EnumerationType enumType, final int memberTypeLength, final int memberStorageTypeId, final HDF5DataTypeVariant typeVariant, final HDF5CompoundMappingHints.EnumReturnType enumReturnType) { return new HDF5MemberByteifyer(null, memberName, enumType.getStorageForm().getStorageSize() * memberTypeLength, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return enumType.getStorageForm().getStorageSize(); } @Override protected int getMemberStorageTypeId() { return memberStorageTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { return getEnumArray(obj).toStorageForm(); } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { final Object enumValueArray = getEnumValue(enumType, byteArr, arrayOffset + offsetInMemory, memberTypeLength, enumReturnType, null); setList(obj, index, enumValueArray); } private HDF5EnumerationValueArray getEnumArray(Object obj) throws IllegalAccessException, IllegalArgumentException { assert obj != null; final Object enumArrayObj = getList(obj, index); return guessEnumArray(enumArrayObj, enumType); } }; } private HDF5MemberByteifyer createByteifyerForArray(final String memberName, final int index, final int offset, int memOffset, final HDF5EnumerationType enumType, final int memberTypeLength, final int memberStorageTypeId, final HDF5DataTypeVariant typeVariant, final HDF5CompoundMappingHints.EnumReturnType enumReturnType) { return new HDF5MemberByteifyer(null, memberName, enumType.getStorageForm().getStorageSize() * memberTypeLength, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return enumType.getStorageForm().getStorageSize(); } @Override protected int getMemberStorageTypeId() { return memberStorageTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { return getEnumArray(obj).toStorageForm(); } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { final Object enumValueArray = getEnumValue(enumType, byteArr, arrayOffset + offsetInMemory, memberTypeLength, enumReturnType, null); setArray(obj, index, enumValueArray); } private HDF5EnumerationValueArray getEnumArray(Object obj) throws IllegalAccessException, IllegalArgumentException { assert obj != null; final Object enumArrayObj = getArray(obj, index); return guessEnumArray(enumArrayObj, enumType); } }; } static HDF5EnumerationValueArray guessEnumArray(final Object enumArrayObj, final HDF5EnumerationType enumType) { if (enumArrayObj instanceof HDF5EnumerationValueArray) { return (HDF5EnumerationValueArray) enumArrayObj; } else if (enumArrayObj instanceof int[]) { return new HDF5EnumerationValueArray(enumType, (int[]) enumArrayObj); } else if (enumArrayObj instanceof String[]) { return new HDF5EnumerationValueArray(enumType, (String[]) enumArrayObj); } else if (enumArrayObj.getClass().isArray() && enumArrayObj.getClass().getComponentType().isEnum()) { return new HDF5EnumerationValueArray(enumType, (Enum[]) enumArrayObj); } else { final String[] options = new String[Array.getLength(enumArrayObj)]; for (int i = 0; i < options.length; ++i) { options[i] = Array.get(enumArrayObj, i).toString(); } return new HDF5EnumerationValueArray(enumType, options); } } static HDF5EnumerationValueArray getEnumArrayFromField(final Object enumArrayObj, final HDF5EnumerationType enumType, final HDF5CompoundMappingHints.EnumReturnType enumReturnType) { switch (enumReturnType) { case HDF5ENUMERATIONVALUE: return (HDF5EnumerationValueArray) enumArrayObj; case STRING: return new HDF5EnumerationValueArray(enumType, (String[]) enumArrayObj); case ORDINAL: return new HDF5EnumerationValueArray(enumType, enumArrayObj); case JAVAENUMERATION: { return new HDF5EnumerationValueArray(enumType, (Enum[]) enumArrayObj); } } throw new Error("Unknown EnumReturnType " + enumReturnType); } static Object getEnumValue(final HDF5EnumerationType enumType, byte[] byteArr, int arrayOffset, final int length, final HDF5CompoundMappingHints.EnumReturnType enumReturnType, Field fieldOrNull) { switch (enumReturnType) { case HDF5ENUMERATIONVALUE: return HDF5EnumerationValueArray.fromStorageForm(enumType, byteArr, arrayOffset, length); case STRING: return HDF5EnumerationValueArray.fromStorageFormToStringArray(enumType, byteArr, arrayOffset, length); case ORDINAL: return HDF5EnumerationValueArray.fromStorageFormToIntArray(enumType, byteArr, arrayOffset, length); case JAVAENUMERATION: { if (fieldOrNull == null) { throw new HDF5JavaException( "JAVAENUMERATIONTYPE only available with access type FIELD"); } final String[] values = HDF5EnumerationValueArray.fromStorageFormToStringArray(enumType, byteArr, arrayOffset, length); @SuppressWarnings("unchecked") final Class> enumClass = (Class>) fieldOrNull.getType().getComponentType(); final Enum[] result = (Enum[]) Array.newInstance(fieldOrNull.getType().getComponentType(), values.length); for (int i = 0; i < result.length; ++i) { result[i] = getValue(enumClass, values[i]); } return result; } } throw new Error("Unknown EnumReturnType " + enumReturnType); } /** * Returns the value as Enum of type enumClass. */ @SuppressWarnings( { "unchecked", "rawtypes" }) private static Enum getValue(Class> enumClass, String value) { return Enum.valueOf((Class) enumClass, value); } } HDF5CompoundMemberByteifyerEnumFactory.java000066400000000000000000000412461256564762100335400ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getArray; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getList; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getMap; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.putMap; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.setArray; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.setList; import static ch.systemsx.cisd.hdf5.HDF5CompoundMappingHints.getEnumReturnType; import java.lang.reflect.Field; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.AccessType; import ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.IHDF5CompoundMemberBytifyerFactory; import ch.systemsx.cisd.hdf5.HDF5CompoundMappingHints.EnumReturnType; import ch.systemsx.cisd.hdf5.HDF5ValueObjectByteifyer.IFileAccessProvider; /** * A {@link HDF5CompoundByteifyerFactory.IHDF5CompoundMemberBytifyerFactory} for * HDF5EnumerationValue. * * @author Bernd Rinn */ class HDF5CompoundMemberByteifyerEnumFactory implements IHDF5CompoundMemberBytifyerFactory { @Override public boolean canHandle(Class clazz, HDF5CompoundMemberInformation memberInfoOrNull) { if (memberInfoOrNull != null) { return ((clazz == HDF5EnumerationValue.class) || clazz.isEnum() || clazz == String.class || Number.class.isAssignableFrom(clazz) || (clazz .isPrimitive() && clazz != boolean.class)) && memberInfoOrNull.getType().getDataClass() == HDF5DataClass.ENUM; } else { return (clazz == HDF5EnumerationValue.class) || clazz.isEnum(); } } @Override public Class tryGetOverrideJavaType(HDF5DataClass dataClass, int rank, int elementSize, HDF5DataTypeVariant typeVariantOrNull) { return null; } @Override public HDF5MemberByteifyer createBytifyer(final AccessType accessType, final Field fieldOrNull, final HDF5CompoundMemberMapping member, final HDF5CompoundMemberInformation compoundMemberInfoOrNull, HDF5EnumerationType compoundMemberInfoEnumTypeOrNull, final Class memberClazz, final int index, final int offset, int memOffset, final IFileAccessProvider fileInfoProvider) { final String memberName = member.getMemberName(); final HDF5EnumerationType enumTypeOrNull = member.tryGetEnumerationType() != null ? member.tryGetEnumerationType() : compoundMemberInfoEnumTypeOrNull; if (enumTypeOrNull == null) { throw new HDF5JavaException("Enumeration type for member '" + memberName + "' not known for member byteifyer."); } switch (accessType) { case FIELD: return createByteifyerForField(fieldOrNull, memberName, offset, memOffset, enumTypeOrNull, member.tryGetTypeVariant(), getEnumReturnTypeFromField(fieldOrNull.getType())); case MAP: return createByteifyerForMap(memberName, offset, memOffset, enumTypeOrNull, member.tryGetTypeVariant(), getEnumReturnType(member)); case LIST: return createByteifyerForList(memberName, index, offset, memOffset, enumTypeOrNull, member.tryGetTypeVariant(), getEnumReturnType(member)); case ARRAY: return createByteifyerForArray(memberName, index, offset, memOffset, enumTypeOrNull, member.tryGetTypeVariant(), getEnumReturnType(member)); default: throw new Error("Unknown access type"); } } /** * Returns the desired enumeration return type. */ static EnumReturnType getEnumReturnTypeFromField(Class type) { final Class clazz = type.isArray() ? type.getComponentType() : type; if (Number.class.isAssignableFrom(clazz) || (clazz.isPrimitive() && clazz != boolean.class)) { return EnumReturnType.ORDINAL; } else if (String.class == clazz) { return EnumReturnType.STRING; } else if (clazz.isEnum()) { return EnumReturnType.JAVAENUMERATION; } { return EnumReturnType.HDF5ENUMERATIONVALUE; } } private HDF5MemberByteifyer createByteifyerForField(final Field field, final String memberName, final int offset, int memOffset, final HDF5EnumerationType enumType, final HDF5DataTypeVariant typeVariant, final EnumReturnType enumReturnType) { ReflectionUtils.ensureAccessible(field); return new HDF5MemberByteifyer(field, memberName, enumType.getStorageForm() .getStorageSize(), offset, memOffset, false, typeVariant) { @Override int getElementSize() { return enumType.getStorageForm().getStorageSize(); } @Override protected int getMemberStorageTypeId() { return enumType.getStorageTypeId(); } @Override protected int getMemberNativeTypeId() { return enumType.getNativeTypeId(); } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { return getEnum(obj).toStorageForm(); } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { final Object enumValue = getEnumValue(enumType, byteArr, arrayOffset + offsetInMemory, enumReturnType, field); field.set(obj, enumValue); } private HDF5EnumerationValue getEnum(Object obj) throws IllegalAccessException, IllegalArgumentException { assert obj != null; final Object enumObj = field.get(obj); if (enumObj instanceof HDF5EnumerationValue) { return (HDF5EnumerationValue) enumObj; } else if (enumObj instanceof Number) { return new HDF5EnumerationValue(enumType, ((Number) enumObj).intValue()); } else { return new HDF5EnumerationValue(enumType, enumObj.toString()); } } @Override HDF5EnumerationType tryGetEnumType() { return enumType; } }; } private HDF5MemberByteifyer createByteifyerForMap(final String memberName, final int offset, int memOffset, final HDF5EnumerationType enumType, final HDF5DataTypeVariant typeVariant, final HDF5CompoundMappingHints.EnumReturnType enumReturnType) { return new HDF5MemberByteifyer(null, memberName, enumType.getStorageForm().getStorageSize(), offset, memOffset, false, typeVariant) { @Override int getElementSize() { return enumType.getStorageForm().getStorageSize(); } @Override protected int getMemberStorageTypeId() { return enumType.getStorageTypeId(); } @Override protected int getMemberNativeTypeId() { return enumType.getNativeTypeId(); } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { return getEnum(obj).toStorageForm(); } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { final Object enumValue = getEnumValue(enumType, byteArr, arrayOffset + offsetInMemory, enumReturnType, null); putMap(obj, memberName, enumValue); } private HDF5EnumerationValue getEnum(Object obj) throws IllegalAccessException, IllegalArgumentException { assert obj != null; final Object enumObj = getMap(obj, memberName); if (enumObj instanceof HDF5EnumerationValue) { return (HDF5EnumerationValue) enumObj; } else if (enumObj instanceof Number) { return new HDF5EnumerationValue(enumType, ((Number) enumObj).intValue()); } else { return new HDF5EnumerationValue(enumType, enumObj.toString()); } } @Override HDF5EnumerationType tryGetEnumType() { return enumType; } }; } private HDF5MemberByteifyer createByteifyerForList(final String memberName, final int index, final int offset, int memOffset, final HDF5EnumerationType enumType, final HDF5DataTypeVariant typeVariant, final HDF5CompoundMappingHints.EnumReturnType enumReturnType) { return new HDF5MemberByteifyer(null, memberName, enumType.getStorageForm().getStorageSize(), offset, memOffset, false, typeVariant) { @Override int getElementSize() { return enumType.getStorageForm().getStorageSize(); } @Override protected int getMemberStorageTypeId() { return enumType.getStorageTypeId(); } @Override protected int getMemberNativeTypeId() { return enumType.getNativeTypeId(); } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { return getEnum(obj).toStorageForm(); } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { final Object enumValue = getEnumValue(enumType, byteArr, arrayOffset + offsetInMemory, enumReturnType, null); setList(obj, index, enumValue); } private HDF5EnumerationValue getEnum(Object obj) throws IllegalAccessException, IllegalArgumentException { assert obj != null; final Object enumObj = getList(obj, index); if (enumObj instanceof HDF5EnumerationValue) { return (HDF5EnumerationValue) enumObj; } else if (enumObj instanceof Number) { return new HDF5EnumerationValue(enumType, ((Number) enumObj).intValue()); } else { return new HDF5EnumerationValue(enumType, enumObj.toString()); } } @Override HDF5EnumerationType tryGetEnumType() { return enumType; } }; } private HDF5MemberByteifyer createByteifyerForArray(final String memberName, final int index, final int offset, int memOffset, final HDF5EnumerationType enumType, final HDF5DataTypeVariant typeVariant, final HDF5CompoundMappingHints.EnumReturnType enumReturnType) { return new HDF5MemberByteifyer(null, memberName, enumType.getStorageForm().getStorageSize(), offset, memOffset, false, typeVariant) { @Override int getElementSize() { return enumType.getStorageForm().getStorageSize(); } @Override protected int getMemberStorageTypeId() { return enumType.getStorageTypeId(); } @Override protected int getMemberNativeTypeId() { return enumType.getNativeTypeId(); } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { return getEnum(obj).toStorageForm(); } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { final Object enumValue = getEnumValue(enumType, byteArr, arrayOffset + offsetInMemory, enumReturnType, null); setArray(obj, index, enumValue); } private HDF5EnumerationValue getEnum(Object obj) throws IllegalAccessException, IllegalArgumentException { assert obj != null; final Object enumObj = getArray(obj, index); if (enumObj instanceof HDF5EnumerationValue) { return (HDF5EnumerationValue) enumObj; } else if (enumObj instanceof Number) { return new HDF5EnumerationValue(enumType, ((Number) enumObj).intValue()); } else { return new HDF5EnumerationValue(enumType, enumObj.toString()); } } @Override HDF5EnumerationType tryGetEnumType() { return enumType; } }; } @SuppressWarnings( { "rawtypes", "unchecked" }) static Object getEnumValue(final HDF5EnumerationType enumType, byte[] byteArr, int arrayOffset, final HDF5CompoundMappingHints.EnumReturnType enumReturnType, Field fieldOrNull) { switch (enumReturnType) { case HDF5ENUMERATIONVALUE: return enumType.createFromStorageForm(byteArr, arrayOffset); case STRING: return enumType.createStringFromStorageForm(byteArr, arrayOffset); case ORDINAL: return enumType.getOrdinalFromStorageForm(byteArr, arrayOffset); case JAVAENUMERATION: { if (fieldOrNull == null) { throw new HDF5JavaException( "JAVAENUMERATIONTYPE only available with access type FIELD"); } final String value = enumType.createStringFromStorageForm(byteArr, arrayOffset); final Class enumClass = (Class) fieldOrNull.getType(); return Enum.valueOf(enumClass, value); } } throw new Error("Unknown EnumReturnType " + enumReturnType); } } HDF5CompoundMemberByteifyerFloatFactory.java000066400000000000000000000524461256564762100337050ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.base.convert.NativeData.FLOAT_SIZE; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getArray; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getList; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getMap; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.putMap; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.setArray; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.setList; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_IEEE_F32LE; import java.lang.reflect.Field; import java.util.IdentityHashMap; import java.util.Map; import ch.systemsx.cisd.base.mdarray.MDFloatArray; import ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.AccessType; import ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.IHDF5CompoundMemberBytifyerFactory; import ch.systemsx.cisd.hdf5.HDF5ValueObjectByteifyer.IFileAccessProvider; import ch.systemsx.cisd.hdf5.hdf5lib.HDFNativeData; /** * A {@link HDF5CompoundByteifyerFactory.IHDF5CompoundMemberBytifyerFactory} for float, * float[], float[][] and MDFloatArray. * * @author Bernd Rinn */ class HDF5CompoundMemberByteifyerFloatFactory implements IHDF5CompoundMemberBytifyerFactory { private static Map, Rank> classToRankMap = new IdentityHashMap, Rank>(); private enum Rank { SCALAR(float.class, 0), ARRAY1D(float[].class, 1), ARRAY2D(float[][].class, 2), ARRAYMD( MDFloatArray.class, -1); private final Class clazz; private final int rank; Rank(Class clazz, int rank) { this.clazz = clazz; this.rank = rank; } int getRank() { return rank; } boolean isScalar() { return rank == 0; } boolean anyRank() { return rank == -1; } Class getClazz() { return clazz; } } static { for (Rank r : Rank.values()) { classToRankMap.put(r.getClazz(), r); } } @Override public boolean canHandle(Class clazz, HDF5CompoundMemberInformation memberInfoOrNull) { final Rank rankOrNull = classToRankMap.get(clazz); if (memberInfoOrNull != null) { final HDF5DataTypeInformation typeInfo = memberInfoOrNull.getType(); if (rankOrNull == null || (typeInfo.getDataClass() != HDF5DataClass.FLOAT && typeInfo.getDataClass() != HDF5DataClass.INTEGER)) { return false; } return rankOrNull.anyRank() || (rankOrNull.getRank() == typeInfo.getDimensions().length) || (rankOrNull.isScalar() && typeInfo.getDimensions().length == 1 && typeInfo .getDimensions()[0] == 1); } else { return rankOrNull != null; } } @Override public Class tryGetOverrideJavaType(HDF5DataClass dataClass, int rank, int elementSize, HDF5DataTypeVariant typeVariantOrNull) { return null; } @Override public HDF5MemberByteifyer createBytifyer(AccessType accessType, Field fieldOrNull, HDF5CompoundMemberMapping member, HDF5CompoundMemberInformation compoundMemberInfoOrNull, HDF5EnumerationType enumTypeOrNull, Class memberClazz, int index, int offset, int memOffset, IFileAccessProvider fileInfoProvider) { final String memberName = member.getMemberName(); final Rank rank = classToRankMap.get(memberClazz); final int len = (compoundMemberInfoOrNull != null) ? compoundMemberInfoOrNull.getType() .getNumberOfElements() : rank.isScalar() ? 1 : member.getMemberTypeLength(); final int[] dimensions = rank.isScalar() ? new int[] { 1 } : member.getMemberTypeDimensions(); final int storageTypeId = member.getStorageDataTypeId(); final int memberTypeId = rank.isScalar() ? H5T_IEEE_F32LE : ((storageTypeId < 0) ? fileInfoProvider .getArrayTypeId(H5T_IEEE_F32LE, dimensions) : storageTypeId); switch (accessType) { case FIELD: return createByteifyerForField(fieldOrNull, memberName, offset, memOffset, dimensions, len, memberTypeId, rank, member.tryGetTypeVariant()); case MAP: return createByteifyerForMap(memberName, offset, memOffset, dimensions, len, memberTypeId, rank, member.tryGetTypeVariant()); case LIST: return createByteifyerForList(memberName, index, offset, memOffset, dimensions, len, memberTypeId, rank, member.tryGetTypeVariant()); case ARRAY: return createByteifyerForArray(memberName, index, offset, memOffset, dimensions, len, memberTypeId, rank, member.tryGetTypeVariant()); default: throw new Error("Unknown access type"); } } private HDF5MemberByteifyer createByteifyerForField(final Field field, final String memberName, final int offset, int memOffset, final int[] dimensions, final int len, final int memberTypeId, final Rank rank, final HDF5DataTypeVariant typeVariant) { ReflectionUtils.ensureAccessible(field); return new HDF5MemberByteifyer(field, memberName, FLOAT_SIZE * len, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 4; } @Override protected int getMemberStorageTypeId() { return memberTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { switch (rank) { case SCALAR: return HDFNativeData.floatToByte(field.getFloat(obj)); case ARRAY1D: return HDFNativeData.floatToByte((float[]) field.get(obj)); case ARRAY2D: { final float[][] array = (float[][]) field.get(obj); MatrixUtils.checkMatrixDimensions(memberName, dimensions, array); return HDFNativeData.floatToByte(MatrixUtils.flatten(array)); } case ARRAYMD: { final MDFloatArray array = (MDFloatArray) field.get(obj); MatrixUtils.checkMDArrayDimensions(memberName, dimensions, array); return HDFNativeData.floatToByte(array.getAsFlatArray()); } default: throw new Error("Unknown rank."); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { switch (rank) { case SCALAR: field.setFloat(obj, HDFNativeData.byteToFloat(byteArr, arrayOffset + offsetInMemory)); break; case ARRAY1D: field.set(obj, HDFNativeData.byteToFloat(byteArr, arrayOffset + offsetInMemory, len)); break; case ARRAY2D: { final float[] array = HDFNativeData .byteToFloat(byteArr, arrayOffset + offsetInMemory, len); field.set(obj, MatrixUtils.shapen(array, dimensions)); break; } case ARRAYMD: { final float[] array = HDFNativeData .byteToFloat(byteArr, arrayOffset + offsetInMemory, len); field.set(obj, new MDFloatArray(array, dimensions)); break; } default: throw new Error("Unknown rank."); } } }; } private HDF5MemberByteifyer createByteifyerForMap(final String memberName, final int offset, int memOffset, final int[] dimensions, final int len, final int memberTypeId, final Rank rank, final HDF5DataTypeVariant typeVariant) { return new HDF5MemberByteifyer(null, memberName, FLOAT_SIZE * len, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 4; } @Override protected int getMemberStorageTypeId() { return memberTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { switch (rank) { case SCALAR: return HDFNativeData.floatToByte(((Number) getMap(obj, memberName)) .floatValue()); case ARRAY1D: return HDFNativeData.floatToByte((float[]) getMap(obj, memberName)); case ARRAY2D: { final float[][] array = (float[][]) getMap(obj, memberName); MatrixUtils.checkMatrixDimensions(memberName, dimensions, array); return HDFNativeData.floatToByte(MatrixUtils.flatten(array)); } case ARRAYMD: { final MDFloatArray array = (MDFloatArray) getMap(obj, memberName); MatrixUtils.checkMDArrayDimensions(memberName, dimensions, array); return HDFNativeData.floatToByte(array.getAsFlatArray()); } default: throw new Error("Unknown rank."); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { switch (rank) { case SCALAR: putMap(obj, memberName, HDFNativeData.byteToFloat(byteArr, arrayOffset + offsetInMemory)); break; case ARRAY1D: putMap(obj, memberName, HDFNativeData.byteToFloat(byteArr, arrayOffset + offsetInMemory, len)); break; case ARRAY2D: { final float[] array = HDFNativeData .byteToFloat(byteArr, arrayOffset + offsetInMemory, len); putMap(obj, memberName, MatrixUtils.shapen(array, dimensions)); break; } case ARRAYMD: { final float[] array = HDFNativeData .byteToFloat(byteArr, arrayOffset + offsetInMemory, len); putMap(obj, memberName, new MDFloatArray(array, dimensions)); break; } default: throw new Error("Unknown rank."); } } }; } private HDF5MemberByteifyer createByteifyerForList(final String memberName, final int index, final int offset, int memOffset, final int[] dimensions, final int len, final int memberTypeId, final Rank rank, final HDF5DataTypeVariant typeVariant) { return new HDF5MemberByteifyer(null, memberName, FLOAT_SIZE * len, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 4; } @Override protected int getMemberStorageTypeId() { return memberTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { switch (rank) { case SCALAR: return HDFNativeData.floatToByte(((Number) getList(obj, index)) .floatValue()); case ARRAY1D: return HDFNativeData.floatToByte((float[]) getList(obj, index)); case ARRAY2D: { final float[][] array = (float[][]) getList(obj, index); MatrixUtils.checkMatrixDimensions(memberName, dimensions, array); return HDFNativeData.floatToByte(MatrixUtils.flatten(array)); } case ARRAYMD: { final MDFloatArray array = (MDFloatArray) getList(obj, index); MatrixUtils.checkMDArrayDimensions(memberName, dimensions, array); return HDFNativeData.floatToByte(array.getAsFlatArray()); } default: throw new Error("Unknown rank."); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { switch (rank) { case SCALAR: setList(obj, index, HDFNativeData.byteToFloat(byteArr, arrayOffset + offsetInMemory)); break; case ARRAY1D: putMap(obj, memberName, HDFNativeData.byteToFloat(byteArr, arrayOffset + offsetInMemory, len)); break; case ARRAY2D: { final float[] array = HDFNativeData .byteToFloat(byteArr, arrayOffset + offsetInMemory, len); setList(obj, index, MatrixUtils.shapen(array, dimensions)); break; } case ARRAYMD: { final float[] array = HDFNativeData .byteToFloat(byteArr, arrayOffset + offsetInMemory, len); setList(obj, index, new MDFloatArray(array, dimensions)); break; } default: throw new Error("Unknown rank."); } } }; } private HDF5MemberByteifyer createByteifyerForArray(final String memberName, final int index, final int offset, int memOffset, final int[] dimensions, final int len, final int memberTypeId, final Rank rank, final HDF5DataTypeVariant typeVariant) { return new HDF5MemberByteifyer(null, memberName, FLOAT_SIZE * len, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 4; } @Override protected int getMemberStorageTypeId() { return memberTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { switch (rank) { case SCALAR: return HDFNativeData.floatToByte(((Number) getArray(obj, index)) .floatValue()); case ARRAY1D: return HDFNativeData.floatToByte((float[]) getArray(obj, index)); case ARRAY2D: { final float[][] array = (float[][]) getArray(obj, index); MatrixUtils.checkMatrixDimensions(memberName, dimensions, array); return HDFNativeData.floatToByte(MatrixUtils.flatten(array)); } case ARRAYMD: { final MDFloatArray array = (MDFloatArray) getArray(obj, index); MatrixUtils.checkMDArrayDimensions(memberName, dimensions, array); return HDFNativeData.floatToByte(array.getAsFlatArray()); } default: throw new Error("Unknown rank."); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { switch (rank) { case SCALAR: setArray(obj, index, HDFNativeData.byteToFloat(byteArr, arrayOffset + offsetInMemory)); break; case ARRAY1D: setArray(obj, index, HDFNativeData.byteToFloat(byteArr, arrayOffset + offsetInMemory, len)); break; case ARRAY2D: { final float[] array = HDFNativeData .byteToFloat(byteArr, arrayOffset + offsetInMemory, len); setArray(obj, index, MatrixUtils.shapen(array, dimensions)); break; } case ARRAYMD: { final float[] array = HDFNativeData .byteToFloat(byteArr, arrayOffset + offsetInMemory, len); setArray(obj, index, new MDFloatArray(array, dimensions)); break; } default: throw new Error("Unknown rank."); } } }; } } HDF5CompoundMemberByteifyerHDF5TimeDurationFactory.java000066400000000000000000000275061256564762100356520ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.base.convert.NativeData.LONG_SIZE; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getArray; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getList; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getMap; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.putMap; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.setArray; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.setList; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_I64LE; import java.lang.reflect.Field; import ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.AccessType; import ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.IHDF5CompoundMemberBytifyerFactory; import ch.systemsx.cisd.hdf5.HDF5ValueObjectByteifyer.IFileAccessProvider; import ch.systemsx.cisd.hdf5.hdf5lib.HDFNativeData; /** * A {@link HDF5CompoundByteifyerFactory.IHDF5CompoundMemberBytifyerFactory} for * {@link HDF5TimeDuration}. * * @author Bernd Rinn */ class HDF5CompoundMemberByteifyerHDF5TimeDurationFactory implements IHDF5CompoundMemberBytifyerFactory { @Override public boolean canHandle(Class clazz, HDF5CompoundMemberInformation memberInfoOrNull) { if (memberInfoOrNull != null) { return (clazz == HDF5TimeDuration.class || Long.class.isAssignableFrom(clazz)) && memberInfoOrNull.getType().isTimeDuration(); } else { return (clazz == HDF5TimeDuration.class); } } @Override public Class tryGetOverrideJavaType(HDF5DataClass dataClass, int rank, int elementSize, HDF5DataTypeVariant typeVariantOrNull) { if (dataClass == HDF5DataClass.INTEGER && rank == 0 && elementSize == 8 && typeVariantOrNull != null && typeVariantOrNull.isTimeDuration()) { return HDF5TimeDuration.class; } else { return null; } } @Override public HDF5MemberByteifyer createBytifyer(AccessType accessType, Field fieldOrNull, HDF5CompoundMemberMapping member, HDF5CompoundMemberInformation compoundMemberInfoOrNull, HDF5EnumerationType enumTypeOrNull, Class memberClazz, int index, int offset, int memOffset, IFileAccessProvider fileInfoProvider) { final String memberName = member.getMemberName(); final HDF5DataTypeVariant typeVariant = HDF5DataTypeVariant.isTypeVariant(member.tryGetTypeVariant()) ? member .tryGetTypeVariant() : HDF5DataTypeVariant.TIME_DURATION_MICROSECONDS; switch (accessType) { case FIELD: return createByteifyerForField(fieldOrNull, memberName, offset, memOffset, typeVariant); case MAP: return createByteifyerForMap(memberName, offset, memOffset, typeVariant); case LIST: return createByteifyerForList(memberName, index, offset, memOffset, typeVariant); case ARRAY: return createByteifyerForArray(memberName, index, offset, memOffset, typeVariant); default: throw new Error("Unknown access type"); } } private HDF5MemberByteifyer createByteifyerForField(final Field field, final String memberName, final int offset, int memOffset, final HDF5DataTypeVariant typeVariant) { ReflectionUtils.ensureAccessible(field); return new HDF5MemberByteifyer(field, memberName, LONG_SIZE, offset, memOffset, false, typeVariant) { final HDF5TimeUnit timeUnit = HDF5DataTypeVariant.getTimeUnit(typeVariant); @Override int getElementSize() { return 8; } @Override protected int getMemberStorageTypeId() { return H5T_STD_I64LE; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { final HDF5TimeDuration duration = (HDF5TimeDuration) field.get(obj); return HDFNativeData.longToByte(timeUnit.convert(duration.getValue(), duration.getUnit())); } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { field.set( obj, new HDF5TimeDuration(HDFNativeData.byteToLong(byteArr, arrayOffset + offsetInMemory), timeUnit)); } }; } private HDF5MemberByteifyer createByteifyerForMap(final String memberName, final int offset, int memOffset, final HDF5DataTypeVariant typeVariant) { return new HDF5MemberByteifyer(null, memberName, LONG_SIZE, offset, memOffset, false, typeVariant) { final HDF5TimeUnit timeUnit = HDF5DataTypeVariant.getTimeUnit(typeVariant); @Override int getElementSize() { return 8; } @Override protected int getMemberStorageTypeId() { return H5T_STD_I64LE; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { final Object durationObj = getMap(obj, memberName); if (durationObj instanceof HDF5TimeDuration) { final HDF5TimeDuration duration = (HDF5TimeDuration) durationObj; return HDFNativeData.longToByte(timeUnit.convert(duration.getValue(), duration.getUnit())); } else { return HDFNativeData.longToByte(((Number) durationObj).longValue()); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { putMap(obj, memberName, new HDF5TimeDuration(HDFNativeData.byteToLong(byteArr, arrayOffset + offsetInMemory), timeUnit)); } }; } private HDF5MemberByteifyer createByteifyerForList(final String memberName, final int index, final int offset, int memOffset, final HDF5DataTypeVariant typeVariant) { return new HDF5MemberByteifyer(null, memberName, LONG_SIZE, offset, memOffset, false, typeVariant) { final HDF5TimeUnit timeUnit = HDF5DataTypeVariant.getTimeUnit(typeVariant); @Override int getElementSize() { return 8; } @Override protected int getMemberStorageTypeId() { return H5T_STD_I64LE; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { final Object durationObj = getList(obj, index); if (durationObj instanceof HDF5TimeDuration) { final HDF5TimeDuration duration = (HDF5TimeDuration) durationObj; return HDFNativeData.longToByte(timeUnit.convert(duration.getValue(), duration.getUnit())); } else { return HDFNativeData.longToByte(((Number) durationObj).longValue()); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { setList(obj, index, new HDF5TimeDuration(HDFNativeData.byteToLong(byteArr, arrayOffset + offsetInMemory), timeUnit)); } }; } private HDF5MemberByteifyer createByteifyerForArray(final String memberName, final int index, final int offset, int memOffset, final HDF5DataTypeVariant typeVariant) { return new HDF5MemberByteifyer(null, memberName, LONG_SIZE, offset, memOffset, false, typeVariant) { final HDF5TimeUnit timeUnit = HDF5DataTypeVariant.getTimeUnit(typeVariant); @Override int getElementSize() { return 8; } @Override protected int getMemberStorageTypeId() { return H5T_STD_I64LE; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { final Object durationObj = getArray(obj, index); if (durationObj instanceof HDF5TimeDuration) { final HDF5TimeDuration duration = (HDF5TimeDuration) durationObj; return HDFNativeData.longToByte(timeUnit.convert(duration.getValue(), duration.getUnit())); } else { return HDFNativeData.longToByte(((Number) durationObj).longValue()); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { setArray( obj, index, new HDF5TimeDuration(HDFNativeData.byteToLong(byteArr, arrayOffset + offsetInMemory), timeUnit)); } }; } } HDF5CompoundMemberByteifyerIntFactory.java000066400000000000000000000517511256564762100333700ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.base.convert.NativeData.INT_SIZE; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getArray; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getList; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getMap; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.putMap; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.setArray; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.setList; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_I32LE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_U32LE; import java.lang.reflect.Field; import java.util.IdentityHashMap; import java.util.Map; import ch.systemsx.cisd.base.mdarray.MDIntArray; import ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.AccessType; import ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.IHDF5CompoundMemberBytifyerFactory; import ch.systemsx.cisd.hdf5.HDF5ValueObjectByteifyer.IFileAccessProvider; import ch.systemsx.cisd.hdf5.hdf5lib.HDFNativeData; /** * A {@link HDF5CompoundByteifyerFactory.IHDF5CompoundMemberBytifyerFactory} for int, * int[], int[][] and MDIntArray. * * @author Bernd Rinn */ class HDF5CompoundMemberByteifyerIntFactory implements IHDF5CompoundMemberBytifyerFactory { private static Map, Rank> classToRankMap = new IdentityHashMap, Rank>(); private enum Rank { SCALAR(int.class, 0), ARRAY1D(int[].class, 1), ARRAY2D(int[][].class, 2), ARRAYMD( MDIntArray.class, -1); private final Class clazz; private final int rank; Rank(Class clazz, int rank) { this.clazz = clazz; this.rank = rank; } int getRank() { return rank; } boolean isScalar() { return rank == 0; } boolean anyRank() { return rank == -1; } Class getClazz() { return clazz; } } static { for (Rank r : Rank.values()) { classToRankMap.put(r.getClazz(), r); } } @Override public boolean canHandle(Class clazz, HDF5CompoundMemberInformation memberInfoOrNull) { final Rank rankOrNull = classToRankMap.get(clazz); if (memberInfoOrNull != null) { final HDF5DataTypeInformation typeInfo = memberInfoOrNull.getType(); if (rankOrNull == null || (typeInfo.getDataClass() != HDF5DataClass.INTEGER && typeInfo.getDataClass() != HDF5DataClass.FLOAT)) { return false; } return rankOrNull.anyRank() || (rankOrNull.getRank() == typeInfo.getDimensions().length) || (rankOrNull.isScalar() && typeInfo.getDimensions().length == 1 && typeInfo .getDimensions()[0] == 1); } else { return rankOrNull != null; } } @Override public Class tryGetOverrideJavaType(HDF5DataClass dataClass, int rank, int elementSize, HDF5DataTypeVariant typeVariantOrNull) { return null; } @Override public HDF5MemberByteifyer createBytifyer(AccessType accessType, Field fieldOrNull, HDF5CompoundMemberMapping member, HDF5CompoundMemberInformation compoundMemberInfoOrNull, HDF5EnumerationType enumTypeOrNull, Class memberClazz, int index, int offset, int memOffset, IFileAccessProvider fileInfoProvider) { final String memberName = member.getMemberName(); final Rank rank = classToRankMap.get(memberClazz); final int len = (compoundMemberInfoOrNull != null) ? compoundMemberInfoOrNull.getType() .getNumberOfElements() : rank.isScalar() ? 1 : member.getMemberTypeLength(); final int[] dimensions = rank.isScalar() ? new int[] { 1 } : member.getMemberTypeDimensions(); final int storageTypeId = member.getStorageDataTypeId(); final int memberTypeId = rank.isScalar() ? member.isUnsigned() ? H5T_STD_U32LE : H5T_STD_I32LE : ((storageTypeId < 0) ? fileInfoProvider.getArrayTypeId( member.isUnsigned() ? H5T_STD_U32LE : H5T_STD_I32LE, dimensions) : storageTypeId); switch (accessType) { case FIELD: return createByteifyerForField(fieldOrNull, memberName, offset, memOffset, dimensions, len, memberTypeId, rank, member.tryGetTypeVariant()); case MAP: return createByteifyerForMap(memberName, offset, memOffset, dimensions, len, memberTypeId, rank, member.tryGetTypeVariant()); case LIST: return createByteifyerForList(memberName, index, offset, memOffset, dimensions, len, memberTypeId, rank, member.tryGetTypeVariant()); case ARRAY: return createByteifyerForArray(memberName, index, offset, memOffset, dimensions, len, memberTypeId, rank, member.tryGetTypeVariant()); default: throw new Error("Unknown access type"); } } private HDF5MemberByteifyer createByteifyerForField(final Field field, final String memberName, final int offset, int memOffset, final int[] dimensions, final int len, final int memberTypeId, final Rank rank, final HDF5DataTypeVariant typeVariant) { ReflectionUtils.ensureAccessible(field); return new HDF5MemberByteifyer(field, memberName, INT_SIZE * len, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 4; } @Override protected int getMemberStorageTypeId() { return memberTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { switch (rank) { case SCALAR: return HDFNativeData.intToByte(field.getInt(obj)); case ARRAY1D: return HDFNativeData.intToByte((int[]) field.get(obj)); case ARRAY2D: { final int[][] array = (int[][]) field.get(obj); MatrixUtils.checkMatrixDimensions(memberName, dimensions, array); return HDFNativeData.intToByte(MatrixUtils.flatten(array)); } case ARRAYMD: { final MDIntArray array = (MDIntArray) field.get(obj); MatrixUtils.checkMDArrayDimensions(memberName, dimensions, array); return HDFNativeData.intToByte(array.getAsFlatArray()); } default: throw new Error("Unknown rank."); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { switch (rank) { case SCALAR: field.setInt(obj, HDFNativeData.byteToInt(byteArr, arrayOffset + offsetInMemory)); break; case ARRAY1D: field.set(obj, HDFNativeData.byteToInt(byteArr, arrayOffset + offsetInMemory, len)); break; case ARRAY2D: { final int[] array = HDFNativeData.byteToInt(byteArr, arrayOffset + offsetInMemory, len); field.set(obj, MatrixUtils.shapen(array, dimensions)); break; } case ARRAYMD: { final int[] array = HDFNativeData.byteToInt(byteArr, arrayOffset + offsetInMemory, len); field.set(obj, new MDIntArray(array, dimensions)); break; } default: throw new Error("Unknown rank."); } } }; } private HDF5MemberByteifyer createByteifyerForMap(final String memberName, final int offset, int memOffset, final int[] dimensions, final int len, final int memberTypeId, final Rank rank, final HDF5DataTypeVariant typeVariant) { return new HDF5MemberByteifyer(null, memberName, INT_SIZE * len, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 4; } @Override protected int getMemberStorageTypeId() { return memberTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { switch (rank) { case SCALAR: return HDFNativeData.intToByte(((Number) getMap(obj, memberName)) .intValue()); case ARRAY1D: return HDFNativeData.intToByte((int[]) getMap(obj, memberName)); case ARRAY2D: { final int[][] array = (int[][]) getMap(obj, memberName); MatrixUtils.checkMatrixDimensions(memberName, dimensions, array); return HDFNativeData.intToByte(MatrixUtils.flatten(array)); } case ARRAYMD: { final MDIntArray array = (MDIntArray) getMap(obj, memberName); MatrixUtils.checkMDArrayDimensions(memberName, dimensions, array); return HDFNativeData.intToByte(array.getAsFlatArray()); } default: throw new Error("Unknown rank."); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { switch (rank) { case SCALAR: putMap(obj, memberName, HDFNativeData.byteToInt(byteArr, arrayOffset + offsetInMemory)); break; case ARRAY1D: putMap(obj, memberName, HDFNativeData.byteToInt(byteArr, arrayOffset + offsetInMemory, len)); break; case ARRAY2D: { final int[] array = HDFNativeData.byteToInt(byteArr, arrayOffset + offsetInMemory, len); putMap(obj, memberName, MatrixUtils.shapen(array, dimensions)); break; } case ARRAYMD: { final int[] array = HDFNativeData.byteToInt(byteArr, arrayOffset + offsetInMemory, len); putMap(obj, memberName, new MDIntArray(array, dimensions)); break; } default: throw new Error("Unknown rank."); } } }; } private HDF5MemberByteifyer createByteifyerForList(final String memberName, final int index, final int offset, int memOffset, final int[] dimensions, final int len, final int memberTypeId, final Rank rank, final HDF5DataTypeVariant typeVariant) { return new HDF5MemberByteifyer(null, memberName, INT_SIZE * len, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 4; } @Override protected int getMemberStorageTypeId() { return memberTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { switch (rank) { case SCALAR: return HDFNativeData.intToByte(((Number) getList(obj, index)) .intValue()); case ARRAY1D: return HDFNativeData.intToByte((int[]) getList(obj, index)); case ARRAY2D: { final int[][] array = (int[][]) getList(obj, index); MatrixUtils.checkMatrixDimensions(memberName, dimensions, array); return HDFNativeData.intToByte(MatrixUtils.flatten(array)); } case ARRAYMD: { final MDIntArray array = (MDIntArray) getList(obj, index); MatrixUtils.checkMDArrayDimensions(memberName, dimensions, array); return HDFNativeData.intToByte(array.getAsFlatArray()); } default: throw new Error("Unknown rank."); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { switch (rank) { case SCALAR: setList(obj, index, HDFNativeData.byteToInt(byteArr, arrayOffset + offsetInMemory)); break; case ARRAY1D: putMap(obj, memberName, HDFNativeData.byteToInt(byteArr, arrayOffset + offsetInMemory, len)); break; case ARRAY2D: { final int[] array = HDFNativeData.byteToInt(byteArr, arrayOffset + offsetInMemory, len); setList(obj, index, MatrixUtils.shapen(array, dimensions)); break; } case ARRAYMD: { final int[] array = HDFNativeData.byteToInt(byteArr, arrayOffset + offsetInMemory, len); setList(obj, index, new MDIntArray(array, dimensions)); break; } default: throw new Error("Unknown rank."); } } }; } private HDF5MemberByteifyer createByteifyerForArray(final String memberName, final int index, final int offset, int memOffset, final int[] dimensions, final int len, final int memberTypeId, final Rank rank, final HDF5DataTypeVariant typeVariant) { return new HDF5MemberByteifyer(null, memberName, INT_SIZE * len, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 4; } @Override protected int getMemberStorageTypeId() { return memberTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { switch (rank) { case SCALAR: return HDFNativeData.intToByte(((Number) getArray(obj, index)) .intValue()); case ARRAY1D: return HDFNativeData.intToByte((int[]) getArray(obj, index)); case ARRAY2D: { final int[][] array = (int[][]) getArray(obj, index); MatrixUtils.checkMatrixDimensions(memberName, dimensions, array); return HDFNativeData.intToByte(MatrixUtils.flatten(array)); } case ARRAYMD: { final MDIntArray array = (MDIntArray) getArray(obj, index); MatrixUtils.checkMDArrayDimensions(memberName, dimensions, array); return HDFNativeData.intToByte(array.getAsFlatArray()); } default: throw new Error("Unknown rank."); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { switch (rank) { case SCALAR: setArray(obj, index, HDFNativeData.byteToInt(byteArr, arrayOffset + offsetInMemory)); break; case ARRAY1D: setArray(obj, index, HDFNativeData.byteToInt(byteArr, arrayOffset + offsetInMemory, len)); break; case ARRAY2D: { final int[] array = HDFNativeData.byteToInt(byteArr, arrayOffset + offsetInMemory, len); setArray(obj, index, MatrixUtils.shapen(array, dimensions)); break; } case ARRAYMD: { final int[] array = HDFNativeData.byteToInt(byteArr, arrayOffset + offsetInMemory, len); setArray(obj, index, new MDIntArray(array, dimensions)); break; } default: throw new Error("Unknown rank."); } } }; } } HDF5CompoundMemberByteifyerLongFactory.java000066400000000000000000000520631256564762100335320ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.base.convert.NativeData.LONG_SIZE; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getArray; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getList; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getMap; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.putMap; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.setArray; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.setList; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_I64LE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_U64LE; import java.lang.reflect.Field; import java.util.IdentityHashMap; import java.util.Map; import ch.systemsx.cisd.base.mdarray.MDLongArray; import ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.AccessType; import ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.IHDF5CompoundMemberBytifyerFactory; import ch.systemsx.cisd.hdf5.HDF5ValueObjectByteifyer.IFileAccessProvider; import ch.systemsx.cisd.hdf5.hdf5lib.HDFNativeData; /** * A {@link HDF5CompoundByteifyerFactory.IHDF5CompoundMemberBytifyerFactory} for long, * long[], long[][] and MDLongArray. * * @author Bernd Rinn */ class HDF5CompoundMemberByteifyerLongFactory implements IHDF5CompoundMemberBytifyerFactory { private static Map, Rank> classToRankMap = new IdentityHashMap, Rank>(); private enum Rank { SCALAR(long.class, 0), ARRAY1D(long[].class, 1), ARRAY2D(long[][].class, 2), ARRAYMD( MDLongArray.class, -1); private final Class clazz; private final int rank; Rank(Class clazz, int rank) { this.clazz = clazz; this.rank = rank; } int getRank() { return rank; } boolean isScalar() { return rank == 0; } boolean anyRank() { return rank == -1; } Class getClazz() { return clazz; } } static { for (Rank r : Rank.values()) { classToRankMap.put(r.getClazz(), r); } } @Override public boolean canHandle(Class clazz, HDF5CompoundMemberInformation memberInfoOrNull) { final Rank rankOrNull = classToRankMap.get(clazz); if (memberInfoOrNull != null) { final HDF5DataTypeInformation typeInfo = memberInfoOrNull.getType(); if (rankOrNull == null || typeInfo.getDataClass() != HDF5DataClass.INTEGER || typeInfo.getElementSize() != LONG_SIZE) { return false; } return rankOrNull.anyRank() || (rankOrNull.getRank() == typeInfo.getDimensions().length) || (rankOrNull.isScalar() && typeInfo.getDimensions().length == 1 && typeInfo .getDimensions()[0] == 1); } else { return rankOrNull != null; } } @Override public Class tryGetOverrideJavaType(HDF5DataClass dataClass, int rank, int elementSize, HDF5DataTypeVariant typeVariantOrNull) { return null; } @Override public HDF5MemberByteifyer createBytifyer(AccessType accessType, Field fieldOrNull, HDF5CompoundMemberMapping member, HDF5CompoundMemberInformation compoundMemberInfoOrNull, HDF5EnumerationType enumTypeOrNull, Class memberClazz, int index, int offset, int memOffset, IFileAccessProvider fileInfoProvider) { final String memberName = member.getMemberName(); final Rank rank = classToRankMap.get(memberClazz); final int len = (compoundMemberInfoOrNull != null) ? compoundMemberInfoOrNull.getType() .getNumberOfElements() : rank.isScalar() ? 1 : member.getMemberTypeLength(); final int[] dimensions = rank.isScalar() ? new int[] { 1 } : member.getMemberTypeDimensions(); final int storageTypeId = member.getStorageDataTypeId(); final int memberTypeId = rank.isScalar() ? member.isUnsigned() ? H5T_STD_U64LE : H5T_STD_I64LE : ((storageTypeId < 0) ? fileInfoProvider.getArrayTypeId( member.isUnsigned() ? H5T_STD_U64LE : H5T_STD_I64LE, dimensions) : storageTypeId); switch (accessType) { case FIELD: return createByteifyerForField(fieldOrNull, memberName, offset, memOffset, dimensions, len, memberTypeId, rank, member.tryGetTypeVariant()); case MAP: return createByteifyerForMap(memberName, offset, memOffset, dimensions, len, memberTypeId, rank, member.tryGetTypeVariant()); case LIST: return createByteifyerForList(memberName, index, offset, memOffset, dimensions, len, memberTypeId, rank, member.tryGetTypeVariant()); case ARRAY: return createByteifyerForArray(memberName, index, offset, memOffset, dimensions, len, memberTypeId, rank, member.tryGetTypeVariant()); default: throw new Error("Unknown access type"); } } private HDF5MemberByteifyer createByteifyerForField(final Field field, final String memberName, final int offset, int memOffset, final int[] dimensions, final int len, final int memberTypeId, final Rank rank, final HDF5DataTypeVariant typeVariant) { ReflectionUtils.ensureAccessible(field); return new HDF5MemberByteifyer(field, memberName, LONG_SIZE * len, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 8; } @Override protected int getMemberStorageTypeId() { return memberTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { switch (rank) { case SCALAR: return HDFNativeData.longToByte(field.getLong(obj)); case ARRAY1D: return HDFNativeData.longToByte((long[]) field.get(obj)); case ARRAY2D: { final long[][] array = (long[][]) field.get(obj); MatrixUtils.checkMatrixDimensions(memberName, dimensions, array); return HDFNativeData.longToByte(MatrixUtils.flatten(array)); } case ARRAYMD: { final MDLongArray array = (MDLongArray) field.get(obj); MatrixUtils.checkMDArrayDimensions(memberName, dimensions, array); return HDFNativeData.longToByte(array.getAsFlatArray()); } default: throw new Error("Unknown rank."); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { switch (rank) { case SCALAR: field.setLong(obj, HDFNativeData.byteToLong(byteArr, arrayOffset + offsetInMemory)); break; case ARRAY1D: field.set(obj, HDFNativeData.byteToLong(byteArr, arrayOffset + offsetInMemory, len)); break; case ARRAY2D: { final long[] array = HDFNativeData.byteToLong(byteArr, arrayOffset + offsetInMemory, len); field.set(obj, MatrixUtils.shapen(array, dimensions)); break; } case ARRAYMD: { final long[] array = HDFNativeData.byteToLong(byteArr, arrayOffset + offsetInMemory, len); field.set(obj, new MDLongArray(array, dimensions)); break; } default: throw new Error("Unknown rank."); } } }; } private HDF5MemberByteifyer createByteifyerForMap(final String memberName, final int offset, int memOffset, final int[] dimensions, final int len, final int memberTypeId, final Rank rank, final HDF5DataTypeVariant typeVariant) { return new HDF5MemberByteifyer(null, memberName, LONG_SIZE * len, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 8; } @Override protected int getMemberStorageTypeId() { return memberTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { switch (rank) { case SCALAR: return HDFNativeData.longToByte(((Number) getMap(obj, memberName)) .longValue()); case ARRAY1D: return HDFNativeData.longToByte((long[]) getMap(obj, memberName)); case ARRAY2D: { final long[][] array = (long[][]) getMap(obj, memberName); MatrixUtils.checkMatrixDimensions(memberName, dimensions, array); return HDFNativeData.longToByte(MatrixUtils.flatten(array)); } case ARRAYMD: { final MDLongArray array = (MDLongArray) getMap(obj, memberName); MatrixUtils.checkMDArrayDimensions(memberName, dimensions, array); return HDFNativeData.longToByte(array.getAsFlatArray()); } default: throw new Error("Unknown rank."); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { switch (rank) { case SCALAR: putMap(obj, memberName, HDFNativeData.byteToLong(byteArr, arrayOffset + offsetInMemory)); break; case ARRAY1D: putMap(obj, memberName, HDFNativeData.byteToLong(byteArr, arrayOffset + offsetInMemory, len)); break; case ARRAY2D: { final long[] array = HDFNativeData.byteToLong(byteArr, arrayOffset + offsetInMemory, len); putMap(obj, memberName, MatrixUtils.shapen(array, dimensions)); break; } case ARRAYMD: { final long[] array = HDFNativeData.byteToLong(byteArr, arrayOffset + offsetInMemory, len); putMap(obj, memberName, new MDLongArray(array, dimensions)); break; } default: throw new Error("Unknown rank."); } } }; } private HDF5MemberByteifyer createByteifyerForList(final String memberName, final int index, final int offset, int memOffset, final int[] dimensions, final int len, final int memberTypeId, final Rank rank, final HDF5DataTypeVariant typeVariant) { return new HDF5MemberByteifyer(null, memberName, LONG_SIZE * len, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 8; } @Override protected int getMemberStorageTypeId() { return memberTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { switch (rank) { case SCALAR: return HDFNativeData.longToByte(((Number) getList(obj, index)) .longValue()); case ARRAY1D: return HDFNativeData.longToByte((long[]) getList(obj, index)); case ARRAY2D: { final long[][] array = (long[][]) getList(obj, index); MatrixUtils.checkMatrixDimensions(memberName, dimensions, array); return HDFNativeData.longToByte(MatrixUtils.flatten(array)); } case ARRAYMD: { final MDLongArray array = (MDLongArray) getList(obj, index); MatrixUtils.checkMDArrayDimensions(memberName, dimensions, array); return HDFNativeData.longToByte(array.getAsFlatArray()); } default: throw new Error("Unknown rank."); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { switch (rank) { case SCALAR: setList(obj, index, HDFNativeData.byteToLong(byteArr, arrayOffset + offsetInMemory)); break; case ARRAY1D: putMap(obj, memberName, HDFNativeData.byteToLong(byteArr, arrayOffset + offsetInMemory, len)); break; case ARRAY2D: { final long[] array = HDFNativeData.byteToLong(byteArr, arrayOffset + offsetInMemory, len); setList(obj, index, MatrixUtils.shapen(array, dimensions)); break; } case ARRAYMD: { final long[] array = HDFNativeData.byteToLong(byteArr, arrayOffset + offsetInMemory, len); setList(obj, index, new MDLongArray(array, dimensions)); break; } default: throw new Error("Unknown rank."); } } }; } private HDF5MemberByteifyer createByteifyerForArray(final String memberName, final int index, final int offset, int memOffset, final int[] dimensions, final int len, final int memberTypeId, final Rank rank, final HDF5DataTypeVariant typeVariant) { return new HDF5MemberByteifyer(null, memberName, LONG_SIZE * len, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 8; } @Override protected int getMemberStorageTypeId() { return memberTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { switch (rank) { case SCALAR: return HDFNativeData.longToByte(((Number) getArray(obj, index)) .longValue()); case ARRAY1D: return HDFNativeData.longToByte((long[]) getArray(obj, index)); case ARRAY2D: { final long[][] array = (long[][]) getArray(obj, index); MatrixUtils.checkMatrixDimensions(memberName, dimensions, array); return HDFNativeData.longToByte(MatrixUtils.flatten(array)); } case ARRAYMD: { final MDLongArray array = (MDLongArray) getArray(obj, index); MatrixUtils.checkMDArrayDimensions(memberName, dimensions, array); return HDFNativeData.longToByte(array.getAsFlatArray()); } default: throw new Error("Unknown rank."); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { switch (rank) { case SCALAR: setArray(obj, index, HDFNativeData.byteToLong(byteArr, arrayOffset + offsetInMemory)); break; case ARRAY1D: setArray(obj, index, HDFNativeData.byteToLong(byteArr, arrayOffset + offsetInMemory, len)); break; case ARRAY2D: { final long[] array = HDFNativeData.byteToLong(byteArr, arrayOffset + offsetInMemory, len); setArray(obj, index, MatrixUtils.shapen(array, dimensions)); break; } case ARRAYMD: { final long[] array = HDFNativeData.byteToLong(byteArr, arrayOffset + offsetInMemory, len); setArray(obj, index, new MDLongArray(array, dimensions)); break; } default: throw new Error("Unknown rank."); } } }; } } HDF5CompoundMemberByteifyerShortFactory.java000066400000000000000000000527621256564762100337400ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.base.convert.NativeData.SHORT_SIZE; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getArray; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getList; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getMap; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.putMap; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.setArray; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.setList; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_I16LE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_U16LE; import java.lang.reflect.Field; import java.util.IdentityHashMap; import java.util.Map; import ch.systemsx.cisd.base.mdarray.MDShortArray; import ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.AccessType; import ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.IHDF5CompoundMemberBytifyerFactory; import ch.systemsx.cisd.hdf5.HDF5ValueObjectByteifyer.IFileAccessProvider; import ch.systemsx.cisd.hdf5.hdf5lib.HDFNativeData; /** * A {@link HDF5CompoundByteifyerFactory.IHDF5CompoundMemberBytifyerFactory} for short, * short[], short[][] and MDShortArray. * * @author Bernd Rinn */ class HDF5CompoundMemberByteifyerShortFactory implements IHDF5CompoundMemberBytifyerFactory { private static Map, Rank> classToRankMap = new IdentityHashMap, Rank>(); private enum Rank { SCALAR(short.class, 0), ARRAY1D(short[].class, 1), ARRAY2D(short[][].class, 2), ARRAYMD( MDShortArray.class, -1); private final Class clazz; private final int rank; Rank(Class clazz, int rank) { this.clazz = clazz; this.rank = rank; } int getRank() { return rank; } boolean isScalar() { return rank == 0; } boolean anyRank() { return rank == -1; } Class getClazz() { return clazz; } } static { for (Rank r : Rank.values()) { classToRankMap.put(r.getClazz(), r); } } @Override public boolean canHandle(Class clazz, HDF5CompoundMemberInformation memberInfoOrNull) { final Rank rankOrNull = classToRankMap.get(clazz); if (memberInfoOrNull != null) { final HDF5DataTypeInformation typeInfo = memberInfoOrNull.getType(); if (rankOrNull == null || typeInfo.getDataClass() != HDF5DataClass.INTEGER || typeInfo.getElementSize() != SHORT_SIZE) { return false; } return rankOrNull.anyRank() || (rankOrNull.getRank() == typeInfo.getDimensions().length) || (rankOrNull.isScalar() && typeInfo.getDimensions().length == 1 && typeInfo .getDimensions()[0] == 1); } else { return rankOrNull != null; } } @Override public Class tryGetOverrideJavaType(HDF5DataClass dataClass, int rank, int elementSize, HDF5DataTypeVariant typeVariantOrNull) { return null; } @Override public HDF5MemberByteifyer createBytifyer(AccessType accessType, Field fieldOrNull, HDF5CompoundMemberMapping member, HDF5CompoundMemberInformation compoundMemberInfoOrNull, HDF5EnumerationType enumTypeOrNull, Class memberClazz, int index, int offset, int memOffset, IFileAccessProvider fileInfoProvider) { final String memberName = member.getMemberName(); final Rank rank = classToRankMap.get(memberClazz); final int len = (compoundMemberInfoOrNull != null) ? compoundMemberInfoOrNull.getType() .getNumberOfElements() : rank.isScalar() ? 1 : member.getMemberTypeLength(); final int[] dimensions = rank.isScalar() ? new int[] { 1 } : member.getMemberTypeDimensions(); final int storageTypeId = member.getStorageDataTypeId(); final int memberTypeId = rank.isScalar() ? (member.isUnsigned() ? H5T_STD_U16LE : H5T_STD_I16LE) : ((storageTypeId < 0) ? fileInfoProvider.getArrayTypeId( member.isUnsigned() ? H5T_STD_U16LE : H5T_STD_I16LE, dimensions) : storageTypeId); switch (accessType) { case FIELD: return createByteifyerForField(fieldOrNull, memberName, offset, memOffset, dimensions, len, memberTypeId, rank, member.tryGetTypeVariant()); case MAP: return createByteifyerForMap(memberName, offset, memOffset, dimensions, len, memberTypeId, rank, member.tryGetTypeVariant()); case LIST: return createByteifyerForList(memberName, index, offset, memOffset, dimensions, len, memberTypeId, rank, member.tryGetTypeVariant()); case ARRAY: return createByteifyerForArray(memberName, index, offset, memOffset, dimensions, len, memberTypeId, rank, member.tryGetTypeVariant()); default: throw new Error("Unknown access type"); } } private HDF5MemberByteifyer createByteifyerForField(final Field field, final String memberName, final int offset, int memOffset, final int[] dimensions, final int len, final int memberTypeId, final Rank rank, final HDF5DataTypeVariant typeVariant) { ReflectionUtils.ensureAccessible(field); return new HDF5MemberByteifyer(field, memberName, SHORT_SIZE * len, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 2; } @Override protected int getMemberStorageTypeId() { return memberTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { switch (rank) { case SCALAR: return HDFNativeData.shortToByte(field.getShort(obj)); case ARRAY1D: return HDFNativeData.shortToByte((short[]) field.get(obj)); case ARRAY2D: { final short[][] array = (short[][]) field.get(obj); MatrixUtils.checkMatrixDimensions(memberName, dimensions, array); return HDFNativeData.shortToByte(MatrixUtils.flatten(array)); } case ARRAYMD: { final MDShortArray array = (MDShortArray) field.get(obj); MatrixUtils.checkMDArrayDimensions(memberName, dimensions, array); return HDFNativeData.shortToByte(array.getAsFlatArray()); } default: throw new Error("Unknown rank."); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { switch (rank) { case SCALAR: field.setShort(obj, HDFNativeData.byteToShort(byteArr, arrayOffset + offsetInMemory)); break; case ARRAY1D: field.set(obj, HDFNativeData.byteToShort(byteArr, arrayOffset + offsetInMemory, len)); break; case ARRAY2D: { final short[] array = HDFNativeData .byteToShort(byteArr, arrayOffset + offsetInMemory, len); field.set(obj, MatrixUtils.shapen(array, dimensions)); break; } case ARRAYMD: { final short[] array = HDFNativeData .byteToShort(byteArr, arrayOffset + offsetInMemory, len); field.set(obj, new MDShortArray(array, dimensions)); break; } default: throw new Error("Unknown rank."); } } }; } private HDF5MemberByteifyer createByteifyerForMap(final String memberName, final int offset, int memOffset, final int[] dimensions, final int len, final int memberTypeId, final Rank rank, final HDF5DataTypeVariant typeVariant) { return new HDF5MemberByteifyer(null, memberName, SHORT_SIZE * len, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 2; } @Override protected int getMemberStorageTypeId() { return memberTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { switch (rank) { case SCALAR: return HDFNativeData.shortToByte(((Number) getMap(obj, memberName)) .shortValue()); case ARRAY1D: return HDFNativeData.shortToByte((short[]) getMap(obj, memberName)); case ARRAY2D: { final short[][] array = (short[][]) getMap(obj, memberName); MatrixUtils.checkMatrixDimensions(memberName, dimensions, array); return HDFNativeData.shortToByte(MatrixUtils.flatten(array)); } case ARRAYMD: { final MDShortArray array = (MDShortArray) getMap(obj, memberName); MatrixUtils.checkMDArrayDimensions(memberName, dimensions, array); return HDFNativeData.shortToByte(array.getAsFlatArray()); } default: throw new Error("Unknown rank."); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { switch (rank) { case SCALAR: putMap(obj, memberName, HDFNativeData.byteToShort(byteArr, arrayOffset + offsetInMemory)); break; case ARRAY1D: putMap(obj, memberName, HDFNativeData.byteToShort(byteArr, arrayOffset + offsetInMemory, len)); break; case ARRAY2D: { final short[] array = HDFNativeData .byteToShort(byteArr, arrayOffset + offsetInMemory, len); putMap(obj, memberName, MatrixUtils.shapen(array, dimensions)); break; } case ARRAYMD: { final short[] array = HDFNativeData .byteToShort(byteArr, arrayOffset + offsetInMemory, len); putMap(obj, memberName, new MDShortArray(array, dimensions)); break; } default: throw new Error("Unknown rank."); } } }; } private HDF5MemberByteifyer createByteifyerForList(final String memberName, final int index, final int offset, int memOffset, final int[] dimensions, final int len, final int memberTypeId, final Rank rank, final HDF5DataTypeVariant typeVariant) { return new HDF5MemberByteifyer(null, memberName, SHORT_SIZE * len, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 2; } @Override protected int getMemberStorageTypeId() { return memberTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { switch (rank) { case SCALAR: return HDFNativeData.shortToByte(((Number) getList(obj, index)) .shortValue()); case ARRAY1D: return HDFNativeData.shortToByte((short[]) getList(obj, index)); case ARRAY2D: { final short[][] array = (short[][]) getList(obj, index); MatrixUtils.checkMatrixDimensions(memberName, dimensions, array); return HDFNativeData.shortToByte(MatrixUtils.flatten(array)); } case ARRAYMD: { final MDShortArray array = (MDShortArray) getList(obj, index); MatrixUtils.checkMDArrayDimensions(memberName, dimensions, array); return HDFNativeData.shortToByte(array.getAsFlatArray()); } default: throw new Error("Unknown rank."); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { switch (rank) { case SCALAR: setList(obj, index, HDFNativeData.byteToShort(byteArr, arrayOffset + offsetInMemory)); break; case ARRAY1D: putMap(obj, memberName, HDFNativeData.byteToShort(byteArr, arrayOffset + offsetInMemory, len)); break; case ARRAY2D: { final short[] array = HDFNativeData .byteToShort(byteArr, arrayOffset + offsetInMemory, len); setList(obj, index, MatrixUtils.shapen(array, dimensions)); break; } case ARRAYMD: { final short[] array = HDFNativeData .byteToShort(byteArr, arrayOffset + offsetInMemory, len); setList(obj, index, new MDShortArray(array, dimensions)); break; } default: throw new Error("Unknown rank."); } } }; } private HDF5MemberByteifyer createByteifyerForArray(final String memberName, final int index, final int offset, int memOffset, final int[] dimensions, final int len, final int memberTypeId, final Rank rank, final HDF5DataTypeVariant typeVariant) { return new HDF5MemberByteifyer(null, memberName, SHORT_SIZE * len, offset, memOffset, false, typeVariant) { @Override int getElementSize() { return 2; } @Override protected int getMemberStorageTypeId() { return memberTypeId; } @Override protected int getMemberNativeTypeId() { return -1; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { switch (rank) { case SCALAR: return HDFNativeData.shortToByte(((Number) getArray(obj, index)) .shortValue()); case ARRAY1D: return HDFNativeData.shortToByte((short[]) getArray(obj, index)); case ARRAY2D: { final short[][] array = (short[][]) getArray(obj, index); MatrixUtils.checkMatrixDimensions(memberName, dimensions, array); return HDFNativeData.shortToByte(MatrixUtils.flatten(array)); } case ARRAYMD: { final MDShortArray array = (MDShortArray) getArray(obj, index); MatrixUtils.checkMDArrayDimensions(memberName, dimensions, array); return HDFNativeData.shortToByte(array.getAsFlatArray()); } default: throw new Error("Unknown rank."); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { switch (rank) { case SCALAR: setArray(obj, index, HDFNativeData.byteToShort(byteArr, arrayOffset + offsetInMemory)); break; case ARRAY1D: setArray(obj, index, HDFNativeData.byteToShort(byteArr, arrayOffset + offsetInMemory, len)); break; case ARRAY2D: { final short[] array = HDFNativeData .byteToShort(byteArr, arrayOffset + offsetInMemory, len); setArray(obj, index, MatrixUtils.shapen(array, dimensions)); break; } case ARRAYMD: { final short[] array = HDFNativeData .byteToShort(byteArr, arrayOffset + offsetInMemory, len); setArray(obj, index, new MDShortArray(array, dimensions)); break; } default: throw new Error("Unknown rank."); } } }; } } HDF5CompoundMemberByteifyerStringFactory.java000066400000000000000000000432601256564762100341000ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getArray; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getList; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.getMap; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.putMap; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.setArray; import static ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.setList; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_REF_OBJ; import java.lang.reflect.Field; import ch.systemsx.cisd.base.convert.NativeData; import ch.systemsx.cisd.base.convert.NativeData.ByteOrder; import ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.AccessType; import ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.IHDF5CompoundMemberBytifyerFactory; import ch.systemsx.cisd.hdf5.HDF5ValueObjectByteifyer.IFileAccessProvider; import ch.systemsx.cisd.hdf5.hdf5lib.HDFNativeData; /** * A {@link HDF5CompoundByteifyerFactory.IHDF5CompoundMemberBytifyerFactory} for String * . * * @author Bernd Rinn */ class HDF5CompoundMemberByteifyerStringFactory implements IHDF5CompoundMemberBytifyerFactory { private static abstract class HDF5StringMemberByteifyer extends HDF5MemberByteifyer { HDF5StringMemberByteifyer(Field fieldOrNull, String memberName, int size, int offset, int memOffset, CharacterEncoding encoding, int maxCharacters, boolean isVariableLengthType, boolean isReferenceType) { super(fieldOrNull, memberName, size, offset, memOffset, encoding, maxCharacters, isVariableLengthType, isReferenceType); } /** * For strings, this is the minimal element size 1 for fixed strings or the size of a * pointer for variable-length strings. */ @Override int getElementSize() { return isVariableLengthType() ? HDFNativeData.getMachineWordSize() : 1; } @Override public boolean mayBeCut() { return true; } @Override protected int getMemberNativeTypeId() { return -1; } } @Override public boolean canHandle(Class clazz, HDF5CompoundMemberInformation memberInfoOrNull) { if (memberInfoOrNull != null) { final HDF5DataClass dataClass = memberInfoOrNull.getType().getDataClass(); return ((clazz == String.class) || (clazz == char[].class)) && (dataClass == HDF5DataClass.STRING || dataClass == HDF5DataClass.REFERENCE); } else { return (clazz == String.class) || (clazz == char[].class); } } @Override public Class tryGetOverrideJavaType(HDF5DataClass dataClass, int rank, int elementSize, HDF5DataTypeVariant typeVariantOrNull) { return null; } @Override public HDF5MemberByteifyer createBytifyer(AccessType accessType, Field fieldOrNull, HDF5CompoundMemberMapping member, HDF5CompoundMemberInformation compoundMemberInfoOrNull, HDF5EnumerationType enumTypeOrNull, Class memberClazz, int index, int offset, int memOffset, IFileAccessProvider fileAccessProvider) { final String memberName = member.getMemberName(); final int maxCharacters = member.getMemberTypeLength(); final boolean isVariableLengthType = member.isVariableLength() || (maxCharacters == 0 && member.tryGetHints() != null && member .tryGetHints().isUseVariableLengthStrings()); final boolean isReferenceType = member.isReference(); // May be -1 if not known final int memberTypeId = isVariableLengthType ? fileAccessProvider.getVariableLengthStringDataTypeId() : member.getStorageDataTypeId(); final CharacterEncoding encoding = isReferenceType ? CharacterEncoding.ASCII : fileAccessProvider .getCharacterEncoding(memberTypeId); final int size = (compoundMemberInfoOrNull != null) ? compoundMemberInfoOrNull.getType().getSize() : encoding.getMaxBytesPerChar() * maxCharacters; final int stringOrRefDataTypeId = (memberTypeId < 0) ? (isReferenceType ? H5T_STD_REF_OBJ : fileAccessProvider .getStringDataTypeId(size)) : memberTypeId; final boolean isCharArray = (memberClazz == char[].class); switch (accessType) { case FIELD: return createByteifyerForField(fieldOrNull, memberName, fileAccessProvider, offset, memOffset, stringOrRefDataTypeId, maxCharacters, size, encoding, isCharArray, isVariableLengthType, isReferenceType); case MAP: return createByteifyerForMap(memberName, fileAccessProvider, offset, memOffset, stringOrRefDataTypeId, maxCharacters, size, encoding, isCharArray, isVariableLengthType, isReferenceType); case LIST: return createByteifyerForList(memberName, fileAccessProvider, index, offset, memOffset, stringOrRefDataTypeId, maxCharacters, size, encoding, isCharArray, isVariableLengthType, isReferenceType); case ARRAY: return createByteifyerForArray(memberName, fileAccessProvider, index, offset, memOffset, stringOrRefDataTypeId, maxCharacters, size, encoding, isCharArray, isVariableLengthType, isReferenceType); default: throw new Error("Unknown access type"); } } private static String refToStr(byte[] byteArr, int offset) { final long reference = NativeData.byteToLong(byteArr, ByteOrder.NATIVE, offset, 1)[0]; return '\0' + Long.toString(reference); } static String bytesToString(byte[] byteArr, final int totalOffset, final int maxIdx, CharacterEncoding encoding, final boolean isVariableLengthType, final boolean isReferenceType) { final String s; if (isVariableLengthType) { s = HDFNativeData.createVLStrFromCompound(byteArr, totalOffset); } else if (isReferenceType) { s = refToStr(byteArr, totalOffset); } else { s = StringUtils.fromBytes0Term(byteArr, totalOffset, maxIdx, encoding); } return s; } private HDF5MemberByteifyer createByteifyerForField(final Field field, final String memberName, final IFileAccessProvider fileAccessProvider, final int offset, int memOffset, final int stringOrRefDataTypeId, final int maxCharacters, final int size, final CharacterEncoding encoding, final boolean isCharArray, final boolean isVariableLengthType, final boolean isReferenceType) { ReflectionUtils.ensureAccessible(field); return new HDF5StringMemberByteifyer(field, memberName, size, offset, memOffset, encoding, maxCharacters, isVariableLengthType, isReferenceType) { @Override protected int getMemberStorageTypeId() { return stringOrRefDataTypeId; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { Object o = field.get(obj); if (o == null) { throw new NullPointerException("Field '" + field.getName() + "' is null"); } final String s = isCharArray ? new String((char[]) o) : o.toString(); if (isVariableLengthType) { final byte[] result = new byte[HDFNativeData.getMachineWordSize()]; HDFNativeData.compoundCpyVLStr(s, result, 0); return result; } else if (isReferenceType) { return fileAccessProvider.createObjectReference(s); } else { return StringUtils.toBytes0Term(s, getMaxCharacters(), encoding); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { final int totalOffset = arrayOffset + offsetInMemory; final int maxIdx = totalOffset + maxCharacters; final String s = bytesToString(byteArr, totalOffset, maxIdx, encoding, isVariableLengthType, isReferenceType); field.set(obj, isCharArray ? s.toCharArray() : s); } }; } private HDF5MemberByteifyer createByteifyerForMap(final String memberName, final IFileAccessProvider fileAccessProvider, final int offset, int memOffset, final int stringOrRefDataTypeId, final int maxCharacters, final int size, final CharacterEncoding encoding, final boolean isCharArray, final boolean isVariableLengthType, final boolean isReferenceType) { return new HDF5StringMemberByteifyer(null, memberName, size, offset, memOffset, encoding, maxCharacters, isVariableLengthType, isReferenceType) { @Override protected int getMemberStorageTypeId() { return stringOrRefDataTypeId; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { final Object o = getMap(obj, memberName); final String s; if (o.getClass() == char[].class) { s = new String((char[]) o); } else { s = o.toString(); } if (isVariableLengthType) { final byte[] result = new byte[HDFNativeData.getMachineWordSize()]; HDFNativeData.compoundCpyVLStr(s, result, 0); return result; } else if (isReferenceType) { return fileAccessProvider.createObjectReference(s); } else { return StringUtils.toBytes0Term(s, getMaxCharacters(), encoding); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { final int totalOffset = arrayOffset + offsetInMemory; final int maxIdx = totalOffset + maxCharacters; final String s = bytesToString(byteArr, totalOffset, maxIdx, encoding, isVariableLengthType, isReferenceType); if (isCharArray) { putMap(obj, memberName, s.toCharArray()); } else { putMap(obj, memberName, s); } } }; } private HDF5MemberByteifyer createByteifyerForList(final String memberName, final IFileAccessProvider fileAccessProvider, final int index, final int offset, int memOffset, final int stringOrRefDataTypeId, final int maxCharacters, final int size, final CharacterEncoding encoding, final boolean isCharArray, final boolean isVariableLengthType, final boolean isReferenceType) { return new HDF5StringMemberByteifyer(null, memberName, size, offset, memOffset, encoding, maxCharacters, isVariableLengthType, isReferenceType) { @Override protected int getMemberStorageTypeId() { return stringOrRefDataTypeId; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { final Object o = getList(obj, index); final String s; if (o.getClass() == char[].class) { s = new String((char[]) o); } else { s = o.toString(); } if (isVariableLengthType) { final byte[] result = new byte[HDFNativeData.getMachineWordSize()]; HDFNativeData.compoundCpyVLStr(s, result, 0); return result; } else if (isReferenceType) { return fileAccessProvider.createObjectReference(s); } else { return StringUtils.toBytes0Term(s, getMaxCharacters(), encoding); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { final int totalOffset = arrayOffset + offsetInMemory; final int maxIdx = totalOffset + maxCharacters; final String s = bytesToString(byteArr, totalOffset, maxIdx, encoding, isVariableLengthType, isReferenceType); if (isCharArray) { setList(obj, index, s.toCharArray()); } else { setList(obj, index, s); } } }; } private HDF5MemberByteifyer createByteifyerForArray(final String memberName, final IFileAccessProvider fileAccessProvider, final int index, final int offset, int memOffset, final int stringOrRefDataTypeId, final int maxCharacters, final int size, final CharacterEncoding encoding, final boolean isCharArray, final boolean isVariableLengthType, final boolean isReferenceType) { return new HDF5StringMemberByteifyer(null, memberName, size, offset, memOffset, encoding, maxCharacters, isVariableLengthType, isReferenceType) { @Override protected int getMemberStorageTypeId() { return stringOrRefDataTypeId; } @Override public byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException { final Object o = getArray(obj, index); final String s; if (o.getClass() == char[].class) { s = new String((char[]) o); } else { s = o.toString(); } if (isVariableLengthType) { final byte[] result = new byte[HDFNativeData.getMachineWordSize()]; HDFNativeData.compoundCpyVLStr(s, result, 0); return result; } else if (isReferenceType) { return fileAccessProvider.createObjectReference(s); } else { return StringUtils.toBytes0Term(s, getMaxCharacters(), encoding); } } @Override public void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException { final int totalOffset = arrayOffset + offsetInMemory; final int maxIdx = totalOffset + maxCharacters; final String s = bytesToString(byteArr, totalOffset, maxIdx, encoding, isVariableLengthType, isReferenceType); if (isCharArray) { setArray(obj, index, s.toCharArray()); } else { setArray(obj, index, s); } } }; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5CompoundMemberInformation.java000066400000000000000000000265531256564762100317710ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.lang.reflect.Field; import java.util.Arrays; import java.util.BitSet; import ch.systemsx.cisd.base.mdarray.MDAbstractArray; import ch.systemsx.cisd.base.mdarray.MDByteArray; import ch.systemsx.cisd.base.mdarray.MDDoubleArray; import ch.systemsx.cisd.base.mdarray.MDFloatArray; import ch.systemsx.cisd.base.mdarray.MDIntArray; import ch.systemsx.cisd.base.mdarray.MDLongArray; import ch.systemsx.cisd.base.mdarray.MDShortArray; import ch.systemsx.cisd.hdf5.HDF5DataTypeInformation.DataTypeInfoOptions; /** * Contains information about one member of an HDF5 compound data type. * * @author Bernd Rinn */ public final class HDF5CompoundMemberInformation implements Comparable { private final String memberName; private final HDF5DataTypeInformation dataTypeInformation; private final int offsetOnDisk; private final int offsetInMemory; private final String[] enumValuesOrNull; HDF5CompoundMemberInformation(String memberName, HDF5DataTypeInformation dataTypeInformation, int offsetOnDisk, int offsetInMemory, String[] enumValuesOrNull) { assert memberName != null; assert dataTypeInformation != null; assert offsetOnDisk >= 0; this.memberName = memberName; this.dataTypeInformation = dataTypeInformation; this.enumValuesOrNull = enumValuesOrNull; this.offsetOnDisk = offsetOnDisk; this.offsetInMemory = PaddingUtils.padOffset(offsetInMemory, dataTypeInformation.getElementSizeForPadding()); } HDF5CompoundMemberInformation(String memberName, HDF5DataTypeInformation dataTypeInformation, int offsetOnDisk, int offsetInMemory) { this(memberName, dataTypeInformation, offsetOnDisk, offsetInMemory, null); } /** * Returns the name of the member. */ public String getName() { return memberName; } /** * Returns the type information of the member. */ public HDF5DataTypeInformation getType() { return dataTypeInformation; } /** * Returns the values of the enumeration type of this compound member, if it is of an * enumeration type and null otherwise. */ public String[] tryGetEnumValues() { return enumValuesOrNull; } /** * Returns the byte offset of this member within the compound data type, 0 meaning that the * member is the first one in the compound data type. * * @deprecated Use {@link #getOffsetOnDisk()} instead. */ @Deprecated public int getOffset() { return offsetOnDisk; } /** * Returns the byte offset of this member within the compound data type on disk. 0 meaning that * the member is the first one in the compound data type. *

* The on-disk representation is packed. */ public int getOffsetOnDisk() { return offsetOnDisk; } /** * Returns the byte offset of this member within the compound data type in memory. 0 meaning * that the member is the first one in the compound data type. *

* The in-memory representation may contain padding to ensure that read access is always * aligned. */ public int getOffsetInMemory() { return offsetInMemory; } /** * Creates the compound member information for the given compoundClass and * members. The returned array will contain the members in the order of the * members. *

* Call Arrays.sort(compoundInformation) to sort the array in alphabetical order of * names. *

* Can be used to compare compound types, e.g. via * {@link java.util.Arrays#equals(Object[], Object[])}. */ public static HDF5CompoundMemberInformation[] create(Class compoundClass, String houseKeepingNameSuffix, final HDF5CompoundMemberMapping... members) { assert compoundClass != null; final HDF5CompoundMemberInformation[] info = new HDF5CompoundMemberInformation[members.length]; int offsetOnDisk = 0; int offsetInMemory = 0; for (int i = 0; i < info.length; ++i) { info[i] = new HDF5CompoundMemberInformation(members[i].getMemberName(), getTypeInformation(compoundClass, houseKeepingNameSuffix, members[i]), offsetOnDisk, offsetInMemory); final int elementSize = info[i].getType().getElementSize(); final int size = info[i].getType().getSize(); offsetOnDisk += size; offsetInMemory = PaddingUtils.padOffset(offsetInMemory + size, elementSize); } Arrays.sort(info); return info; } private static HDF5DataTypeInformation getTypeInformation(Class compoundClass, String houseKeepingNameSuffix, final HDF5CompoundMemberMapping member) { final Field fieldOrNull = member.tryGetField(compoundClass); final Class fieldTypeOrNull = (fieldOrNull == null) ? null : fieldOrNull.getType(); final HDF5DataTypeInformation typeInfo; if (fieldTypeOrNull == boolean.class) { typeInfo = new HDF5DataTypeInformation(HDF5DataClass.BOOLEAN, houseKeepingNameSuffix, 1, false); } else if (fieldTypeOrNull == byte.class || fieldTypeOrNull == byte[].class || fieldTypeOrNull == byte[][].class || fieldTypeOrNull == MDByteArray.class) { typeInfo = new HDF5DataTypeInformation(HDF5DataClass.INTEGER, houseKeepingNameSuffix, 1, false == member.isUnsigned()); } else if (fieldTypeOrNull == short.class || fieldTypeOrNull == short[].class || fieldTypeOrNull == short[][].class || fieldTypeOrNull == MDShortArray.class) { typeInfo = new HDF5DataTypeInformation(HDF5DataClass.INTEGER, houseKeepingNameSuffix, 2, false == member.isUnsigned()); } else if (fieldTypeOrNull == int.class || fieldTypeOrNull == int[].class || fieldTypeOrNull == int[][].class || fieldTypeOrNull == MDIntArray.class) { typeInfo = new HDF5DataTypeInformation(HDF5DataClass.INTEGER, houseKeepingNameSuffix, 4, false == member.isUnsigned()); } else if (fieldTypeOrNull == long.class || fieldTypeOrNull == long[].class || fieldTypeOrNull == long[][].class || fieldTypeOrNull == MDLongArray.class) { typeInfo = new HDF5DataTypeInformation(HDF5DataClass.INTEGER, houseKeepingNameSuffix, 8, false == member.isUnsigned()); } else if (fieldTypeOrNull == BitSet.class) { typeInfo = new HDF5DataTypeInformation(HDF5DataClass.BITFIELD, houseKeepingNameSuffix, 8, member.getMemberTypeLength() / 64 + (member.getMemberTypeLength() % 64 != 0 ? 1 : 0), false); } else if (fieldTypeOrNull == float.class || fieldTypeOrNull == float[].class || fieldTypeOrNull == float[][].class || fieldTypeOrNull == MDFloatArray.class) { typeInfo = new HDF5DataTypeInformation(HDF5DataClass.FLOAT, houseKeepingNameSuffix, 4, true); } else if (fieldTypeOrNull == double.class || fieldTypeOrNull == double[].class || fieldTypeOrNull == double[][].class || fieldTypeOrNull == MDDoubleArray.class) { typeInfo = new HDF5DataTypeInformation(HDF5DataClass.FLOAT, houseKeepingNameSuffix, 8, true); } else if (fieldTypeOrNull == String.class || fieldTypeOrNull == char[].class) { if (member.isReference()) { typeInfo = new HDF5DataTypeInformation(HDF5DataClass.REFERENCE, houseKeepingNameSuffix, HDF5BaseReader.REFERENCE_SIZE_IN_BYTES, false); } else { typeInfo = new HDF5DataTypeInformation(HDF5DataClass.STRING, houseKeepingNameSuffix, member.getMemberTypeLength(), false); } } else if (fieldTypeOrNull == HDF5EnumerationValue.class) { final DataTypeInfoOptions options = new DataTypeInfoOptions("UNKNOWN".equals(member.tryGetEnumerationType() .getName()) == false, member.tryGetTypeVariant() != null); typeInfo = new HDF5DataTypeInformation( options.knowsDataTypePath() ? HDF5Utils.createDataTypePath( HDF5Utils.ENUM_PREFIX, houseKeepingNameSuffix, member .tryGetEnumerationType().getName()) : null, options, HDF5DataClass.ENUM, houseKeepingNameSuffix, member .tryGetEnumerationType().getStorageForm().getStorageSize(), false); if (options.knowsDataTypeVariant()) { typeInfo.setTypeVariant(member.tryGetTypeVariant()); } } else { typeInfo = new HDF5DataTypeInformation(HDF5DataClass.OTHER, houseKeepingNameSuffix, -1, false); } if (fieldTypeOrNull != null && (fieldTypeOrNull.isArray() && fieldTypeOrNull != char[].class) || MDAbstractArray.class.isAssignableFrom(fieldTypeOrNull)) { typeInfo.setDimensions(member.getMemberTypeDimensions()); } return typeInfo; } // // Object // @Override public boolean equals(Object obj) { if (obj == null || obj instanceof HDF5CompoundMemberInformation == false) { return false; } final HDF5CompoundMemberInformation that = (HDF5CompoundMemberInformation) obj; return memberName.equals(that.memberName) && dataTypeInformation.equals(that.dataTypeInformation); } @Override public int hashCode() { return (17 * 59 + memberName.hashCode()) * 59 + dataTypeInformation.hashCode(); } @Override public String toString() { return memberName + ":" + dataTypeInformation.toString(); } // // Comparable // @Override public int compareTo(HDF5CompoundMemberInformation o) { return memberName.compareTo(o.memberName); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5CompoundMemberMapping.java000066400000000000000000001651511256564762100310750ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.lang.reflect.Array; import java.lang.reflect.Field; import java.util.ArrayList; import java.util.BitSet; import java.util.Collection; import java.util.Collections; import java.util.Comparator; import java.util.HashMap; import java.util.IdentityHashMap; import java.util.Iterator; import java.util.List; import java.util.Map; import java.util.Map.Entry; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import org.apache.commons.lang.StringUtils; import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel; import ch.systemsx.cisd.base.mdarray.MDAbstractArray; /** * A class that maps a Java field to a member of a HDF5 compound data type. *

* Example on how to use: * * 

 * static class Record
 *     {
 *         int i;
 * 
 *         String s;
 * 
 *         HDF5EnumerationValue e;
 * 
 *         Record(int i, String s, HDF5EnumerationValue e)
 *         {
 *             this.i = i;
 *             this.e = e;
 *             this.s = s;
 *         }
 * 
 *         Record()
 *         {
 *         }
 * 
 *         static HDF5CompoundType<Record> getHDF5Type(HDF5Reader reader)
 *         {
 *             final HDF5EnumerationType enumType = reader.getEnumType("someEnumType", new String[]
 *                 { "1", "Two", "THREE" });
 *             return reader.getCompoundType(Record.class, mapping("i"), 
 *                      mapping("s", 20), mapping("e", enumType));
 *         }
 * 
 *     }
 *         
 *     ...
 *         
 *     final HDF5Writer writer = new HDF5Writer(new File("test.h5").open();
 *     final HDF5CompoundType<Record> compoundType = Record.getHDF5Type(writer);
 *     final HDF5EnumerationType enumType = writer.getEnumType("someEnumType");
 *     Record[] array =
 *             new Record[]
 *                 {
 *                         new Record(1, "some text",
 *                                 new HDF5EnumerationValue(enumType, "THREE")),
 *                         new Record(2, "some note",
 *                                 new HDF5EnumerationValue(enumType, "1")), };
 *     writer.writeCompound("/testCompound", compoundType, recordWritten);
 *     writer.close();
 *
* * A simpler form is to let JHDF5 infer the mapping between fields in the Java object and members of * the compound data type, see {@link #inferMapping(Class)} and {@link #inferMapping(Class, Map)} * * @author Bernd Rinn */ public final class HDF5CompoundMemberMapping { private final String memberName; private final int storageDataTypeId; private final Field fieldOrNull; private String fieldName; private Class memberClassOrNull; private String enumTypeNameOrNull; private int memberTypeLength; private boolean unsigned; private boolean variableLength; private boolean reference; private int[] memberTypeDimensions; private HDF5EnumerationType enumTypeOrNull; private HDF5DataTypeVariant typeVariantOrNull; private HDF5CompoundMappingHints hintsOrNull; /** * Adds a member mapping for memberName. * * @param memberName The name of the member in the compound type. field in the Java class. Will * also be used to find the name of the field in the Java class if not overridden by * {@link #fieldName(String)}. */ public static HDF5CompoundMemberMapping mapping(String memberName) { return new HDF5CompoundMemberMapping(memberName); } /** * Adds a member mapping for fieldName. * * @param fieldName The name of the field in the Java class. * @param memberName The name of the member in the compound type. * @param memberClass The class of the member. Only used if the compound pojo class is a map. * For restrictions on the type, see above. * @param memberDimensions The dimensions of the compound type (i.e. length of the String or * dimensions of the array). * @param storageDataTypeId The storage data type id of the member, if known, or -1 else * @param unsigned If true, map to an unsigned integer type. * @param variableLength if true, map to a variable-length string type. * @param reference if true, map to a reference type. * @param typeVariantOrNull The data type variant of this mapping or null */ static HDF5CompoundMemberMapping mappingArrayWithStorageId(String fieldName, String memberName, Class memberClass, int[] memberDimensions, int storageDataTypeId, boolean unsigned, boolean variableLength, boolean reference, HDF5DataTypeVariant typeVariantOrNull) { return new HDF5CompoundMemberMapping(fieldName, null, memberClass, memberName, null, null, memberDimensions, storageDataTypeId, unsigned, variableLength, reference, typeVariantOrNull); } /** * Adds a member mapping for fieldName. Only suitable for Enumeration arrays. * * @param fieldName The name of the field in the Java class. * @param memberName The name of the member in the compound type. * @param enumType The enumeration type in the HDF5 file. * @param memberTypeDimensions The dimensions of the array in the compound type. * @param storageTypeId the id of the storage type of this member. * @param typeVariantOrNull The data type variant of this mapping or null */ static HDF5CompoundMemberMapping mappingWithStorageTypeId(String fieldName, String memberName, HDF5EnumerationType enumType, int[] memberTypeDimensions, int storageTypeId, HDF5DataTypeVariant typeVariantOrNull) { assert enumType != null; return new HDF5CompoundMemberMapping(fieldName, null, HDF5EnumerationValueArray.class, memberName, enumType, null, memberTypeDimensions, storageTypeId, false, false, false, typeVariantOrNull); } /** * Returns the inferred compound member mapping for the given pojoClass. This method * honors the annotations {@link CompoundType} and {@link CompoundElement}. *

* Note 1: All fields that correspond to members with a variable length (e.g. Strings, * primitive arrays and matrices and objects of type MDXXXArray) need to be * annotated with {@link CompoundElement} specifying their dimensions using * {@link CompoundElement#dimensions()}. . *

* Note 2: pojoClass containing HDF5 enumerations cannot have their mapping * inferred as the HDF5 enumeration type needs to be explicitly specified in the mapping. *

* Example 1: * * 

     * class Record1
     * {
     *     @CompoundElement(dimension = 10)
     *     String s;
     * 
     *     float f;
     * }
     *
* * will lead to: * * 
     * inferMapping(Record1.class) -> { mapping("s", 10), mapping("f") }
     *
* * Example 2: * * 
     * @CompoundType(mapAllFields = false)
     * class Record2
     * {
     *     @CompoundElement(memberName = "someString", dimension = 10)
     *     String s;
     * 
     *     float f;
     * }
     *
* * will lead to: * * 
     * inferMapping(Record2.class) -> { mapping("s", "someString", 10) }
     *
*/ public static HDF5CompoundMemberMapping[] inferMapping(final Class pojoClass) { return inferMapping(pojoClass, (HDF5CompoundMappingHints) null); } /** * Returns the inferred compound member mapping for the given pojoClass. This method * honors the annotations {@link CompoundType} and {@link CompoundElement}. *

* Note 1: All fields that correspond to members with a dimension (e.g. Strings, * primitive arrays and matrices and objects of type MDXXXArray) need to be * annotated with {@link CompoundElement} specifying their dimensions using * {@link CompoundElement#dimensions()}. Strings can alternatively also be annotated as * CompoundElement.variableLength = true. *

* Note 2: pojoClass containing HDF5 enumerations need to have their * {@link HDF5EnumerationType} specified in the fieldNameToEnumTypeMapOrNull. You may * use {@link #inferEnumerationTypeMap(Object, IHDF5EnumTypeRetriever)} to create * fieldNameToEnumTypeMapOrNull. *

* Example 1: * * 

     * class Record1
     * {
     *     @CompoundElement(dimension = 10)
     *     String s;
     * 
     *     float f;
     * }
     *
* * will lead to: * * 
     * inferMapping(Record1.class) -> { mapping("s", 10), mapping("f") }
     *
* * Example 2: * * 
     * @CompoundType(mapAllFields = false)
     * class Record2
     * {
     *     @CompoundElement(memberName = "someString", dimension = 10)
     *     String s;
     * 
     *     float f;
     * }
     *
* * will lead to: * * 
     * inferMapping(Record2.class) -> { mapping("s", "someString", 10) }
     *
*/ public static HDF5CompoundMemberMapping[] inferMapping(final Class pojoClass, final Map fieldNameToEnumTypeMapOrNull) { return inferMapping(pojoClass, new HDF5CompoundMappingHints().enumTypeMapping(fieldNameToEnumTypeMapOrNull)); } /** * Returns the inferred compound member mapping for the given pojoClass. This method * honors the annotations {@link CompoundType} and {@link CompoundElement}. *

* Note 1: All fields that correspond to members with a dimension (e.g. Strings, * primitive arrays and matrices and objects of type MDXXXArray) need to be * annotated with {@link CompoundElement} specifying their dimensions using * {@link CompoundElement#dimensions()}. Strings can alternatively also be annotated as * CompoundElement.variableLength = true. *

* Note 2: pojoClass containing HDF5 enumerations need to have their * {@link HDF5EnumerationType} specified in the fieldNameToEnumTypeMapOrNull. You may * use {@link #inferEnumerationTypeMap(Object, IHDF5EnumTypeRetriever)} to create * fieldNameToEnumTypeMapOrNull. *

* Example 1: * * 

     * class Record1
     * {
     *     @CompoundElement(dimension = 10)
     *     String s;
     * 
     *     float f;
     * }
     *
* * will lead to: * * 
     * inferMapping(Record1.class) -> { mapping("s", 10), mapping("f") }
     *
* * Example 2: * * 
     * @CompoundType(mapAllFields = false)
     * class Record2
     * {
     *     @CompoundElement(memberName = "someString", dimension = 10)
     *     String s;
     * 
     *     float f;
     * }
     *
* * will lead to: * * 
     * inferMapping(Record2.class) -> { mapping("s", "someString", 10) }
     *
*/ public static HDF5CompoundMemberMapping[] inferMapping(final Class pojoClass, final HDF5CompoundMappingHints hintsOrNull) { final List result = new ArrayList(pojoClass.getDeclaredFields().length); final CompoundType ct = pojoClass.getAnnotation(CompoundType.class); final boolean includeAllFields = (ct != null) ? ct.mapAllFields() : true; for (Class c = pojoClass; c != null; c = c.getSuperclass()) { for (Field f : c.getDeclaredFields()) { final HDF5EnumerationType enumTypeOrNull = (hintsOrNull != null) ? hintsOrNull.tryGetEnumType(f.getName()) : null; final CompoundElement e = f.getAnnotation(CompoundElement.class); if (e != null) { result.add(new HDF5CompoundMemberMapping(f.getName(), f, f.getType(), StringUtils.defaultIfEmpty(e.memberName(), f.getName()), enumTypeOrNull, e.typeName(), e.dimensions(), e.unsigned(), e .variableLength(), e.reference(), HDF5DataTypeVariant .unmaskNone(e.typeVariant()))); } else if (includeAllFields) { final boolean variableLength = (hintsOrNull == null) ? false : hintsOrNull .isUseVariableLengthStrings(); result.add(new HDF5CompoundMemberMapping(f.getName(), f, f.getType(), f .getName(), enumTypeOrNull, null, new int[0], false, variableLength, false, null)); } } } return result.toArray(new HDF5CompoundMemberMapping[result.size()]); } /** * @see #inferMapping(Class, Map)

* This method is using pojo to infer length and dimension information. */ public static HDF5CompoundMemberMapping[] inferMapping(final Object pojo, final Map fieldNameToEnumTypeMapOrNull) { return inferMapping(pojo, fieldNameToEnumTypeMapOrNull, false); } /** * This method is using pojo to infer length and dimension information. * * @param pojo The popo to infer member names, length and dimension information from. * @param fieldNameToEnumTypeMapOrNull The map to get member name to enumeration type mapping * from. * @param useVariableLengthStringTypes If true, use variable-length string types * for all strings in the pojo template. * @see #inferMapping(Class, Map)

*/ public static HDF5CompoundMemberMapping[] inferMapping(final Object pojo, final Map fieldNameToEnumTypeMapOrNull, final boolean useVariableLengthStringTypes) { final HDF5CompoundMemberMapping[] result = inferMapping(pojo.getClass(), fieldNameToEnumTypeMapOrNull); for (HDF5CompoundMemberMapping m : result) { try { final Class memberClass = m.tryGetMemberClass(); if (m.getMemberTypeDimensions().length == 0) { if (memberClass == String.class) { ReflectionUtils.ensureAccessible(m.fieldOrNull); if (useVariableLengthStringTypes) { m.variableLength(true); } else { final String value = (String) (m.fieldOrNull.get(pojo)); m.length(value != null ? value.length() : 0); } } else if (memberClass.isArray()) { if (memberClass.isArray()) { ReflectionUtils.ensureAccessible(m.fieldOrNull); final Object o = m.fieldOrNull.get(pojo); final int dimX = Array.getLength(o); if (memberClass.getComponentType().isArray() == false) { m.length(dimX); } else if (dimX > 0) { final Object firstElement = Array.get(o, 0); if (firstElement != null) { final int dimY = Array.getLength(firstElement); m.dimensions(new int[] { dimX, dimY }); } } } } else if (MDAbstractArray.class.isAssignableFrom(memberClass)) { ReflectionUtils.ensureAccessible(m.fieldOrNull); final Object o = m.fieldOrNull.get(pojo); m.dimensions(((MDAbstractArray) o).dimensions()); } } } catch (IllegalAccessException ex) { throw CheckedExceptionTunnel.wrapIfNecessary(ex); } } return result; } /** * This method is using pojo to infer length and dimension information. * * @param pojo The popo arrau to infer member names, length and dimension information from. * @param fieldNameToEnumTypeMapOrNull The map to get member name to enumeration type mapping * from. * @see #inferMapping(Class, Map)

*/ public static HDF5CompoundMemberMapping[] inferMapping(final Object[] pojo, final Map fieldNameToEnumTypeMapOrNull) { return inferMapping(pojo, fieldNameToEnumTypeMapOrNull); } /** * This method is using pojo to infer length and dimension information. * * @param pojo The popo arrau to infer member names, length and dimension information from. * @param fieldNameToEnumTypeMapOrNull The map to get member name to enumeration type mapping * from. * @param useVariableLengthStringTypes If true, use variable-length string types * for all strings in the pojo template. * @see #inferMapping(Class, Map)

*/ public static HDF5CompoundMemberMapping[] inferMapping(final Object[] pojo, final Map fieldNameToEnumTypeMapOrNull, final boolean useVariableLengthStringTypes) { final HDF5CompoundMemberMapping[] result = inferMapping(pojo.getClass().getComponentType(), fieldNameToEnumTypeMapOrNull); for (HDF5CompoundMemberMapping m : result) { try { final Class memberClass = m.tryGetMemberClass(); if (m.getMemberTypeDimensions().length == 0) { if (memberClass == String.class) { ReflectionUtils.ensureAccessible(m.fieldOrNull); if (useVariableLengthStringTypes) { m.variableLength(true); } else { int maxLen = 0; for (int i = 0; i < pojo.length; ++i) { maxLen = Math.max(maxLen, ((String) (m.fieldOrNull.get(pojo[i]))).length()); } m.length(maxLen); } } else if (memberClass.isArray()) { if (memberClass.isArray() && pojo.length > 0) { ReflectionUtils.ensureAccessible(m.fieldOrNull); final Object o = m.fieldOrNull.get(pojo[0]); final int dimX = Array.getLength(o); if (memberClass.getComponentType().isArray() == false) { m.length(dimX); } else if (dimX > 0) { final Object firstElement = Array.get(o, 0); if (firstElement != null) { final int dimY = Array.getLength(firstElement); m.dimensions(new int[] { dimX, dimY }); } } } } else if (MDAbstractArray.class.isAssignableFrom(memberClass) && pojo.length > 0) { ReflectionUtils.ensureAccessible(m.fieldOrNull); final Object o = m.fieldOrNull.get(pojo[0]); m.dimensions(((MDAbstractArray) o).dimensions()); } } } catch (IllegalAccessException ex) { throw CheckedExceptionTunnel.wrapIfNecessary(ex); } } return result; } /** * Adds the given hintsOrNull to all mapping. * * @return mapping. */ public static HDF5CompoundMemberMapping[] addHints(HDF5CompoundMemberMapping[] mapping, HDF5CompoundMappingHints hintsOrNull) { if (hintsOrNull != null) { for (HDF5CompoundMemberMapping m : mapping) { m.hints(hintsOrNull); } } return mapping; } /** * Returns the inferred compound member mapping for the given compoundMap. All * entries that correspond to members with length or dimension information take this information * from the values supplied. *

* Example: * * 

     * Map<String, Object> mw = new HashMap<String, Object>();
     * mw.put("date", new Date());
     * mw.put("temperatureInDegreeCelsius", 19.5f);
     * mw.put("voltagesInMilliVolts", new double[][] { 1, 2, 3 }, { 4, 5, 6 } });
     *
* * will lead to: * * 
     * inferMapping(mw) -> { mapping("date").memberClass(Date.class), 
     *                       mapping("temperatureInDegreeCelsius").memberClass(float.class), 
     *                       mapping("voltagesInMilliVolts").memberClass(double[][].class).dimensions(new int[] { 3, 3 } }
     *
*/ public static HDF5CompoundMemberMapping[] inferMapping(final Map compoundMap) { return inferMapping(compoundMap, (HDF5CompoundMappingHints) null); } /** * Returns the inferred compound member mapping for the given compoundMap. All * entries that correspond to members with length or dimension information take this information * from the values supplied. *

* Example: * * 

     * Map<String, Object> mw = new HashMap<String, Object>();
     * mw.put("date", new Date());
     * mw.put("temperatureInDegreeCelsius", 19.5f);
     * mw.put("voltagesInMilliVolts", new double[][] { 1, 2, 3 }, { 4, 5, 6 } });
     *
* * will lead to: * * 
     * inferMapping(mw) -> { mapping("date").memberClass(Date.class), 
     *                       mapping("temperatureInDegreeCelsius").memberClass(float.class), 
     *                       mapping("voltagesInMilliVolts").memberClass(double[][].class).dimensions(new int[] { 3, 3 } }
     *
*/ public static HDF5CompoundMemberMapping[] inferMapping(final Map compoundMap, final HDF5CompoundMappingHints hintsOrNull) { final List result = inferMapping(compoundMap.size(), compoundMap.entrySet(), hintsOrNull); Collections.sort(result, new Comparator() { @Override public int compare(HDF5CompoundMemberMapping o1, HDF5CompoundMemberMapping o2) { return o1.memberName.compareTo(o2.memberName); } }); return result.toArray(new HDF5CompoundMemberMapping[result.size()]); } /** * Returns the inferred compound member mapping for the given memberNames and * memberValues. All entries that correspond to members with length or dimension * information take this information from the values supplied. *

* Example: * * 

     * List<String> n = Arrays.asList("date", "temperatureInDegreeCelsius", "voltagesInMilliVolts");
     * List<Object> l = Arrays. <Object>asList(new Date(), 19.5f, new double[][] { 1, 2, 3 }, { 4, 5, 6 } });
     *
* * will lead to: * * 
     * inferMapping(n, l) -> { mapping("date").memberClass(Date.class), 
     *                       mapping("temperatureInDegreeCelsius").memberClass(float.class), 
     *                       mapping("voltagesInMilliVolts").memberClass(double[][].class).dimensions(new int[] { 3, 3 } }
     *
*/ public static HDF5CompoundMemberMapping[] inferMapping(final List memberNames, final List memberValues) { return inferMapping(memberNames, memberValues, (HDF5CompoundMappingHints) null); } /** * Returns the inferred compound member mapping for the given memberNames and * memberValues. All entries that correspond to members with length or dimension * information take this information from the values supplied. *

* Example: * * 

     * List<String> n = Arrays.asList("date", "temperatureInDegreeCelsius", "voltagesInMilliVolts");
     * List<Object> l = Arrays. <Object>asList(new Date(), 19.5f, new double[][] { 1, 2, 3 }, { 4, 5, 6 } });
     *
* * will lead to: * * 
     * inferMapping(n, l) -> { mapping("date").memberClass(Date.class), 
     *                       mapping("temperatureInDegreeCelsius").memberClass(float.class), 
     *                       mapping("voltagesInMilliVolts").memberClass(double[][].class).dimensions(new int[] { 3, 3 } }
     *
*/ public static HDF5CompoundMemberMapping[] inferMapping(final List memberNames, final List memberValues, final HDF5CompoundMappingHints hintsOrNull) { assert memberNames != null; assert memberValues != null; assert memberNames.size() == memberValues.size(); final List result = inferMapping(memberNames.size(), createEntryIterable(memberNames, memberValues), hintsOrNull); return result.toArray(new HDF5CompoundMemberMapping[result.size()]); } /** * Returns the inferred compound member mapping for the given memberNames and * memberValues. All entries that correspond to members with length or dimension * information take this information from the values supplied. *

* Example: * * 

     * String[] n = new String[] { "date", "temperatureInDegreeCelsius", "voltagesInMilliVolts" };
     * Object[] l = new Object[] { new Date(), 19.5f, new double[][] { 1, 2, 3 }, { 4, 5, 6 } } };
     *
* * will lead to: * * 
     * inferMapping(n, l) -> { mapping("date").memberClass(Date.class), 
     *                       mapping("temperatureInDegreeCelsius").memberClass(float.class), 
     *                       mapping("voltagesInMilliVolts").memberClass(double[][].class).dimensions(new int[] { 3, 3 } }
     *
*/ public static HDF5CompoundMemberMapping[] inferMapping(final String[] memberNames, final Object[] memberValues) { return inferMapping(memberNames, memberValues, (HDF5CompoundMappingHints) null); } /** * Returns the inferred compound member mapping for the given memberNames and * memberValues. All entries that correspond to members with length or dimension * information take this information from the values supplied. *

* Example: * * 

     * String[] n = new String[] { "date", "temperatureInDegreeCelsius", "voltagesInMilliVolts" };
     * Object[] l = new Object[] { new Date(), 19.5f, new double[][] { 1, 2, 3 }, { 4, 5, 6 } } };
     *
* * will lead to: * * 
     * inferMapping(n, l) -> { mapping("date").memberClass(Date.class), 
     *                       mapping("temperatureInDegreeCelsius").memberClass(float.class), 
     *                       mapping("voltagesInMilliVolts").memberClass(double[][].class).dimensions(new int[] { 3, 3 } }
     *
*/ public static HDF5CompoundMemberMapping[] inferMapping(final String[] memberNames, final Object[] memberValues, final HDF5CompoundMappingHints hints) { assert memberNames != null; assert memberValues != null; assert memberNames.length == memberValues.length; final List result = inferMapping(memberNames.length, createEntryIterable(memberNames, memberValues), hints); return result.toArray(new HDF5CompoundMemberMapping[result.size()]); } private static Iterable> createEntryIterable( final List memberNames, final List memberValues) { return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { int idx = -1; @Override public boolean hasNext() { return idx < memberNames.size() - 1; } @Override public Entry next() { ++idx; return new Entry() { @Override public String getKey() { return memberNames.get(idx); } @Override public Object getValue() { return memberValues.get(idx); } @Override public Object setValue(Object value) { throw new UnsupportedOperationException(); } }; } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } private static Iterable> createEntryIterable(final String[] memberNames, final Object[] memberValues) { return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { int idx = -1; @Override public boolean hasNext() { return idx < memberNames.length - 1; } @Override public Entry next() { ++idx; return new Entry() { @Override public String getKey() { return memberNames[idx]; } @Override public Object getValue() { return memberValues[idx]; } @Override public Object setValue(Object value) { throw new UnsupportedOperationException(); } }; } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } private static List inferMapping(final int size, final Iterable> entries, final HDF5CompoundMappingHints hintsOrNull) { final List result = new ArrayList(size); for (Map.Entry entry : entries) { final String memberName = entry.getKey(); final Object memberValue = entry.getValue(); final Class memberClass = HDF5Utils.unwrapClass(memberValue.getClass()); HDF5DataTypeVariant variantOrNull; if (memberClass == HDF5TimeDuration.class) { variantOrNull = ((HDF5TimeDuration) memberValue).getUnit().getTypeVariant(); } else { variantOrNull = null; } if (memberClass.isArray()) { final int lenx = Array.getLength(memberValue); if (lenx > 0 && Array.get(memberValue, 0).getClass().isArray()) { final int leny = Array.getLength(Array.get(memberValue, 0)); result.add(new HDF5CompoundMemberMapping(memberName, memberClass, memberName, null, null, new int[] { lenx, leny }, variantOrNull)); } else { result.add(new HDF5CompoundMemberMapping(memberName, memberClass, memberName, null, null, new int[] { lenx }, variantOrNull)); } } else if (MDAbstractArray.class.isInstance(memberValue)) { result.add(new HDF5CompoundMemberMapping(memberName, memberClass, memberName, null, null, ((MDAbstractArray) memberValue).dimensions(), variantOrNull)); } else { HDF5EnumerationType enumTypeOrNull = null; final boolean variableLength = (hintsOrNull == null) ? false : hintsOrNull.isUseVariableLengthStrings(); final int[] dimensions; if (memberClass == HDF5EnumerationValue.class) { enumTypeOrNull = ((HDF5EnumerationValue) memberValue).getType(); dimensions = new int[0]; } else if (memberClass == HDF5EnumerationValueArray.class) { enumTypeOrNull = ((HDF5EnumerationValueArray) memberValue).getType(); dimensions = new int[] { ((HDF5EnumerationValueArray) memberValue).getLength() }; } else if (memberClass == String.class) { dimensions = (variableLength) ? new int[0] : new int[] { ((String) memberValue).length() }; } else if (memberClass == BitSet.class) { final int len = ((BitSet) memberValue).length(); dimensions = new int[] { len > 0 ? len : 1 }; } else { dimensions = new int[0]; } result.add(new HDF5CompoundMemberMapping(memberName, memberClass, memberName, enumTypeOrNull, null, dimensions, false, variableLength, variantOrNull) .hints(hintsOrNull)); } } return result; } /** * Infers a name for a compound type from the given memberNames by concatenating * them. * * @param memberNames The names of the members to use to build the compound type name from. * @param sort If true, the names will be sorted before they are concatenated. */ public static String constructCompoundTypeName(final Collection memberNames, boolean sort) { final Collection names = sort ? sort(memberNames) : memberNames; final StringBuilder b = new StringBuilder(); for (String name : names) { b.append(name); b.append(':'); } b.setLength(b.length() - 1); return b.toString(); } private static List sort(Collection memberNames) { final List names = new ArrayList(memberNames); Collections.sort(names); return names; } /** * Infers the map from field names to {@link HDF5EnumerationType}s for the given pojo * object. */ public static Map inferEnumerationTypeMap(T pojo, IHDF5EnumTypeRetriever enumTypeRetriever) { Map resultOrNull = null; for (Class c = pojo.getClass(); c != null; c = c.getSuperclass()) { for (Field f : c.getDeclaredFields()) { if (f.getType() == HDF5EnumerationValue.class) { ReflectionUtils.ensureAccessible(f); try { if (resultOrNull == null) { resultOrNull = new HashMap(); } resultOrNull.put(f.getName(), ((HDF5EnumerationValue) f.get(pojo)).getType()); } catch (IllegalArgumentException ex) { throw new Error(ex); } catch (IllegalAccessException ex) { throw new Error(ex); } } if (f.getType().isEnum()) { ReflectionUtils.ensureAccessible(f); try { if (resultOrNull == null) { resultOrNull = new HashMap(); } resultOrNull.put(f.getName(), enumTypeRetriever.getType(f.getType() .getSimpleName(), ReflectionUtils.getEnumOptions(asEnumClass(f)))); } catch (IllegalArgumentException ex) { throw new Error(ex); } } if (f.getType() == HDF5EnumerationValueArray.class) { ReflectionUtils.ensureAccessible(f); try { if (resultOrNull == null) { resultOrNull = new HashMap(); } resultOrNull.put(f.getName(), ((HDF5EnumerationValueArray) f.get(pojo)).getType()); } catch (IllegalArgumentException ex) { throw new Error(ex); } catch (IllegalAccessException ex) { throw new Error(ex); } } } } return resultOrNull; } @SuppressWarnings("unchecked") private static Class> asEnumClass(Field f) { return (Class>) f.getType(); } @SuppressWarnings("rawtypes") private final static IdentityHashMap typeVariantMap = new IdentityHashMap(); static { typeVariantMap.put(java.util.Date.class, HDF5DataTypeVariant.TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH); typeVariantMap.put(HDF5TimeDuration.class, HDF5DataTypeVariant.TIME_DURATION_MICROSECONDS); } /** * A {@link HDF5CompoundMemberMapping} that allows to provide an explicit memberName * that differs from the fieldName and the maximal length in case of a String member. * * @param fieldName The name of the field in the clazz * @param memberClassOrNull The class of the member, if a map is used as the compound pojo. * @param memberName The name of the member in the HDF5 compound data type. * @param memberTypeDimensions The dimensions of the member type, or 0 for a scalar value. */ private HDF5CompoundMemberMapping(String fieldName) { this(fieldName, null, null, fieldName, null, null, new int[0], -1, false, false, false, null); } /** * A {@link HDF5CompoundMemberMapping} that allows to provide an explicit memberName * that differs from the fieldName and the maximal length in case of a String member. * * @param fieldName The name of the field in the clazz * @param memberClassOrNull The class of the member, if a map is used as the compound pojo. * @param memberName The name of the member in the HDF5 compound data type. * @param enumTypeOrNull The HDF5 enumeration type of this member. * @param enumTypeNameOrNull The name to be used for the HDF5 enumeration type. * @param memberTypeDimensions The dimensions of the member type, or 0 for a scalar value. * @param unsigned If true, the type will be mapped to an unsigned integer type. * @param typeVariantOrNull The data type variant of this mapping, or null if this * mapping has no type variant. */ private HDF5CompoundMemberMapping(String fieldName, Class memberClassOrNull, String memberName, HDF5EnumerationType enumTypeOrNull, String enumTypeNameOrNull, int[] memberTypeDimensions, HDF5DataTypeVariant typeVariantOrNull) { this(fieldName, null, memberClassOrNull, memberName, enumTypeOrNull, enumTypeNameOrNull, memberTypeDimensions, -1, false, false, false, typeVariantOrNull); } /** * A {@link HDF5CompoundMemberMapping} that allows to provide an explicit memberName * that differs from the fieldName and the maximal length in case of a String member. * * @param fieldName The name of the field in the clazz * @param memberClassOrNull The class of the member, if a map is used as the compound pojo. * @param memberName The name of the member in the HDF5 compound data type. * @param enumTypeOrNull The HDF5 enumeration type of this member. * @param enumTypeNameOrNull The name to be used for the HDF5 enumeration type. * @param memberTypeDimensions The dimensions of the member type, or 0 for a scalar value. * @param unsigned If true, the type will be mapped to an unsigned integer type. * @param variableLength If true, the type will be mapped to a variable-length * type. * @param typeVariantOrNull The data type variant of this mapping, or null if this * mapping has no type variant. */ private HDF5CompoundMemberMapping(String fieldName, Class memberClassOrNull, String memberName, HDF5EnumerationType enumTypeOrNull, String enumTypeNameOrNull, int[] memberTypeDimensions, boolean unsigned, boolean variableLength, HDF5DataTypeVariant typeVariantOrNull) { this(fieldName, null, memberClassOrNull, memberName, enumTypeOrNull, enumTypeNameOrNull, memberTypeDimensions, -1, unsigned, variableLength, false, typeVariantOrNull); } /** * A {@link HDF5CompoundMemberMapping} that allows to provide an explicit memberName * that differs from the fieldName and the maximal length in case of a String member. * * @param fieldName The name of the field in the clazz * @param fieldOrNull The {@link Field} in the compound class (may be null) * @param memberClassOrNull The class of the member, if a map is used as the compound pojo. * @param memberName The name of the member in the HDF5 compound data type. * @param enumTypeOrNull The HDF5 enumeration type of this member. * @param enumTypeNameOrNull The name to be used for the HDF5 enumeration type. * @param memberTypeDimensions The dimensions of the member type, or 0 for a scalar value. * @param unsigned If true, the type will be mapped to an unsigned integer type. * @param variableLength If true, the type will be mapped to a variable-length * type. * @param reference If true, the type will be mapped to a reference type. type. * @param typeVariantOrNull The data type variant of this mapping, or null if this * mapping has no type variant. */ private HDF5CompoundMemberMapping(String fieldName, Field fieldOrNull, Class memberClassOrNull, String memberName, HDF5EnumerationType enumTypeOrNull, String enumTypeNameOrNull, int[] memberTypeDimensions, boolean unsigned, boolean variableLength, boolean reference, HDF5DataTypeVariant typeVariantOrNull) { this(fieldName, fieldOrNull, memberClassOrNull, memberName, enumTypeOrNull, enumTypeNameOrNull, memberTypeDimensions, -1, unsigned, variableLength, reference, typeVariantOrNull); } /** * A {@link HDF5CompoundMemberMapping} that allows to provide an explicit memberName * that differs from the fieldName and the maximal length in case of a String member. * * @param fieldName The name of the field in the clazz * @param fieldOrNull The {@link Field} in the compound class (may be null) * @param memberClassOrNull The class of the member, if a map is used as the compound pojo. * @param memberName The name of the member in the HDF5 compound data type. * @param enumTypeOrNull The enumeation type (only for enumerations, obviously). * @param enumTypeNameOrNull The name of the committed HDF5 enum type. * @param memberTypeDimensions The dimensions of the member type, or 0 for a scalar value. * @param unsigned If true, the type will be mapped to an unsigned integer type. * @param variableLength If true, the type will be mapped to a variable-length * string type. * @param reference If true, the type will be mapped to a reference type. * @param storageMemberTypeId The storage data type id of member, or -1, if not available */ private HDF5CompoundMemberMapping(String fieldName, Field fieldOrNull, Class memberClassOrNull, String memberName, HDF5EnumerationType enumTypeOrNull, String enumTypeNameOrNull, int[] memberTypeDimensions, int storageMemberTypeId, boolean unsigned, boolean variableLength, boolean reference, HDF5DataTypeVariant typeVariantOrNull) { this.fieldOrNull = fieldOrNull; this.fieldName = fieldName; this.memberClassOrNull = memberClassOrNull; this.memberName = memberName; this.enumTypeOrNull = enumTypeOrNull; this.enumTypeNameOrNull = enumTypeNameOrNull; this.memberTypeDimensions = memberTypeDimensions; this.memberTypeLength = MDAbstractArray.getLength(memberTypeDimensions); this.storageDataTypeId = storageMemberTypeId; this.unsigned = unsigned; this.variableLength = variableLength; this.reference = reference; if (typeVariantMap.containsKey(typeVariantOrNull)) { this.typeVariantOrNull = typeVariantMap.get(typeVariantOrNull); } else { this.typeVariantOrNull = HDF5DataTypeVariant.maskNull(typeVariantOrNull); } } /** * Sets the field name in the Java class to use for the mapping, overriding the member name * which is used by default to find the field. */ @SuppressWarnings("hiding") public HDF5CompoundMemberMapping fieldName(String fieldName) { this.fieldName = fieldName; return this; } /** * Sets the name to be used for the comitted HDF5 datatype (for Java enum types only, overriding * the simple class name which is used by default as the type name. */ public HDF5CompoundMemberMapping enumTypeName(String enumTypeName) { this.enumTypeNameOrNull = (enumTypeName != null && enumTypeName.length() == 0) ? null : enumTypeName; return this; } String tryGetEnumTypeName() { return enumTypeNameOrNull; } Field tryGetField(Class clazz, boolean skipChecks) throws HDF5JavaException { return tryGetField(clazz, clazz, skipChecks); } Field tryGetField(Class clazz) throws HDF5JavaException { return tryGetField(clazz, clazz, false); } private Field tryGetField(Class clazz, Class searchClass, boolean skipChecks) throws HDF5JavaException { try { final Field field = clazz.getDeclaredField(fieldName); final boolean isArray = isArray(field); if (skipChecks == false) { if (memberTypeLength > 1) { if (field.getType() != String.class && false == isArray) { throw new HDF5JavaException("Field '" + fieldName + "' of class '" + clazz.getCanonicalName() + "' is no String or array, but a length > 1 is given."); } } else if (memberTypeLength == 0 && (isFixedLengthString(field) || isArray)) { throw new HDF5JavaException("Field '" + fieldName + "' of class '" + clazz.getCanonicalName() + "' is a String or array, but a length == 0 is given."); } } return field; } catch (NoSuchFieldException ex) { final Class superClassOrNull = clazz.getSuperclass(); if (superClassOrNull == null || superClassOrNull == Object.class) { return null; } else { return tryGetField(superClassOrNull, searchClass, skipChecks); } } } private boolean isArray(final Field field) { final Class fieldType = field.getType(); return fieldType.isArray() || MDAbstractArray.class.isAssignableFrom(fieldType) || field.getType() == java.util.BitSet.class || field.getType() == HDF5EnumerationValueArray.class; } private boolean isFixedLengthString(final Field field) { return (field.getType() == String.class && false == variableLength && false == reference) && (hintsOrNull != null && false == hintsOrNull.isUseVariableLengthStrings()); } String getMemberName() { return memberName; } /** * Sets the member class to use for the mapping. */ public HDF5CompoundMemberMapping memberClass(Class memberClass) { this.memberClassOrNull = memberClass; return this; } public Class tryGetMemberClass() { return memberClassOrNull; } /** * Sets the length of the member type to use for the mapping. Must be set for String, BitSet. * Can be used as a convenience method replacing {@link #dimensions(int[])} for array members of * rank 1. */ @SuppressWarnings("hiding") public HDF5CompoundMemberMapping length(int memberTypeLength) { return dimensions(new int[] { memberTypeLength }); } int getMemberTypeLength() { return memberTypeLength; } /** * Sets the dimensions of the member type to use for the mapping. Convenience method replacing * {@link #dimensions(int[])} for array members of rank 2. */ public HDF5CompoundMemberMapping dimensions(int memberTypeDimensionX, int memberTypeDimensionY) { this.memberTypeDimensions = new int[] { memberTypeDimensionX, memberTypeDimensionY }; this.memberTypeLength = MDAbstractArray.getLength(memberTypeDimensions); return this; } /** * Sets the dimensions of the member type to use for the mapping. Must be set for array members * of rank N. */ @SuppressWarnings("hiding") public HDF5CompoundMemberMapping dimensions(int[] memberTypeDimensions) { this.memberTypeDimensions = memberTypeDimensions; this.memberTypeLength = MDAbstractArray.getLength(memberTypeDimensions); if (enumTypeOrNull != null) { checkEnumArrayRank(); this.memberClassOrNull = HDF5EnumerationValueArray.class; } return this; } /** * Sets this field to an unsigned type. Must be an integer. */ public HDF5CompoundMemberMapping unsigned() { this.unsigned = true; return this; } /** * Sets this field to an unsigned type, if unsigned is true. Must be an * integer. */ public HDF5CompoundMemberMapping unsigned(@SuppressWarnings("hiding") boolean unsigned) { this.unsigned = unsigned; return this; } /** * Returns true if this field should be mapped to an unsigned integer. */ boolean isUnsigned() { return this.unsigned; } /** * Sets this field to a variable-length type. Must be a string. */ public HDF5CompoundMemberMapping variableLength() { this.variableLength = true; return this; } /** * Sets this field to a variable-length type, if variableLength is true. * Must be a string. */ public HDF5CompoundMemberMapping variableLength(@SuppressWarnings("hiding") boolean variableLength) { this.variableLength = variableLength; return this; } /** * Returns true if this field should be mapped to a variable-length string. */ public boolean isVariableLength() { return this.variableLength; } /** * Sets this field to a reference type. Must be a string. */ public HDF5CompoundMemberMapping reference() { this.reference = true; return this; } /** * Sets this field to a reference type, if reference is true. Must be a * string. */ public HDF5CompoundMemberMapping reference(@SuppressWarnings("hiding") boolean reference) { this.reference = reference; return this; } /** * Returns true if this field should be mapped to a refernce type. */ public boolean isReference() { return this.reference; } /** * Sets mapping hints for this mapping. */ public HDF5CompoundMemberMapping hints(HDF5CompoundMappingHints hints) { this.hintsOrNull = hints; return this; } private void checkEnumArrayRank() { if (memberTypeDimensions != null && memberTypeDimensions.length > 1) { throw new HDF5JavaException("Enumeration arrays only supported with rank 1 [rank=" + memberTypeDimensions.length + "]"); } } int[] getMemberTypeDimensions() { return memberTypeDimensions; } int getStorageDataTypeId() { return storageDataTypeId; } /** * Sets the enumeration type to use for the mapping. Must be set for enumeration members. */ public HDF5CompoundMemberMapping enumType(HDF5EnumerationType enumType) { this.enumTypeOrNull = enumType; checkEnumArrayRank(); this.memberClassOrNull = (memberTypeLength == 0) ? HDF5EnumerationValue.class : HDF5EnumerationValueArray.class; return this; } HDF5EnumerationType tryGetEnumerationType() { return enumTypeOrNull; } void setEnumerationType(HDF5EnumerationType enumType) { this.enumTypeOrNull = enumType; } HDF5CompoundMappingHints tryGetHints() { return hintsOrNull; } /** * Sets the data type variant to use for the mapping. */ public HDF5CompoundMemberMapping typeVariant(HDF5DataTypeVariant typeVariant) { this.typeVariantOrNull = typeVariant; return this; } HDF5DataTypeVariant tryGetTypeVariant() { return typeVariantOrNull; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5CompoundReader.java000066400000000000000000000762471256564762100275630ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_ARRAY; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_COMPOUND; import java.util.Iterator; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.base.mdarray.MDAbstractArray; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.hdf5.HDF5BaseReader.DataSpaceParameters; import ch.systemsx.cisd.hdf5.HDF5DataTypeInformation.DataTypeInfoOptions; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; /** * The implementation of {@link IHDF5CompoundReader}. * * @author Bernd Rinn */ class HDF5CompoundReader extends HDF5CompoundInformationRetriever implements IHDF5CompoundReader { HDF5CompoundReader(HDF5BaseReader baseReader, IHDF5EnumReader enumReader) { super(baseReader, enumReader); } @Override public T getAttr(final String objectPath, final String attributeName, final HDF5CompoundType type) throws HDF5JavaException { return primGetCompoundAttribute(objectPath, attributeName, type, null); } @Override public T getAttr(final String objectPath, final String attributeName, final Class pojoClass) throws HDF5JavaException { baseReader.checkOpen(); final HDF5CompoundType attributeCompoundType = getAttributeType(objectPath, attributeName, pojoClass); attributeCompoundType.checkMappingComplete(); return primGetCompoundAttribute(objectPath, attributeName, attributeCompoundType, null); } @Override public T[] getArrayAttr(String objectPath, String attributeName, HDF5CompoundType type) throws HDF5JavaException { return primGetCompoundArrayAttribute(objectPath, attributeName, type, null); } @Override public T[] getArrayAttr(String objectPath, String attributeName, Class pojoClass) throws HDF5JavaException { baseReader.checkOpen(); final HDF5CompoundType attributeCompoundType = getAttributeType(objectPath, attributeName, pojoClass); attributeCompoundType.checkMappingComplete(); return primGetCompoundArrayAttribute(objectPath, attributeName, attributeCompoundType, null); } @Override public MDArray getMDArrayAttr(String objectPath, String attributeName, HDF5CompoundType type) throws HDF5JavaException { return primGetCompoundMDArrayAttribute(objectPath, attributeName, type, null); } @Override public MDArray getMDArrayAttr(String objectPath, String attributeName, Class pojoClass) throws HDF5JavaException { baseReader.checkOpen(); final HDF5CompoundType attributeCompoundType = getAttributeType(objectPath, attributeName, pojoClass); attributeCompoundType.checkMappingComplete(); return primGetCompoundMDArrayAttribute(objectPath, attributeName, attributeCompoundType, null); } private T primGetCompoundAttribute(final String objectPath, final String attributeName, final HDF5CompoundType type, final IByteArrayInspector inspectorOrNull) throws HDF5JavaException { final ICallableWithCleanUp readRunnable = new ICallableWithCleanUp() { @Override public T call(final ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int storageDataTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, registry); checkCompoundType(storageDataTypeId, objectPath, type); final int nativeDataTypeId = type.getNativeTypeId(); final byte[] byteArr = baseReader.h5.readAttributeAsByteArray(attributeId, nativeDataTypeId, type.getObjectByteifyer().getRecordSizeInMemory()); if (inspectorOrNull != null) { inspectorOrNull.inspect(byteArr); } final T scalar = type.getObjectByteifyer().arrayifyScalar(storageDataTypeId, byteArr, type.getCompoundType()); baseReader.h5.reclaimCompoundVL(type, byteArr); return scalar; } }; return baseReader.runner.call(readRunnable); } private T[] primGetCompoundArrayAttribute(final String objectPath, final String attributeName, final HDF5CompoundType type, final IByteArrayInspector inspectorOrNull) throws HDF5JavaException { final ICallableWithCleanUp readRunnable = new ICallableWithCleanUp() { @Override public T[] call(final ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); final int attributeId = baseReader.h5.openAttribute(dataSetId, attributeName, registry); final int storageDataTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, registry); final int nativeDataTypeId = baseReader.h5.getNativeDataType(storageDataTypeId, registry); final int len; final int compoundTypeId; if (baseReader.h5.getClassType(storageDataTypeId) == H5T_ARRAY) { final int[] arrayDimensions = baseReader.h5.getArrayDimensions(storageDataTypeId); len = HDF5Utils.getOneDimensionalArraySize(arrayDimensions); compoundTypeId = baseReader.h5.getBaseDataType(storageDataTypeId, registry); if (baseReader.h5.getClassType(compoundTypeId) != H5T_COMPOUND) { throw new HDF5JavaException("Attribute '" + attributeName + "' of object '" + objectPath + "' is not of type compound array."); } } else { if (baseReader.h5.getClassType(storageDataTypeId) != H5T_COMPOUND) { throw new HDF5JavaException("Attribute '" + attributeName + "' of object '" + objectPath + "' is not of type compound array."); } compoundTypeId = storageDataTypeId; final long[] arrayDimensions = baseReader.h5.getDataDimensionsForAttribute(attributeId, registry); len = HDF5Utils.getOneDimensionalArraySize(arrayDimensions); } checkCompoundType(compoundTypeId, objectPath, type); final byte[] byteArr = baseReader.h5.readAttributeAsByteArray(attributeId, nativeDataTypeId, len * type.getRecordSizeInMemory()); if (inspectorOrNull != null) { inspectorOrNull.inspect(byteArr); } final T[] array = type.getObjectByteifyer().arrayify(storageDataTypeId, byteArr, type.getCompoundType()); baseReader.h5.reclaimCompoundVL(type, byteArr); return array; } }; return baseReader.runner.call(readRunnable); } private MDArray primGetCompoundMDArrayAttribute(final String objectPath, final String attributeName, final HDF5CompoundType type, final IByteArrayInspector inspectorOrNull) throws HDF5JavaException { final ICallableWithCleanUp> readRunnable = new ICallableWithCleanUp>() { @Override public MDArray call(final ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); final int attributeId = baseReader.h5.openAttribute(dataSetId, attributeName, registry); final int storageDataTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, registry); final int nativeDataTypeId = baseReader.h5.getNativeDataType(storageDataTypeId, registry); final int len; final int[] arrayDimensions; final int compoundTypeId; if (baseReader.h5.getClassType(storageDataTypeId) == H5T_ARRAY) { arrayDimensions = baseReader.h5.getArrayDimensions(storageDataTypeId); len = MDAbstractArray.getLength(arrayDimensions); compoundTypeId = baseReader.h5.getBaseDataType(storageDataTypeId, registry); if (baseReader.h5.getClassType(compoundTypeId) != H5T_COMPOUND) { throw new HDF5JavaException("Attribute '" + attributeName + "' of object '" + objectPath + "' is not of type compound array."); } } else { if (baseReader.h5.getClassType(storageDataTypeId) != H5T_COMPOUND) { throw new HDF5JavaException("Attribute '" + attributeName + "' of object '" + objectPath + "' is not of type compound array."); } compoundTypeId = storageDataTypeId; arrayDimensions = MDAbstractArray.toInt(baseReader.h5.getDataDimensionsForAttribute( attributeId, registry)); len = MDAbstractArray.getLength(arrayDimensions); } checkCompoundType(compoundTypeId, objectPath, type); final byte[] byteArr = baseReader.h5.readAttributeAsByteArray(attributeId, nativeDataTypeId, len * type.getRecordSizeInMemory()); if (inspectorOrNull != null) { inspectorOrNull.inspect(byteArr); } final MDArray array = new MDArray(type.getObjectByteifyer().arrayify( storageDataTypeId, byteArr, type.getCompoundType()), arrayDimensions); baseReader.h5.reclaimCompoundVL(type, byteArr); return array; } }; return baseReader.runner.call(readRunnable); } @Override public T read(final String objectPath, final HDF5CompoundType type) throws HDF5JavaException { return read(objectPath, type, null); } @Override public T read(final String objectPath, final Class pojoClass) throws HDF5JavaException { baseReader.checkOpen(); final HDF5CompoundType dataSetCompoundType = getDataSetType(objectPath, pojoClass); dataSetCompoundType.checkMappingComplete(); return read(objectPath, dataSetCompoundType, null); } @Override public T read(final String objectPath, final HDF5CompoundType type, final IByteArrayInspector inspectorOrNull) throws HDF5JavaException { baseReader.checkOpen(); type.check(baseReader.fileId); return primReadCompound(objectPath, -1, -1, type, inspectorOrNull); } @Override public T[] readArray(final String objectPath, final HDF5CompoundType type) throws HDF5JavaException { return readArray(objectPath, type, null); } @Override public T[] readArray(final String objectPath, final HDF5CompoundType type, final IByteArrayInspector inspectorOrNull) throws HDF5JavaException { baseReader.checkOpen(); type.check(baseReader.fileId); return primReadCompoundArray(objectPath, -1, -1, type, inspectorOrNull); } @Override public T[] readArray(final String objectPath, final Class pojoClass) throws HDF5JavaException { baseReader.checkOpen(); final HDF5CompoundType dataSetCompoundType = getDataSetType(objectPath, pojoClass); dataSetCompoundType.checkMappingComplete(); return readArray(objectPath, dataSetCompoundType, null); } @Override public T[] readArrayBlock(final String objectPath, final HDF5CompoundType type, final int blockSize, final long blockNumber) throws HDF5JavaException { return readArrayBlock(objectPath, type, blockSize, blockNumber, null); } @Override public T[] readArrayBlock(final String objectPath, final HDF5CompoundType type, final int blockSize, final long blockNumber, final IByteArrayInspector inspectorOrNull) throws HDF5JavaException { baseReader.checkOpen(); type.check(baseReader.fileId); return primReadCompoundArray(objectPath, blockSize, blockSize * blockNumber, type, inspectorOrNull); } @Override public T[] readArrayBlockWithOffset(final String objectPath, final HDF5CompoundType type, final int blockSize, final long offset) throws HDF5JavaException { return readArrayBlockWithOffset(objectPath, type, blockSize, offset, null); } @Override public T[] readArrayBlockWithOffset(final String objectPath, final HDF5CompoundType type, final int blockSize, final long offset, final IByteArrayInspector inspectorOrNull) throws HDF5JavaException { baseReader.checkOpen(); type.check(baseReader.fileId); return primReadCompoundArray(objectPath, blockSize, offset, type, inspectorOrNull); } @Override public Iterable> getArrayBlocks(final String objectPath, final HDF5CompoundType type) throws HDF5JavaException { return getArrayBlocks(objectPath, type, null); } @Override public Iterable> getArrayBlocks(final String objectPath, final HDF5CompoundType type, final IByteArrayInspector inspectorOrNull) throws HDF5JavaException { baseReader.checkOpen(); type.check(baseReader.fileId); final HDF5NaturalBlock1DParameters params = new HDF5NaturalBlock1DParameters(baseReader.getDataSetInformation(objectPath)); return primGetCompoundArrayNaturalBlocks(objectPath, type, params, inspectorOrNull); } private Iterable> primGetCompoundArrayNaturalBlocks( final String objectPath, final HDF5CompoundType type, final HDF5NaturalBlock1DParameters params, final IByteArrayInspector inspectorOrNull) { return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlock1DParameters.HDF5NaturalBlock1DIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5DataBlock next() { final long offset = index.computeOffsetAndSizeGetOffset(); final T[] block = readArrayBlockWithOffset(objectPath, type, index.getBlockSize(), offset, inspectorOrNull); return new HDF5DataBlock(block, index.getAndIncIndex(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } @Override public Iterable> getArrayBlocks(String objectPath, Class pojoClass) throws HDF5JavaException { baseReader.checkOpen(); final HDF5NaturalBlock1DParameters params = new HDF5NaturalBlock1DParameters(baseReader.getDataSetInformation(objectPath)); final HDF5CompoundType dataSetCompoundType = getDataSetType(objectPath, pojoClass); dataSetCompoundType.checkMappingComplete(); return primGetCompoundArrayNaturalBlocks(objectPath, dataSetCompoundType, params, null); } private T primReadCompound(final String objectPath, final int blockSize, final long offset, final HDF5CompoundType type, final IByteArrayInspector inspectorOrNull) throws HDF5JavaException { final ICallableWithCleanUp readRunnable = new ICallableWithCleanUp() { @Override public T call(final ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final int storageDataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); checkCompoundType(storageDataTypeId, objectPath, type); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockSize, registry); final int nativeDataTypeId = type.getNativeTypeId(); final byte[] byteArr = new byte[spaceParams.blockSize * type.getObjectByteifyer().getRecordSizeInMemory()]; baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, byteArr); if (inspectorOrNull != null) { inspectorOrNull.inspect(byteArr); } final T scalar = type.getObjectByteifyer().arrayifyScalar(storageDataTypeId, byteArr, type.getCompoundType()); baseReader.h5.reclaimCompoundVL(type, byteArr); return scalar; } }; return baseReader.runner.call(readRunnable); } private T[] primReadCompoundArray(final String objectPath, final int blockSize, final long offset, final HDF5CompoundType type, final IByteArrayInspector inspectorOrNull) throws HDF5JavaException { final ICallableWithCleanUp readRunnable = new ICallableWithCleanUp() { @Override public T[] call(final ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final int storageDataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); checkCompoundType(storageDataTypeId, objectPath, type); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockSize, registry); final int nativeDataTypeId = type.getNativeTypeId(); final byte[] byteArr = new byte[spaceParams.blockSize * type.getObjectByteifyer().getRecordSizeInMemory()]; baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, byteArr); if (inspectorOrNull != null) { inspectorOrNull.inspect(byteArr); } final T[] array = type.getObjectByteifyer().arrayify(storageDataTypeId, byteArr, type.getCompoundType()); baseReader.h5.reclaimCompoundVL(type, byteArr); return array; } }; return baseReader.runner.call(readRunnable); } private void checkCompoundType(final int dataTypeId, final String path, final HDF5CompoundType type) throws HDF5JavaException { final boolean isCompound = (baseReader.h5.getClassType(dataTypeId) == H5T_COMPOUND); if (isCompound == false) { throw new HDF5JavaException("Data set '" + path + "' is no compound."); } if (type.isRequireTypesToBeEqual()) { final boolean isEqual = (baseReader.h5.dataTypesAreEqual(dataTypeId, type.getStorageTypeId())); if (isEqual == false) { throw new HDF5JavaException("The compound type '" + type.getName() + "' does not equal the compound type of data set '" + path + "'."); } } } @Override public MDArray readMDArray(final String objectPath, final HDF5CompoundType type) throws HDF5JavaException { return readMDArrayBlockWithOffset(objectPath, type, null, null, null); } @Override public MDArray readMDArray(final String objectPath, final HDF5CompoundType type, final IByteArrayInspector inspectorOrNull) throws HDF5JavaException { return readMDArrayBlockWithOffset(objectPath, type, null, null, inspectorOrNull); } @Override public MDArray readMDArray(String objectPath, Class pojoClass) throws HDF5JavaException { final HDF5CompoundType dataSetCompoundType = getDataSetType(objectPath, pojoClass); dataSetCompoundType.checkMappingComplete(); return readMDArrayBlockWithOffset(objectPath, dataSetCompoundType, null, null, null); } @Override public MDArray readMDArrayBlock(final String objectPath, final HDF5CompoundType type, final int[] blockDimensions, final long[] blockNumber) throws HDF5JavaException { return readMDArrayBlock(objectPath, type, blockDimensions, blockNumber, null); } @Override public MDArray readMDArrayBlock(final String objectPath, final HDF5CompoundType type, final int[] blockDimensions, final long[] blockNumber, final IByteArrayInspector inspectorOrNull) throws HDF5JavaException { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockDimensions[i] * blockNumber[i]; } return readMDArrayBlockWithOffset(objectPath, type, blockDimensions, offset, inspectorOrNull); } @Override public MDArray readMDArrayBlockWithOffset(final String objectPath, final HDF5CompoundType type, final int[] blockDimensions, final long[] offset) throws HDF5JavaException { return readMDArrayBlockWithOffset(objectPath, type, blockDimensions, offset, null); } @Override public MDArray readMDArrayBlockWithOffset(final String objectPath, final HDF5CompoundType type, final int[] dimensionsOrNull, final long[] offsetOrNull, final IByteArrayInspector inspectorOrNull) throws HDF5JavaException { baseReader.checkOpen(); type.check(baseReader.fileId); final ICallableWithCleanUp> readRunnable = new ICallableWithCleanUp>() { @Override public MDArray call(final ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final int storageDataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); checkCompoundType(storageDataTypeId, objectPath, type); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offsetOrNull, dimensionsOrNull, registry); final int nativeDataTypeId = type.getNativeTypeId(); final byte[] byteArr = new byte[spaceParams.blockSize * type.getObjectByteifyer().getRecordSizeInMemory()]; baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, byteArr); if (inspectorOrNull != null) { inspectorOrNull.inspect(byteArr); } final MDArray array = new MDArray(type.getObjectByteifyer().arrayify( storageDataTypeId, byteArr, type.getCompoundType()), spaceParams.dimensions); baseReader.h5.reclaimCompoundVL(type, byteArr); return array; } }; return baseReader.runner.call(readRunnable); } @Override public Iterable>> getMDArrayBlocks(final String objectPath, final HDF5CompoundType type) throws HDF5JavaException { return getMDArrayBlocks(objectPath, type, null); } @Override public Iterable>> getMDArrayBlocks(final String objectPath, final HDF5CompoundType type, final IByteArrayInspector inspectorOrNull) throws HDF5JavaException { baseReader.checkOpen(); type.check(baseReader.fileId); final HDF5NaturalBlockMDParameters params = new HDF5NaturalBlockMDParameters(baseReader.getDataSetInformation(objectPath, DataTypeInfoOptions.MINIMAL, true)); return primGetCompoundMDArrayNaturalBlocks(objectPath, type, params, inspectorOrNull); } private Iterable>> primGetCompoundMDArrayNaturalBlocks( final String objectPath, final HDF5CompoundType type, final HDF5NaturalBlockMDParameters params, final IByteArrayInspector inspectorOrNull) { return new Iterable>>() { @Override public Iterator>> iterator() { return new Iterator>>() { final HDF5NaturalBlockMDParameters.HDF5NaturalBlockMDIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5MDDataBlock> next() { final long[] offset = index.computeOffsetAndSizeGetOffsetClone(); final MDArray block = readMDArrayBlockWithOffset(objectPath, type, index.getBlockSize(), offset, inspectorOrNull); return new HDF5MDDataBlock>(block, index.getIndexClone(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } @Override public Iterable>> getMDArrayBlocks(String objectPath, Class pojoClass) throws HDF5JavaException { baseReader.checkOpen(); final HDF5NaturalBlockMDParameters params = new HDF5NaturalBlockMDParameters(baseReader.getDataSetInformation(objectPath)); final HDF5CompoundType dataSetCompoundType = getDataSetType(objectPath, pojoClass); dataSetCompoundType.checkMappingComplete(); return primGetCompoundMDArrayNaturalBlocks(objectPath, dataSetCompoundType, params, null); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5CompoundType.java000066400000000000000000000313271256564762100272700ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.lang.reflect.Field; import java.util.Collections; import java.util.HashMap; import java.util.HashSet; import java.util.Iterator; import java.util.LinkedHashMap; import java.util.List; import java.util.Map; import java.util.Set; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import org.apache.commons.lang.ArrayUtils; import ch.systemsx.cisd.hdf5.HDF5DataTypeInformation.DataTypeInfoOptions; /** * The definition of a HDF5 compound type. For information on how to create and work with compound * types, have a look at {@link IHDF5CompoundInformationRetriever}. The simplest way of creating a * compound type for a Java class, is * {@link IHDF5CompoundInformationRetriever#getInferredType(Class)}. *

* Once you have a compound type, you may use methods like * {@link IHDF5CompoundReader#read(String, HDF5CompoundType)} and * {@link IHDF5CompoundWriter#write(String, HDF5CompoundType, Object)} and to read and write them. * * @author Bernd Rinn */ public class HDF5CompoundType extends HDF5DataType { interface IHDF5InternalCompoundMemberInformationRetriever { HDF5CompoundMemberInformation[] getCompoundMemberInformation( final DataTypeInfoOptions dataTypeInfoOptions); } private final String nameOrNull; private final Class compoundType; private final boolean mapAllFields; private final HDF5ValueObjectByteifyer objectByteifyer; private final IHDF5InternalCompoundMemberInformationRetriever informationRetriever; private final boolean requireTypesToBeEqual; /** * Creates a new {@link HDF5CompoundType} for the given compoundType and the mapping * defined by members. * * @param nameOrNull The name of this type, or null, if it is not known. * @param storageTypeId The storage data type id. * @param nativeTypeId The native (memory) data type id. * @param compoundType The Java type that corresponds to this type. * @param requireEqualsType If true, check that this type is equal to the type it * is used to read. * @param objectByteifer The byteifer to use to convert between the Java object and the HDF5 * file. * @param informationRetriever A role that allows to retrieve compound member information for a * given compound type id. * @param baseReader The base reader that this types was derived from. */ HDF5CompoundType(int fileId, int storageTypeId, int nativeTypeId, String nameOrNull, Class compoundType, boolean requireEqualsType, HDF5ValueObjectByteifyer objectByteifer, IHDF5InternalCompoundMemberInformationRetriever informationRetriever, HDF5BaseReader baseReader) { super(fileId, storageTypeId, nativeTypeId, baseReader); assert compoundType != null; assert objectByteifer != null; assert informationRetriever != null; this.nameOrNull = nameOrNull; this.compoundType = compoundType; final CompoundType ct = compoundType.getAnnotation(CompoundType.class); this.requireTypesToBeEqual = requireEqualsType; this.mapAllFields = (ct == null) || ct.mapAllFields(); this.objectByteifyer = objectByteifer; this.informationRetriever = informationRetriever; } /** * Returns the Java type of the compound. */ public Class getCompoundType() { return compoundType; } /** * Returns the size of the record on disk (in bytes). * * @deprecated Use {@link #getRecordSizeOnDisk()} instead. */ @Deprecated public int getRecordSize() { return getRecordSizeOnDisk(); } /** * Returns the size of the record on disk (in bytes). */ public int getRecordSizeOnDisk() { return objectByteifyer.getRecordSizeOnDisk(); } /** * Returns the size of the record in memory (in bytes). */ public int getRecordSizeInMemory() { return objectByteifyer.getRecordSizeInMemory(); } /** * Returns an array with the {@link HDF5CompoundMemberInformation} of all compound members. */ public HDF5CompoundMemberInformation[] getCompoundMemberInformation() { return getCompoundMemberInformation(DataTypeInfoOptions.DEFAULT); } /** * Returns an array with the {@link HDF5CompoundMemberInformation} of all compound members. */ public HDF5CompoundMemberInformation[] getCompoundMemberInformation( final DataTypeInfoOptions options) { return informationRetriever.getCompoundMemberInformation(options); } /** * Returns true, if the mapping between the in-memory and the on-disk * representation is incomplete, that is if either {@link #isDiskRepresentationIncomplete()} or * {@link #isMemoryRepresentationIncomplete()} returns true. */ public boolean isMappingIncomplete() { return isMemoryRepresentationIncomplete() || isDiskRepresentationIncomplete(); } /** * Returns true if there are compound members in the on-disk representation that * are not mapped to fields in the in-memory representation. */ public boolean isMemoryRepresentationIncomplete() { return objectByteifyer.hasUnmappedMembers(); } /** * Returns true, if this type is expected to be equal to the type of a data set it * is used to read. */ public boolean isRequireTypesToBeEqual() { return requireTypesToBeEqual; } /** * Returns an array with the names of compound members that are not mapped to the in-memory * representation. If no members are unmapped, an empty array is returned. */ public String[] getUnmappedCompoundMemberNames() { return objectByteifyer.getUnmappedMembers(); } private Map getCompoundMemberInformationMap() { final Map result = new HashMap(); for (HDF5CompoundMemberInformation info : getCompoundMemberInformation()) { result.put(info.getName(), info); } return result; } /** * Returns an with the {@link HDF5CompoundMemberInformation} of compound members that are not * mapped to the in-memory representation. If no members are unmapped, an empty array is * returned. */ public HDF5CompoundMemberInformation[] getUnmappedCompoundMemberInformation() { final String[] unmappedCompoundMemberNames = getUnmappedCompoundMemberNames(); if (unmappedCompoundMemberNames.length > 0) { final Map compoundMemberInfoMap = getCompoundMemberInformationMap(); final HDF5CompoundMemberInformation[] result = new HDF5CompoundMemberInformation[unmappedCompoundMemberNames.length]; int idx = 0; for (String name : unmappedCompoundMemberNames) { result[idx++] = compoundMemberInfoMap.get(name); } return result; } else { return new HDF5CompoundMemberInformation[0]; } } /** * Returns true if there are fields in the in-memory representation that are not * mapped to any compound member in the on-disk representation. */ public boolean isDiskRepresentationIncomplete() { return getUnmappedFields().isEmpty() == false; } /** * Checks whether the mapping between the on-disk representation and the in-memory * representation is complete. * * @throws HDF5JavaException if {@link #isMappingIncomplete()} returns true. */ public void checkMappingComplete() throws HDF5JavaException { final String[] unmappedMembers = getUnmappedCompoundMemberNames(); final String[] unmappedFields = getUnmappedFieldNames(); if ((unmappedMembers.length > 0 && mapAllFields) || unmappedFields.length > 0) { final StringBuilder b = new StringBuilder(); b.append("Incomplete mapping for compound type '"); b.append(getName()); b.append("': "); if (unmappedMembers.length > 0) { b.append("unmapped members: "); b.append(ArrayUtils.toString(unmappedMembers)); } if (unmappedMembers.length > 0 && unmappedFields.length > 0) { b.append(", "); } if (unmappedFields.length > 0) { b.append("unmapped fields: "); b.append(ArrayUtils.toString(unmappedFields)); } throw new HDF5JavaException(b.toString()); } } /** * Returns an array with names of fields of the in-memory representation that do not map to any * compound member in the on-disk representation. */ public String[] getUnmappedFieldNames() { final Set unmappedFields = getUnmappedFields(); final String[] result = new String[unmappedFields.size()]; int idx = 0; for (Field field : unmappedFields) { result[idx++] = field.getName(); } return result; } private Set getUnmappedFields() { if (Map.class.isAssignableFrom(compoundType) || List.class.isAssignableFrom(compoundType) || compoundType == Object[].class) { return Collections.emptySet(); } else { final Set fieldSet = new HashSet(ReflectionUtils.getFieldMap(compoundType, false).values()); // If the compound type is annotated with @CompoundType(mapAllFields = false) // then remove all fields that do not have an @CompoundElement annotation if (mapAllFields == false) { final Iterator it = fieldSet.iterator(); while (it.hasNext()) { final Field f = it.next(); final CompoundElement ce = f.getAnnotation(CompoundElement.class); if (ce == null) { it.remove(); } } } for (HDF5MemberByteifyer byteifyer : objectByteifyer.getByteifyers()) { fieldSet.remove(byteifyer.tryGetField()); } return fieldSet; } } /** * Returns the byteifyer to convert between the Java type and the HDF5 type. */ HDF5ValueObjectByteifyer getObjectByteifyer() { return objectByteifyer; } @Override public String tryGetName() { return nameOrNull; } /** * Returns the map of member names to enumeration types (only enum members will have an entry in * the map). */ public Map getEnumTypeMap() { final HDF5MemberByteifyer[] bytefier = objectByteifyer.getByteifyers(); final Map result = new LinkedHashMap(); int idx = 0; for (HDF5CompoundMemberInformation info : getCompoundMemberInformation(DataTypeInfoOptions.MINIMAL)) { if (info.getType().getDataClass() == HDF5DataClass.ENUM) { result.put(info.getName(), bytefier[idx].tryGetEnumType()); } ++idx; } return result; } @Override public String toString() { if (nameOrNull != null) { return "HDF5CompoundType [nameOrNull=" + nameOrNull + ", compoundType=" + compoundType.getSimpleName() + ", objectByteifyer=" + objectByteifyer + "]"; } else { return "HDF5CompoundType [compoundType=" + compoundType.getSimpleName() + ", objectByteifyer=" + objectByteifyer + "]"; } } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5CompoundWriter.java000066400000000000000000001225451256564762100276260ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.hdf5lib.H5D.H5Dwrite; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_ALL; import java.util.List; import java.util.Map; import ch.systemsx.cisd.base.mdarray.MDAbstractArray; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.hdf5.HDF5DataTypeInformation.DataTypeInfoOptions; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; /** * The implementation of {@link IHDF5CompoundWriter}. * * @author Bernd Rinn */ class HDF5CompoundWriter extends HDF5CompoundReader implements IHDF5CompoundWriter { private final HDF5BaseWriter baseWriter; HDF5CompoundWriter(HDF5BaseWriter baseWriter, IHDF5EnumWriter enumWriter) { super(baseWriter, enumWriter); this.baseWriter = baseWriter; } private HDF5CompoundType getType(final String nameOrNull, final boolean anonymousType, Class pojoClass, final boolean requireEqualsType, HDF5CompoundMemberMapping... members) { baseWriter.checkOpen(); final HDF5ValueObjectByteifyer objectByteifyer = baseWriter.createCompoundByteifyers(pojoClass, members, null); final String dataTypeName = anonymousType ? null : (nameOrNull != null) ? nameOrNull : deriveCompoundNameFromClass(pojoClass); final int storageDataTypeId = getOrCreateCompoundDataType(dataTypeName, objectByteifyer, baseWriter.keepDataSetIfExists); final int nativeDataTypeId = baseWriter.createNativeCompoundDataType(objectByteifyer); return new HDF5CompoundType(baseWriter.fileId, storageDataTypeId, nativeDataTypeId, dataTypeName, pojoClass, requireEqualsType, objectByteifyer, new HDF5CompoundType.IHDF5InternalCompoundMemberInformationRetriever() { @Override public HDF5CompoundMemberInformation[] getCompoundMemberInformation( final DataTypeInfoOptions dataTypeOptions) { return HDF5CompoundWriter.this.getCompoundMemberInformation( storageDataTypeId, nameOrNull, dataTypeOptions); } }, baseReader); } @Override public HDF5CompoundType getType(final String name, final Class pojoClass, boolean requireTypesToBeEqual, final HDF5CompoundMemberMapping... members) { return getType(name, false, pojoClass, requireTypesToBeEqual, members); } @Override public HDF5CompoundType getType(final String name, Class pojoClass, HDF5CompoundMemberMapping... members) { return getType(name, false, pojoClass, true, members); } @Override public HDF5CompoundType getAnonType(Class pojoClass, HDF5CompoundMemberMapping... members) { return getType(null, true, pojoClass, true, members); } @Override public HDF5CompoundType getInferredAnonType(Class pojoClass, HDF5CompoundMappingHints hints) { return getType( null, true, pojoClass, true, addEnumTypes(HDF5CompoundMemberMapping.addHints( HDF5CompoundMemberMapping.inferMapping(pojoClass), hints))); } @Override public HDF5CompoundType getInferredAnonType(Class pojoClass) { return getInferredAnonType(pojoClass, null); } @Override public HDF5CompoundType getInferredAnonType(T template) { return getInferredAnonType(template, null); } @Override @SuppressWarnings( { "unchecked", "rawtypes" }) public HDF5CompoundType getInferredAnonType(T pojo, HDF5CompoundMappingHints hints) { if (Map.class.isInstance(pojo)) { return (HDF5CompoundType) getType( null, true, Map.class, true, addEnumTypes(HDF5CompoundMemberMapping.addHints( HDF5CompoundMemberMapping.inferMapping((Map) pojo), hints))); } else { final Class pojoClass = (Class) pojo.getClass(); return getType(null, true, pojoClass, true, addEnumTypes(HDF5CompoundMemberMapping.addHints(HDF5CompoundMemberMapping .inferMapping(pojo, HDF5CompoundMemberMapping.inferEnumerationTypeMap( pojo, enumTypeRetriever), HDF5CompoundMappingHints .isUseVariableLengthStrings(hints)), hints))); } } private HDF5CompoundType getType(final String name, final boolean anonymousType, final HDF5CompoundType templateType) { baseWriter.checkOpen(); templateType.checkOpen(); final HDF5ValueObjectByteifyer objectByteifyer = templateType.getObjectByteifyer(); final String dataTypeName = anonymousType ? null : (name == null) ? templateType.getName() : name; final int storageDataTypeId = getOrCreateCompoundDataType(dataTypeName, objectByteifyer, baseWriter.keepDataSetIfExists); return getType(dataTypeName, storageDataTypeId, templateType.getCompoundType(), true, objectByteifyer); } @Override public HDF5CompoundType getInferredAnonType(T[] template) { return getInferredAnonType(template, null); } @Override @SuppressWarnings( { "unchecked", "rawtypes" }) public HDF5CompoundType getInferredAnonType(T[] template, HDF5CompoundMappingHints hints) { final Class componentType = template.getClass().getComponentType(); if (template.length == 0) { return (HDF5CompoundType) getInferredAnonType(componentType, hints); } if (Map.class.isAssignableFrom(componentType)) { return (HDF5CompoundType) getType( null, true, Map.class, true, addEnumTypes(HDF5CompoundMemberMapping.addHints( HDF5CompoundMemberMapping.inferMapping((Map) template[0]), hints))); } else { return (HDF5CompoundType) getType(null, true, componentType, true, addEnumTypes(HDF5CompoundMemberMapping.addHints(HDF5CompoundMemberMapping .inferMapping(template, HDF5CompoundMemberMapping .inferEnumerationTypeMap(template, enumTypeRetriever), hints == null ? false : hints.isUseVariableLengthStrings()), hints))); } } @Override @SuppressWarnings("unchecked") public HDF5CompoundType> getInferredAnonType(List memberNames, List template, HDF5CompoundMappingHints hints) { final HDF5CompoundType type = getType(null, true, List.class, true, HDF5CompoundMemberMapping.addHints( HDF5CompoundMemberMapping.inferMapping(memberNames, template), hints)); return (HDF5CompoundType>) type; } @Override public HDF5CompoundType> getInferredAnonType(List memberNames, List template) { return getInferredAnonType(memberNames, template, null); } @Override public HDF5CompoundType getInferredAnonType(String[] memberNames, Object[] template) { return getInferredAnonType(memberNames, template, null); } @Override @SuppressWarnings("unchecked") public HDF5CompoundType getInferredAnonType(String[] memberNames, Object[] template, HDF5CompoundMappingHints hints) { final HDF5CompoundType type = getType(null, true, List.class, true, HDF5CompoundMemberMapping.addHints( HDF5CompoundMemberMapping.inferMapping(memberNames, template), hints)); return (HDF5CompoundType) type; } @Override public HDF5CompoundType getClonedType(final HDF5CompoundType templateType) { return getType(null, false, templateType); } private String deriveCompoundNameFromClass(Class pojoClass) { final CompoundType ct = pojoClass.getAnnotation(CompoundType.class); final String name = (ct != null) ? ct.name() : ""; return name.length() == 0 ? pojoClass.getSimpleName() : name; } private int getOrCreateCompoundDataType(final String dataTypeName, final HDF5ValueObjectByteifyer objectByteifyer, boolean committedDataTypeHasPreference) { final boolean dataTypeNameGiven = (dataTypeName != null && "UNKNOWN".equals(dataTypeName) == false); final String dataTypePath = dataTypeNameGiven ? HDF5Utils.createDataTypePath(HDF5Utils.COMPOUND_PREFIX, baseWriter.houseKeepingNameSuffix, dataTypeName) : null; final int committedStorageDataTypeId = dataTypeNameGiven ? baseWriter.getDataTypeId(dataTypePath) : -1; final boolean typeExists = (committedStorageDataTypeId >= 0); int storageDataTypeId = committedStorageDataTypeId; final boolean commitType; if (((typeExists == false) || (committedDataTypeHasPreference == false))) { storageDataTypeId = baseWriter.createStorageCompoundDataType(objectByteifyer); final boolean typesAreEqual = typeExists && baseWriter.h5.dataTypesAreEqual(committedStorageDataTypeId, storageDataTypeId); commitType = dataTypeNameGiven && ((typeExists == false) || (typesAreEqual == false)); if (typeExists && commitType) { final String replacementDataTypePath = baseWriter.moveLinkOutOfTheWay(dataTypePath); baseReader.renameNamedDataType(dataTypePath, replacementDataTypePath); } if (typesAreEqual) { storageDataTypeId = committedStorageDataTypeId; } } else { commitType = false; } if (commitType) { baseWriter.commitDataType(dataTypePath, storageDataTypeId); final HDF5EnumerationValueArray typeVariants = tryCreateDataTypeVariantArray(objectByteifyer); if (typeVariants != null) { baseWriter.setEnumArrayAttribute(dataTypePath, HDF5Utils .getTypeVariantMembersAttributeName(baseWriter.houseKeepingNameSuffix), typeVariants); } } return storageDataTypeId; } private HDF5EnumerationValueArray tryCreateDataTypeVariantArray( final HDF5ValueObjectByteifyer objectByteifyer) { final byte[] typeVariantOrdinals = new byte[objectByteifyer.getByteifyers().length]; boolean hasTypeVariants = false; for (int i = 0; i < typeVariantOrdinals.length; ++i) { typeVariantOrdinals[i] = (byte) objectByteifyer.getByteifyers()[i].getTypeVariant().ordinal(); hasTypeVariants |= HDF5DataTypeVariant.isTypeVariant(typeVariantOrdinals[i]); } return hasTypeVariants ? new HDF5EnumerationValueArray(baseWriter.typeVariantDataType, typeVariantOrdinals) : null; } @Override public void setAttr(final String objectPath, final String attributeName, final HDF5CompoundType type, final T data) { primSetCompoundAttribute(objectPath, attributeName, type, data, null); } @Override public void setAttr(final String objectPath, final String attributeName, final T data) { final HDF5CompoundType inferredCompoundType = getInferredType(data); inferredCompoundType.checkMappingComplete(); primSetCompoundAttribute(objectPath, attributeName, inferredCompoundType, data, null); } @Override public void setArrayAttr(String objectPath, String attributeName, HDF5CompoundType type, T[] value) { baseWriter.setCompoundArrayAttribute(objectPath, attributeName, type, value, null); } @Override public void setArrayAttr(String objectPath, String attributeName, T[] value) { @SuppressWarnings("unchecked") final HDF5CompoundType inferredCompoundType = getInferredType((Class) value.getClass().getComponentType()); inferredCompoundType.checkMappingComplete(); baseWriter.setCompoundArrayAttribute(objectPath, attributeName, inferredCompoundType, value, null); } @Override public void setMDArrayAttr(String objectPath, String attributeName, HDF5CompoundType type, MDArray value) { baseWriter.setCompoundMDArrayAttribute(objectPath, attributeName, type, value, null); } @Override public void setMDArrayAttr(String objectPath, String attributeName, MDArray value) { @SuppressWarnings("unchecked") final HDF5CompoundType inferredCompoundType = getInferredType((Class) value.getAsFlatArray().getClass().getComponentType()); inferredCompoundType.checkMappingComplete(); baseWriter.setCompoundMDArrayAttribute(objectPath, attributeName, inferredCompoundType, value, null); } private void primSetCompoundAttribute(final String objectPath, final String attributeName, final HDF5CompoundType type, final T data, final IByteArrayInspector inspectorOrNull) { baseWriter.checkOpen(); type.check(baseWriter.fileId); @SuppressWarnings("unchecked") final byte[] byteArray = ((HDF5CompoundType) type).getObjectByteifyer().byteify(type.getStorageTypeId(), data); if (inspectorOrNull != null) { inspectorOrNull.inspect(byteArray); } final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { 1 }, registry); baseWriter.setAttribute(objectPath, attributeName, type.getStorageTypeId(), type.getNativeTypeId(), dataSpaceId, byteArray, registry); } else { baseWriter.setAttribute(objectPath, attributeName, type.getStorageTypeId(), type.getNativeTypeId(), -1, byteArray, registry); } baseWriter.h5.reclaimCompoundVL(type, byteArray); return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void write(final String objectPath, final HDF5CompoundType type, final T data) { primWriteCompound(objectPath, type, data, null); } @Override public void write(final String objectPath, final HDF5CompoundType type, final T data, final IByteArrayInspector inspectorOrNull) { primWriteCompound(objectPath, type, data, inspectorOrNull); } private void primWriteCompound(final String objectPath, final HDF5CompoundType type, final T data, final IByteArrayInspector inspectorOrNull) { baseWriter.checkOpen(); type.check(baseWriter.fileId); @SuppressWarnings("unchecked") final byte[] byteArray = ((HDF5CompoundType) type).getObjectByteifyer().byteify(type.getStorageTypeId(), data); if (inspectorOrNull != null) { inspectorOrNull.inspect(byteArray); } baseWriter.writeScalar(objectPath, type.getStorageTypeId(), type.getNativeTypeId(), byteArray); baseWriter.h5.reclaimCompoundVL(type, byteArray); } @Override public void write(String objectPath, T data) { final HDF5CompoundType inferredCompoundType = getInferredType(data); inferredCompoundType.checkMappingComplete(); primWriteCompound(objectPath, inferredCompoundType, data, null); } @Override public void writeArray(final String objectPath, final HDF5CompoundType type, final T[] data) { primWriteCompoundArray(objectPath, type, data, HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION, null); } @Override public void writeArray(final String objectPath, final HDF5CompoundType type, final T[] data, final HDF5GenericStorageFeatures features) { primWriteCompoundArray(objectPath, type, data, features, null); } @Override public void writeArray(final String objectPath, final HDF5CompoundType type, final T[] data, final HDF5GenericStorageFeatures features, final IByteArrayInspector inspectorOrNull) { primWriteCompoundArray(objectPath, type, data, features, inspectorOrNull); } private void primWriteCompoundArray(final String objectPath, final HDF5CompoundType type, final T[] data, final HDF5GenericStorageFeatures features, final IByteArrayInspector inspectorOrNull) { assert objectPath != null; assert type != null; assert data != null; baseWriter.checkOpen(); type.check(baseWriter.fileId); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(final ICleanUpRegistry registry) { final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, type.getStorageTypeId(), new long[] { data.length }, type.getObjectByteifyer() .getRecordSizeOnDisk(), features, registry); @SuppressWarnings("unchecked") final byte[] byteArray = ((HDF5CompoundType) type).getObjectByteifyer().byteify( type.getStorageTypeId(), data); if (inspectorOrNull != null) { inspectorOrNull.inspect(byteArray); } H5Dwrite(dataSetId, type.getNativeTypeId(), H5S_ALL, H5S_ALL, H5P_DEFAULT, byteArray); baseWriter.h5.reclaimCompoundVL(type, byteArray); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeArray(String objectPath, T[] data) { writeArray(objectPath, data, HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION); } @Override public void writeArray(String objectPath, T[] data, HDF5GenericStorageFeatures features) { assert data != null && data.length > 0; final HDF5CompoundType inferredCompoundType = getInferredType(data); inferredCompoundType.checkMappingComplete(); primWriteCompoundArray(objectPath, inferredCompoundType, data, features, null); } @Override public void writeArrayBlock(final String objectPath, final HDF5CompoundType type, final T[] data, final long blockNumber) { writeArrayBlock(objectPath, type, data, blockNumber, null); } @Override public void writeArrayBlock(final String objectPath, final HDF5CompoundType type, final T[] data, final long blockNumber, final IByteArrayInspector inspectorOrNull) { assert objectPath != null; assert type != null; assert data != null; assert blockNumber >= 0; baseWriter.checkOpen(); type.check(baseWriter.fileId); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(final ICleanUpRegistry registry) { final long size = data.length; final long[] dimensions = new long[] { size }; final long[] offset = new long[] { size * blockNumber }; final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, new long[] { data.length * (blockNumber + 1) }, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, dimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(dimensions, registry); final byte[] byteArray = type.getObjectByteifyer().byteify(type.getStorageTypeId(), data); if (inspectorOrNull != null) { inspectorOrNull.inspect(byteArray); } H5Dwrite(dataSetId, type.getNativeTypeId(), memorySpaceId, dataSpaceId, H5P_DEFAULT, byteArray); baseWriter.h5.reclaimCompoundVL(type, byteArray); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeArrayBlockWithOffset(final String objectPath, final HDF5CompoundType type, final T[] data, final long offset) { writeArrayBlockWithOffset(objectPath, type, data, offset, null); } @Override public void writeArrayBlockWithOffset(final String objectPath, final HDF5CompoundType type, final T[] data, final long offset, final IByteArrayInspector inspectorOrNull) { assert objectPath != null; assert type != null; assert data != null; assert offset >= 0; baseWriter.checkOpen(); type.check(baseWriter.fileId); final long size = data.length; final long[] dimensions = new long[] { size }; final long[] offsetArray = new long[] { offset }; final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(final ICleanUpRegistry registry) { final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, new long[] { offset + data.length }, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offsetArray, dimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(dimensions, registry); final byte[] byteArray = type.getObjectByteifyer().byteify(type.getStorageTypeId(), data); if (inspectorOrNull != null) { inspectorOrNull.inspect(byteArray); } H5Dwrite(dataSetId, type.getNativeTypeId(), memorySpaceId, dataSpaceId, H5P_DEFAULT, byteArray); baseWriter.h5.reclaimCompoundVL(type, byteArray); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createArray(String objectPath, HDF5CompoundType type, int size) { createArray(objectPath, type, size, HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION); } @Override public void createArray(final String objectPath, final HDF5CompoundType type, final long size, final int blockSize) { createArray(objectPath, type, size, blockSize, HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION); } @Override public void createArray(final String objectPath, final HDF5CompoundType type, final long size, final int blockSize, final HDF5GenericStorageFeatures features) { assert objectPath != null; assert type != null; assert size >= 0; assert blockSize >= 0 && (blockSize <= size || size == 0); baseWriter.checkOpen(); type.check(baseWriter.fileId); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(final ICleanUpRegistry registry) { baseWriter.createDataSet(objectPath, type.getStorageTypeId(), features, new long[] { size }, new long[] { blockSize }, type.getObjectByteifyer().getRecordSizeOnDisk(), registry); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createArray(final String objectPath, final HDF5CompoundType type, final long size, final HDF5GenericStorageFeatures features) { assert objectPath != null; assert type != null; assert size >= 0; baseWriter.checkOpen(); type.check(baseWriter.fileId); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(final ICleanUpRegistry registry) { if (features.requiresChunking()) { baseWriter.createDataSet(objectPath, type.getStorageTypeId(), features, new long[] { 0 }, new long[] { size }, type.getObjectByteifyer().getRecordSizeOnDisk(), registry); } else { baseWriter.createDataSet(objectPath, type.getStorageTypeId(), features, new long[] { size }, null, type.getObjectByteifyer().getRecordSizeOnDisk(), registry); } return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeMDArray(final String objectPath, final HDF5CompoundType type, final MDArray data) { writeMDArray(objectPath, type, data, HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION); } @Override public void writeMDArray(final String objectPath, final HDF5CompoundType type, final MDArray data, final HDF5GenericStorageFeatures features) { writeMDArray(objectPath, type, data, features, null); } @Override public void writeMDArray(final String objectPath, final HDF5CompoundType type, final MDArray data, final HDF5GenericStorageFeatures features, final IByteArrayInspector inspectorOrNull) { assert objectPath != null; assert type != null; assert data != null; baseWriter.checkOpen(); type.check(baseWriter.fileId); primWriteCompoundMDArray(objectPath, type, data, features, inspectorOrNull); } private void primWriteCompoundMDArray(final String objectPath, final HDF5CompoundType type, final MDArray data, final HDF5GenericStorageFeatures features, final IByteArrayInspector inspectorOrNull) { final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(final ICleanUpRegistry registry) { final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, type.getStorageTypeId(), MDAbstractArray.toLong(data.dimensions()), type .getObjectByteifyer().getRecordSizeOnDisk(), features, registry); final byte[] byteArray = type.getObjectByteifyer().byteify(type.getStorageTypeId(), data.getAsFlatArray()); if (inspectorOrNull != null) { inspectorOrNull.inspect(byteArray); } H5Dwrite(dataSetId, type.getNativeTypeId(), H5S_ALL, H5S_ALL, H5P_DEFAULT, byteArray); baseWriter.h5.reclaimCompoundVL(type, byteArray); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeMDArrayBlock(final String objectPath, final HDF5CompoundType type, final MDArray data, final long[] blockNumber) { writeMDArrayBlock(objectPath, type, data, blockNumber, null); } @Override public void writeMDArrayBlock(final String objectPath, final HDF5CompoundType type, final MDArray data, final long[] blockNumber, final IByteArrayInspector inspectorOrNull) { final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; final long[] dataSetDimensions = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; dataSetDimensions[i] = offset[i] + dimensions[i]; } writeCompoundMDArrayBlockWithOffset(objectPath, type, data.getAsFlatArray(), dimensions, offset, dataSetDimensions, inspectorOrNull); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final HDF5CompoundType type, final MDArray data, final long[] offset) { writeMDArrayBlockWithOffset(objectPath, type, data, offset, null); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final HDF5CompoundType type, final MDArray data, final long[] offset, final IByteArrayInspector inspectorOrNull) { final long[] dimensions = data.longDimensions(); final long[] dataSetDimensions = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + dimensions[i]; } writeCompoundMDArrayBlockWithOffset(objectPath, type, data.getAsFlatArray(), dimensions, offset, dataSetDimensions, inspectorOrNull); } private void writeCompoundMDArrayBlockWithOffset(final String objectPath, final HDF5CompoundType type, final T[] data, final long[] dimensions, final long[] offset, final long[] dataSetDimensions, final IByteArrayInspector inspectorOrNull) { assert objectPath != null; assert type != null; assert data != null; assert offset != null; baseWriter.checkOpen(); type.check(baseWriter.fileId); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(final ICleanUpRegistry registry) { final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, dimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(dimensions, registry); final byte[] byteArray = type.getObjectByteifyer().byteify(type.getStorageTypeId(), data); if (inspectorOrNull != null) { inspectorOrNull.inspect(byteArray); } H5Dwrite(dataSetId, type.getNativeTypeId(), memorySpaceId, dataSpaceId, H5P_DEFAULT, byteArray); baseWriter.h5.reclaimCompoundVL(type, byteArray); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final HDF5CompoundType type, final MDArray data, final int[] blockDimensions, final long[] offset, final int[] memoryOffset) { writeMDArrayBlockWithOffset(objectPath, type, data, blockDimensions, offset, memoryOffset, null); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final HDF5CompoundType type, final MDArray data, final int[] blockDimensions, final long[] offset, final int[] memoryOffset, final IByteArrayInspector inspectorOrNull) { assert objectPath != null; assert type != null; assert data != null; assert offset != null; baseWriter.checkOpen(); type.check(baseWriter.fileId); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(final ICleanUpRegistry registry) { final long[] memoryDimensions = data.longDimensions(); final long[] longBlockDimensions = MDAbstractArray.toLong(blockDimensions); final long[] dataSetDimensions = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + blockDimensions[i]; } final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, longBlockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(memoryDimensions, registry); baseWriter.h5.setHyperslabBlock(memorySpaceId, MDAbstractArray.toLong(memoryOffset), longBlockDimensions); final byte[] byteArray = type.getObjectByteifyer().byteify(type.getStorageTypeId(), data.getAsFlatArray()); if (inspectorOrNull != null) { inspectorOrNull.inspect(byteArray); } H5Dwrite(dataSetId, type.getNativeTypeId(), memorySpaceId, dataSpaceId, H5P_DEFAULT, byteArray); baseWriter.h5.reclaimCompoundVL(type, byteArray); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createMDArray(String objectPath, HDF5CompoundType type, int[] dimensions) { createMDArray(objectPath, type, dimensions, HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final HDF5CompoundType type, final long[] dimensions, final int[] blockDimensions) { createMDArray(objectPath, type, dimensions, blockDimensions, HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final HDF5CompoundType type, final long[] dimensions, final int[] blockDimensions, final HDF5GenericStorageFeatures features) { assert objectPath != null; assert type != null; assert dimensions != null; assert blockDimensions != null; baseWriter.checkOpen(); type.check(baseWriter.fileId); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(final ICleanUpRegistry registry) { baseWriter.createDataSet(objectPath, type.getStorageTypeId(), features, dimensions, MDAbstractArray.toLong(blockDimensions), type .getObjectByteifyer().getRecordSizeOnDisk(), registry); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createMDArray(final String objectPath, final HDF5CompoundType type, final int[] dimensions, final HDF5GenericStorageFeatures features) { assert objectPath != null; assert type != null; assert dimensions != null; baseWriter.checkOpen(); type.check(baseWriter.fileId); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(final ICleanUpRegistry registry) { if (features.requiresChunking()) { final long[] nullDimensions = new long[dimensions.length]; baseWriter.createDataSet(objectPath, type.getStorageTypeId(), features, nullDimensions, MDAbstractArray.toLong(dimensions), type .getObjectByteifyer().getRecordSizeOnDisk(), registry); } else { baseWriter.createDataSet(objectPath, type.getStorageTypeId(), features, MDAbstractArray.toLong(dimensions), null, type.getObjectByteifyer() .getRecordSizeOnDisk(), registry); } return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeMDArray(String objectPath, MDArray data) { writeMDArray(objectPath, data, HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION); } @Override public void writeMDArray(String objectPath, MDArray data, HDF5GenericStorageFeatures features) { assert objectPath != null; assert data != null && data.size() > 0; baseWriter.checkOpen(); final HDF5CompoundType inferredCompoundType = getInferredType(data.getAsFlatArray()); inferredCompoundType.checkMappingComplete(); primWriteCompoundMDArray(objectPath, inferredCompoundType, data, features, null); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5DataBlock.java000066400000000000000000000037641256564762100264720ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; /** * A class that is used for iterating over a data set block by block, using * natural data blocks. The Natural block for chunked data sets is a chunk, for * non-chunked data sets it is the complete array. *

* The pattern for using this class is: * * 

 * for (HDF5DataBlock<int[]> block : reader.getIntNaturalBlocks(dsName1D))
 * {
 *     float[] naturalBlock = block.getData();
 *     ... work on naturalBlock, use block.getIndex() and block.getOffset() where needed ...
 * }
 *
* * Note: If the size of the data set is not an integer number of blocks, then the last block * will be smaller than the natural block size. * * @author Bernd Rinn */ public final class HDF5DataBlock { private final T data; private final long offset; private final long index; HDF5DataBlock(T block, long index, long offset) { this.data = block; this.index = index; this.offset = offset; } /** * Returns the data block itself. */ public T getData() { return data; } /** * Returns the offset of this block in the data set. */ public long getOffset() { return offset; } /** * Returns the iteration index of this block, starting with 0. */ public long getIndex() { return index; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5DataClass.java000066400000000000000000000230411256564762100264730ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_BITFIELD; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_COMPOUND; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_ENUM; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_FLOAT; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_INTEGER; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_OPAQUE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_REFERENCE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STRING; import java.util.BitSet; import java.util.Map; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDByteArray; import ch.systemsx.cisd.base.mdarray.MDDoubleArray; import ch.systemsx.cisd.base.mdarray.MDFloatArray; import ch.systemsx.cisd.base.mdarray.MDIntArray; import ch.systemsx.cisd.base.mdarray.MDLongArray; import ch.systemsx.cisd.base.mdarray.MDShortArray; import ch.systemsx.cisd.hdf5.HDF5CompoundByteifyerFactory.IHDF5CompoundMemberBytifyerFactory; /** * Identifies the class of a data type. Note that for array types the class of the elements is * identified. * * @author Bernd Rinn */ public enum HDF5DataClass { // Implementation note: The order matters! ENUM needs to be before INTEGER, as H5Tdetect_class // will return TRUE for ENUM arrays when trying to detect an INTEGER class. BITFIELD(H5T_BITFIELD, new BasicJavaTypeProvider(BitSet.class, null, null, null)), ENUM( H5T_ENUM, new BasicJavaTypeProvider(HDF5EnumerationValue.class, HDF5EnumerationValueArray.class, null, null)), INTEGER(H5T_INTEGER, new IntJavaTypeProvider()), FLOAT(H5T_FLOAT, new FloatJavaTypeProvider()), STRING( H5T_STRING, new BasicJavaTypeProvider(String.class, String[].class, String[][].class, MDArray.class)), OPAQUE(H5T_OPAQUE, new BasicJavaTypeProvider(byte.class, byte[].class, byte[][].class, MDByteArray.class)), BOOLEAN(-1, new BasicJavaTypeProvider(boolean.class, BitSet.class, null, null)), COMPOUND( H5T_COMPOUND, new BasicJavaTypeProvider(Map.class, Map[].class, Map[][].class, MDArray.class)), REFERENCE(H5T_REFERENCE, new BasicJavaTypeProvider( String.class, String[].class, String[][].class, MDArray.class)), OTHER(-1, new BasicJavaTypeProvider(null, null, null, null)); /** * A role that can provide a java type for a data class, rank and element size. */ interface IHDF5JavaTypeProvider { Class tryGetJavaType(int rank, int elementSize, HDF5DataTypeVariant typeVariantOrNull); } private final int id; private final IHDF5JavaTypeProvider typeProvider; HDF5DataClass(int id, IHDF5JavaTypeProvider typeProvider) { this.id = id; this.typeProvider = typeProvider; } int getId() { return id; } /** * Returns a {@link IHDF5JavaTypeProvider} that returns the default Java type for this data * class. *

* Overriding the default for particular choices should be done by one of the * {@link IHDF5CompoundMemberBytifyerFactory}s in * {@link IHDF5CompoundMemberBytifyerFactory#tryGetOverrideJavaType(HDF5DataClass, int, int, HDF5DataTypeVariant)}. */ IHDF5JavaTypeProvider getJavaTypeProvider() { return typeProvider; } /** * Returns the {@link HDF5DataClass} for the given data classId. *

* Note: This method will never return {@link #BOOLEAN}, but instead it will return * {@link #ENUM} for a boolean value as boolean values are actually enums in the HDF5 file. */ static HDF5DataClass classIdToDataClass(final int classId) { for (HDF5DataClass clazz : values()) { if (clazz.id == classId) { return clazz; } } return OTHER; } // // Auxiliary classes // private static class BasicJavaTypeProvider implements IHDF5JavaTypeProvider { private final Class javaTypeScalarOrNull; private final Class javaType1DArrayOrNull; private final Class javaType2DArrayOrNull; private final Class javaTypeMDArrayOrNull; BasicJavaTypeProvider(Class javaTypeScalarOrNull, Class javaType1DArrayOrNull, Class javaType2DArrayOrNull, Class javaTypeMDArrayOrNull) { this.javaTypeScalarOrNull = javaTypeScalarOrNull; this.javaType1DArrayOrNull = javaType1DArrayOrNull; this.javaType2DArrayOrNull = javaType2DArrayOrNull; this.javaTypeMDArrayOrNull = javaTypeMDArrayOrNull; } @Override public Class tryGetJavaType(int rank, int elementSize, HDF5DataTypeVariant typeVariantOrNull) { if (rank == 0) { return javaTypeScalarOrNull; } else if (rank == 1) { return javaType1DArrayOrNull; } else if (rank == 2) { return javaType2DArrayOrNull; } else { return javaTypeMDArrayOrNull; } } } private static class IntJavaTypeProvider implements IHDF5JavaTypeProvider { @Override public Class tryGetJavaType(int rank, int elementSize, HDF5DataTypeVariant typeVariantOrNull) { if (rank == 0) { switch (elementSize) { case 1: return byte.class; case 2: return short.class; case 4: return int.class; case 8: return long.class; default: return null; } } else if (rank == 1) { switch (elementSize) { case 1: return byte[].class; case 2: return short[].class; case 4: return int[].class; case 8: return long[].class; default: return null; } } else if (rank == 2) { switch (elementSize) { case 1: return byte[][].class; case 2: return short[][].class; case 4: return int[][].class; case 8: return long[][].class; default: return null; } } else { switch (elementSize) { case 1: return MDByteArray.class; case 2: return MDShortArray.class; case 4: return MDIntArray.class; case 8: return MDLongArray.class; default: return null; } } } } private static class FloatJavaTypeProvider implements IHDF5JavaTypeProvider { @Override public Class tryGetJavaType(int rank, int elementSize, HDF5DataTypeVariant typeVariantOrNull) { if (rank == 0) { switch (elementSize) { case 4: return float.class; case 8: return double.class; default: return null; } } else if (rank == 1) { switch (elementSize) { case 4: return float[].class; case 8: return double[].class; default: return null; } } else if (rank == 2) { switch (elementSize) { case 4: return float[][].class; case 8: return double[][].class; default: return null; } } else { switch (elementSize) { case 4: return MDFloatArray.class; case 8: return MDDoubleArray.class; default: return null; } } } } }libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5DataSetInformation.java000066400000000000000000000137751256564762100304040ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import org.apache.commons.lang.ArrayUtils; import org.apache.commons.lang.builder.EqualsBuilder; import org.apache.commons.lang.builder.HashCodeBuilder; /** * A class that holds relevant information about a data set. * * @author Bernd Rinn */ public final class HDF5DataSetInformation { private final HDF5DataTypeInformation typeInformation; private long[] dimensions; private long[] maxDimensions; private HDF5StorageLayout storageLayout = HDF5StorageLayout.NOT_APPLICABLE; private int[] chunkSizesOrNull; HDF5DataSetInformation(HDF5DataTypeInformation typeInformation, HDF5DataTypeVariant typeVariantOrNull) { this.typeInformation = typeInformation; if (typeVariantOrNull != null) { typeInformation.setTypeVariant(typeVariantOrNull); } } /** * Returns the data type information for the data set. */ public HDF5DataTypeInformation getTypeInformation() { return typeInformation; } /** * Returns the data type variant of this data set, or null, if this data set is not * tagged with a type variant. */ public HDF5DataTypeVariant tryGetTypeVariant() { return typeInformation.tryGetTypeVariant(); } /** * Returns true, if the data set is a time stamp, or false otherwise. */ public boolean isTimeStamp() { return typeInformation.isTimeStamp(); } /** * Returns true, if the data set is a time duration, or false * otherwise. */ public boolean isTimeDuration() { return typeInformation.isTimeDuration(); } /** * Returns the time unit of the data set, if the data set is a time duration, or * null otherwise. */ public HDF5TimeUnit tryGetTimeUnit() { return typeInformation.tryGetTimeUnit(); } /** * Returns the array dimensions of the data set. */ public long[] getDimensions() { return dimensions; } void setDimensions(long[] dimensions) { this.dimensions = dimensions; } /** * Returns the largest possible array dimensions of the data set. */ public long[] getMaxDimensions() { return maxDimensions; } void setMaxDimensions(long[] maxDimensions) { this.maxDimensions = maxDimensions; } void setStorageLayout(HDF5StorageLayout storageLayout) { this.storageLayout = storageLayout; } /** * Returns the storage layout of the data set in the HDF5 file. */ public HDF5StorageLayout getStorageLayout() { return storageLayout; } /** * Returns the chunk size in each array dimension of the data set, or null, if the * data set is not of {@link HDF5StorageLayout#CHUNKED}. */ public int[] tryGetChunkSizes() { return chunkSizesOrNull; } void setChunkSizes(int[] chunkSizes) { this.chunkSizesOrNull = chunkSizes; } /** * Returns the rank (number of axis) of this data set. */ public int getRank() { return dimensions.length; } /** * Returns true, if the rank of this data set is 0. */ public boolean isScalar() { return dimensions.length == 0; } /** * Returns true, if this data set type has a sign anf false otherwise. */ public boolean isSigned() { return typeInformation.isSigned(); } /** * Returns the one-dimensional length of the multi-dimensional array defined by * dimensions. */ private static long getLength(final long[] dimensions) { assert dimensions != null; if (dimensions.length == 0) // NULL data space needs to be treated differently { return 0; } long length = dimensions[0]; for (int i = 1; i < dimensions.length; ++i) { length *= dimensions[i]; } return length; } /** * Returns the total number of elements of this data set. */ public long getNumberOfElements() { return getLength(dimensions); } /** * Returns the total size (in bytes) of this data set. */ public long getSize() { return getLength(dimensions) * typeInformation.getElementSize(); } // // Object // @Override public boolean equals(Object obj) { if (obj == null || obj instanceof HDF5DataSetInformation == false) { return false; } final HDF5DataSetInformation that = (HDF5DataSetInformation) obj; final EqualsBuilder builder = new EqualsBuilder(); builder.append(typeInformation, that.typeInformation); builder.append(dimensions, that.dimensions); builder.append(maxDimensions, that.maxDimensions); return builder.isEquals(); } @Override public int hashCode() { final HashCodeBuilder builder = new HashCodeBuilder(); builder.append(typeInformation); builder.append(dimensions); builder.append(maxDimensions); return builder.toHashCode(); } @Override public String toString() { return typeInformation.toString() + ":" + ArrayUtils.toString(dimensions); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5DataType.java000066400000000000000000000115351256564762100263540ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.hdf5.HDF5DataTypeInformation.DataTypeInfoOptions; /** * The abstract base class of Java wrappers for HDF data types. * * @author Bernd Rinn */ public abstract class HDF5DataType { private int fileId; private int storageTypeId; private int nativeTypeId; private final HDF5BaseReader baseReader; HDF5DataType(int fileId, int storageTypeId, int nativeTypeId, HDF5BaseReader baseReader) { assert fileId >= 0; this.fileId = fileId; this.storageTypeId = storageTypeId; this.nativeTypeId = nativeTypeId; this.baseReader = baseReader; baseReader.fileRegistry.registerCleanUp(new Runnable() { @Override public void run() { HDF5DataType.this.fileId = -1; HDF5DataType.this.storageTypeId = -1; HDF5DataType.this.nativeTypeId = -1; } }); } /** * Returns the storage data type id of this type. */ int getStorageTypeId() { return storageTypeId; } /** * Returns the native data type id of this type. */ int getNativeTypeId() { return nativeTypeId; } /** * Checks whether this type is for file expectedFileId. * * @throws HDF5JavaException If this type is not for file expectedFileId. */ void check(final int expectedFileId) throws HDF5JavaException { if (fileId < 0) { throw new HDF5JavaException("Type " + getName() + " is closed."); } if (fileId != expectedFileId) { throw new HDF5JavaException("Type " + getName() + " is not from this file."); } } /** * Checks whether this type is open. * * @throws HDF5JavaException If this type is not open. */ void checkOpen() throws HDF5JavaException { if (fileId < 0) { throw new HDF5JavaException("Type " + getName() + " is closed."); } } /** * Returns a name for this type, or null if this type has no name. */ public abstract String tryGetName(); /** * Returns a name for this type, or UNKNOWNnull, if this type is not a comitted * data type. */ public String tryGetDataTypePath() { return getDataTypeInformation(DataTypeInfoOptions.PATH).tryGetDataTypePath(); } /** * Returns the data type information for this data type. * * @param dataTypeInfoOptions The options that decide how much information to fetch. */ public HDF5DataTypeInformation getDataTypeInformation( final DataTypeInfoOptions dataTypeInfoOptions) { return baseReader.getDataTypeInformation(storageTypeId, dataTypeInfoOptions); } /** * Returns the data type information (with {@link DataTypeInfoOptions#DEFAULT}) for this data * type. */ public HDF5DataTypeInformation getDataTypeInformation() { return baseReader.getDataTypeInformation(storageTypeId, DataTypeInfoOptions.DEFAULT); } // // Object // @Override public int hashCode() { final int prime = 31; int result = 1; result = prime * result + fileId; result = prime * result + storageTypeId; return result; } @Override public boolean equals(Object obj) { if (this == obj) { return true; } if (obj == null) { return false; } if (getClass() != obj.getClass()) { return false; } HDF5DataType other = (HDF5DataType) obj; if (fileId != other.fileId) { return false; } if (storageTypeId != other.storageTypeId) { return false; } return true; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5DataTypeInformation.java000066400000000000000000000437671256564762100305760ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import org.apache.commons.lang.ObjectUtils; import ch.systemsx.cisd.base.mdarray.MDAbstractArray; import ch.systemsx.cisd.hdf5.hdf5lib.HDFNativeData; /** * A class that holds relevant information about a data type. * * @author Bernd Rinn */ public final class HDF5DataTypeInformation { /** * An object that represents the options for a data type information object. * * @author Bernd Rinn */ public static final class DataTypeInfoOptions { public static final DataTypeInfoOptions MINIMAL = new DataTypeInfoOptions(false, false); public static final DataTypeInfoOptions ALL = new DataTypeInfoOptions(true, true); public static final DataTypeInfoOptions DEFAULT = new DataTypeInfoOptions(false, true); public static final DataTypeInfoOptions PATH = new DataTypeInfoOptions(true, false); private boolean knowsDataTypePath; private boolean knowsDataTypeVariant; DataTypeInfoOptions(boolean knowsDataTypePath, boolean knowsDataTypeVariant) { this.knowsDataTypePath = knowsDataTypePath; this.knowsDataTypeVariant = knowsDataTypeVariant; } DataTypeInfoOptions() { knowsDataTypePath = false; knowsDataTypeVariant = true; } public DataTypeInfoOptions path(boolean readDataTypePath) { this.knowsDataTypePath = readDataTypePath; return this; } public DataTypeInfoOptions path() { this.knowsDataTypePath = true; return this; } public DataTypeInfoOptions variant(boolean readDataTypeVariant) { this.knowsDataTypeVariant = readDataTypeVariant; return this; } public DataTypeInfoOptions noVariant() { this.knowsDataTypeVariant = false; return this; } public DataTypeInfoOptions all() { this.knowsDataTypePath = true; this.knowsDataTypeVariant = true; return this; } public DataTypeInfoOptions nothing() { this.knowsDataTypePath = false; this.knowsDataTypeVariant = false; return this; } public boolean knowsDataTypePath() { return knowsDataTypePath; } public boolean knowsDataTypeVariant() { return knowsDataTypeVariant; } } /** * Returns a new {@link DataTypeInfoOptions} object. */ public static DataTypeInfoOptions options() { return new DataTypeInfoOptions(); } private final boolean arrayType; private final boolean signed; private final boolean variableLengthString; private final String dataTypePathOrNull; private final String nameOrNull; private final HDF5DataClass dataClass; private int elementSize; private int numberOfElements; private CharacterEncoding encoding; private int[] dimensions; private String opaqueTagOrNull; private final DataTypeInfoOptions options; private HDF5DataTypeVariant typeVariantOrNull; HDF5DataTypeInformation(String dataTypePathOrNull, DataTypeInfoOptions options, HDF5DataClass dataClass, String houseKeepingNameSuffix, int elementSize, boolean signed) { this(dataTypePathOrNull, options, dataClass, CharacterEncoding.ASCII, houseKeepingNameSuffix, elementSize, 1, new int[0], false, signed, false, null); } HDF5DataTypeInformation(HDF5DataClass dataClass, String houseKeepingNameSuffix, int elementSize, boolean signed) { this(null, DataTypeInfoOptions.ALL, dataClass, CharacterEncoding.ASCII, houseKeepingNameSuffix, elementSize, 1, new int[0], false, signed, false, null); } HDF5DataTypeInformation(HDF5DataClass dataClass, String houseKeepingNameSuffix, int elementSize, int numberOfElements, boolean signed) { this(null, DataTypeInfoOptions.ALL, dataClass, CharacterEncoding.ASCII, houseKeepingNameSuffix, elementSize, numberOfElements, new int[] { numberOfElements }, false, signed, false, null); } HDF5DataTypeInformation(String dataTypePathOrNull, DataTypeInfoOptions options, HDF5DataClass dataClass, CharacterEncoding encoding, String houseKeepingNameSuffix, int elementSize, boolean signed, boolean variableLengthString, String opaqueTagOrNull) { this(dataTypePathOrNull, options, dataClass, encoding, houseKeepingNameSuffix, elementSize, 1, new int[0], false, signed, variableLengthString, opaqueTagOrNull); } HDF5DataTypeInformation(String dataTypePathOrNull, DataTypeInfoOptions options, HDF5DataClass dataClass, CharacterEncoding encoding, String houseKeepingNameSuffix, int elementSize, int[] dimensions, boolean arrayType, boolean signed, boolean variableLengthString) { this(dataTypePathOrNull, options, dataClass, encoding, houseKeepingNameSuffix, elementSize, MDAbstractArray.getLength(dimensions), dimensions, arrayType, signed, variableLengthString, null); } private HDF5DataTypeInformation(String dataTypePathOrNull, DataTypeInfoOptions options, HDF5DataClass dataClass, CharacterEncoding encoding, String houseKeepingNameSuffix, int elementSize, int numberOfElements, int[] dimensions, boolean arrayType, boolean signed, boolean variableLengthString, String opaqueTagOrNull) { if (dataClass == HDF5DataClass.BOOLEAN || dataClass == HDF5DataClass.STRING) { this.dataTypePathOrNull = null; this.nameOrNull = null; } else { this.dataTypePathOrNull = dataTypePathOrNull; this.nameOrNull = HDF5Utils.tryGetDataTypeNameFromPath(dataTypePathOrNull, houseKeepingNameSuffix, dataClass); } this.arrayType = arrayType; this.signed = signed; this.variableLengthString = variableLengthString; this.dataClass = dataClass; this.elementSize = elementSize; this.numberOfElements = numberOfElements; this.dimensions = dimensions; this.encoding = encoding; this.opaqueTagOrNull = opaqueTagOrNull; this.options = options; } /** * Returns the raw data class (INTEGER, FLOAT, ...) of this type. *

* May differ from {@link #getDataClass()} if it is the type of a scaled enum ( * {@link HDF5DataTypeVariant#ENUM} or a scaled bitfield (@link * {@link HDF5DataTypeVariant#BITFIELD}. */ public HDF5DataClass getRawDataClass() { return dataClass; } /** * Returns the data class (INTEGER, FLOAT, ...) of this type. */ public HDF5DataClass getDataClass() { if (typeVariantOrNull == HDF5DataTypeVariant.ENUM) { return HDF5DataClass.ENUM; } else if (typeVariantOrNull == HDF5DataTypeVariant.BITFIELD) { return HDF5DataClass.BITFIELD; } else { return dataClass; } } /** * Returns the size of one element (in bytes) of this type. For strings, the total length. */ public int getElementSize() { return elementSize; } /** * The length that is usable. Usually equals to {@link #getElementSize()}, except for Strings, * where it takes into account the character encoding. */ public int getUsableLength() { if (dataClass == HDF5DataClass.STRING && elementSize > 0) { return variableLengthString ? -1 : elementSize / encoding.getMaxBytesPerChar(); } else { return elementSize; } } /** * The element size as is relevant for padding to ensure memory alignment. */ public int getElementSizeForPadding() { // Variable-length strings store a pointer. if (variableLengthString) { return HDFNativeData.getMachineWordSize(); } // Fixed-length strings are accessing single bytes. if (dataClass == HDF5DataClass.STRING) { return 1; } // Otherwise: use elementSize. return elementSize; } void setElementSize(int elementSize) { this.elementSize = elementSize; } /** * Returns the number of elements of this type. *

* This will be 1 except for array data types. */ public int getNumberOfElements() { return numberOfElements; } /** * Returns the total size (in bytes) of this data set. */ public int getSize() { return elementSize * numberOfElements; } /** * Returns the rank (number of dimensions) of this type (0 for a scalar type). */ public int getRank() { return dimensions.length; } /** * Returns the dimensions along each axis of this type (an empty array for a scalar type). */ public int[] getDimensions() { return dimensions; } void setDimensions(int[] dimensions) { this.dimensions = dimensions; this.numberOfElements = MDAbstractArray.getLength(dimensions); } /** * Returns true if this type is an HDF5 array type. */ public boolean isArrayType() { return arrayType; } /** * Returns true if this type is an HDF5 VL (variable-length) type. * * @deprecated Use {@link #isVariableLengthString()} instead. */ @Deprecated public boolean isVariableLengthType() { return variableLengthString; } /** * Returns true, if this data set type has a sign anf false otherwise. */ public boolean isSigned() { return signed; } /** * Returns true, if this data set type is a variable-length string, or * false otherwise. */ public boolean isVariableLengthString() { return variableLengthString; } /** * Returns the tag of an opaque data type, or null, if this data type is not * opaque. */ public String tryGetOpaqueTag() { return opaqueTagOrNull; } /** * Returns whether the data type path has been determined. *

* A return value of true does not necessarily mean that * {@link #tryGetDataTypePath()} will return a value other than null, but a return * value of false means that this method will always return null. */ public boolean knowsDataTypePath() { return options.knowsDataTypePath(); } /** * If this is a committed (named) data type and {@link #knowsDataTypePath()} == * true, return the path of the data type. Otherwise null is returned. */ public String tryGetDataTypePath() { return dataTypePathOrNull; } /** * Returns the name of this datatype, if it is a committed data type. */ public String tryGetName() { return nameOrNull; } /** * Returns whether the data type variant has been determined. *

* A return value of true does not necessarily mean that * {@link #tryGetTypeVariant()} will return a value other than null, but a return * value of false means that this method will always return null. */ public boolean knowsDataTypeVariant() { return options.knowsDataTypeVariant; } /** * Returns the {@link HDF5DataTypeVariant}, or null, if this type has no variant or * {@link #knowsDataTypeVariant()} == false. */ public HDF5DataTypeVariant tryGetTypeVariant() { if (typeVariantOrNull == null && options.knowsDataTypeVariant()) { return HDF5DataTypeVariant.NONE; } else { return typeVariantOrNull; } } private HDF5DataTypeVariant tryGetTypeVariantReplaceNoneWithNull() { return (typeVariantOrNull == HDF5DataTypeVariant.NONE) ? null : typeVariantOrNull; } void setTypeVariant(HDF5DataTypeVariant typeVariant) { this.typeVariantOrNull = typeVariant; } /** * Returns true, if the data set is a time stamp, or false otherwise. */ public boolean isTimeStamp() { return (typeVariantOrNull != null) ? typeVariantOrNull.isTimeStamp() : false; } /** * Returns true, if the data set is a time duration, or false * otherwise. */ public boolean isTimeDuration() { return (typeVariantOrNull != null) ? typeVariantOrNull.isTimeDuration() : false; } /** * Returns the time unit of the data set, if the data set is a time duration, or * null otherwise. */ public HDF5TimeUnit tryGetTimeUnit() { return (typeVariantOrNull != null) ? typeVariantOrNull.tryGetTimeUnit() : null; } /** * Returns true, if the data set is an enumeration type. */ public boolean isEnum() { return getDataClass() == HDF5DataClass.ENUM; } /** * Returns true, if the data set is a bitfield type. */ public boolean isBitField() { return getDataClass() == HDF5DataClass.BITFIELD; } /** * Returns an appropriate Java type, or null, if this HDF5 type has no appropriate * Java type. */ public Class tryGetJavaType() { final int rank = (dimensions.length == 1 && dimensions[0] == 1) ? 0 : dimensions.length; final Class overrideDataTypeOrNull = HDF5CompoundByteifyerFactory.tryGetOverrideJavaType(dataClass, rank, elementSize, typeVariantOrNull); if (overrideDataTypeOrNull != null) { return overrideDataTypeOrNull; } else { return dataClass.getJavaTypeProvider().tryGetJavaType(rank, elementSize, typeVariantOrNull); } } // // Object // @Override public boolean equals(Object obj) { if (obj == null || obj instanceof HDF5DataTypeInformation == false) { return false; } final HDF5DataTypeInformation that = (HDF5DataTypeInformation) obj; final HDF5DataTypeVariant thisTypeVariant = tryGetTypeVariant(); final HDF5DataTypeVariant thatTypeVariant = that.tryGetTypeVariant(); return dataClass.equals(that.dataClass) && elementSize == that.elementSize && encoding == that.encoding && numberOfElements == that.numberOfElements && ObjectUtils.equals(nameOrNull, that.nameOrNull) && ObjectUtils.equals(dataTypePathOrNull, that.dataTypePathOrNull) && ObjectUtils.equals(thisTypeVariant, thatTypeVariant); } @Override public int hashCode() { final HDF5DataTypeVariant typeVariant = tryGetTypeVariant(); return ((((((17 * 59 + dataClass.hashCode()) * 59 + elementSize) * 59 + ObjectUtils .hashCode(encoding)) * 59 + numberOfElements) * 59 + ObjectUtils .hashCode(nameOrNull)) * 59 + ObjectUtils.hashCode(dataTypePathOrNull) * 59) + ObjectUtils.hashCode(typeVariant); } @Override public String toString() { final String name; if (nameOrNull != null) { name = "<" + nameOrNull + ">"; } else { name = ""; } final HDF5DataTypeVariant variantOrNull = tryGetTypeVariantReplaceNoneWithNull(); if (numberOfElements == 1) { if (variantOrNull != null) { return name + dataClass + "(" + getUsableLength() + ")/" + variantOrNull.toString(); } else { return name + dataClass + "(" + getUsableLength() + ")"; } } else if (dimensions.length == 1) { if (variantOrNull != null) { return name + dataClass + "(" + getUsableLength() + ", #" + numberOfElements + ")/" + variantOrNull.toString(); } else { return name + dataClass + "(" + getUsableLength() + ", #" + numberOfElements + ")"; } } else { final StringBuilder builder = new StringBuilder(); builder.append(name); builder.append(dataClass.toString()); builder.append('('); builder.append(getUsableLength()); builder.append(", ["); for (int d : dimensions) { builder.append(d); builder.append(','); } if (dimensions.length > 0) { builder.setLength(builder.length() - 1); } builder.append(']'); builder.append(')'); if (typeVariantOrNull != null) { builder.append('/'); builder.append(typeVariantOrNull.toString()); } return builder.toString(); } } }libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5DataTypeVariant.java000066400000000000000000000136231256564762100277010ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.util.Arrays; import java.util.BitSet; import java.util.Date; import java.util.HashSet; import java.util.Set; /** * An enum of all type variants. Type variants contain additional information on how to interpret a * data set, similar to the tag for the opaque type. * * @author Bernd Rinn */ public enum HDF5DataTypeVariant { // // Implementation note: Never change the order or the names of the values or else old files will // be interpreted wrongly! // // Appending of new type variants at the end of the list is fine. // /** * Used for data sets that encode time stamps as number of milli-seconds since midnight, January * 1, 1970 UTC (aka "start of the epoch"). */ TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH(long.class, Long.class, Date.class), /** * A time duration in micro-seconds. */ TIME_DURATION_MICROSECONDS(HDF5Utils.allTimeDurationTypes), /** * A time duration in milli-seconds. */ TIME_DURATION_MILLISECONDS(HDF5Utils.allTimeDurationTypes), /** * A time duration in seconds. */ TIME_DURATION_SECONDS(HDF5Utils.allTimeDurationTypes), /** * A time duration in minutes. */ TIME_DURATION_MINUTES(HDF5Utils.allTimeDurationTypes), /** * A time duration in hours. */ TIME_DURATION_HOURS(HDF5Utils.allTimeDurationTypes), /** * A time duration in days. */ TIME_DURATION_DAYS(HDF5Utils.allTimeDurationTypes), /** * An enumeration. */ ENUM(HDF5EnumerationValue.class, HDF5EnumerationValueArray.class), /** * No type variant. */ NONE, BITFIELD(BitSet.class); private Set> compatibleTypes; private HDF5DataTypeVariant(Class... compatibleTypes) { this.compatibleTypes = new HashSet>(Arrays.asList(compatibleTypes)); } /** * Returns true, if typeVariantOrNull is not * nullNONE. */ public static boolean isTypeVariant(HDF5DataTypeVariant typeVariantOrNull) { return (typeVariantOrNull != null) && typeVariantOrNull.isTypeVariant(); } /** * Returns true, if typeVariantOrdinal does not * represent NONE. */ public static boolean isTypeVariant(int typeVariantOrdinal) { return typeVariantOrdinal != NONE.ordinal(); } /** * Returns typeVariantOrNull, if it is not null, and NONE * otherwise. */ public static HDF5DataTypeVariant maskNull(HDF5DataTypeVariant typeVariantOrNull) { return (typeVariantOrNull != null) ? typeVariantOrNull : NONE; } /** * Returns typeVariantOrNull, if it is not NONE, and null * otherwise. */ public static HDF5DataTypeVariant unmaskNone(HDF5DataTypeVariant typeVariantOrNull) { return (typeVariantOrNull != NONE) ? typeVariantOrNull : null; } /** * Returns true, if this type variant is not NONE. */ public boolean isTypeVariant() { return this != NONE; } /** * Returns true, if the type variant denoted by typeVariantOrdinal * corresponds to a time duration. */ public static boolean isTimeDuration(final int typeVariantOrdinal) { return typeVariantOrdinal >= TIME_DURATION_MICROSECONDS.ordinal() && typeVariantOrdinal <= TIME_DURATION_DAYS.ordinal(); } /** * Returns true if type is compatible with this type variant. */ public boolean isCompatible(Class type) { return compatibleTypes.contains(type); } /** * Returns the time unit for the given typeVariant. Note that it is an error * if typeVariant does not correspond to a time unit. */ public static HDF5TimeUnit getTimeUnit(final HDF5DataTypeVariant typeVariant) { return HDF5TimeUnit.values()[typeVariant.ordinal() - HDF5DataTypeVariant.TIME_DURATION_MICROSECONDS.ordinal()]; } /** * Returns the time unit for the given typeVariantOrdinal. Note that it is an error * if typeVariantOrdinal does not correspond to a time unit. */ public static HDF5TimeUnit getTimeUnit(final int typeVariantOrdinal) { return HDF5TimeUnit.values()[typeVariantOrdinal - HDF5DataTypeVariant.TIME_DURATION_MICROSECONDS.ordinal()]; } /** * Returns true, if this type variant corresponds to a time stamp. */ public boolean isTimeStamp() { return this == TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH; } /** * Returns true, if this type variant corresponds to a time duration. */ public boolean isTimeDuration() { return isTimeDuration(ordinal()); } /** * Returns the time unit for this type variant or null, if this type variant is not * a time unit. */ public HDF5TimeUnit tryGetTimeUnit() { final int ordinal = ordinal(); return isTimeDuration(ordinal) ? getTimeUnit(ordinal) : null; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5DateTimeReader.java000066400000000000000000000633221256564762100274610ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_INT64; import java.util.Date; import java.util.Iterator; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDLongArray; import ch.systemsx.cisd.hdf5.HDF5BaseReader.DataSpaceParameters; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; /** * The implementation of {@link IHDF5DateTimeReader}. * * @author Bernd Rinn */ class HDF5DateTimeReader implements IHDF5DateTimeReader { private final HDF5BaseReader baseReader; private final HDF5LongReader longReader; HDF5DateTimeReader(HDF5BaseReader baseReader, HDF5LongReader longReader) { assert baseReader != null; assert longReader != null; this.baseReader = baseReader; this.longReader = longReader; } @Override public long getAttrAsLong(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public Long call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); baseReader.checkIsTimeStamp(objectPath, attributeName, objectId, registry); final long[] data = baseReader.h5 .readAttributeAsLongArray(attributeId, H5T_NATIVE_INT64, 1); return data[0]; } }; return baseReader.runner.call(getAttributeRunnable); } @Override public Date getAttr(String objectPath, String attributeName) { return new Date(getAttrAsLong(objectPath, attributeName)); } @Override public long[] getArrayAttrAsLong(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public long[] call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); baseReader.checkIsTimeStamp(objectPath, attributeName, objectId, registry); return longReader.getLongArrayAttribute(objectId, attributeName, registry); } }; return baseReader.runner.call(getAttributeRunnable); } @Override public MDLongArray getMDArrayAttrAsLong(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public MDLongArray call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); baseReader.checkIsTimeStamp(objectPath, attributeName, objectId, registry); return longReader.getLongMDArrayAttribute(objectId, attributeName, registry); } }; return baseReader.runner.call(getAttributeRunnable); } @Override public Date[] getArrayAttr(String objectPath, String attributeName) { final long[] timeStampArray = getArrayAttrAsLong(objectPath, attributeName); return timeStampsToDates(timeStampArray); } @Override public MDArray getMDArrayAttr(String objectPath, String attributeName) { final MDLongArray timeStampArray = getMDArrayAttrAsLong(objectPath, attributeName); return timeStampsToDates(timeStampArray); } @Override public boolean isTimeStamp(String objectPath, String attributeName) throws HDF5JavaException { final HDF5DataTypeVariant typeVariantOrNull = baseReader.tryGetTypeVariant(objectPath, attributeName); return typeVariantOrNull != null && typeVariantOrNull.isTimeStamp(); } @Override public boolean isTimeStamp(final String objectPath) throws HDF5JavaException { final HDF5DataTypeVariant typeVariantOrNull = baseReader.tryGetTypeVariant(objectPath); return typeVariantOrNull != null && typeVariantOrNull.isTimeStamp(); } @Override public long readTimeStamp(final String objectPath) throws HDF5JavaException { baseReader.checkOpen(); assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public Long call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); baseReader.checkIsTimeStamp(objectPath, dataSetId, registry); final long[] data = new long[1]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_INT64, data); return data[0]; } }; return baseReader.runner.call(readCallable); } @Override public long[] readTimeStampArray(final String objectPath) throws HDF5JavaException { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public long[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); baseReader.checkIsTimeStamp(objectPath, dataSetId, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); final long[] data = new long[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_INT64, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return data; } }; return baseReader.runner.call(readCallable); } @Override public long[] readTimeStampArrayBlock(final String objectPath, final int blockSize, final long blockNumber) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public long[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); baseReader.checkIsTimeStamp(objectPath, dataSetId, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, blockNumber * blockSize, blockSize, registry); final long[] data = new long[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_INT64, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return data; } }; return baseReader.runner.call(readCallable); } @Override public long[] readTimeStampArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public long[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); baseReader.checkIsTimeStamp(objectPath, dataSetId, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockSize, registry); final long[] data = new long[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_INT64, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return data; } }; return baseReader.runner.call(readCallable); } @Override public Date readDate(final String objectPath) throws HDF5JavaException { return new Date(readTimeStamp(objectPath)); } @Override public Date[] readDateArray(final String objectPath) throws HDF5JavaException { final long[] timeStampArray = readTimeStampArray(objectPath); return timeStampsToDates(timeStampArray); } @Override public MDLongArray readTimeStampMDArray(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public MDLongArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); baseReader.checkIsTimeStamp(objectPath, dataSetId, registry); return longReader.readLongMDArray(dataSetId, registry); } }; return baseReader.runner.call(readCallable); } @Override public MDLongArray readTimeStampMDArrayBlock(final String objectPath, final int[] blockDimensions, final long[] blockNumber) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readTimeStampMDArrayBlockWithOffset(objectPath, blockDimensions, offset); } @Override public MDLongArray readTimeStampMDArrayBlockWithOffset(final String objectPath, final int[] blockDimensions, final long[] offset) { assert objectPath != null; assert blockDimensions != null; assert offset != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public MDLongArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); baseReader.checkIsTimeStamp(objectPath, dataSetId, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockDimensions, registry); final long[] dataBlock = new long[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_INT64, spaceParams.memorySpaceId, spaceParams.dataSpaceId, dataBlock); return new MDLongArray(dataBlock, blockDimensions); } }; return baseReader.runner.call(readCallable); } @Override public int[] readToMDArrayWithOffset(final String objectPath, final MDLongArray array, final int[] memoryOffset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); baseReader.checkIsTimeStamp(objectPath, dataSetId, registry); final DataSpaceParameters spaceParams = baseReader.getBlockSpaceParameters(dataSetId, memoryOffset, array .dimensions(), registry); final int nativeDataTypeId = baseReader.getNativeDataTypeId(dataSetId, H5T_NATIVE_INT64, registry); baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, array. getAsFlatArray()); return MDArray.toInt(spaceParams.dimensions); } }; return baseReader.runner.call(readCallable); } @Override public int[] readToMDArrayBlockWithOffset(final String objectPath, final MDLongArray array, final int[] blockDimensions, final long[] offset, final int[] memoryOffset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); baseReader.checkIsTimeStamp(objectPath, dataSetId, registry); final DataSpaceParameters spaceParams = baseReader.getBlockSpaceParameters(dataSetId, memoryOffset, array .dimensions(), offset, blockDimensions, registry); final int nativeDataTypeId = baseReader.getNativeDataTypeId(dataSetId, H5T_NATIVE_INT64, registry); baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, array .getAsFlatArray()); return MDArray.toInt(spaceParams.dimensions); } }; return baseReader.runner.call(readCallable); } @Override public Iterable> getTimeStampArrayNaturalBlocks(final String dataSetPath) throws HDF5JavaException { final HDF5NaturalBlock1DParameters params = new HDF5NaturalBlock1DParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlock1DParameters.HDF5NaturalBlock1DIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5DataBlock next() { final long offset = index.computeOffsetAndSizeGetOffset(); final long[] block = readTimeStampArrayBlockWithOffset(dataSetPath, index.getBlockSize(), offset); return new HDF5DataBlock(block, index.getAndIncIndex(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } @Override public Date[] readDateArrayBlock(String objectPath, int blockSize, long blockNumber) { final long[] timestampArray = readTimeStampArrayBlock(objectPath, blockSize, blockNumber); return timeStampsToDates(timestampArray); } @Override public Date[] readDateArrayBlockWithOffset(String objectPath, int blockSize, long offset) { final long[] timestampArray = readTimeStampArrayBlockWithOffset(objectPath, blockSize, offset); return timeStampsToDates(timestampArray); } @Override public Iterable> getDateArrayNaturalBlocks(final String dataSetPath) throws HDF5JavaException { final HDF5NaturalBlock1DParameters params = new HDF5NaturalBlock1DParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlock1DParameters.HDF5NaturalBlock1DIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5DataBlock next() { final long offset = index.computeOffsetAndSizeGetOffset(); final long[] block = readTimeStampArrayBlockWithOffset(dataSetPath, index.getBlockSize(), offset); return new HDF5DataBlock(timeStampsToDates(block), index.getAndIncIndex(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } @Override public Iterable> getTimeStampMDArrayNaturalBlocks( final String dataSetPath) { baseReader.checkOpen(); final HDF5NaturalBlockMDParameters params = new HDF5NaturalBlockMDParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlockMDParameters.HDF5NaturalBlockMDIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5MDDataBlock next() { final long[] offset = index.computeOffsetAndSizeGetOffsetClone(); final MDLongArray data = readTimeStampMDArrayBlockWithOffset(dataSetPath, index.getBlockSize(), offset); return new HDF5MDDataBlock(data, index.getIndexClone(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } private static Date[] timeStampsToDates(final long[] timeStampArray) { assert timeStampArray != null; final Date[] dateArray = new Date[timeStampArray.length]; for (int i = 0; i < dateArray.length; ++i) { dateArray[i] = new Date(timeStampArray[i]); } return dateArray; } private static MDArray timeStampsToDates(final MDLongArray timeStampArray) { assert timeStampArray != null; final long[] timeStampsFlat = timeStampArray.getAsFlatArray(); final MDArray dateArray = new MDArray(Date.class, timeStampArray.dimensions()); final Date[] datesFlat = dateArray.getAsFlatArray(); for (int i = 0; i < datesFlat.length; ++i) { datesFlat[i] = new Date(timeStampsFlat[i]); } return dateArray; } @Override public MDArray readDateMDArray(String objectPath) { final MDLongArray timeStampArray = readTimeStampMDArray(objectPath); return timeStampsToDates(timeStampArray); } @Override public MDArray readDateMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber) { final MDLongArray timeStampArray = readTimeStampMDArrayBlock(objectPath, blockDimensions, blockNumber); return timeStampsToDates(timeStampArray); } @Override public MDArray readDateMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset) { final MDLongArray timeStampArray = readTimeStampMDArrayBlockWithOffset(objectPath, blockDimensions, offset); return timeStampsToDates(timeStampArray); } @Override public Iterable>> getDateMDArrayNaturalBlocks( final String dataSetPath) { baseReader.checkOpen(); final HDF5NaturalBlockMDParameters params = new HDF5NaturalBlockMDParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>>() { @Override public Iterator>> iterator() { return new Iterator>>() { final HDF5NaturalBlockMDParameters.HDF5NaturalBlockMDIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5MDDataBlock> next() { final long[] offset = index.computeOffsetAndSizeGetOffsetClone(); final MDLongArray data = readTimeStampMDArrayBlockWithOffset(dataSetPath, index.getBlockSize(), offset); return new HDF5MDDataBlock>(timeStampsToDates(data), index.getIndexClone(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5DateTimeWriter.java000066400000000000000000000704041256564762100275320ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.HDF5IntStorageFeatures.INT_NO_COMPRESSION; import static ch.systemsx.cisd.hdf5.hdf5lib.H5D.H5Dwrite; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_ALL; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_INT64; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_I64LE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_U64LE; import java.util.Date; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDLongArray; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; import ch.systemsx.cisd.hdf5.hdf5lib.HDFNativeData; /** * Implementation of {@link IHDF5DateTimeWriter}. * * @author Bernd Rinn */ public class HDF5DateTimeWriter extends HDF5DateTimeReader implements IHDF5DateTimeWriter { private final HDF5BaseWriter baseWriter; HDF5DateTimeWriter(HDF5BaseWriter baseWriter, HDF5LongReader longReader) { super(baseWriter, longReader); assert baseWriter != null; this.baseWriter = baseWriter; } @Override public void setAttr(final String objectPath, final String name, final long timeStamp) { assert objectPath != null; assert name != null; baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { 1 }, registry); baseWriter .setAttribute( objectPath, name, HDF5DataTypeVariant.TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH, H5T_STD_I64LE, H5T_NATIVE_INT64, dataSpaceId, new long[] { timeStamp }, registry); } else { baseWriter .setAttribute( objectPath, name, HDF5DataTypeVariant.TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH, H5T_STD_I64LE, H5T_NATIVE_INT64, -1, new long[] { timeStamp }, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void setAttr(String objectPath, String name, Date date) { setAttr(objectPath, name, date.getTime()); } @Override public void setArrayAttr(String objectPath, String name, Date[] dates) { setArrayAttr(objectPath, name, datesToTimeStamps(dates)); } @Override public void setArrayAttr(final String objectPath, final String name, final long[] timeStamps) { assert objectPath != null; assert name != null; assert timeStamps != null; baseWriter.checkOpen(); final ICallableWithCleanUp setAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { timeStamps.length }, registry); baseWriter .setAttribute( objectPath, name, HDF5DataTypeVariant.TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH, H5T_STD_I64LE, H5T_NATIVE_INT64, dataSpaceId, timeStamps, registry); } else { final int memoryTypeId = baseWriter.h5.createArrayType(H5T_NATIVE_INT64, timeStamps.length, registry); final int storageTypeId = baseWriter.h5.createArrayType(H5T_STD_I64LE, timeStamps.length, registry); baseWriter .setAttribute( objectPath, name, HDF5DataTypeVariant.TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH, storageTypeId, memoryTypeId, -1, timeStamps, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(setAttributeRunnable); } @Override public void setMDArrayAttr(final String objectPath, final String name, final MDLongArray timeStamps) { assert objectPath != null; assert name != null; assert timeStamps != null; baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(timeStamps.longDimensions(), registry); baseWriter .setAttribute( objectPath, name, HDF5DataTypeVariant.TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH, H5T_STD_I64LE, H5T_NATIVE_INT64, dataSpaceId, timeStamps.getAsFlatArray(), registry); } else { final int memoryTypeId = baseWriter.h5.createArrayType(H5T_NATIVE_INT64, timeStamps.dimensions(), registry); final int storageTypeId = baseWriter.h5.createArrayType(H5T_STD_I64LE, timeStamps.dimensions(), registry); baseWriter .setAttribute( objectPath, name, HDF5DataTypeVariant.TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH, storageTypeId, memoryTypeId, -1, timeStamps.getAsFlatArray(), registry); } return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void setMDArrayAttr(String objectPath, String name, MDArray value) { setMDArrayAttr(objectPath, name, datesToTimeStamps(value)); } @Override public void write(final String objectPath, final long timeStamp) { assert objectPath != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeScalarRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.writeScalar(objectPath, H5T_STD_I64LE, H5T_NATIVE_INT64, HDFNativeData.longToByte(timeStamp), true, true, registry); baseWriter.setTypeVariant(dataSetId, HDF5DataTypeVariant.TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH, registry); return null; // Nothing to return. } }; baseWriter.runner.call(writeScalarRunnable); } @Override public void createArray(String objectPath, int size) { createArray(objectPath, size, HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION); } @Override public void createArray(final String objectPath, final long size, final int blockSize) { createArray(objectPath, size, blockSize, HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION); } @Override public void createArray(final String objectPath, final int size, final HDF5GenericStorageFeatures features) { assert objectPath != null; assert size >= 0; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int longBytes = 8; final int dataSetId; if (features.requiresChunking()) { dataSetId = baseWriter.createDataSet(objectPath, H5T_STD_I64LE, features, new long[] { 0 }, new long[] { size }, longBytes, registry); } else { dataSetId = baseWriter.createDataSet(objectPath, H5T_STD_I64LE, features, new long[] { size }, null, longBytes, registry); } baseWriter.setTypeVariant(dataSetId, HDF5DataTypeVariant.TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH, registry); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createArray(final String objectPath, final long length, final int blockSize, final HDF5GenericStorageFeatures features) { assert objectPath != null; assert length >= 0; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int longBytes = 8; final int dataSetId = baseWriter.createDataSet(objectPath, H5T_STD_I64LE, features, new long[] { length }, new long[] { blockSize }, longBytes, registry); baseWriter.setTypeVariant(dataSetId, HDF5DataTypeVariant.TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH, registry); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeArray(final String objectPath, final long[] timeStamps) { writeArray(objectPath, timeStamps, HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION); } @Override public void writeArray(final String objectPath, final long[] timeStamps, final HDF5GenericStorageFeatures features) { assert objectPath != null; assert timeStamps != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int longBytes = 8; final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, H5T_STD_I64LE, new long[] { timeStamps.length }, longBytes, features, registry); H5Dwrite(dataSetId, H5T_NATIVE_INT64, H5S_ALL, H5S_ALL, H5P_DEFAULT, timeStamps); baseWriter.setTypeVariant(dataSetId, HDF5DataTypeVariant.TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH, registry); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeArrayBlock(final String objectPath, final long[] data, final long blockNumber) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] dimensions = new long[] { data.length }; final long[] slabStartOrNull = new long[] { data.length * blockNumber }; final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, new long[] { data.length * (blockNumber + 1) }, -1, registry); baseWriter.checkIsTimeStamp(objectPath, dataSetId, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, slabStartOrNull, dimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(dimensions, registry); H5Dwrite(dataSetId, H5T_NATIVE_INT64, memorySpaceId, dataSpaceId, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeArrayBlockWithOffset(final String objectPath, final long[] data, final int dataSize, final long offset) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] blockDimensions = new long[] { dataSize }; final long[] slabStartOrNull = new long[] { offset }; final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, new long[] { offset + dataSize }, -1, registry); baseWriter.checkIsTimeStamp(objectPath, dataSetId, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, slabStartOrNull, blockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(blockDimensions, registry); H5Dwrite(dataSetId, H5T_NATIVE_INT64, memorySpaceId, dataSpaceId, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void write(final String objectPath, final Date date) { write(objectPath, date.getTime()); } @Override public void writeArray(final String objectPath, final Date[] dates) { writeArray(objectPath, datesToTimeStamps(dates)); } @Override public void writeArray(final String objectPath, final Date[] dates, final HDF5GenericStorageFeatures features) { writeArray(objectPath, datesToTimeStamps(dates), features); } @Override public void writeMDArray(final String objectPath, final MDLongArray data, final HDF5IntStorageFeatures features) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, features.isSigned() ? H5T_STD_I64LE : H5T_STD_U64LE, data.longDimensions(), 8, features, registry); H5Dwrite(dataSetId, H5T_NATIVE_INT64, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.getAsFlatArray()); baseWriter.setTypeVariant(dataSetId, HDF5DataTypeVariant.TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH, registry); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createMDArray(final String objectPath, final int[] dimensions) { createMDArray(objectPath, dimensions, INT_NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions) { createMDArray(objectPath, dimensions, blockDimensions, INT_NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final int[] dimensions, final HDF5IntStorageFeatures features) { assert objectPath != null; assert dimensions != null; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId; if (features.requiresChunking()) { final long[] nullDimensions = new long[dimensions.length]; dataSetId = baseWriter.createDataSet(objectPath, features.isSigned() ? H5T_STD_I64LE : H5T_STD_U64LE, features, nullDimensions, MDArray.toLong(dimensions), 8, registry); } else { dataSetId = baseWriter.createDataSet(objectPath, features.isSigned() ? H5T_STD_I64LE : H5T_STD_U64LE, features, MDArray.toLong(dimensions), null, 8, registry); } baseWriter.setTypeVariant(dataSetId, HDF5DataTypeVariant.TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH, registry); return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void createMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions, final HDF5IntStorageFeatures features) { assert objectPath != null; assert dimensions != null; assert blockDimensions != null; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.createDataSet(objectPath, features.isSigned() ? H5T_STD_I64LE : H5T_STD_U64LE, features, dimensions, MDArray.toLong(blockDimensions), 8, registry); baseWriter.setTypeVariant(dataSetId, HDF5DataTypeVariant.TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH, registry); return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void writeMDArrayBlock(final String objectPath, final MDLongArray data, final long[] blockNumber) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeMDArrayBlockWithOffset(objectPath, data, offset); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final MDLongArray data, final long[] offset) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] dimensions = data.longDimensions(); assert dimensions.length == offset.length; final long[] dataSetDimensions = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + dimensions[i]; } final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, dimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(dimensions, registry); H5Dwrite(dataSetId, H5T_NATIVE_INT64, memorySpaceId, dataSpaceId, H5P_DEFAULT, data.getAsFlatArray()); baseWriter.setTypeVariant(dataSetId, HDF5DataTypeVariant.TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH, registry); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final MDLongArray data, final int[] blockDimensions, final long[] offset, final int[] memoryOffset) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] memoryDimensions = data.longDimensions(); assert memoryDimensions.length == offset.length; final long[] longBlockDimensions = MDArray.toLong(blockDimensions); assert longBlockDimensions.length == offset.length; final long[] dataSetDimensions = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + blockDimensions[i]; } final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, longBlockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(memoryDimensions, registry); baseWriter.h5.setHyperslabBlock(memorySpaceId, MDArray.toLong(memoryOffset), longBlockDimensions); H5Dwrite(dataSetId, H5T_NATIVE_INT64, memorySpaceId, dataSpaceId, H5P_DEFAULT, data.getAsFlatArray()); baseWriter.setTypeVariant(dataSetId, HDF5DataTypeVariant.TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH, registry); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeMDArray(final String objectPath, final MDArray data, final HDF5IntStorageFeatures features) { writeMDArray(objectPath, datesToTimeStamps(data), features); } @Override public void writeMDArrayBlock(final String objectPath, final MDArray data, final long[] blockNumber) { writeMDArrayBlock(objectPath, datesToTimeStamps(data), blockNumber); } @Override public void writeMDArrayBlockWithOffset(String objectPath, MDArray data, long[] offset) { writeMDArrayBlockWithOffset(objectPath, datesToTimeStamps(data), offset); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final MDArray data, final int[] blockDimensions, final long[] offset, final int[] memoryOffset) { writeMDArrayBlockWithOffset(objectPath, datesToTimeStamps(data), blockDimensions, offset, memoryOffset); } private static long[] datesToTimeStamps(Date[] dates) { assert dates != null; final long[] timestamps = new long[dates.length]; for (int i = 0; i < timestamps.length; ++i) { timestamps[i] = dates[i].getTime(); } return timestamps; } private static MDLongArray datesToTimeStamps(MDArray dates) { assert dates != null; final Date[] datesFlat = dates.getAsFlatArray(); final MDLongArray timestamps = new MDLongArray(dates.dimensions()); final long[] timestampsFlat = timestamps.getAsFlatArray(); for (int i = 0; i < timestampsFlat.length; ++i) { timestampsFlat[i] = datesFlat[i].getTime(); } return timestamps; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5DoubleReader.java000066400000000000000000001024551256564762100272000ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.MatrixUtils.cardinalityBoundIndices; import static ch.systemsx.cisd.hdf5.MatrixUtils.checkBoundIndices; import static ch.systemsx.cisd.hdf5.MatrixUtils.createFullBlockDimensionsAndOffset; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_ARRAY; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_DOUBLE; import java.util.Arrays; import java.util.Iterator; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import ncsa.hdf.hdf5lib.exceptions.HDF5SpaceRankMismatch; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDDoubleArray; import ch.systemsx.cisd.hdf5.HDF5BaseReader.DataSpaceParameters; import ch.systemsx.cisd.hdf5.HDF5DataTypeInformation.DataTypeInfoOptions; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; import ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants; /** * The implementation of {@link IHDF5DoubleReader}. * * @author Bernd Rinn */ class HDF5DoubleReader implements IHDF5DoubleReader { private final HDF5BaseReader baseReader; HDF5DoubleReader(HDF5BaseReader baseReader) { assert baseReader != null; this.baseReader = baseReader; } // For Unit tests only. HDF5BaseReader getBaseReader() { return baseReader; } // ///////////////////// // Attributes // ///////////////////// @Override public double getAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public Double call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final double[] data = baseReader.h5.readAttributeAsDoubleArray(attributeId, H5T_NATIVE_DOUBLE, 1); return data[0]; } }; return baseReader.runner.call(getAttributeRunnable); } @Override public double[] getArrayAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public double[] call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); return getDoubleArrayAttribute(objectId, attributeName, registry); } }; return baseReader.runner.call(getAttributeRunnable); } @Override public MDDoubleArray getMDArrayAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public MDDoubleArray call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); return getDoubleMDArrayAttribute(objectId, attributeName, registry); } }; return baseReader.runner.call(getAttributeRunnable); } @Override public double[][] getMatrixAttr(final String objectPath, final String attributeName) throws HDF5JavaException { final MDDoubleArray array = getMDArrayAttr(objectPath, attributeName); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } // ///////////////////// // Data Sets // ///////////////////// @Override public double read(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public Double call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final double[] data = new double[1]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_DOUBLE, data); return data[0]; } }; return baseReader.runner.call(readCallable); } @Override public double[] readArray(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public double[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); return readDoubleArray(dataSetId, registry); } }; return baseReader.runner.call(readCallable); } private double[] readDoubleArray(int dataSetId, ICleanUpRegistry registry) { try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); final double[] data = new double[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_DOUBLE, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return data; } catch (HDF5LibraryException ex) { if (ex.getMajorErrorNumber() == HDF5Constants.H5E_DATATYPE && ex.getMinorErrorNumber() == HDF5Constants.H5E_CANTINIT) { // Check whether it is an array data type. final int dataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); if (baseReader.h5.getClassType(dataTypeId) == HDF5Constants.H5T_ARRAY) { return readDoubleArrayFromArrayType(dataSetId, dataTypeId, registry); } } throw ex; } } private double[] readDoubleArrayFromArrayType(int dataSetId, final int dataTypeId, ICleanUpRegistry registry) { final int spaceId = baseReader.h5.createScalarDataSpace(); final int[] dimensions = baseReader.h5.getArrayDimensions(dataTypeId); final double[] data = new double[HDF5Utils.getOneDimensionalArraySize(dimensions)]; final int memoryDataTypeId = baseReader.h5.createArrayType(H5T_NATIVE_DOUBLE, data.length, registry); baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceId, spaceId, data); return data; } @Override public int[] readToMDArrayWithOffset(final String objectPath, final MDDoubleArray array, final int[] memoryOffset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getBlockSpaceParameters(dataSetId, memoryOffset, array .dimensions(), registry); final int nativeDataTypeId = baseReader.getNativeDataTypeId(dataSetId, H5T_NATIVE_DOUBLE, registry); baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, array. getAsFlatArray()); return MDArray.toInt(spaceParams.dimensions); } }; return baseReader.runner.call(readCallable); } @Override public int[] readToMDArrayBlockWithOffset(final String objectPath, final MDDoubleArray array, final int[] blockDimensions, final long[] offset, final int[] memoryOffset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getBlockSpaceParameters(dataSetId, memoryOffset, array .dimensions(), offset, blockDimensions, registry); final int nativeDataTypeId = baseReader.getNativeDataTypeId(dataSetId, H5T_NATIVE_DOUBLE, registry); baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, array .getAsFlatArray()); return MDArray.toInt(spaceParams.dimensions); } }; return baseReader.runner.call(readCallable); } @Override public double[] readArrayBlock(final String objectPath, final int blockSize, final long blockNumber) { return readArrayBlockWithOffset(objectPath, blockSize, blockNumber * blockSize); } @Override public double[] readArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public double[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockSize, registry); final double[] data = new double[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_DOUBLE, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return data; } }; return baseReader.runner.call(readCallable); } @Override public double[][] readMatrix(final String objectPath) throws HDF5JavaException { final MDDoubleArray array = readMDArray(objectPath); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public double[][] readMatrixBlock(final String objectPath, final int blockSizeX, final int blockSizeY, final long blockNumberX, final long blockNumberY) throws HDF5JavaException { final MDDoubleArray array = readMDArrayBlock(objectPath, new int[] { blockSizeX, blockSizeY }, new long[] { blockNumberX, blockNumberY }); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public double[][] readMatrixBlockWithOffset(final String objectPath, final int blockSizeX, final int blockSizeY, final long offsetX, final long offsetY) throws HDF5JavaException { final MDDoubleArray array = readMDArrayBlockWithOffset(objectPath, new int[] { blockSizeX, blockSizeY }, new long[] { offsetX, offsetY }); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public MDDoubleArray readMDArraySlice(String objectPath, IndexMap boundIndices) { baseReader.checkOpen(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; final int cardBoundIndices = cardinalityBoundIndices(boundIndices); checkBoundIndices(objectPath, fullDimensions, cardBoundIndices); final int[] effectiveBlockDimensions = new int[fullBlockDimensions.length - cardBoundIndices]; Arrays.fill(effectiveBlockDimensions, -1); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, null, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDDoubleArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); if (fullBlockDimensions.length == cardBoundIndices) // no free indices { return new MDDoubleArray(result.getAsFlatArray(), new int[] { 1 }); } else { return new MDDoubleArray(result.getAsFlatArray(), effectiveBlockDimensions); } } @Override public MDDoubleArray readMDArraySlice(String objectPath, long[] boundIndices) { baseReader.checkOpen(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; final int cardBoundIndices = cardinalityBoundIndices(boundIndices); checkBoundIndices(objectPath, fullDimensions, boundIndices); final int[] effectiveBlockDimensions = new int[fullBlockDimensions.length - cardBoundIndices]; Arrays.fill(effectiveBlockDimensions, -1); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, null, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDDoubleArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); if (fullBlockDimensions.length == cardBoundIndices) // no free indices { return new MDDoubleArray(result.getAsFlatArray(), new int[] { 1 }); } else { return new MDDoubleArray(result.getAsFlatArray(), effectiveBlockDimensions); } } @Override public MDDoubleArray readMDArray(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public MDDoubleArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); return readDoubleMDArray(dataSetId, registry); } }; return baseReader.runner.call(readCallable); } MDDoubleArray readDoubleMDArray(int dataSetId, ICleanUpRegistry registry) { try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); final double[] data = new double[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_DOUBLE, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return new MDDoubleArray(data, spaceParams.dimensions); } catch (HDF5LibraryException ex) { if (ex.getMajorErrorNumber() == HDF5Constants.H5E_DATATYPE && ex.getMinorErrorNumber() == HDF5Constants.H5E_CANTINIT) { // Check whether it is an array data type. final int dataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); if (baseReader.h5.getClassType(dataTypeId) == HDF5Constants.H5T_ARRAY) { return readDoubleMDArrayFromArrayType(dataSetId, dataTypeId, registry); } } throw ex; } } private MDDoubleArray readDoubleMDArrayFromArrayType(int dataSetId, final int dataTypeId, ICleanUpRegistry registry) { final int[] arrayDimensions = baseReader.h5.getArrayDimensions(dataTypeId); final int memoryDataTypeId = baseReader.h5.createArrayType(H5T_NATIVE_DOUBLE, arrayDimensions, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); if (spaceParams.blockSize == 0) { final int spaceId = baseReader.h5.createScalarDataSpace(); final double[] data = new double[MDArray.getLength(arrayDimensions)]; baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceId, spaceId, data); return new MDDoubleArray(data, arrayDimensions); } else { final double[] data = new double[MDArray.getLength(arrayDimensions) * spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return new MDDoubleArray(data, MatrixUtils.concat(MDArray.toInt(spaceParams.dimensions), arrayDimensions)); } } @Override public MDDoubleArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, IndexMap boundIndices) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readSlicedMDArrayBlockWithOffset(objectPath, blockDimensions, offset, boundIndices); } @Override public MDDoubleArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, long[] boundIndices) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readSlicedMDArrayBlockWithOffset(objectPath, blockDimensions, offset, boundIndices); } @Override public MDDoubleArray readMDArrayBlock(final String objectPath, final int[] blockDimensions, final long[] blockNumber) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readMDArrayBlockWithOffset(objectPath, blockDimensions, offset); } @Override public MDDoubleArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, IndexMap boundIndices) { baseReader.checkOpen(); final int[] effectiveBlockDimensions = blockDimensions.clone(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; checkBoundIndices(objectPath, fullDimensions, blockDimensions, cardinalityBoundIndices(boundIndices)); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, offset, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDDoubleArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); return new MDDoubleArray(result.getAsFlatArray(), effectiveBlockDimensions); } @Override public MDDoubleArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, long[] boundIndices) { baseReader.checkOpen(); final int[] effectiveBlockDimensions = blockDimensions.clone(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; checkBoundIndices(objectPath, fullDimensions, blockDimensions, cardinalityBoundIndices(boundIndices)); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, offset, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDDoubleArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); return new MDDoubleArray(result.getAsFlatArray(), effectiveBlockDimensions); } @Override public MDDoubleArray readMDArrayBlockWithOffset(final String objectPath, final int[] blockDimensions, final long[] offset) { assert objectPath != null; assert blockDimensions != null; assert offset != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public MDDoubleArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockDimensions, registry); final double[] dataBlock = new double[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_DOUBLE, spaceParams.memorySpaceId, spaceParams.dataSpaceId, dataBlock); return new MDDoubleArray(dataBlock, spaceParams.dimensions); } catch (HDF5SpaceRankMismatch ex) { final HDF5DataSetInformation info = baseReader.getDataSetInformation(objectPath, DataTypeInfoOptions.MINIMAL, false); if (ex.getSpaceRankExpected() - ex.getSpaceRankFound() == info .getTypeInformation().getRank()) { return readMDArrayBlockOfArrays(dataSetId, blockDimensions, offset, info, ex.getSpaceRankFound(), registry); } else { throw ex; } } } }; return baseReader.runner.call(readCallable); } private MDDoubleArray readMDArrayBlockOfArrays(final int dataSetId, final int[] blockDimensions, final long[] offset, final HDF5DataSetInformation info, final int spaceRank, final ICleanUpRegistry registry) { final int[] arrayDimensions = info.getTypeInformation().getDimensions(); int[] effectiveBlockDimensions = blockDimensions; // We do not support block-wise reading of array types, check // that we do not have to and bail out otherwise. for (int i = 0; i < arrayDimensions.length; ++i) { final int j = spaceRank + i; if (effectiveBlockDimensions[j] < 0) { if (effectiveBlockDimensions == blockDimensions) { effectiveBlockDimensions = blockDimensions.clone(); } effectiveBlockDimensions[j] = arrayDimensions[i]; } if (effectiveBlockDimensions[j] != arrayDimensions[i]) { throw new HDF5JavaException( "Block-wise reading of array type data sets is not supported."); } } final int[] spaceBlockDimensions = Arrays.copyOfRange(effectiveBlockDimensions, 0, spaceRank); final long[] spaceOfs = Arrays.copyOfRange(offset, 0, spaceRank); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, spaceOfs, spaceBlockDimensions, registry); final double[] dataBlock = new double[spaceParams.blockSize * info.getTypeInformation().getNumberOfElements()]; final int memoryDataTypeId = baseReader.h5.createArrayType(H5T_NATIVE_DOUBLE, info.getTypeInformation() .getDimensions(), registry); baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, dataBlock); return new MDDoubleArray(dataBlock, effectiveBlockDimensions); } @Override public Iterable> getArrayNaturalBlocks(final String dataSetPath) throws HDF5JavaException { baseReader.checkOpen(); final HDF5NaturalBlock1DParameters params = new HDF5NaturalBlock1DParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlock1DParameters.HDF5NaturalBlock1DIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5DataBlock next() { final long offset = index.computeOffsetAndSizeGetOffset(); final double[] block = readArrayBlockWithOffset(dataSetPath, index .getBlockSize(), offset); return new HDF5DataBlock(block, index.getAndIncIndex(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } @Override public Iterable> getMDArrayNaturalBlocks(final String dataSetPath) { baseReader.checkOpen(); final HDF5NaturalBlockMDParameters params = new HDF5NaturalBlockMDParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlockMDParameters.HDF5NaturalBlockMDIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5MDDataBlock next() { final long[] offset = index.computeOffsetAndSizeGetOffsetClone(); final MDDoubleArray data = readMDArrayBlockWithOffset(dataSetPath, index .getBlockSize(), offset); return new HDF5MDDataBlock(data, index .getIndexClone(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } double[] getDoubleArrayAttribute(final int objectId, final String attributeName, ICleanUpRegistry registry) { final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, registry); final int memoryTypeId; final int len; if (baseReader.h5.getClassType(attributeTypeId) == H5T_ARRAY) { final int[] arrayDimensions = baseReader.h5.getArrayDimensions(attributeTypeId); if (arrayDimensions.length != 1) { throw new HDF5JavaException( "Array needs to be of rank 1, but is of rank " + arrayDimensions.length); } len = arrayDimensions[0]; memoryTypeId = baseReader.h5.createArrayType(H5T_NATIVE_DOUBLE, len, registry); } else { final long[] arrayDimensions = baseReader.h5.getDataDimensionsForAttribute(attributeId, registry); memoryTypeId = H5T_NATIVE_DOUBLE; len = HDF5Utils.getOneDimensionalArraySize(arrayDimensions); } final double[] data = baseReader.h5.readAttributeAsDoubleArray(attributeId, memoryTypeId, len); return data; } MDDoubleArray getDoubleMDArrayAttribute(final int objectId, final String attributeName, ICleanUpRegistry registry) { try { final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, registry); final int memoryTypeId; final int[] arrayDimensions; if (baseReader.h5.getClassType(attributeTypeId) == H5T_ARRAY) { arrayDimensions = baseReader.h5.getArrayDimensions(attributeTypeId); memoryTypeId = baseReader.h5.createArrayType(H5T_NATIVE_DOUBLE, arrayDimensions, registry); } else { arrayDimensions = MDArray.toInt(baseReader.h5.getDataDimensionsForAttribute( attributeId, registry)); memoryTypeId = H5T_NATIVE_DOUBLE; } final int len = MDArray.getLength(arrayDimensions); final double[] data = baseReader.h5.readAttributeAsDoubleArray(attributeId, memoryTypeId, len); return new MDDoubleArray(data, arrayDimensions); } catch (IllegalArgumentException ex) { throw new HDF5JavaException(ex.getMessage()); } } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5DoubleWriter.java000066400000000000000000000662551256564762100272610ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.HDF5FloatStorageFeatures.FLOAT_NO_COMPRESSION; import static ch.systemsx.cisd.hdf5.hdf5lib.H5D.H5Dwrite; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_ALL; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_DOUBLE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_IEEE_F64LE; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDDoubleArray; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; /** * The implementation of {@link IHDF5DoubleWriter}. * * @author Bernd Rinn */ class HDF5DoubleWriter extends HDF5DoubleReader implements IHDF5DoubleWriter { private final HDF5BaseWriter baseWriter; HDF5DoubleWriter(HDF5BaseWriter baseWriter) { super(baseWriter); assert baseWriter != null; this.baseWriter = baseWriter; } // ///////////////////// // Attributes // ///////////////////// @Override public void setAttr(final String objectPath, final String name, final double value) { assert objectPath != null; assert name != null; baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { 1 }, registry); baseWriter.setAttribute(objectPath, name, H5T_IEEE_F64LE, H5T_NATIVE_DOUBLE, dataSpaceId, new double[] { value }, registry); } else { baseWriter.setAttribute(objectPath, name, H5T_IEEE_F64LE, H5T_NATIVE_DOUBLE, -1, new double[] { value }, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void setArrayAttr(final String objectPath, final String name, final double[] value) { assert objectPath != null; assert name != null; assert value != null; baseWriter.checkOpen(); final ICallableWithCleanUp setAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { value.length }, registry); baseWriter.setAttribute(objectPath, name, H5T_IEEE_F64LE, H5T_NATIVE_DOUBLE, dataSpaceId, value, registry); } else { final int memoryTypeId = baseWriter.h5.createArrayType(H5T_NATIVE_DOUBLE, value.length, registry); final int storageTypeId = baseWriter.h5.createArrayType(H5T_IEEE_F64LE, value.length, registry); baseWriter.setAttribute(objectPath, name, storageTypeId, memoryTypeId, -1, value, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(setAttributeRunnable); } @Override public void setMDArrayAttr(final String objectPath, final String name, final MDDoubleArray value) { assert objectPath != null; assert name != null; assert value != null; baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(value.longDimensions(), registry); baseWriter.setAttribute(objectPath, name, H5T_IEEE_F64LE, H5T_NATIVE_DOUBLE, dataSpaceId, value.getAsFlatArray(), registry); } else { final int memoryTypeId = baseWriter.h5.createArrayType(H5T_NATIVE_DOUBLE, value.dimensions(), registry); final int storageTypeId = baseWriter.h5.createArrayType(H5T_IEEE_F64LE, value.dimensions(), registry); baseWriter.setAttribute(objectPath, name, storageTypeId, memoryTypeId, -1, value.getAsFlatArray(), registry); } return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void setMatrixAttr(final String objectPath, final String name, final double[][] value) { setMDArrayAttr(objectPath, name, new MDDoubleArray(value)); } // ///////////////////// // Data Sets // ///////////////////// @Override public void write(final String objectPath, final double value) { assert objectPath != null; baseWriter.checkOpen(); baseWriter.writeScalar(objectPath, H5T_IEEE_F64LE, H5T_NATIVE_DOUBLE, value); } @Override public void writeArray(final String objectPath, final double[] data) { writeArray(objectPath, data, FLOAT_NO_COMPRESSION); } @Override public void writeArray(final String objectPath, final double[] data, final HDF5FloatStorageFeatures features) { assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, H5T_IEEE_F64LE, new long[] { data.length }, 8, features, registry); H5Dwrite(dataSetId, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createArray(final String objectPath, final int size) { createArray(objectPath, size, FLOAT_NO_COMPRESSION); } @Override public void createArray(final String objectPath, final long size, final int blockSize) { createArray(objectPath, size, blockSize, FLOAT_NO_COMPRESSION); } @Override public void createArray(final String objectPath, final int size, final HDF5FloatStorageFeatures features) { assert objectPath != null; assert size >= 0; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (features.requiresChunking()) { baseWriter.createDataSet(objectPath, H5T_IEEE_F64LE, features, new long[] { 0 }, new long[] { size }, 8, registry); } else { baseWriter.createDataSet(objectPath, H5T_IEEE_F64LE, features, new long[] { size }, null, 8, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void createArray(final String objectPath, final long size, final int blockSize, final HDF5FloatStorageFeatures features) { assert objectPath != null; assert size >= 0; assert blockSize >= 0 && (blockSize <= size || size == 0); baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { baseWriter.createDataSet(objectPath, H5T_IEEE_F64LE, features, new long[] { size }, new long[] { blockSize }, 8, registry); return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void writeArrayBlock(final String objectPath, final double[] data, final long blockNumber) { writeArrayBlockWithOffset(objectPath, data, data.length, data.length * blockNumber); } @Override public void writeArrayBlockWithOffset(final String objectPath, final double[] data, final int dataSize, final long offset) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] blockDimensions = new long[] { dataSize }; final long[] slabStartOrNull = new long[] { offset }; final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, new long[] { offset + dataSize }, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, slabStartOrNull, blockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(blockDimensions, registry); H5Dwrite(dataSetId, H5T_NATIVE_DOUBLE, memorySpaceId, dataSpaceId, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } /** * Writes out a double matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ @Override public void writeMatrix(final String objectPath, final double[][] data) { writeMatrix(objectPath, data, FLOAT_NO_COMPRESSION); } @Override public void writeMatrix(final String objectPath, final double[][] data, final HDF5FloatStorageFeatures features) { assert objectPath != null; assert data != null; assert HDF5Utils.areMatrixDimensionsConsistent(data); writeMDArray(objectPath, new MDDoubleArray(data), features); } @Override public void createMatrix(final String objectPath, final int sizeX, final int sizeY) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; createMDArray(objectPath, new int[] { sizeX, sizeY }); } @Override public void createMatrix(final String objectPath, final int sizeX, final int sizeY, final HDF5FloatStorageFeatures features) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; createMDArray(objectPath, new int[] { sizeX, sizeY }, features); } @Override public void createMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; assert blockSizeX >= 0 && (blockSizeX <= sizeX || sizeX == 0); assert blockSizeY >= 0 && (blockSizeY <= sizeY || sizeY == 0); createMDArray(objectPath, new long[] { sizeX, sizeY }, new int[] { blockSizeX, blockSizeY }); } @Override public void createMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY, final HDF5FloatStorageFeatures features) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; assert blockSizeX >= 0 && (blockSizeX <= sizeX || sizeX == 0); assert blockSizeY >= 0 && (blockSizeY <= sizeY || sizeY == 0); createMDArray(objectPath, new long[] { sizeX, sizeY }, new int[] { blockSizeX, blockSizeY }, features); } @Override public void writeMatrixBlock(final String objectPath, final double[][] data, final long blockNumberX, final long blockNumberY) { assert objectPath != null; assert data != null; writeMDArrayBlock(objectPath, new MDDoubleArray(data), new long[] { blockNumberX, blockNumberY }); } @Override public void writeMatrixBlockWithOffset(final String objectPath, final double[][] data, final long offsetX, final long offsetY) { assert objectPath != null; assert data != null; writeMDArrayBlockWithOffset(objectPath, new MDDoubleArray(data, new int[] { data.length, data[0].length }), new long[] { offsetX, offsetY }); } @Override public void writeMatrixBlockWithOffset(final String objectPath, final double[][] data, final int dataSizeX, final int dataSizeY, final long offsetX, final long offsetY) { assert objectPath != null; assert data != null; writeMDArrayBlockWithOffset(objectPath, new MDDoubleArray(data, new int[] { dataSizeX, dataSizeY }), new long[] { offsetX, offsetY }); } @Override public void writeMDArray(final String objectPath, final MDDoubleArray data) { writeMDArray(objectPath, data, FLOAT_NO_COMPRESSION); } @Override public void writeMDArraySlice(String objectPath, MDDoubleArray data, IndexMap boundIndices) { baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), null, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDDoubleArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArraySlice(String objectPath, MDDoubleArray data, long[] boundIndices) { baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), null, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDDoubleArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArray(final String objectPath, final MDDoubleArray data, final HDF5FloatStorageFeatures features) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, H5T_IEEE_F64LE, data.longDimensions(), 8, features, registry); H5Dwrite(dataSetId, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createMDArray(final String objectPath, final int[] dimensions) { createMDArray(objectPath, dimensions, FLOAT_NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions) { createMDArray(objectPath, dimensions, blockDimensions, FLOAT_NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final int[] dimensions, final HDF5FloatStorageFeatures features) { assert objectPath != null; assert dimensions != null; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (features.requiresChunking()) { final long[] nullDimensions = new long[dimensions.length]; baseWriter.createDataSet(objectPath, H5T_IEEE_F64LE, features, nullDimensions, MDArray.toLong(dimensions), 8, registry); } else { baseWriter.createDataSet(objectPath, H5T_IEEE_F64LE, features, MDArray.toLong(dimensions), null, 8, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void createMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions, final HDF5FloatStorageFeatures features) { assert objectPath != null; assert dimensions != null; assert blockDimensions != null; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { baseWriter.createDataSet(objectPath, H5T_IEEE_F64LE, features, dimensions, MDArray.toLong(blockDimensions), 8, registry); return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void writeMDArrayBlock(final String objectPath, final MDDoubleArray data, final long[] blockNumber) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeMDArrayBlockWithOffset(objectPath, data, offset); } @Override public void writeSlicedMDArrayBlock(final String objectPath, final MDDoubleArray data, final long[] blockNumber, IndexMap boundIndices) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeSlicedMDArrayBlockWithOffset(objectPath, data, offset, boundIndices); } @Override public void writeSlicedMDArrayBlock(String objectPath, MDDoubleArray data, long[] blockNumber, long[] boundIndices) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeSlicedMDArrayBlockWithOffset(objectPath, data, offset, boundIndices); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final MDDoubleArray data, final long[] offset) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] dimensions = data.longDimensions(); assert dimensions.length == offset.length; final long[] dataSetDimensions = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + dimensions[i]; } final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, dimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(dimensions, registry); H5Dwrite(dataSetId, H5T_NATIVE_DOUBLE, memorySpaceId, dataSpaceId, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeSlicedMDArrayBlockWithOffset(String objectPath, MDDoubleArray data, long[] offset, IndexMap boundIndices) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), offset, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDDoubleArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeSlicedMDArrayBlockWithOffset(String objectPath, MDDoubleArray data, long[] offset, long[] boundIndices) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), offset, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDDoubleArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final MDDoubleArray data, final int[] blockDimensions, final long[] offset, final int[] memoryOffset) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] memoryDimensions = data.longDimensions(); assert memoryDimensions.length == offset.length; final long[] longBlockDimensions = MDArray.toLong(blockDimensions); assert longBlockDimensions.length == offset.length; final long[] dataSetDimensions = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + blockDimensions[i]; } final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, longBlockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(memoryDimensions, registry); baseWriter.h5.setHyperslabBlock(memorySpaceId, MDArray.toLong(memoryOffset), longBlockDimensions); H5Dwrite(dataSetId, H5T_NATIVE_DOUBLE, memorySpaceId, dataSpaceId, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5EnumReader.java000066400000000000000000001037561256564762100266770ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.HDF5Utils.ENUM_PREFIX; import static ch.systemsx.cisd.hdf5.HDF5Utils.createDataTypePath; import java.util.Iterator; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.hdf5.HDF5BaseReader.DataSpaceParameters; import ch.systemsx.cisd.hdf5.HDF5DataTypeInformation.DataTypeInfoOptions; import ch.systemsx.cisd.hdf5.HDF5EnumerationType.EnumStorageForm; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; /** * The implementation of {@link IHDF5EnumReader}. * * @author Bernd Rinn */ class HDF5EnumReader implements IHDF5EnumReader { protected final HDF5BaseReader baseReader; HDF5EnumReader(HDF5BaseReader baseReader) { assert baseReader != null; this.baseReader = baseReader; } // ///////////////////// // Types // ///////////////////// @Override public HDF5EnumerationType getType(final String name) { baseReader.checkOpen(); final String dataTypePath = createDataTypePath(ENUM_PREFIX, baseReader.houseKeepingNameSuffix, name); final int storageDataTypeId = baseReader.getDataTypeId(dataTypePath); return baseReader.getEnumTypeForStorageDataType(name, storageDataTypeId, true, null, null, baseReader.fileRegistry); } @Override public HDF5EnumerationType getType(final String name, final String[] values) throws HDF5JavaException { return getType(name, values, true); } @Override public > HDF5EnumerationType getType(final Class enumClass) throws HDF5JavaException { return getType(enumClass.getSimpleName(), ReflectionUtils.getEnumOptions(enumClass), true); } @Override public HDF5EnumerationType getType(final Class> enumClass, final boolean check) throws HDF5JavaException { return getType(enumClass.getSimpleName(), ReflectionUtils.getEnumOptions(enumClass), check); } @Override public HDF5EnumerationType getType(final String name, final Class> enumClass) throws HDF5JavaException { return getType(name, ReflectionUtils.getEnumOptions(enumClass), true); } @Override public > HDF5EnumerationType getType(final String name, final Class enumClass, final boolean check) throws HDF5JavaException { return getType(name, ReflectionUtils.getEnumOptions(enumClass), check); } @Override public HDF5EnumerationType getType(final String name, final String[] values, final boolean check) throws HDF5JavaException { baseReader.checkOpen(); final HDF5EnumerationType dataType = getType(name); if (check) { baseReader.checkEnumValues(dataType.getStorageTypeId(), values, name); } return dataType; } @Override public HDF5EnumerationType getType(EnumerationType genericType) throws HDF5JavaException { return getType(genericType, true); } @Override public HDF5EnumerationType getType(EnumerationType genericType, boolean check) throws HDF5JavaException { baseReader.checkOpen(); final HDF5EnumerationType dataType = getType(genericType.tryGetName()); if (check) { baseReader.checkEnumValues(dataType.getStorageTypeId(), genericType.getValueArray(), genericType.tryGetName()); } return dataType; } @Override public HDF5EnumerationType getDataSetType(final String dataSetPath) { baseReader.checkOpen(); final ICallableWithCleanUp readEnumTypeCallable = new ICallableWithCleanUp() { @Override public HDF5EnumerationType call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, dataSetPath, registry); return getEnumTypeForDataSetId(dataSetId, dataSetPath, baseReader.isScaledEnum(dataSetId, registry), registry); } }; return baseReader.runner.call(readEnumTypeCallable); } private HDF5EnumerationType getEnumTypeForDataSetId(final int objectId, final String objectName, final boolean scaledEnum, final ICleanUpRegistry registry) { if (scaledEnum) { final String enumTypeName = baseReader.getStringAttribute(objectId, objectName, HDF5Utils .getEnumTypeNameAttributeName(baseReader.houseKeepingNameSuffix), false, registry); return getType(enumTypeName); } else { final int storageDataTypeId = baseReader.h5.getDataTypeForDataSet(objectId, baseReader.fileRegistry); return baseReader.getEnumTypeForStorageDataType(null, storageDataTypeId, true, objectName, null, baseReader.fileRegistry); } } @Override public HDF5EnumerationType getAttributeType(final String dataSetPath, final String attributeName) { baseReader.checkOpen(); final ICallableWithCleanUp readEnumTypeCallable = new ICallableWithCleanUp() { @Override public HDF5EnumerationType call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, dataSetPath, registry); final int attributeId = baseReader.h5.openAttribute(dataSetId, attributeName, registry); final int storageDataTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, baseReader.fileRegistry); return baseReader.getEnumTypeForStorageDataType(null, storageDataTypeId, true, dataSetPath, attributeName, baseReader.fileRegistry); } }; return baseReader.runner.call(readEnumTypeCallable); } // ///////////////////// // Attributes // ///////////////////// @Override public String getAttrAsString(final String objectPath, final String attributeName) throws HDF5JavaException { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp readRunnable = new ICallableWithCleanUp() { @Override public String call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int storageDataTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, registry); final int nativeDataTypeId = baseReader.h5.getNativeDataType(storageDataTypeId, registry); final int enumDataTypeId = baseReader.getEnumDataTypeId(storageDataTypeId, registry); final int size = baseReader.h5.getDataTypeSize(enumDataTypeId); final byte[] data = baseReader.h5.readAttributeAsByteArray(attributeId, nativeDataTypeId, size); final String value = baseReader.h5.getNameForEnumOrCompoundMemberIndex(enumDataTypeId, EnumerationType.fromStorageForm(data, 0, size)); if (value == null) { throw new HDF5JavaException("Attribute " + attributeName + " of object " + objectPath + " needs to be an Enumeration."); } return value; } }; return baseReader.runner.call(readRunnable); } @Override public HDF5EnumerationValue getAttr(final String objectPath, final String attributeName) throws HDF5JavaException { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp readRunnable = new ICallableWithCleanUp() { @Override public HDF5EnumerationValue call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int storageDataTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, baseReader.fileRegistry); final int enumTypeId = baseReader.getEnumDataTypeId(storageDataTypeId, baseReader.fileRegistry); final HDF5EnumerationType enumType = baseReader.getEnumTypeForStorageDataType(null, enumTypeId, true, objectPath, attributeName, baseReader.fileRegistry); final int nativeDataTypeId; if (storageDataTypeId != enumTypeId) // Array data type { nativeDataTypeId = baseReader.h5 .getNativeDataType(storageDataTypeId, registry); } else { nativeDataTypeId = enumType.getNativeTypeId(); } final int enumOrdinal = baseReader.getEnumOrdinal(attributeId, nativeDataTypeId, enumType); return new HDF5EnumerationValue(enumType, enumOrdinal); } }; return baseReader.runner.call(readRunnable); } @Override public > T getAttr(String objectPath, String attributeName, Class enumClass) throws HDF5JavaException { final String value = getAttrAsString(objectPath, attributeName); try { return Enum.valueOf(enumClass, value); } catch (IllegalArgumentException ex) { throw new HDF5JavaException("The Java enum class " + enumClass.getCanonicalName() + " has no value '" + value + "'."); } } @Override public HDF5EnumerationValueArray getArrayAttr(final String objectPath, final String attributeName) throws HDF5JavaException { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp readRunnable = new ICallableWithCleanUp() { @Override public HDF5EnumerationValueArray call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); return baseReader.getEnumValueArray(attributeId, objectPath, attributeName, registry); } }; return baseReader.runner.call(readRunnable); } public String[] getEnumArrayAttributeAsString(final String objectPath, final String attributeName) throws HDF5JavaException { final HDF5EnumerationValueArray array = getArrayAttr(objectPath, attributeName); return array.toStringArray(); } @Override public HDF5EnumerationValueMDArray getMDArrayAttr(final String objectPath, final String attributeName) throws HDF5JavaException { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp readRunnable = new ICallableWithCleanUp() { @Override public HDF5EnumerationValueMDArray call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); return baseReader.getEnumValueMDArray(attributeId, objectPath, attributeName, registry); } }; return baseReader.runner.call(readRunnable); } // ///////////////////// // Data Sets // ///////////////////// @Override public String readAsString(final String objectPath) throws HDF5JavaException { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public String call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final int storageDataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); final int nativeDataTypeId = baseReader.h5.getNativeDataType(storageDataTypeId, registry); final int size = baseReader.h5.getDataTypeSize(nativeDataTypeId); final byte[] data = new byte[size]; baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, data); final String value = baseReader.h5.getNameForEnumOrCompoundMemberIndex(storageDataTypeId, EnumerationType.fromStorageForm(data)); if (value == null) { throw new HDF5JavaException(objectPath + " needs to be an Enumeration."); } return value; } }; return baseReader.runner.call(writeRunnable); } @Override public > T read(String objectPath, Class enumClass) throws HDF5JavaException { final String value = readAsString(objectPath); try { return Enum.valueOf(enumClass, value); } catch (IllegalArgumentException ex) { throw new HDF5JavaException("The Java enum class " + enumClass.getCanonicalName() + " has no value '" + value + "'."); } } @Override public HDF5EnumerationValue read(final String objectPath) throws HDF5JavaException { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readRunnable = new ICallableWithCleanUp() { @Override public HDF5EnumerationValue call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final HDF5EnumerationType enumType = getEnumTypeForDataSetId(dataSetId, objectPath, false, registry); return readEnumValue(dataSetId, enumType); } }; return baseReader.runner.call(readRunnable); } @Override public HDF5EnumerationValue read(final String objectPath, final HDF5EnumerationType enumType) throws HDF5JavaException { assert objectPath != null; assert enumType != null; baseReader.checkOpen(); enumType.check(baseReader.fileId); final ICallableWithCleanUp readRunnable = new ICallableWithCleanUp() { @Override public HDF5EnumerationValue call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); return readEnumValue(dataSetId, enumType); } }; return baseReader.runner.call(readRunnable); } private HDF5EnumerationValue readEnumValue(final int dataSetId, final HDF5EnumerationType enumType) { final byte[] data = new byte[enumType.getStorageForm().getStorageSize()]; baseReader.h5.readDataSet(dataSetId, enumType.getNativeTypeId(), data); return new HDF5EnumerationValue(enumType, EnumerationType.fromStorageForm(data)); } @Override public HDF5EnumerationValueArray readArray(final String objectPath, final HDF5EnumerationType enumTypeOrNull) throws HDF5JavaException { assert objectPath != null; baseReader.checkOpen(); if (enumTypeOrNull != null) { enumTypeOrNull.check(baseReader.fileId); } final ICallableWithCleanUp readRunnable = new ICallableWithCleanUp() { @Override public HDF5EnumerationValueArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final long[] dimensions = baseReader.h5.getDataDimensions(dataSetId, registry); final boolean scaledEnum = baseReader.isScaledEnum(dataSetId, registry); final HDF5EnumerationType actualEnumType = (enumTypeOrNull == null) ? getEnumTypeForDataSetId(dataSetId, objectPath, scaledEnum, registry) : enumTypeOrNull; final int arraySize = HDF5Utils.getOneDimensionalArraySize(dimensions); final EnumStorageForm storageForm = actualEnumType.getStorageForm(); final byte[] data = new byte[arraySize * storageForm.getStorageSize()]; if (scaledEnum) { baseReader.h5.readDataSet(dataSetId, actualEnumType .getStorageForm().getIntNativeTypeId(), data); } else { baseReader.h5.readDataSet(dataSetId, actualEnumType.getNativeTypeId(), data); } return new HDF5EnumerationValueArray(actualEnumType, EnumerationType.fromStorageForm(data, storageForm)); } }; return baseReader.runner.call(readRunnable); } @Override public HDF5EnumerationValueArray readArray(final String objectPath) throws HDF5JavaException { return readArray(objectPath, (HDF5EnumerationType) null); } @Override public HDF5EnumerationValueArray readArrayBlockWithOffset(final String objectPath, final HDF5EnumerationType enumTypeOrNull, final int blockSize, final long offset) { assert objectPath != null; baseReader.checkOpen(); if (enumTypeOrNull != null) { enumTypeOrNull.check(baseReader.fileId); } final ICallableWithCleanUp readRunnable = new ICallableWithCleanUp() { @Override public HDF5EnumerationValueArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockSize, registry); final boolean scaledEnum = baseReader.isScaledEnum(dataSetId, registry); final HDF5EnumerationType actualEnumType = (enumTypeOrNull == null) ? getEnumTypeForDataSetId(dataSetId, objectPath, scaledEnum, registry) : enumTypeOrNull; final byte[] data = new byte[spaceParams.blockSize * actualEnumType.getStorageForm().getStorageSize()]; if (scaledEnum) { baseReader.h5.readDataSet(dataSetId, actualEnumType .getStorageForm().getIntNativeTypeId(), spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); } else { baseReader.h5.readDataSet(dataSetId, actualEnumType.getNativeTypeId(), spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); } return new HDF5EnumerationValueArray(actualEnumType, EnumerationType.fromStorageForm(data, actualEnumType.getStorageForm())); } }; return baseReader.runner.call(readRunnable); } @Override public HDF5EnumerationValueArray readArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset) { return readArrayBlockWithOffset(objectPath, (HDF5EnumerationType) null, blockSize, offset); } @Override public HDF5EnumerationValueArray readArrayBlock(final String objectPath, final int blockSize, final long blockNumber) { return readArrayBlockWithOffset(objectPath, (HDF5EnumerationType) null, blockSize, blockNumber * blockSize); } @Override public HDF5EnumerationValueArray readArrayBlock(final String objectPath, final HDF5EnumerationType enumType, final int blockSize, final long blockNumber) { return readArrayBlockWithOffset(objectPath, enumType, blockSize, blockNumber * blockSize); } @Override public HDF5EnumerationValueMDArray readMDArray(final String objectPath) throws HDF5JavaException { return readMDArray(objectPath, (HDF5EnumerationType) null); } @Override public HDF5EnumerationValueMDArray readMDArray(final String objectPath, final HDF5EnumerationType enumTypeOrNull) throws HDF5JavaException { return readMDArrayBlockWithOffset(objectPath, enumTypeOrNull, null, null); } @Override public HDF5EnumerationValueMDArray readMDArrayBlockWithOffset(final String objectPath, final HDF5EnumerationType enumTypeOrNull, final int[] blockDimensionsOrNull, final long[] offsetOrNull) { assert objectPath != null; baseReader.checkOpen(); if (enumTypeOrNull != null) { enumTypeOrNull.check(baseReader.fileId); } final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public HDF5EnumerationValueMDArray call(final ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final boolean scaledEnum = baseReader.isScaledEnum(dataSetId, registry); final HDF5EnumerationType actualEnumType = (enumTypeOrNull == null) ? getEnumTypeForDataSetId(dataSetId, objectPath, scaledEnum, registry) : enumTypeOrNull; final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offsetOrNull, blockDimensionsOrNull, registry); final EnumStorageForm storageForm = actualEnumType.getStorageForm(); final byte[] byteArr = new byte[spaceParams.blockSize * storageForm.getStorageSize()]; if (scaledEnum) { baseReader.h5 .readDataSet(dataSetId, storageForm.getIntNativeTypeId(), spaceParams.memorySpaceId, spaceParams.dataSpaceId, byteArr); } else { baseReader.h5 .readDataSet(dataSetId, actualEnumType.getNativeTypeId(), spaceParams.memorySpaceId, spaceParams.dataSpaceId, byteArr); } return new HDF5EnumerationValueMDArray(actualEnumType, EnumerationType.fromStorageForm(byteArr, spaceParams.dimensions, storageForm)); } }; return baseReader.runner.call(writeRunnable); } @Override public HDF5EnumerationValueMDArray readMDArrayBlock(String objectPath, HDF5EnumerationType type, int[] blockDimensions, long[] blockNumber) throws HDF5JavaException { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockDimensions[i] * blockNumber[i]; } return readMDArrayBlockWithOffset(objectPath, type, blockDimensions, offset); } @Override public HDF5EnumerationValueMDArray readMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber) throws HDF5JavaException { return readMDArrayBlock(objectPath, null, blockDimensions, blockNumber); } @Override public HDF5EnumerationValueMDArray readMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset) throws HDF5JavaException { return readMDArrayBlockWithOffset(objectPath, null, blockDimensions, offset); } @Override public Iterable> getArrayBlocks( final String objectPath, final HDF5EnumerationType enumTypeOrNull) throws HDF5JavaException { baseReader.checkOpen(); final HDF5NaturalBlock1DParameters params = new HDF5NaturalBlock1DParameters(baseReader.getDataSetInformation(objectPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlock1DParameters.HDF5NaturalBlock1DIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5DataBlock next() { final long offset = index.computeOffsetAndSizeGetOffset(); final HDF5EnumerationValueArray block = readArrayBlockWithOffset(objectPath, enumTypeOrNull, index.getBlockSize(), offset); return new HDF5DataBlock(block, index.getAndIncIndex(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } @Override public Iterable> getArrayBlocks(final String objectPath) throws HDF5JavaException { return getArrayBlocks(objectPath, (HDF5EnumerationType) null); } @Override public Iterable getMDArrayBlocks(final String objectPath, final HDF5EnumerationType enumTypeOrNull) throws HDF5JavaException { final HDF5NaturalBlockMDParameters params = new HDF5NaturalBlockMDParameters(baseReader.getDataSetInformation(objectPath, DataTypeInfoOptions.MINIMAL, true)); return new Iterable() { @Override public Iterator iterator() { return new Iterator() { final HDF5NaturalBlockMDParameters.HDF5NaturalBlockMDIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5MDEnumBlock next() { final long[] offset = index.computeOffsetAndSizeGetOffsetClone(); final HDF5EnumerationValueMDArray block = readMDArrayBlockWithOffset(objectPath, enumTypeOrNull, index.getBlockSize(), offset); return new HDF5MDEnumBlock(block, index.getIndexClone(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } @Override public Iterable getMDArrayBlocks(String objectPath) throws HDF5JavaException { return getMDArrayBlocks(objectPath, null); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5EnumWriter.java000066400000000000000000001110761256564762100267430ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.hdf5lib.H5D.H5Dwrite; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_ALL; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.base.mdarray.MDAbstractArray; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDByteArray; import ch.systemsx.cisd.base.mdarray.MDIntArray; import ch.systemsx.cisd.base.mdarray.MDShortArray; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; /** * The implementation of {@link IHDF5EnumWriter}. * * @author Bernd Rinn */ class HDF5EnumWriter extends HDF5EnumReader implements IHDF5EnumWriter { private final HDF5BaseWriter baseWriter; HDF5EnumWriter(HDF5BaseWriter baseWriter) { super(baseWriter); this.baseWriter = baseWriter; } // ///////////////////// // Value creation // ///////////////////// @Override public HDF5EnumerationValue newVal(String typeName, String[] options, String value) { return new HDF5EnumerationValue(getType(typeName, options), value); } @Override public HDF5EnumerationValue newVal(String typeName, String[] options, int value) { return new HDF5EnumerationValue(getType(typeName, options), value); } @Override public HDF5EnumerationValue newVal(String typeName, String[] options, short value) { return new HDF5EnumerationValue(getType(typeName, options), value); } @Override public HDF5EnumerationValue newVal(String typeName, String[] options, byte value) { return new HDF5EnumerationValue(getType(typeName, options), value); } @Override public > HDF5EnumerationValue newVal(String typeName, Enum value) { return new HDF5EnumerationValue(getType(typeName, getEnumClass(value)), value); } @Override public HDF5EnumerationValueArray newArray(String typeName, String[] options, String[] values) { return new HDF5EnumerationValueArray(getType(typeName, options), values); } @Override public HDF5EnumerationValueArray newArray(String typeName, String[] options, int[] values) { return new HDF5EnumerationValueArray(getType(typeName, options), values); } @Override public HDF5EnumerationValueArray newArray(String typeName, String[] options, short[] values) { return new HDF5EnumerationValueArray(getType(typeName, options), values); } @Override public HDF5EnumerationValueArray newArray(String typeName, String[] options, byte[] values) { return new HDF5EnumerationValueArray(getType(typeName, options), values); } @Override public > HDF5EnumerationValueArray newArray(String typeName, Enum[] values) { return new HDF5EnumerationValueArray(getType(typeName, getEnumClass(values)), values); } @Override public HDF5EnumerationValueMDArray newMDArray(String typeName, String[] options, MDArray values) { return new HDF5EnumerationValueMDArray(getType(typeName, options), values); } @Override public HDF5EnumerationValueMDArray newMDArray(String typeName, String[] options, MDIntArray values) { return new HDF5EnumerationValueMDArray(getType(typeName, options), values); } @Override public HDF5EnumerationValueMDArray newMDArray(String typeName, String[] options, MDShortArray values) { return new HDF5EnumerationValueMDArray(getType(typeName, options), values); } @Override public HDF5EnumerationValueMDArray newMDArray(String typeName, String[] options, MDByteArray values) { return new HDF5EnumerationValueMDArray(getType(typeName, options), values); } @Override public > HDF5EnumerationValueMDArray newMDArray(String typeName, MDArray> values) { return new HDF5EnumerationValueMDArray(getType(typeName, getEnumClass(values)), values); } @Override public HDF5EnumerationValue newAnonVal(String[] options, String value) { return new HDF5EnumerationValue(getAnonType(options), value); } @Override public HDF5EnumerationValue newAnonVal(String[] options, int value) { return new HDF5EnumerationValue(getAnonType(options), value); } @Override public HDF5EnumerationValue newAnonVal(String[] options, short value) { return new HDF5EnumerationValue(getAnonType(options), value); } @Override public HDF5EnumerationValue newAnonVal(String[] options, byte value) { return new HDF5EnumerationValue(getAnonType(options), value); } @Override public > HDF5EnumerationValue newAnonVal(Enum value) { return new HDF5EnumerationValue(getAnonType(getEnumClass(value)), value); } @Override public > HDF5EnumerationValue newVal(Enum value) { return new HDF5EnumerationValue(getType(getEnumClass(value)), value); } @Override public HDF5EnumerationValueArray newAnonArray(String[] options, String[] values) { return new HDF5EnumerationValueArray(getAnonType(options), values); } @Override public HDF5EnumerationValueArray newAnonArray(String[] options, int[] values) { return new HDF5EnumerationValueArray(getAnonType(options), values); } @Override public HDF5EnumerationValueArray newAnonArray(String[] options, short[] values) { return new HDF5EnumerationValueArray(getAnonType(options), values); } @Override public HDF5EnumerationValueArray newAnonArray(String[] options, byte[] values) { return new HDF5EnumerationValueArray(getAnonType(options), values); } @Override public > HDF5EnumerationValueArray newAnonArray(Enum[] values) { return new HDF5EnumerationValueArray(getAnonType(getEnumClass(values)), values); } @Override public > HDF5EnumerationValueArray newArray(Enum[] values) { return new HDF5EnumerationValueArray(getType(getEnumClass(values)), values); } @Override public HDF5EnumerationValueMDArray newAnonMDArray(String[] options, MDArray values) { return new HDF5EnumerationValueMDArray(getAnonType(options), values); } @Override public HDF5EnumerationValueMDArray newAnonMDArray(String[] options, MDIntArray values) { return new HDF5EnumerationValueMDArray(getAnonType(options), values); } @Override public HDF5EnumerationValueMDArray newAnonMDArray(String[] options, MDShortArray values) { return new HDF5EnumerationValueMDArray(getAnonType(options), values); } @Override public HDF5EnumerationValueMDArray newAnonMDArray(String[] options, MDByteArray values) { return new HDF5EnumerationValueMDArray(getAnonType(options), values); } @Override public > HDF5EnumerationValueMDArray newAnonMDArray(MDArray> values) { return new HDF5EnumerationValueMDArray(getAnonType(getEnumClass(values)), values); } @Override public > HDF5EnumerationValueMDArray newMDArray(MDArray> values) { return new HDF5EnumerationValueMDArray(getType(getEnumClass(values)), values); } @SuppressWarnings("unchecked") private > Class> getEnumClass(final Enum value) { return (Class>) value.getClass(); } @SuppressWarnings("unchecked") private > Class> getEnumClass(Enum[] data) { return (Class>) data.getClass().getComponentType(); } @SuppressWarnings("unchecked") private > Class> getEnumClass(MDArray> data) { return (Class>) data.getAsFlatArray().getClass().getComponentType(); } // ///////////////////// // Types // ///////////////////// @Override public HDF5EnumerationType getAnonType(String[] values) throws HDF5JavaException { return getType(null, values, false); } @Override public HDF5EnumerationType getAnonType(final Class> enumClass) throws HDF5JavaException { return getType(null, ReflectionUtils.getEnumOptions(enumClass)); } @Override public HDF5EnumerationType getType(final String name, final String[] values) throws HDF5JavaException { return getType(name, values, true); } @Override public HDF5EnumerationType getType(final String nameOrNull, final String[] values, final boolean check) throws HDF5JavaException { baseWriter.checkOpen(); final int storageDataTypeId = getOrCreateEnumDataType(nameOrNull, values, baseWriter.keepDataSetIfExists, check); final int nativeDataTypeId = baseWriter.h5.getNativeDataType(storageDataTypeId, baseWriter.fileRegistry); return new HDF5EnumerationType(baseWriter.fileId, storageDataTypeId, nativeDataTypeId, (nameOrNull == null) ? "__anonymous__" : nameOrNull, values, baseWriter); } @Override public HDF5EnumerationType getType(EnumerationType genericType, boolean check) throws HDF5JavaException { baseWriter.checkOpen(); final int storageDataTypeId = getOrCreateEnumDataType(genericType.tryGetName(), genericType.getValueArray(), baseWriter.keepDataSetIfExists, check); final int nativeDataTypeId = baseWriter.h5.getNativeDataType(storageDataTypeId, baseWriter.fileRegistry); return new HDF5EnumerationType(baseWriter.fileId, storageDataTypeId, nativeDataTypeId, (genericType.tryGetName() == null) ? new EnumerationType("__anonymous__", genericType.getValueArray()) : genericType, baseWriter); } @Override public HDF5EnumerationType getType(final String name, final Class> enumClass) throws HDF5JavaException { return getType(name, ReflectionUtils.getEnumOptions(enumClass), true); } @Override public > HDF5EnumerationType getType(final String name, final Class enumClass, final boolean check) throws HDF5JavaException { return getType(name, ReflectionUtils.getEnumOptions(enumClass), check); } @Override public > HDF5EnumerationType getType(final Class enumClass) throws HDF5JavaException { return getType(enumClass.getSimpleName(), ReflectionUtils.getEnumOptions(enumClass), true); } @Override public HDF5EnumerationType getType(final Class> enumClass, final boolean check) throws HDF5JavaException { return getType(enumClass.getSimpleName(), ReflectionUtils.getEnumOptions(enumClass), check); } private int getOrCreateEnumDataType(final String dataTypeNameOrNull, final String[] values, boolean committedDataTypeHasPreference, boolean checkIfExists) { final String dataTypePathOrNull = (dataTypeNameOrNull == null) ? null : HDF5Utils.createDataTypePath( HDF5Utils.ENUM_PREFIX, baseWriter.houseKeepingNameSuffix, dataTypeNameOrNull); final int committedStorageDataTypeId = (dataTypePathOrNull == null) ? -1 : baseWriter.getDataTypeId(dataTypePathOrNull); final boolean typeExists = (committedStorageDataTypeId >= 0); int storageDataTypeId = committedStorageDataTypeId; final boolean commitType; if ((typeExists == false) || (committedDataTypeHasPreference == false)) { storageDataTypeId = baseWriter.h5.createDataTypeEnum(values, baseWriter.fileRegistry); final boolean typesAreEqual = typeExists && baseWriter.h5.dataTypesAreEqual(committedStorageDataTypeId, storageDataTypeId); commitType = (dataTypeNameOrNull != null) && ((typeExists == false) || (typesAreEqual == false)); if (typeExists && commitType) { final String replacementDataTypePath = baseWriter.moveLinkOutOfTheWay(dataTypePathOrNull); baseWriter.renameNamedDataType(dataTypePathOrNull, replacementDataTypePath); } if (typesAreEqual) { storageDataTypeId = committedStorageDataTypeId; } } else { commitType = false; if (checkIfExists) { baseWriter.checkEnumValues(storageDataTypeId, values, dataTypeNameOrNull); } } if (commitType) { baseWriter.commitDataType(dataTypePathOrNull, storageDataTypeId); } return storageDataTypeId; } // ///////////////////// // Attributes // ///////////////////// @Override public void setAttr(final String objectPath, final String name, final HDF5EnumerationValue value) { assert objectPath != null; assert name != null; assert value != null; baseWriter.checkOpen(); value.getType().check(baseWriter.fileId); final int storageDataTypeId = value.getType().getStorageTypeId(); final int nativeDataTypeId = value.getType().getNativeTypeId(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { 1 }, registry); baseWriter.setAttribute(objectPath, name, storageDataTypeId, nativeDataTypeId, dataSpaceId, value.toStorageForm(), registry); } else { baseWriter.setAttribute(objectPath, name, storageDataTypeId, nativeDataTypeId, -1, value.toStorageForm(), registry); } return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void setAttr(String objectPath, String name, Enum value) throws HDF5JavaException { setAttr(objectPath, name, new HDF5EnumerationValue(getType(getEnumClass(value)), value)); } @Override public void setArrayAttr(final String objectPath, final String name, final HDF5EnumerationValueArray value) { baseWriter.setEnumArrayAttribute(objectPath, name, value); } @Override public void setMDArrayAttr(String objectPath, String name, HDF5EnumerationValueMDArray value) { baseWriter.setEnumMDArrayAttribute(objectPath, name, value); } // ///////////////////// // Data Sets // ///////////////////// @Override public void write(final String objectPath, final HDF5EnumerationValue value) throws HDF5JavaException { assert objectPath != null; assert value != null; baseWriter.checkOpen(); value.getType().check(baseWriter.fileId); final int storageDataTypeId = value.getType().getStorageTypeId(); final int nativeDataTypeId = value.getType().getNativeTypeId(); baseWriter.writeScalar(objectPath, storageDataTypeId, nativeDataTypeId, value.toStorageForm()); } @Override public void write(final String objectPath, final Enum value) throws HDF5JavaException { write(objectPath, new HDF5EnumerationValue(getType(getEnumClass(value)), value)); } @Override public void writeArray(final String objectPath, final HDF5EnumerationValueArray data) throws HDF5JavaException { writeArray(objectPath, data, HDF5IntStorageFeatures.INT_NO_COMPRESSION); } @Override public void writeArray(final String objectPath, final HDF5EnumerationValueArray data, final HDF5IntStorageFeatures features) throws HDF5JavaException { assert objectPath != null; assert data != null; baseWriter.checkOpen(); data.getType().check(baseWriter.fileId); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (features.isScaling()) { features.checkScalingOK(baseWriter.fileFormat); final HDF5IntStorageFeatures actualFeatures = HDF5IntStorageFeatures.createDeflateAndIntegerScaling( features.getDeflateLevel(), data.getType().getEnumType() .getNumberOfBits(), baseWriter.keepDataIfExists(features)); final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, data.getType() .getIntStorageTypeId(), new long[] { data.getLength() }, data.getStorageForm().getStorageSize(), actualFeatures, registry); H5Dwrite(dataSetId, data.getType().getIntNativeTypeId(), H5S_ALL, H5S_ALL, H5P_DEFAULT, data.toStorageForm()); baseWriter.setTypeVariant(dataSetId, HDF5DataTypeVariant.ENUM, registry); baseWriter.setStringAttribute(dataSetId, HDF5Utils .getEnumTypeNameAttributeName(baseWriter.houseKeepingNameSuffix), data.getType().getName(), data.getType().getName().length(), true, registry); } else { final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, data.getType() .getStorageTypeId(), new long[] { data.getLength() }, data.getStorageForm().getStorageSize(), features, registry); H5Dwrite(dataSetId, data.getType().getNativeTypeId(), H5S_ALL, H5S_ALL, H5P_DEFAULT, data.toStorageForm()); } return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public HDF5EnumerationType createArray(final String objectPath, final HDF5EnumerationType enumType, final int size) { return createArray(objectPath, enumType, size, HDF5IntStorageFeatures.INT_NO_COMPRESSION); } @Override public HDF5EnumerationType createArray(final String objectPath, final HDF5EnumerationType enumType, final long size, final int blockSize) { return createArray(objectPath, enumType, size, blockSize, HDF5IntStorageFeatures.INT_NO_COMPRESSION); } @Override public HDF5EnumerationType createArray(final String objectPath, final HDF5EnumerationType enumType, final long size, final int blockSize, final HDF5IntStorageFeatures features) { baseWriter.checkOpen(); enumType.check(baseWriter.fileId); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (features.isScaling()) { features.checkScalingOK(baseWriter.fileFormat); final HDF5IntStorageFeatures actualCompression = HDF5IntStorageFeatures.createDeflateAndIntegerScaling(features .getDeflateLevel(), enumType.getEnumType() .getNumberOfBits()); final int dataSetId = baseWriter.createDataSet(objectPath, enumType.getIntStorageTypeId(), actualCompression, new long[] { size }, new long[] { blockSize }, enumType.getStorageForm() .getStorageSize(), registry); baseWriter.setTypeVariant(dataSetId, HDF5DataTypeVariant.ENUM, registry); baseWriter.setStringAttribute(dataSetId, HDF5Utils .getEnumTypeNameAttributeName(baseWriter.houseKeepingNameSuffix), enumType.getName(), enumType.getName().length(), true, registry); } else { baseWriter.createDataSet(objectPath, enumType.getStorageTypeId(), features, new long[] { size }, new long[] { blockSize }, enumType.getStorageForm().getStorageSize(), registry); } return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); return enumType; } @Override public HDF5EnumerationType createArray(final String objectPath, final HDF5EnumerationType enumType, final long size, final HDF5IntStorageFeatures features) { baseWriter.checkOpen(); enumType.check(baseWriter.fileId); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (features.requiresChunking()) { create(new long[] { 0 }, new long[] { size }, registry); } else { create(new long[] { size }, null, registry); } return null; // Nothing to return. } private void create(final long[] dimensions, final long[] blockDimensionsOrNull, final ICleanUpRegistry registry) { if (features.isScaling()) { features.checkScalingOK(baseWriter.fileFormat); final HDF5IntStorageFeatures actualCompression = HDF5IntStorageFeatures.createDeflateAndIntegerScaling(features .getDeflateLevel(), enumType.getEnumType() .getNumberOfBits()); final int dataSetId = baseWriter.createDataSet(objectPath, enumType.getIntStorageTypeId(), actualCompression, dimensions, blockDimensionsOrNull, enumType .getStorageForm().getStorageSize(), registry); baseWriter.setTypeVariant(dataSetId, HDF5DataTypeVariant.ENUM, registry); baseWriter.setStringAttribute(dataSetId, HDF5Utils .getEnumTypeNameAttributeName(baseWriter.houseKeepingNameSuffix), enumType.getName(), enumType.getName().length(), true, registry); } else { baseWriter.createDataSet(objectPath, enumType.getStorageTypeId(), features, dimensions, blockDimensionsOrNull, enumType.getStorageForm() .getStorageSize(), registry); } } }; baseWriter.runner.call(createRunnable); return enumType; } @Override public void writeArrayBlock(final String objectPath, final HDF5EnumerationValueArray data, final long blockNumber) { assert objectPath != null; assert data != null; writeArrayBlockWithOffset(objectPath, data, data.getLength(), data.getLength() * blockNumber); } @Override public void writeArrayBlockWithOffset(final String objectPath, final HDF5EnumerationValueArray data, final int dataSize, final long offset) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); data.getType().check(baseWriter.fileId); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] blockDimensions = new long[] { dataSize }; final long[] slabStartOrNull = new long[] { offset }; final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, new long[] { offset + dataSize }, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, slabStartOrNull, blockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(blockDimensions, registry); if (baseWriter.isScaledEnum(dataSetId, registry)) { H5Dwrite(dataSetId, data.getType().getIntNativeTypeId(), memorySpaceId, dataSpaceId, H5P_DEFAULT, data.toStorageForm()); } else { H5Dwrite(dataSetId, data.getType().getNativeTypeId(), memorySpaceId, dataSpaceId, H5P_DEFAULT, data.toStorageForm()); } return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeMDArray(final String objectPath, final HDF5EnumerationValueMDArray data) throws HDF5JavaException { writeMDArray(objectPath, data, HDF5IntStorageFeatures.INT_NO_COMPRESSION); } @Override public void writeMDArray(final String objectPath, final HDF5EnumerationValueMDArray data, final HDF5IntStorageFeatures features) throws HDF5JavaException { assert objectPath != null; assert data != null; baseWriter.checkOpen(); data.getType().check(baseWriter.fileId); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (features.isScaling()) { features.checkScalingOK(baseWriter.fileFormat); final HDF5IntStorageFeatures actualFeatures = HDF5IntStorageFeatures.createDeflateAndIntegerScaling( features.getDeflateLevel(), data.getType().getEnumType() .getNumberOfBits(), baseWriter.keepDataIfExists(features)); final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, data.getType() .getIntStorageTypeId(), data.longDimensions(), data .getStorageForm().getStorageSize(), actualFeatures, registry); H5Dwrite(dataSetId, data.getType().getIntNativeTypeId(), H5S_ALL, H5S_ALL, H5P_DEFAULT, data.toStorageForm()); baseWriter.setTypeVariant(dataSetId, HDF5DataTypeVariant.ENUM, registry); baseWriter.setStringAttribute(dataSetId, HDF5Utils .getEnumTypeNameAttributeName(baseWriter.houseKeepingNameSuffix), data.getType().getName(), data.getType().getName().length(), true, registry); } else { final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, data.getType() .getStorageTypeId(), data.longDimensions(), data .getStorageForm().getStorageSize(), features, registry); H5Dwrite(dataSetId, data.getType().getNativeTypeId(), H5S_ALL, H5S_ALL, H5P_DEFAULT, data.toStorageForm()); } return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } private void writeEnumMDArrayBlockWithOffset(final String objectPath, final HDF5EnumerationType enumType, final byte[] data, final long[] dimensions, final long[] offset, final long[] dataSetDimensions) { assert objectPath != null; assert enumType != null; assert data != null; assert offset != null; baseWriter.checkOpen(); enumType.check(baseWriter.fileId); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(final ICleanUpRegistry registry) { final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, dimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(dimensions, registry); H5Dwrite(dataSetId, enumType.getNativeTypeId(), memorySpaceId, dataSpaceId, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final HDF5EnumerationValueMDArray data, final long[] offset) { final long[] dimensions = data.longDimensions(); final long[] dataSetDimensions = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + dimensions[i]; } writeEnumMDArrayBlockWithOffset(objectPath, data.getType(), data.toStorageForm(), dimensions, offset, dataSetDimensions); } @Override public void writeMDArrayBlock(String objectPath, HDF5EnumerationValueMDArray data, long[] blockNumber) { final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; final long[] dataSetDimensions = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; dataSetDimensions[i] = offset[i] + dimensions[i]; } writeEnumMDArrayBlockWithOffset(objectPath, data.getType(), data.toStorageForm(), dimensions, offset, dataSetDimensions); } @Override public HDF5EnumerationType createMDArray(String objectPath, HDF5EnumerationType enumType, int[] dimensions) { return createMDArray(objectPath, enumType, dimensions, HDF5IntStorageFeatures.INT_NO_COMPRESSION); } @Override public HDF5EnumerationType createMDArray(String objectPath, HDF5EnumerationType enumType, long[] dimensions, int[] blockDimensions) { return createMDArray(objectPath, enumType, dimensions, blockDimensions, HDF5IntStorageFeatures.INT_NO_COMPRESSION); } @Override public HDF5EnumerationType createMDArray(final String objectPath, final HDF5EnumerationType enumType, final long[] dimensions, final int[] blockDimensions, final HDF5IntStorageFeatures features) { assert objectPath != null; assert enumType != null; assert dimensions != null; assert blockDimensions != null; baseWriter.checkOpen(); enumType.check(baseWriter.fileId); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(final ICleanUpRegistry registry) { baseWriter.createDataSet(objectPath, enumType.getStorageTypeId(), features, dimensions, MDAbstractArray.toLong(blockDimensions), enumType .getStorageForm().getStorageSize(), registry); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); return enumType; } @Override public HDF5EnumerationType createMDArray(final String objectPath, final HDF5EnumerationType enumType, final int[] dimensions, final HDF5IntStorageFeatures features) { assert objectPath != null; assert enumType != null; assert dimensions != null; baseWriter.checkOpen(); enumType.check(baseWriter.fileId); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(final ICleanUpRegistry registry) { if (features.requiresChunking()) { final long[] nullDimensions = new long[dimensions.length]; baseWriter.createDataSet(objectPath, enumType.getStorageTypeId(), features, nullDimensions, MDAbstractArray.toLong(dimensions), enumType .getStorageForm().getStorageSize(), registry); } else { baseWriter.createDataSet(objectPath, enumType.getStorageTypeId(), features, MDAbstractArray.toLong(dimensions), null, enumType.getStorageForm() .getStorageSize(), registry); } return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); return enumType; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5EnumerationType.java000066400000000000000000000143461256564762100277740ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_INT16; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_INT32; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_INT8; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_U16LE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_U32LE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_U8LE; import java.util.Iterator; import java.util.List; import ch.systemsx.cisd.hdf5.hdf5lib.HDFNativeData; /** * A class that represents an enumeration for a given HDF5 file and values array. * * @author Bernd Rinn */ public final class HDF5EnumerationType extends HDF5DataType implements Iterable { /** * The storage form (as size in bytes) of an enumeration type. */ public enum EnumStorageForm { /** * One byte, for up to 255 alternatives. */ BYTE(1, H5T_NATIVE_INT8, H5T_STD_U8LE), /** * Two bytes, for up to 65535 alternatives. */ SHORT(2, H5T_NATIVE_INT16, H5T_STD_U16LE), /** * Four bytes, for more than 65535 alternatives. */ INT(4, H5T_NATIVE_INT32, H5T_STD_U32LE); private final byte storageSize; private final int intNativeType; private final int intStorageType; EnumStorageForm(int storageSize, int intNativeType, int intStorageType) { this.storageSize = (byte) storageSize; this.intNativeType = intNativeType; this.intStorageType = intStorageType; } /** * Return the number of bytes (1, 2 or 4) of this storage form. */ public byte getStorageSize() { return storageSize; } int getIntNativeTypeId() { return intNativeType; } int getIntStorageTypeId() { return intStorageType; } } private final EnumerationType enumType; /** * Returns the storage data type id of the corresponding integer type of this type. */ int getIntStorageTypeId() { return getStorageForm().getIntStorageTypeId(); } /** * Returns the native data type id of the corresponding integer type of this type. */ int getIntNativeTypeId() { return getStorageForm().getIntNativeTypeId(); } HDF5EnumerationType(int fileId, int storageTypeId, int nativeTypeId, String nameOrNull, String[] values, HDF5BaseReader baseReader) { super(fileId, storageTypeId, nativeTypeId, baseReader); assert values != null; this.enumType = new EnumerationType(nameOrNull, values); } HDF5EnumerationType(int fileId, int storageTypeId, int nativeTypeId, EnumerationType enumType, HDF5BaseReader baseReader) { super(fileId, storageTypeId, nativeTypeId, baseReader); assert enumType != null; this.enumType = enumType; } EnumerationType getEnumType() { return enumType; } /** * Returns the ordinal value for the given string value, if value is a * member of the enumeration, and null otherwise. */ public Integer tryGetIndexForValue(String value) { return enumType.tryGetIndexForValue(value); } /** * Returns the name of this type, if it exists and null otherwise. */ @Override public String tryGetName() { return enumType.tryGetName(); } /** * Returns the allowed values of this enumeration type. */ public List getValues() { return enumType.getValues(); } /** * Returns the (file-independent) {@link EnumerationType} of this (file-dependen) * {@link HDF5EnumerationType}. */ public EnumerationType getEnumerationType() { return enumType; } /** * Returns the {@link EnumStorageForm} of this enumeration type. */ public EnumStorageForm getStorageForm() { return enumType.getStorageForm(); } HDF5EnumerationValue createFromStorageForm(byte[] data, int offset) { return new HDF5EnumerationValue(this, getOrdinalFromStorageForm(data, offset)); } String createStringFromStorageForm(byte[] data, int offset) { return enumType.createStringFromStorageForm(data, offset); } int getOrdinalFromStorageForm(byte[] data, int offset) { switch (getStorageForm()) { case BYTE: return data[offset]; case SHORT: return HDFNativeData.byteToShort(data, offset); case INT: return HDFNativeData.byteToInt(data, offset); } throw new Error("Illegal storage form (" + getStorageForm() + ".)"); } // // Iterable // /** * Returns an {@link Iterator} over all values of this enumeration type. * {@link Iterator#remove()} is not allowed and will throw an * {@link UnsupportedOperationException}. */ @Override public Iterator iterator() { return enumType.iterator(); } @Override public int hashCode() { return enumType.hashCode(); } @Override public boolean equals(Object obj) { if (this == obj) { return true; } if (getClass() != obj.getClass()) { return false; } final HDF5EnumerationType other = (HDF5EnumerationType) obj; return enumType.equals(other.enumType); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5EnumerationValue.java000066400000000000000000000117241256564762100301240ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; /** * A class the represents an HDF enumeration value. * * @author Bernd Rinn */ public final class HDF5EnumerationValue { private final HDF5EnumerationType type; private final int ordinal; /** * Creates an enumeration value. * * @param type The enumeration type of this value. * @param value The value in the type. * @throws IllegalArgumentException If the ordinal is outside of the range of allowed * values of the type. */ public HDF5EnumerationValue(HDF5EnumerationType type, Enum value) throws IllegalArgumentException { this(type, value.name()); } /** * Creates an enumeration value. * * @param type The enumeration type of this value. * @param ordinal The ordinal value of the value in the type. * @throws IllegalArgumentException If the ordinal is outside of the range of allowed * values of the type. */ public HDF5EnumerationValue(HDF5EnumerationType type, int ordinal) throws IllegalArgumentException { assert type != null; if (ordinal < 0 || ordinal >= type.getEnumType().getValueArray().length) { throw new IllegalArgumentException("valueIndex " + ordinal + " out of allowed range [0.." + (type.getEnumType().getValueArray().length - 1) + "] of type '" + type.getName() + "'."); } this.type = type; this.ordinal = ordinal; } /** * Creates an enumeration value. * * @param type The enumeration type of this value. * @param value The string value (needs to be one of the values of type). * @throws IllegalArgumentException If the value is not one of the values of * type. */ public HDF5EnumerationValue(HDF5EnumerationType type, String value) throws IllegalArgumentException { assert type != null; assert value != null; final Integer valueIndexOrNull = type.tryGetIndexForValue(value); if (valueIndexOrNull == null) { throw new IllegalArgumentException("Value '" + value + "' is not allowed for type '" + type.getName() + "'."); } this.type = type; this.ordinal = valueIndexOrNull; } /** * Returns the type of this enumeration value. */ public HDF5EnumerationType getType() { return type; } /** * Returns the string value. */ public String getValue() { return type.getEnumType().getValueArray()[ordinal]; } /** * Returns the ordinal value. */ public int getOrdinal() { return ordinal; } /** * Returns the value as Enum of type enumClass. */ public > T getValue(Class enumClass) { return Enum.valueOf(enumClass, getValue()); } /** * Returns a description of this value. */ public String getDescription() { return type.getName() + " [" + type.getEnumType().getValueArray()[ordinal] + "]"; } byte[] toStorageForm() { return type.getEnumType().toStorageForm(ordinal); } // // Object // @Override public int hashCode() { final int prime = 31; int result = 1; result = prime * result + ((type == null) ? 0 : type.hashCode()); result = prime * result + ordinal; return result; } @Override public boolean equals(Object obj) { if (this == obj) { return true; } if (obj == null) { return false; } if (getClass() != obj.getClass()) { return false; } HDF5EnumerationValue other = (HDF5EnumerationValue) obj; if (type == null) { if (other.type != null) { return false; } } else if (type.equals(other.type) == false) { return false; } if (ordinal != other.ordinal) { return false; } return true; } @Override public String toString() { return getValue(); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5EnumerationValueArray.java000066400000000000000000000471111256564762100311220ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.lang.reflect.Array; import java.util.Iterator; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.base.convert.NativeData; import ch.systemsx.cisd.base.convert.NativeData.ByteOrder; import ch.systemsx.cisd.hdf5.HDF5EnumerationType.EnumStorageForm; import ch.systemsx.cisd.hdf5.hdf5lib.HDFNativeData; /** * A class the represents an array of HDF enumeration values. * * @author Bernd Rinn */ public class HDF5EnumerationValueArray implements Iterable { private final HDF5EnumerationType type; private final int length; private EnumStorageForm storageForm; private byte[] bArrayOrNull; private short[] sArrayOrNull; private int[] iArrayOrNull; HDF5EnumerationValueArray(HDF5EnumerationType type, Object array) throws IllegalArgumentException { this.type = type; if (array instanceof byte[]) { final byte[] bArray = (byte[]) array; this.length = bArray.length; setOrdinalArray(bArray); } else if (array instanceof short[]) { final short[] sArray = (short[]) array; this.length = sArray.length; setOrdinalArray(sArray); } else if (array instanceof int[]) { final int[] iArray = (int[]) array; this.length = iArray.length; setOrdinalArray(iArray); } else { throw new IllegalArgumentException("array is of illegal type " + array.getClass().getCanonicalName()); } } /** * Creates an enumeration value array. * * @param type The enumeration type of this value. * @param ordinalArray The array of ordinal values in the type. * @throws IllegalArgumentException If any of the ordinals in the ordinalArray is * outside of the range of allowed values of the type. */ public HDF5EnumerationValueArray(HDF5EnumerationType type, byte[] ordinalArray) throws IllegalArgumentException { this.type = type; this.length = ordinalArray.length; setOrdinalArray(ordinalArray); } /** * Creates an enumeration value array. * * @param type The enumeration type of this value. * @param ordinalArray The array of ordinal values in the type. * @throws IllegalArgumentException If any of the ordinals in the ordinalArray is * outside of the range of allowed values of the type. */ public HDF5EnumerationValueArray(HDF5EnumerationType type, short[] ordinalArray) throws IllegalArgumentException { this.type = type; this.length = ordinalArray.length; setOrdinalArray(ordinalArray); } /** * Creates an enumeration value array. * * @param type The enumeration type of this value. * @param ordinalArray The array of ordinal values in the type. * @throws IllegalArgumentException If any of the ordinals in the ordinalArray is * outside of the range of allowed values of the type. */ public HDF5EnumerationValueArray(HDF5EnumerationType type, int[] ordinalArray) throws IllegalArgumentException { this.type = type; this.length = ordinalArray.length; setOrdinalArray(ordinalArray); } /** * Creates an enumeration value array. * * @param type The enumeration type of this value. * @param valueArray The array of enum values (each one needs to be one of the values of * type). * @throws IllegalArgumentException If any of the values in the valueArray is not one * of the values of type. */ public HDF5EnumerationValueArray(HDF5EnumerationType type, Enum[] valueArray) throws IllegalArgumentException { this(type, toString(valueArray)); } private static String[] toString(Enum[] valueArray) { final String[] result = new String[valueArray.length]; for (int i = 0; i < valueArray.length; ++i) { result[i] = valueArray[i].name(); } return result; } /** * Creates an enumeration value array. * * @param type The enumeration type of this value. * @param valueArray The array of string values (each one needs to be one of the values of * type). * @throws IllegalArgumentException If any of the values in the valueArray is not one * of the values of type. */ public HDF5EnumerationValueArray(HDF5EnumerationType type, String[] valueArray) throws IllegalArgumentException { this.type = type; this.length = valueArray.length; map(valueArray); } private void map(String[] array) throws IllegalArgumentException { if (type.getEnumType().getValueArray().length < Byte.MAX_VALUE) { storageForm = EnumStorageForm.BYTE; bArrayOrNull = new byte[array.length]; for (int i = 0; i < array.length; ++i) { final Integer indexOrNull = type.tryGetIndexForValue(array[i]); if (indexOrNull == null) { throw new IllegalArgumentException("Value '" + array[i] + "' is not allowed for type '" + type.getName() + "'."); } bArrayOrNull[i] = indexOrNull.byteValue(); } sArrayOrNull = null; iArrayOrNull = null; } else if (type.getEnumType().getValueArray().length < Short.MAX_VALUE) { storageForm = EnumStorageForm.SHORT; bArrayOrNull = null; sArrayOrNull = new short[array.length]; for (int i = 0; i < array.length; ++i) { final Integer indexOrNull = type.tryGetIndexForValue(array[i]); if (indexOrNull == null) { throw new IllegalArgumentException("Value '" + array[i] + "' is not allowed for type '" + type.getName() + "'."); } sArrayOrNull[i] = indexOrNull.shortValue(); } iArrayOrNull = null; } else { storageForm = EnumStorageForm.INT; bArrayOrNull = null; sArrayOrNull = null; iArrayOrNull = new int[array.length]; for (int i = 0; i < array.length; ++i) { final Integer indexOrNull = type.tryGetIndexForValue(array[i]); if (indexOrNull == null) { throw new IllegalArgumentException("Value '" + array[i] + "' is not allowed for type '" + type.getName() + "'."); } iArrayOrNull[i] = indexOrNull.intValue(); } } } private void setOrdinalArray(byte[] array) { if (type.getEnumType().getValueArray().length < Byte.MAX_VALUE) { storageForm = EnumStorageForm.BYTE; bArrayOrNull = array; checkOrdinalArray(bArrayOrNull); sArrayOrNull = null; iArrayOrNull = null; } else if (type.getEnumType().getValueArray().length < Short.MAX_VALUE) { storageForm = EnumStorageForm.SHORT; bArrayOrNull = null; sArrayOrNull = toShortArray(array); checkOrdinalArray(sArrayOrNull); iArrayOrNull = null; } else { storageForm = EnumStorageForm.INT; bArrayOrNull = null; sArrayOrNull = null; iArrayOrNull = toIntArray(array); checkOrdinalArray(iArrayOrNull); } } private void setOrdinalArray(short[] array) throws IllegalArgumentException { if (type.getEnumType().getValueArray().length < Byte.MAX_VALUE) { storageForm = EnumStorageForm.BYTE; bArrayOrNull = toByteArray(array); checkOrdinalArray(bArrayOrNull); sArrayOrNull = null; iArrayOrNull = null; } else if (type.getEnumType().getValueArray().length < Short.MAX_VALUE) { storageForm = EnumStorageForm.SHORT; bArrayOrNull = null; sArrayOrNull = array; checkOrdinalArray(sArrayOrNull); iArrayOrNull = null; } else { storageForm = EnumStorageForm.INT; bArrayOrNull = null; sArrayOrNull = null; iArrayOrNull = toIntArray(array); checkOrdinalArray(iArrayOrNull); } } private void setOrdinalArray(int[] array) throws IllegalArgumentException { if (type.getEnumType().getValueArray().length < Byte.MAX_VALUE) { storageForm = EnumStorageForm.BYTE; bArrayOrNull = toByteArray(array); checkOrdinalArray(bArrayOrNull); sArrayOrNull = null; iArrayOrNull = null; } else if (type.getEnumType().getValueArray().length < Short.MAX_VALUE) { storageForm = EnumStorageForm.SHORT; bArrayOrNull = null; sArrayOrNull = toShortArray(array); checkOrdinalArray(sArrayOrNull); iArrayOrNull = null; } else { storageForm = EnumStorageForm.INT; bArrayOrNull = null; sArrayOrNull = null; iArrayOrNull = array; checkOrdinalArray(iArrayOrNull); } } private byte[] toByteArray(short[] array) throws IllegalArgumentException { final byte[] bArray = new byte[array.length]; for (int i = 0; i < array.length; ++i) { bArray[i] = (byte) array[i]; if (bArray[i] != array[i]) { throw new IllegalArgumentException("Value " + array[i] + " cannot be stored in byte array"); } } return bArray; } private byte[] toByteArray(int[] array) throws IllegalArgumentException { final byte[] bArray = new byte[array.length]; for (int i = 0; i < array.length; ++i) { bArray[i] = (byte) array[i]; if (bArray[i] != array[i]) { throw new IllegalArgumentException("Value " + array[i] + " cannot be stored in byte array"); } } return bArray; } private short[] toShortArray(byte[] array) { final short[] sArray = new short[array.length]; for (int i = 0; i < array.length; ++i) { sArray[i] = array[i]; } return sArray; } private short[] toShortArray(int[] array) throws IllegalArgumentException { final short[] sArray = new short[array.length]; for (int i = 0; i < array.length; ++i) { sArray[i] = (short) array[i]; if (sArray[i] != array[i]) { throw new IllegalArgumentException("Value " + array[i] + " cannot be stored in short array"); } } return sArray; } private int[] toIntArray(byte[] array) { final int[] iArray = new int[array.length]; for (int i = 0; i < array.length; ++i) { iArray[i] = array[i]; } return iArray; } private int[] toIntArray(short[] array) { final int[] iArray = new int[array.length]; for (int i = 0; i < array.length; ++i) { iArray[i] = array[i]; } return iArray; } private void checkOrdinalArray(byte[] array) throws IllegalArgumentException { for (int i = 0; i < array.length; ++i) { if (array[i] < 0 || array[i] >= type.getEnumType().getValueArray().length) { throw new IllegalArgumentException("valueIndex " + array[i] + " out of allowed range [0.." + (type.getEnumType().getValueArray().length - 1) + "] of type '" + type.getName() + "'."); } } } private void checkOrdinalArray(short[] array) throws IllegalArgumentException { for (int i = 0; i < array.length; ++i) { if (array[i] < 0 || array[i] >= type.getEnumType().getValueArray().length) { throw new IllegalArgumentException("valueIndex " + array[i] + " out of allowed range [0.." + (type.getEnumType().getValueArray().length - 1) + "] of type '" + type.getName() + "'."); } } } private void checkOrdinalArray(int[] array) throws IllegalArgumentException { for (int i = 0; i < array.length; ++i) { if (array[i] < 0 || array[i] >= type.getEnumType().getValueArray().length) { throw new IllegalArgumentException("valueIndex " + array[i] + " out of allowed range [0.." + (type.getEnumType().getValueArray().length - 1) + "] of type '" + type.getName() + "'."); } } } EnumStorageForm getStorageForm() { return storageForm; } byte[] getStorageFormBArray() { return bArrayOrNull; } short[] getStorageFormSArray() { return sArrayOrNull; } int[] getStorageFormIArray() { return iArrayOrNull; } /** * Returns the type of this enumeration array. */ public HDF5EnumerationType getType() { return type; } /** * Returns the number of members of this enumeration array. */ public int getLength() { return length; } /** * Returns the ordinal value for the arrayIndex. * * @param arrayIndex The index in the array to get the ordinal for. */ public int getOrdinal(int arrayIndex) { if (bArrayOrNull != null) { return bArrayOrNull[arrayIndex]; } else if (sArrayOrNull != null) { return sArrayOrNull[arrayIndex]; } else { return iArrayOrNull[arrayIndex]; } } /** * Returns the string value for arrayIndex. * * @param arrayIndex The index in the array to get the value for. */ public String getValue(int arrayIndex) { return type.getValues().get(getOrdinal(arrayIndex)); } /** * Returns the value as Enum of type enumClass. * * @param enumClass The class to return the value as. * @param arrayIndex The index in the array to get the value for. */ public > T getValue(Class enumClass, int arrayIndex) { return Enum.valueOf(enumClass, getValue(arrayIndex)); } /** * Returns the string values for all elements of this array. */ public String[] toStringArray() { final int len = getLength(); final String[] values = new String[len]; for (int i = 0; i < len; ++i) { values[i] = getValue(i); } return values; } /** * Returns the values for all elements of this array as Enums of type enumClass. */ public > T[] toEnumArray(Class enumClass) { final int len = getLength(); @SuppressWarnings("unchecked") final T[] result = (T[]) Array.newInstance(enumClass, len); for (int i = 0; i < len; ++i) { try { result[i] = Enum.valueOf(enumClass, getValue(i)); } catch (IllegalArgumentException ex) { throw new HDF5JavaException("The Java enum class " + enumClass.getCanonicalName() + " has no value '" + getValue(i) + "'."); } } return result; } byte[] toStorageForm() { switch (getStorageForm()) { case BYTE: return getStorageFormBArray(); case SHORT: return NativeData.shortToByte(getStorageFormSArray(), ByteOrder.NATIVE); case INT: return NativeData.intToByte(getStorageFormIArray(), ByteOrder.NATIVE); } throw new Error("Illegal storage form (" + getStorageForm() + ".)"); } static HDF5EnumerationValueArray fromStorageForm(HDF5EnumerationType enumType, byte[] data, int offset, int len) { switch (enumType.getStorageForm()) { case BYTE: final byte[] subArray = new byte[len]; System.arraycopy(data, offset, subArray, 0, len); return new HDF5EnumerationValueArray(enumType, subArray); case SHORT: return new HDF5EnumerationValueArray(enumType, HDFNativeData.byteToShort(data, offset, len)); case INT: return new HDF5EnumerationValueArray(enumType, HDFNativeData.byteToInt(data, offset, len)); } throw new Error("Illegal storage form (" + enumType.getStorageForm() + ".)"); } static String[] fromStorageFormToStringArray(HDF5EnumerationType enumType, byte[] data, int offset, int len) { final String[] valueArray = new String[len]; for (int i = 0; i < len; ++i) { valueArray[i] = enumType.createStringFromStorageForm(data, offset + i); } return valueArray; } static int[] fromStorageFormToIntArray(HDF5EnumerationType enumType, byte[] data, int offset, int len) { final int[] valueArray = new int[len]; for (int i = 0; i < len; ++i) { valueArray[i] = enumType.getOrdinalFromStorageForm(data, offset + i); } return valueArray; } // // Iterable // @Override public Iterator iterator() { return new Iterator() { private int index = 0; @Override public boolean hasNext() { return index < length; } @Override public String next() { return getValue(index++); } @Override public void remove() throws UnsupportedOperationException { throw new UnsupportedOperationException(); } }; } @Override public String toString() { final StringBuilder b = new StringBuilder(); b.append(type.getName()); b.append(" ["); for (String value : this) { b.append(value); b.append(","); } b.setLength(b.length() - 1); b.append("]"); return b.toString(); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5EnumerationValueMDArray.java000066400000000000000000000626321256564762100313500ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.util.Iterator; import ch.systemsx.cisd.base.convert.NativeData; import ch.systemsx.cisd.base.convert.NativeData.ByteOrder; import ch.systemsx.cisd.base.mdarray.MDAbstractArray; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDByteArray; import ch.systemsx.cisd.base.mdarray.MDIntArray; import ch.systemsx.cisd.base.mdarray.MDShortArray; import ch.systemsx.cisd.hdf5.HDF5EnumerationType.EnumStorageForm; import ch.systemsx.cisd.hdf5.hdf5lib.HDFNativeData; /** * A class that represents a multi-dimensional array of HDF enumeration values. * * @author Bernd Rinn */ public class HDF5EnumerationValueMDArray implements Iterable.ArrayEntry> { private final HDF5EnumerationType type; private EnumStorageForm storageForm; private MDByteArray bArrayOrNull; private MDShortArray sArrayOrNull; private MDIntArray iArrayOrNull; /** * Creates an enumeration value array. * * @param type The enumeration type of this value. * @param ordinalArray The array of ordinal values in the type. Has to be one of * {@link MDByteArray}, {@link MDShortArray} or {@link MDIntArray}. * @throws IllegalArgumentException If any of the ordinals in the ordinalArray is * outside of the range of allowed values of the type. */ public HDF5EnumerationValueMDArray(HDF5EnumerationType type, MDAbstractArray ordinalArray) throws IllegalArgumentException { this.type = type; if (ordinalArray instanceof MDByteArray) { final MDByteArray bArray = (MDByteArray) ordinalArray; setOrdinalArray(bArray); } else if (ordinalArray instanceof MDShortArray) { final MDShortArray sArray = (MDShortArray) ordinalArray; setOrdinalArray(sArray); } else if (ordinalArray instanceof MDIntArray) { final MDIntArray iArray = (MDIntArray) ordinalArray; setOrdinalArray(iArray); } else if (ordinalArray instanceof MDArray) { final MDArray concreteArray = (MDArray) ordinalArray; if (concreteArray.getAsFlatArray().getClass().getComponentType() == String.class) { @SuppressWarnings("unchecked") final MDArray sArray = (MDArray) concreteArray; map(sArray); } else if (concreteArray.getAsFlatArray().getClass().getComponentType().isEnum()) { @SuppressWarnings("unchecked") final MDArray> eArray = (MDArray>) concreteArray; map(toString(eArray)); } else { throw new IllegalArgumentException("array has illegal component type " + concreteArray.getAsFlatArray().getClass().getComponentType() .getCanonicalName()); } } else { throw new IllegalArgumentException("array is of illegal type " + ordinalArray.getClass().getCanonicalName()); } } /** * Creates an empty array with given rank. */ public HDF5EnumerationValueMDArray(int rank) { this.type = null; storageForm = EnumStorageForm.BYTE; this.bArrayOrNull = new MDByteArray(new int[rank]); } /** * Creates an enumeration value array. * * @param type The enumeration type of this value. * @param ordinalArray The array of ordinal values in the type. * @throws IllegalArgumentException If any of the ordinals in the ordinalArray is * outside of the range of allowed values of the type. */ public HDF5EnumerationValueMDArray(HDF5EnumerationType type, MDByteArray ordinalArray) throws IllegalArgumentException { this.type = type; setOrdinalArray(ordinalArray); } /** * Creates an enumeration value array. * * @param type The enumeration type of this value. * @param ordinalArray The array of ordinal values in the type. * @throws IllegalArgumentException If any of the ordinals in the ordinalArray is * outside of the range of allowed values of the type. */ public HDF5EnumerationValueMDArray(HDF5EnumerationType type, MDShortArray ordinalArray) throws IllegalArgumentException { this.type = type; setOrdinalArray(ordinalArray); } /** * Creates an enumeration value array. * * @param type The enumeration type of this value. * @param ordinalArray The array of ordinal values in the type. * @throws IllegalArgumentException If any of the ordinals in the ordinalArray is * outside of the range of allowed values of the type. */ public HDF5EnumerationValueMDArray(HDF5EnumerationType type, MDIntArray ordinalArray) throws IllegalArgumentException { this.type = type; setOrdinalArray(ordinalArray); } private static MDArray toString(MDArray> valueArray) { final Enum[] flatEnumArray = valueArray.getAsFlatArray(); final MDArray result = new MDArray(String.class, valueArray.dimensions()); final String[] flatStringArray = result.getAsFlatArray(); for (int i = 0; i < flatEnumArray.length; ++i) { flatStringArray[i] = flatEnumArray[i].name(); } return result; } private void map(MDArray array) throws IllegalArgumentException { final String[] flatArray = array.getAsFlatArray(); if (type.getEnumType().getValueArray().length < Byte.MAX_VALUE) { storageForm = EnumStorageForm.BYTE; bArrayOrNull = new MDByteArray(array.dimensions()); final byte[] flatBArray = bArrayOrNull.getAsFlatArray(); for (int i = 0; i < flatArray.length; ++i) { final Integer indexOrNull = type.tryGetIndexForValue(flatArray[i]); if (indexOrNull == null) { throw new IllegalArgumentException("Value '" + flatArray[i] + "' is not allowed for type '" + type.getName() + "'."); } flatBArray[i] = indexOrNull.byteValue(); } sArrayOrNull = null; iArrayOrNull = null; } else if (type.getEnumType().getValueArray().length < Short.MAX_VALUE) { storageForm = EnumStorageForm.SHORT; bArrayOrNull = null; sArrayOrNull = new MDShortArray(array.dimensions()); final short[] flatSArray = sArrayOrNull.getAsFlatArray(); for (int i = 0; i < flatArray.length; ++i) { final Integer indexOrNull = type.tryGetIndexForValue(flatArray[i]); if (indexOrNull == null) { throw new IllegalArgumentException("Value '" + flatArray[i] + "' is not allowed for type '" + type.getName() + "'."); } flatSArray[i] = indexOrNull.shortValue(); } iArrayOrNull = null; } else { storageForm = EnumStorageForm.INT; bArrayOrNull = null; sArrayOrNull = null; iArrayOrNull = new MDIntArray(array.dimensions()); final int[] flatIArray = iArrayOrNull.getAsFlatArray(); for (int i = 0; i < flatIArray.length; ++i) { final Integer indexOrNull = type.tryGetIndexForValue(flatArray[i]); if (indexOrNull == null) { throw new IllegalArgumentException("Value '" + flatArray[i] + "' is not allowed for type '" + type.getName() + "'."); } flatIArray[i] = indexOrNull.intValue(); } } } private void setOrdinalArray(MDByteArray array) { if (type.getEnumType().getValueArray().length < Byte.MAX_VALUE) { storageForm = EnumStorageForm.BYTE; bArrayOrNull = array; checkOrdinalArray(bArrayOrNull); sArrayOrNull = null; iArrayOrNull = null; } else if (type.getEnumType().getValueArray().length < Short.MAX_VALUE) { storageForm = EnumStorageForm.SHORT; bArrayOrNull = null; sArrayOrNull = toShortArray(array); checkOrdinalArray(sArrayOrNull); iArrayOrNull = null; } else { storageForm = EnumStorageForm.INT; bArrayOrNull = null; sArrayOrNull = null; iArrayOrNull = toIntArray(array); checkOrdinalArray(iArrayOrNull); } } private void setOrdinalArray(MDShortArray array) throws IllegalArgumentException { if (type.getEnumType().getValueArray().length < Byte.MAX_VALUE) { storageForm = EnumStorageForm.BYTE; bArrayOrNull = toByteArray(array); checkOrdinalArray(bArrayOrNull); sArrayOrNull = null; iArrayOrNull = null; } else if (type.getEnumType().getValueArray().length < Short.MAX_VALUE) { storageForm = EnumStorageForm.SHORT; bArrayOrNull = null; sArrayOrNull = array; checkOrdinalArray(sArrayOrNull); iArrayOrNull = null; } else { storageForm = EnumStorageForm.INT; bArrayOrNull = null; sArrayOrNull = null; iArrayOrNull = toIntArray(array); checkOrdinalArray(iArrayOrNull); } } private void setOrdinalArray(MDIntArray array) throws IllegalArgumentException { if (type.getEnumType().getValueArray().length < Byte.MAX_VALUE) { storageForm = EnumStorageForm.BYTE; bArrayOrNull = toByteArray(array); checkOrdinalArray(bArrayOrNull); sArrayOrNull = null; iArrayOrNull = null; } else if (type.getEnumType().getValueArray().length < Short.MAX_VALUE) { storageForm = EnumStorageForm.SHORT; bArrayOrNull = null; sArrayOrNull = toShortArray(array); checkOrdinalArray(sArrayOrNull); iArrayOrNull = null; } else { storageForm = EnumStorageForm.INT; bArrayOrNull = null; sArrayOrNull = null; iArrayOrNull = array; checkOrdinalArray(iArrayOrNull); } } private MDByteArray toByteArray(MDShortArray array) throws IllegalArgumentException { final short[] flatSourceArray = array.getAsFlatArray(); final MDByteArray bArray = new MDByteArray(array.dimensions()); final byte[] flatTargetArray = bArray.getAsFlatArray(); for (int i = 0; i < flatSourceArray.length; ++i) { flatTargetArray[i] = (byte) flatSourceArray[i]; if (flatTargetArray[i] != flatSourceArray[i]) { throw new IllegalArgumentException("Value " + flatSourceArray[i] + " cannot be stored in byte array"); } } return bArray; } private MDByteArray toByteArray(MDIntArray array) throws IllegalArgumentException { final int[] flatSourceArray = array.getAsFlatArray(); final MDByteArray bArray = new MDByteArray(array.dimensions()); final byte[] flatTargetArray = bArray.getAsFlatArray(); for (int i = 0; i < flatSourceArray.length; ++i) { flatTargetArray[i] = (byte) flatSourceArray[i]; if (flatTargetArray[i] != flatSourceArray[i]) { throw new IllegalArgumentException("Value " + flatSourceArray[i] + " cannot be stored in byte array"); } } return bArray; } private MDShortArray toShortArray(MDByteArray array) { final byte[] flatSourceArray = array.getAsFlatArray(); final MDShortArray sArray = new MDShortArray(array.dimensions()); final short[] flatTargetArray = sArray.getAsFlatArray(); for (int i = 0; i < flatSourceArray.length; ++i) { flatTargetArray[i] = flatSourceArray[i]; } return sArray; } private MDShortArray toShortArray(MDIntArray array) throws IllegalArgumentException { final int[] flatSourceArray = array.getAsFlatArray(); final MDShortArray sArray = new MDShortArray(array.dimensions()); final short[] flatTargetArray = sArray.getAsFlatArray(); for (int i = 0; i < flatSourceArray.length; ++i) { flatTargetArray[i] = (short) flatSourceArray[i]; if (flatSourceArray[i] != flatTargetArray[i]) { throw new IllegalArgumentException("Value " + flatSourceArray[i] + " cannot be stored in short array"); } } return sArray; } private MDIntArray toIntArray(MDByteArray array) { final byte[] flatSourceArray = array.getAsFlatArray(); final MDIntArray iArray = new MDIntArray(array.dimensions()); final int[] flatTargetArray = iArray.getAsFlatArray(); for (int i = 0; i < flatSourceArray.length; ++i) { flatTargetArray[i] = flatSourceArray[i]; } return iArray; } private MDIntArray toIntArray(MDShortArray array) { final short[] flatSourceArray = array.getAsFlatArray(); final MDIntArray iArray = new MDIntArray(array.dimensions()); final int[] flatTargetArray = iArray.getAsFlatArray(); for (int i = 0; i < flatSourceArray.length; ++i) { flatTargetArray[i] = flatSourceArray[i]; } return iArray; } private void checkOrdinalArray(MDByteArray array) throws IllegalArgumentException { final byte[] flatArray = array.getAsFlatArray(); for (int i = 0; i < flatArray.length; ++i) { if (flatArray[i] < 0 || flatArray[i] >= type.getEnumType().getValueArray().length) { throw new IllegalArgumentException("valueIndex " + flatArray[i] + " out of allowed range [0.." + (type.getEnumType().getValueArray().length - 1) + "] of type '" + type.getName() + "'."); } } } private void checkOrdinalArray(MDShortArray array) throws IllegalArgumentException { final short[] flatArray = array.getAsFlatArray(); for (int i = 0; i < flatArray.length; ++i) { if (flatArray[i] < 0 || flatArray[i] >= type.getEnumType().getValueArray().length) { throw new IllegalArgumentException("valueIndex " + flatArray[i] + " out of allowed range [0.." + (type.getEnumType().getValueArray().length - 1) + "] of type '" + type.getName() + "'."); } } } private void checkOrdinalArray(MDIntArray array) throws IllegalArgumentException { final int[] flatArray = array.getAsFlatArray(); for (int i = 0; i < flatArray.length; ++i) { if (flatArray[i] < 0 || flatArray[i] >= type.getEnumType().getValueArray().length) { throw new IllegalArgumentException("valueIndex " + flatArray[i] + " out of allowed range [0.." + (type.getEnumType().getValueArray().length - 1) + "] of type '" + type.getName() + "'."); } } } EnumStorageForm getStorageForm() { return storageForm; } /** * Returns the type of this enumeration array. */ public HDF5EnumerationType getType() { return type; } /** * Returns the number of elements of this enumeration array. */ public int size() { return getOrdinalValues().size(); } /** * Returns the extent of this enum array along its dim-th axis. */ public int size(int dim) { assert dim < dimensions().length; return dimensions()[dim]; } /** * Returns the rank of this multi-dimensional enumeration array. */ public int rank() { return dimensions().length; } /** * Returns the dimensions of this enumeration array. */ public int[] dimensions() { return getOrdinalValues().dimensions(); } /** * Returns the dimensions of this enumeration array as a long. */ public long[] longDimensions() { return getOrdinalValues().longDimensions(); } /** * Returns the ordinal value for the arrayIndex. * * @param arrayIndex The index in the array to get the ordinal for. */ public int getOrdinal(int arrayIndex) { if (bArrayOrNull != null) { return bArrayOrNull.get(arrayIndex); } else if (sArrayOrNull != null) { return sArrayOrNull.get(arrayIndex); } else { return iArrayOrNull.get(arrayIndex); } } /** * Returns the ordinal value for the arrayIndex. * * @param arrayIndexX The x index in the array to get the ordinal for. * @param arrayIndexY The y index in the array to get the ordinal for. */ public int getOrdinal(int arrayIndexX, int arrayIndexY) { if (bArrayOrNull != null) { return bArrayOrNull.get(arrayIndexX, arrayIndexY); } else if (sArrayOrNull != null) { return sArrayOrNull.get(arrayIndexX, arrayIndexY); } else { return iArrayOrNull.get(arrayIndexX, arrayIndexY); } } /** * Returns the ordinal value for the arrayIndex. * * @param arrayIndices The indices in the array to get the ordinal for. */ public int getOrdinal(int... arrayIndices) { if (bArrayOrNull != null) { return bArrayOrNull.get(arrayIndices); } else if (sArrayOrNull != null) { return sArrayOrNull.get(arrayIndices); } else { return iArrayOrNull.get(arrayIndices); } } /** * Returns the string value for arrayIndex. * * @param arrayIndex The index in the array to get the value for. */ public String getValue(int arrayIndex) { return type.getValues().get(getOrdinal(arrayIndex)); } /** * Returns the string value for arrayIndex. * * @param arrayIndexX The x index in the array to get the value for. * @param arrayIndexY The y index in the array to get the value for. */ public String getValue(int arrayIndexX, int arrayIndexY) { return type.getValues().get(getOrdinal(arrayIndexX, arrayIndexY)); } /** * Returns the string value for arrayIndex. * * @param arrayIndices The indices in the array to get the value for. */ public String getValue(int... arrayIndices) { return type.getValues().get(getOrdinal(arrayIndices)); } /** * Returns the value as Enum of type enumClass. * * @param enumClass The class to return the value as. * @param arrayIndices The indices in the array to get the value for. */ public > T getValue(Class enumClass, int... arrayIndices) { return Enum.valueOf(enumClass, getValue(arrayIndices)); } /** * Returns the string values for all elements of this array. */ public MDArray toStringArray() { final int len = size(); final MDArray values = new MDArray(String.class, dimensions()); final String[] flatValues = values.getAsFlatArray(); for (int i = 0; i < len; ++i) { flatValues[i] = getValue(i); } return values; } /** * Returns the values for all elements of this array as an enum array with enums of type * enumClass. */ public > MDArray toEnumArray(Class enumClass) { final int len = size(); final MDArray values = new MDArray(enumClass, dimensions()); final T[] flatValues = values.getAsFlatArray(); for (int i = 0; i < len; ++i) { flatValues[i] = Enum.valueOf(enumClass, getValue(i)); } return values; } /** * Returns the ordinal values for all elements of this array. */ public MDAbstractArray getOrdinalValues() { switch (getStorageForm()) { case BYTE: return bArrayOrNull; case SHORT: return sArrayOrNull; case INT: return iArrayOrNull; } throw new Error("Illegal storage form."); } byte[] toStorageForm() { switch (getStorageForm()) { case BYTE: return bArrayOrNull.getAsFlatArray(); case SHORT: return NativeData.shortToByte(sArrayOrNull.getAsFlatArray(), ByteOrder.NATIVE); case INT: return NativeData.intToByte(iArrayOrNull.getAsFlatArray(), ByteOrder.NATIVE); } throw new Error("Illegal storage form (" + getStorageForm() + ".)"); } static HDF5EnumerationValueMDArray fromStorageForm(HDF5EnumerationType enumType, byte[] data, int offset, int[] dimensions, int len) { switch (enumType.getStorageForm()) { case BYTE: final byte[] subArray = new byte[len]; System.arraycopy(data, offset, subArray, 0, len); return new HDF5EnumerationValueMDArray(enumType, new MDByteArray(subArray, dimensions)); case SHORT: return new HDF5EnumerationValueMDArray(enumType, new MDShortArray( HDFNativeData.byteToShort(data, offset, len), dimensions)); case INT: return new HDF5EnumerationValueMDArray(enumType, new MDIntArray( HDFNativeData.byteToInt(data, offset, len), dimensions)); } throw new Error("Illegal storage form (" + enumType.getStorageForm() + ".)"); } // // Iterable // @Override public Iterator.ArrayEntry> iterator() { return toStringArray().iterator(); } // // Object // @Override public String toString() { return toStringArray().toString(); } @Override public int hashCode() { final int prime = 31; int result = 1; result = prime * result + ((bArrayOrNull == null) ? 0 : bArrayOrNull.hashCode()); result = prime * result + ((iArrayOrNull == null) ? 0 : iArrayOrNull.hashCode()); result = prime * result + ((sArrayOrNull == null) ? 0 : sArrayOrNull.hashCode()); result = prime * result + ((storageForm == null) ? 0 : storageForm.hashCode()); result = prime * result + ((type == null) ? 0 : type.hashCode()); return result; } @Override public boolean equals(Object obj) { if (this == obj) { return true; } if (obj == null) { return false; } if (getClass() != obj.getClass()) { return false; } HDF5EnumerationValueMDArray other = (HDF5EnumerationValueMDArray) obj; if (bArrayOrNull == null) { if (other.bArrayOrNull != null) { return false; } } else if (false == bArrayOrNull.equals(other.bArrayOrNull)) { return false; } if (iArrayOrNull == null) { if (other.iArrayOrNull != null) { return false; } } else if (false == iArrayOrNull.equals(other.iArrayOrNull)) { return false; } if (sArrayOrNull == null) { if (other.sArrayOrNull != null) { return false; } } else if (false == sArrayOrNull.equals(other.sArrayOrNull)) { return false; } if (storageForm != other.storageForm) { return false; } if (type == null) { if (other.type != null) { return false; } } else if (false == type.equals(other.type)) { return false; } return true; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5Factory.java000066400000000000000000000102421256564762100262420ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.io.File; /** * A static wrapper for the {@link IHDF5Factory} for creating writers and readers of HDF5 files. For * straight-forward creation, see methods {@link #open(File)} and {@link #openForReading(File)}. If * you need full control over the creation process, see the methods {@link #configure(File)} and * {@link #configureForReading(File)}. * * @author Bernd Rinn */ public final class HDF5Factory { /** * Opens an HDF5 file for writing and reading. If the file does not yet exist, it * will be created. */ public static IHDF5Writer open(File file) { return HDF5FactoryProvider.get().open(file); } /** * Opens an HDF5 file named filePath for writing and reading. If the file does not * yet exist, it will be created. */ public static IHDF5Writer open(String filePath) { return HDF5FactoryProvider.get().open(new File(filePath)); } /** * Opens an HDF5 file for reading. It is an error if the file does not exist. */ public static IHDF5Reader openForReading(File file) { return HDF5FactoryProvider.get().openForReading(file); } /** * Opens an HDF5 file named filePath for reading. It is an error if the file does not * exist. */ public static IHDF5Reader openForReading(String filePath) { return HDF5FactoryProvider.get().openForReading(new File(filePath)); } /** * Opens a configurator for an HDF5 file for writing and reading. Configure the * writer as you need and then call {@link IHDF5WriterConfigurator#writer()} in order to start * reading and writing the file. */ public static IHDF5WriterConfigurator configure(File file) { return HDF5FactoryProvider.get().configure(file); } /** * Opens a configurator for an HDF5 file named filePath for writing and reading. * Configure the writer as you need and then call {@link IHDF5WriterConfigurator#writer()} in * order to start reading and writing the file. */ public static IHDF5WriterConfigurator configure(String filePath) { return HDF5FactoryProvider.get().configure(new File(filePath)); } /** * Opens a configurator for an HDF5 file for reading. Configure the reader as you * need and then call {@link IHDF5ReaderConfigurator#reader()} in order to start reading the * file. */ public static IHDF5ReaderConfigurator configureForReading(File file) { return HDF5FactoryProvider.get().configureForReading(file); } /** * Opens a configurator for an HDF5 file named filePath for reading. Configure the * reader as you need and then call {@link IHDF5ReaderConfigurator#reader()} in order to start * reading the file. */ public static IHDF5ReaderConfigurator configureForReading(String filePath) { return HDF5FactoryProvider.get().configureForReading(new File(filePath)); } /** * Returns true, if the file is an HDF5 file and false * otherwise. */ public static boolean isHDF5File(File file) { return HDF5FactoryProvider.get().isHDF5File(file); } /** * Returns true, if the file named filePath is an HDF5 file and * false otherwise. */ public static boolean isHDF5File(String filePath) { return HDF5FactoryProvider.get().isHDF5File(new File(filePath)); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5FactoryProvider.java000066400000000000000000000046701256564762100277650ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.io.File; import ch.systemsx.cisd.hdf5.hdf5lib.H5F; /** * Provides access to a factory for HDF5 readers and writers. * * @author Bernd Rinn */ public final class HDF5FactoryProvider { private static class HDF5Factory implements IHDF5Factory { @Override public IHDF5WriterConfigurator configure(File file) { return new HDF5WriterConfigurator(file); } @Override public IHDF5ReaderConfigurator configureForReading(File file) { return new HDF5ReaderConfigurator(file); } @Override public IHDF5Writer open(File file) { return new HDF5WriterConfigurator(file).writer(); } @Override public IHDF5Reader openForReading(File file) { return new HDF5ReaderConfigurator(file).reader(); } @Override public boolean isHDF5File(File file) { return H5F.H5Fis_hdf5(file.getPath()); } } /** * The (only) instance of the factory. */ private static IHDF5Factory factory = new HDF5Factory(); private HDF5FactoryProvider() { // Not to be instantiated. } /** * Returns the {@link IHDF5Factory}. This is your access to creation of {@link IHDF5Reader} and * {@link IHDF5Writer} instances. */ public static synchronized IHDF5Factory get() { return factory; } /** * Sets the {@link IHDF5Factory}. In normal operation this method is not used, but it is a hook * that can be used if you need to track or influence the factory's operation, for example for * mocking in unit tests. */ public static synchronized void set(IHDF5Factory factory) { HDF5FactoryProvider.factory = factory; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5FileLevelReadOnlyHandler.java000066400000000000000000000030441256564762100314400ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.io.File; /** * Implementation of {@link IHDF5FileLevelReadOnlyHandler} * * @author Bernd Rinn */ class HDF5FileLevelReadOnlyHandler implements IHDF5FileLevelReadOnlyHandler { private final HDF5BaseReader baseReader; HDF5FileLevelReadOnlyHandler(HDF5BaseReader baseReader) { assert baseReader != null; this.baseReader = baseReader; } @Override public boolean isPerformNumericConversions() { return baseReader.performNumericConversions; } @Override public boolean isClosed() { return baseReader.isClosed(); } @Override public String getHouseKeepingNameSuffix() { return baseReader.houseKeepingNameSuffix; } @Override public File getFile() { return baseReader.hdf5File; } @Override public void close() { baseReader.close(); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5FileLevelReadWriteHandler.java000066400000000000000000000040331256564762100316100ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.io.Flushable; import ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator.FileFormat; /** * Implementation of {@link IHDF5FileLevelReadWriteHandler}. * * @author Bernd Rinn */ final class HDF5FileLevelReadWriteHandler extends HDF5FileLevelReadOnlyHandler implements IHDF5FileLevelReadWriteHandler { private final HDF5BaseWriter baseWriter; HDF5FileLevelReadWriteHandler(HDF5BaseWriter baseWriter) { super(baseWriter); assert baseWriter != null; this.baseWriter = baseWriter; } // ///////////////////// // Configuration // ///////////////////// @Override public boolean isUseExtendableDataTypes() { return baseWriter.useExtentableDataTypes; } @Override public FileFormat getFileFormat() { return baseWriter.fileFormat; } // ///////////////////// // File // ///////////////////// @Override public void flush() { baseWriter.checkOpen(); baseWriter.flush(); } @Override public void flushSyncBlocking() { baseWriter.checkOpen(); baseWriter.flushSyncBlocking(); } @Override public boolean addFlushable(Flushable flushable) { return baseWriter.addFlushable(flushable); } @Override public boolean removeFlushable(Flushable flushable) { return baseWriter.removeFlushable(flushable); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5FloatReader.java000066400000000000000000001022351256564762100270270ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.MatrixUtils.cardinalityBoundIndices; import static ch.systemsx.cisd.hdf5.MatrixUtils.checkBoundIndices; import static ch.systemsx.cisd.hdf5.MatrixUtils.createFullBlockDimensionsAndOffset; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_ARRAY; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_FLOAT; import java.util.Arrays; import java.util.Iterator; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import ncsa.hdf.hdf5lib.exceptions.HDF5SpaceRankMismatch; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDFloatArray; import ch.systemsx.cisd.hdf5.HDF5BaseReader.DataSpaceParameters; import ch.systemsx.cisd.hdf5.HDF5DataTypeInformation.DataTypeInfoOptions; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; import ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants; /** * The implementation of {@link IHDF5FloatReader}. * * @author Bernd Rinn */ class HDF5FloatReader implements IHDF5FloatReader { private final HDF5BaseReader baseReader; HDF5FloatReader(HDF5BaseReader baseReader) { assert baseReader != null; this.baseReader = baseReader; } // For Unit tests only. HDF5BaseReader getBaseReader() { return baseReader; } // ///////////////////// // Attributes // ///////////////////// @Override public float getAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public Float call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final float[] data = baseReader.h5.readAttributeAsFloatArray(attributeId, H5T_NATIVE_FLOAT, 1); return data[0]; } }; return baseReader.runner.call(getAttributeRunnable); } @Override public float[] getArrayAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public float[] call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); return getFloatArrayAttribute(objectId, attributeName, registry); } }; return baseReader.runner.call(getAttributeRunnable); } @Override public MDFloatArray getMDArrayAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public MDFloatArray call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); return getFloatMDArrayAttribute(objectId, attributeName, registry); } }; return baseReader.runner.call(getAttributeRunnable); } @Override public float[][] getMatrixAttr(final String objectPath, final String attributeName) throws HDF5JavaException { final MDFloatArray array = getMDArrayAttr(objectPath, attributeName); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } // ///////////////////// // Data Sets // ///////////////////// @Override public float read(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public Float call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final float[] data = new float[1]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_FLOAT, data); return data[0]; } }; return baseReader.runner.call(readCallable); } @Override public float[] readArray(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public float[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); return readFloatArray(dataSetId, registry); } }; return baseReader.runner.call(readCallable); } private float[] readFloatArray(int dataSetId, ICleanUpRegistry registry) { try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); final float[] data = new float[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_FLOAT, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return data; } catch (HDF5LibraryException ex) { if (ex.getMajorErrorNumber() == HDF5Constants.H5E_DATATYPE && ex.getMinorErrorNumber() == HDF5Constants.H5E_CANTINIT) { // Check whether it is an array data type. final int dataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); if (baseReader.h5.getClassType(dataTypeId) == HDF5Constants.H5T_ARRAY) { return readFloatArrayFromArrayType(dataSetId, dataTypeId, registry); } } throw ex; } } private float[] readFloatArrayFromArrayType(int dataSetId, final int dataTypeId, ICleanUpRegistry registry) { final int spaceId = baseReader.h5.createScalarDataSpace(); final int[] dimensions = baseReader.h5.getArrayDimensions(dataTypeId); final float[] data = new float[HDF5Utils.getOneDimensionalArraySize(dimensions)]; final int memoryDataTypeId = baseReader.h5.createArrayType(H5T_NATIVE_FLOAT, data.length, registry); baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceId, spaceId, data); return data; } @Override public int[] readToMDArrayWithOffset(final String objectPath, final MDFloatArray array, final int[] memoryOffset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getBlockSpaceParameters(dataSetId, memoryOffset, array .dimensions(), registry); final int nativeDataTypeId = baseReader.getNativeDataTypeId(dataSetId, H5T_NATIVE_FLOAT, registry); baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, array. getAsFlatArray()); return MDArray.toInt(spaceParams.dimensions); } }; return baseReader.runner.call(readCallable); } @Override public int[] readToMDArrayBlockWithOffset(final String objectPath, final MDFloatArray array, final int[] blockDimensions, final long[] offset, final int[] memoryOffset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getBlockSpaceParameters(dataSetId, memoryOffset, array .dimensions(), offset, blockDimensions, registry); final int nativeDataTypeId = baseReader.getNativeDataTypeId(dataSetId, H5T_NATIVE_FLOAT, registry); baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, array .getAsFlatArray()); return MDArray.toInt(spaceParams.dimensions); } }; return baseReader.runner.call(readCallable); } @Override public float[] readArrayBlock(final String objectPath, final int blockSize, final long blockNumber) { return readArrayBlockWithOffset(objectPath, blockSize, blockNumber * blockSize); } @Override public float[] readArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public float[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockSize, registry); final float[] data = new float[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_FLOAT, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return data; } }; return baseReader.runner.call(readCallable); } @Override public float[][] readMatrix(final String objectPath) throws HDF5JavaException { final MDFloatArray array = readMDArray(objectPath); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public float[][] readMatrixBlock(final String objectPath, final int blockSizeX, final int blockSizeY, final long blockNumberX, final long blockNumberY) throws HDF5JavaException { final MDFloatArray array = readMDArrayBlock(objectPath, new int[] { blockSizeX, blockSizeY }, new long[] { blockNumberX, blockNumberY }); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public float[][] readMatrixBlockWithOffset(final String objectPath, final int blockSizeX, final int blockSizeY, final long offsetX, final long offsetY) throws HDF5JavaException { final MDFloatArray array = readMDArrayBlockWithOffset(objectPath, new int[] { blockSizeX, blockSizeY }, new long[] { offsetX, offsetY }); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public MDFloatArray readMDArraySlice(String objectPath, IndexMap boundIndices) { baseReader.checkOpen(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; final int cardBoundIndices = cardinalityBoundIndices(boundIndices); checkBoundIndices(objectPath, fullDimensions, cardBoundIndices); final int[] effectiveBlockDimensions = new int[fullBlockDimensions.length - cardBoundIndices]; Arrays.fill(effectiveBlockDimensions, -1); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, null, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDFloatArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); if (fullBlockDimensions.length == cardBoundIndices) // no free indices { return new MDFloatArray(result.getAsFlatArray(), new int[] { 1 }); } else { return new MDFloatArray(result.getAsFlatArray(), effectiveBlockDimensions); } } @Override public MDFloatArray readMDArraySlice(String objectPath, long[] boundIndices) { baseReader.checkOpen(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; final int cardBoundIndices = cardinalityBoundIndices(boundIndices); checkBoundIndices(objectPath, fullDimensions, boundIndices); final int[] effectiveBlockDimensions = new int[fullBlockDimensions.length - cardBoundIndices]; Arrays.fill(effectiveBlockDimensions, -1); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, null, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDFloatArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); if (fullBlockDimensions.length == cardBoundIndices) // no free indices { return new MDFloatArray(result.getAsFlatArray(), new int[] { 1 }); } else { return new MDFloatArray(result.getAsFlatArray(), effectiveBlockDimensions); } } @Override public MDFloatArray readMDArray(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public MDFloatArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); return readFloatMDArray(dataSetId, registry); } }; return baseReader.runner.call(readCallable); } MDFloatArray readFloatMDArray(int dataSetId, ICleanUpRegistry registry) { try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); final float[] data = new float[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_FLOAT, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return new MDFloatArray(data, spaceParams.dimensions); } catch (HDF5LibraryException ex) { if (ex.getMajorErrorNumber() == HDF5Constants.H5E_DATATYPE && ex.getMinorErrorNumber() == HDF5Constants.H5E_CANTINIT) { // Check whether it is an array data type. final int dataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); if (baseReader.h5.getClassType(dataTypeId) == HDF5Constants.H5T_ARRAY) { return readFloatMDArrayFromArrayType(dataSetId, dataTypeId, registry); } } throw ex; } } private MDFloatArray readFloatMDArrayFromArrayType(int dataSetId, final int dataTypeId, ICleanUpRegistry registry) { final int[] arrayDimensions = baseReader.h5.getArrayDimensions(dataTypeId); final int memoryDataTypeId = baseReader.h5.createArrayType(H5T_NATIVE_FLOAT, arrayDimensions, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); if (spaceParams.blockSize == 0) { final int spaceId = baseReader.h5.createScalarDataSpace(); final float[] data = new float[MDArray.getLength(arrayDimensions)]; baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceId, spaceId, data); return new MDFloatArray(data, arrayDimensions); } else { final float[] data = new float[MDArray.getLength(arrayDimensions) * spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return new MDFloatArray(data, MatrixUtils.concat(MDArray.toInt(spaceParams.dimensions), arrayDimensions)); } } @Override public MDFloatArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, IndexMap boundIndices) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readSlicedMDArrayBlockWithOffset(objectPath, blockDimensions, offset, boundIndices); } @Override public MDFloatArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, long[] boundIndices) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readSlicedMDArrayBlockWithOffset(objectPath, blockDimensions, offset, boundIndices); } @Override public MDFloatArray readMDArrayBlock(final String objectPath, final int[] blockDimensions, final long[] blockNumber) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readMDArrayBlockWithOffset(objectPath, blockDimensions, offset); } @Override public MDFloatArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, IndexMap boundIndices) { baseReader.checkOpen(); final int[] effectiveBlockDimensions = blockDimensions.clone(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; checkBoundIndices(objectPath, fullDimensions, blockDimensions, cardinalityBoundIndices(boundIndices)); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, offset, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDFloatArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); return new MDFloatArray(result.getAsFlatArray(), effectiveBlockDimensions); } @Override public MDFloatArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, long[] boundIndices) { baseReader.checkOpen(); final int[] effectiveBlockDimensions = blockDimensions.clone(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; checkBoundIndices(objectPath, fullDimensions, blockDimensions, cardinalityBoundIndices(boundIndices)); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, offset, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDFloatArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); return new MDFloatArray(result.getAsFlatArray(), effectiveBlockDimensions); } @Override public MDFloatArray readMDArrayBlockWithOffset(final String objectPath, final int[] blockDimensions, final long[] offset) { assert objectPath != null; assert blockDimensions != null; assert offset != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public MDFloatArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockDimensions, registry); final float[] dataBlock = new float[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_FLOAT, spaceParams.memorySpaceId, spaceParams.dataSpaceId, dataBlock); return new MDFloatArray(dataBlock, spaceParams.dimensions); } catch (HDF5SpaceRankMismatch ex) { final HDF5DataSetInformation info = baseReader.getDataSetInformation(objectPath, DataTypeInfoOptions.MINIMAL, false); if (ex.getSpaceRankExpected() - ex.getSpaceRankFound() == info .getTypeInformation().getRank()) { return readMDArrayBlockOfArrays(dataSetId, blockDimensions, offset, info, ex.getSpaceRankFound(), registry); } else { throw ex; } } } }; return baseReader.runner.call(readCallable); } private MDFloatArray readMDArrayBlockOfArrays(final int dataSetId, final int[] blockDimensions, final long[] offset, final HDF5DataSetInformation info, final int spaceRank, final ICleanUpRegistry registry) { final int[] arrayDimensions = info.getTypeInformation().getDimensions(); int[] effectiveBlockDimensions = blockDimensions; // We do not support block-wise reading of array types, check // that we do not have to and bail out otherwise. for (int i = 0; i < arrayDimensions.length; ++i) { final int j = spaceRank + i; if (effectiveBlockDimensions[j] < 0) { if (effectiveBlockDimensions == blockDimensions) { effectiveBlockDimensions = blockDimensions.clone(); } effectiveBlockDimensions[j] = arrayDimensions[i]; } if (effectiveBlockDimensions[j] != arrayDimensions[i]) { throw new HDF5JavaException( "Block-wise reading of array type data sets is not supported."); } } final int[] spaceBlockDimensions = Arrays.copyOfRange(effectiveBlockDimensions, 0, spaceRank); final long[] spaceOfs = Arrays.copyOfRange(offset, 0, spaceRank); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, spaceOfs, spaceBlockDimensions, registry); final float[] dataBlock = new float[spaceParams.blockSize * info.getTypeInformation().getNumberOfElements()]; final int memoryDataTypeId = baseReader.h5.createArrayType(H5T_NATIVE_FLOAT, info.getTypeInformation() .getDimensions(), registry); baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, dataBlock); return new MDFloatArray(dataBlock, effectiveBlockDimensions); } @Override public Iterable> getArrayNaturalBlocks(final String dataSetPath) throws HDF5JavaException { baseReader.checkOpen(); final HDF5NaturalBlock1DParameters params = new HDF5NaturalBlock1DParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlock1DParameters.HDF5NaturalBlock1DIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5DataBlock next() { final long offset = index.computeOffsetAndSizeGetOffset(); final float[] block = readArrayBlockWithOffset(dataSetPath, index .getBlockSize(), offset); return new HDF5DataBlock(block, index.getAndIncIndex(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } @Override public Iterable> getMDArrayNaturalBlocks(final String dataSetPath) { baseReader.checkOpen(); final HDF5NaturalBlockMDParameters params = new HDF5NaturalBlockMDParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlockMDParameters.HDF5NaturalBlockMDIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5MDDataBlock next() { final long[] offset = index.computeOffsetAndSizeGetOffsetClone(); final MDFloatArray data = readMDArrayBlockWithOffset(dataSetPath, index .getBlockSize(), offset); return new HDF5MDDataBlock(data, index .getIndexClone(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } float[] getFloatArrayAttribute(final int objectId, final String attributeName, ICleanUpRegistry registry) { final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, registry); final int memoryTypeId; final int len; if (baseReader.h5.getClassType(attributeTypeId) == H5T_ARRAY) { final int[] arrayDimensions = baseReader.h5.getArrayDimensions(attributeTypeId); if (arrayDimensions.length != 1) { throw new HDF5JavaException( "Array needs to be of rank 1, but is of rank " + arrayDimensions.length); } len = arrayDimensions[0]; memoryTypeId = baseReader.h5.createArrayType(H5T_NATIVE_FLOAT, len, registry); } else { final long[] arrayDimensions = baseReader.h5.getDataDimensionsForAttribute(attributeId, registry); memoryTypeId = H5T_NATIVE_FLOAT; len = HDF5Utils.getOneDimensionalArraySize(arrayDimensions); } final float[] data = baseReader.h5.readAttributeAsFloatArray(attributeId, memoryTypeId, len); return data; } MDFloatArray getFloatMDArrayAttribute(final int objectId, final String attributeName, ICleanUpRegistry registry) { try { final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, registry); final int memoryTypeId; final int[] arrayDimensions; if (baseReader.h5.getClassType(attributeTypeId) == H5T_ARRAY) { arrayDimensions = baseReader.h5.getArrayDimensions(attributeTypeId); memoryTypeId = baseReader.h5.createArrayType(H5T_NATIVE_FLOAT, arrayDimensions, registry); } else { arrayDimensions = MDArray.toInt(baseReader.h5.getDataDimensionsForAttribute( attributeId, registry)); memoryTypeId = H5T_NATIVE_FLOAT; } final int len = MDArray.getLength(arrayDimensions); final float[] data = baseReader.h5.readAttributeAsFloatArray(attributeId, memoryTypeId, len); return new MDFloatArray(data, arrayDimensions); } catch (IllegalArgumentException ex) { throw new HDF5JavaException(ex.getMessage()); } } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5FloatStorageFeatures.java000066400000000000000000001056551256564762100307410ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_FLOAT; /** * An object representing the storage features that are to be used for a float data set. *

* The ..._KEEP variants denote that the specified storage features should only be * applied if a new data set has to be created. If the data set already exists, it will be kept with * whatever storage features it has. * Note that this may lead to an exception if the existing data set is non-extendable and the * dimensions of the new data set differ from the dimensions of the existing data set. *

* The ..._DELETE variants denote that the specified storage features should always be * applied. If the data set already exists, it will be deleted before the new data set is written. * This is the default behavior. However, if the * {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} setting is given, the * ..._DELETE variant can be used to override this setting on a case-by-case basis. *

* The available storage layouts are {@link HDF5StorageLayout#COMPACT}, * {@link HDF5StorageLayout#CONTIGUOUS} or {@link HDF5StorageLayout#CHUNKED} can be chosen. Only * {@link HDF5StorageLayout#CHUNKED} is extendable and can be compressed. *

* Two types of compressions are supported: deflation (the method used by gzip) * and scaling, which can be used if the accuracy of the values are smaller than what the * atomic data type can store. Note that scaling in general is a lossy compression * while deflation is always lossless. Scaling compression is only available with HDF5 * 1.8 and newer. Trying to use scaling in strict HDF5 1.6 compatibility mode will throw an * {@link IllegalStateException}. *

* For deflation the deflation level can be chosen to get the right balance between speed of * compression and compression ratio. Often the {@link #DEFAULT_DEFLATION_LEVEL} will be the right * choice. *

* For scaling, the scaling factor can be chosen that determines the accuracy of the values * saved. For float values, the scaling factor determines the number of significant digits of the * numbers. It is guaranteed that {@literal |f_real - f_saved| < 10^(-scalingFactor)}. * The algorithm used for scale compression is: *

    *
  1. Calculate the minimum value of all values
    2. *
  2. Subtract the minimum value from all values
    3. *
  3. Multiply all values obtained in step 2 with {@literal 10^scalingFactor}
    4. *
  4. Round the values obtained in step 3 to the nearest integer value
    5. *
  5. Store the minimum found in step 1 and the values obtained in step 4
    6. *
* This algorithm is known as GRIB D-scaling. * * @author Bernd Rinn */ public final class HDF5FloatStorageFeatures extends HDF5AbstractStorageFeatures { /** * Represents 'no compression', use default storage layout. */ public static final HDF5FloatStorageFeatures FLOAT_NO_COMPRESSION = new HDF5FloatStorageFeatures(null, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents 'no compression', use default storage layout. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5FloatStorageFeatures FLOAT_NO_COMPRESSION_KEEP = new HDF5FloatStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents 'no compression', use default storage layout. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5FloatStorageFeatures FLOAT_NO_COMPRESSION_DELETE = new HDF5FloatStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents a compact storage layout. */ public static final HDF5FloatStorageFeatures FLOAT_COMPACT = new HDF5FloatStorageFeatures( HDF5StorageLayout.COMPACT, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents a compact storage layout. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5FloatStorageFeatures FLOAT_COMPACT_KEEP = new HDF5FloatStorageFeatures( HDF5StorageLayout.COMPACT, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents a compact storage layout. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5FloatStorageFeatures FLOAT_COMPACT_DELETE = new HDF5FloatStorageFeatures(HDF5StorageLayout.COMPACT, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents a contiguous storage layout. */ public static final HDF5FloatStorageFeatures FLOAT_CONTIGUOUS = new HDF5FloatStorageFeatures( HDF5StorageLayout.CONTIGUOUS, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents a contiguous storage layout. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5FloatStorageFeatures FLOAT_CONTIGUOUS_KEEP = new HDF5FloatStorageFeatures(HDF5StorageLayout.CONTIGUOUS, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents a contiguous storage layout. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5FloatStorageFeatures FLOAT_CONTIGUOUS_DELETE = new HDF5FloatStorageFeatures(HDF5StorageLayout.CONTIGUOUS, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents a chunked storage layout. */ public static final HDF5FloatStorageFeatures FLOAT_CHUNKED = new HDF5FloatStorageFeatures( HDF5StorageLayout.CHUNKED, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents a chunked storage layout. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5FloatStorageFeatures FLOAT_CHUNKED_KEEP = new HDF5FloatStorageFeatures( HDF5StorageLayout.CHUNKED, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents a chunked storage layout. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5FloatStorageFeatures FLOAT_CHUNKED_DELETE = new HDF5FloatStorageFeatures(HDF5StorageLayout.CHUNKED, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents 'standard compression', that is deflation with the default deflation level. */ public static final HDF5FloatStorageFeatures FLOAT_DEFLATE = new HDF5FloatStorageFeatures(null, DEFAULT_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents 'standard compression' with a pre-filter shuffle, that is deflation with the * default deflation level. */ public static final HDF5FloatStorageFeatures FLOAT_SHUFFLE_DEFLATE = new HDF5FloatStorageFeatures(null, DataSetReplacementPolicy.USE_WRITER_DEFAULT, true, DEFAULT_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents 'standard compression', that is deflation with the default deflation level. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5FloatStorageFeatures FLOAT_DEFLATE_KEEP = new HDF5FloatStorageFeatures( null, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, DEFAULT_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents 'standard compression', that is deflation with the default deflation level. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5FloatStorageFeatures FLOAT_DEFLATE_DELETE = new HDF5FloatStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, DEFAULT_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents 'maximal compression', that is deflation with the maximal deflation level. */ public static final HDF5FloatStorageFeatures FLOAT_DEFLATE_MAX = new HDF5FloatStorageFeatures( null, MAX_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents 'maximal compression', that is deflation with the maximal deflation level. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5FloatStorageFeatures FLOAT_DEFLATE_MAX_KEEP = new HDF5FloatStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, MAX_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents 'maximal compression', that is deflation with the maximal deflation level. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5FloatStorageFeatures FLOAT_DEFLATE_MAX_DELETE = new HDF5FloatStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, MAX_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents scaling with scaling factor 1 for float values. */ public static final HDF5FloatStorageFeatures FLOAT_SCALING1 = new HDF5FloatStorageFeatures( null, NO_DEFLATION_LEVEL, (byte) 1); /** * Represents scaling with scaling factor 1 for float values. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5FloatStorageFeatures FLOAT_SCALING1_KEEP = new HDF5FloatStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, NO_DEFLATION_LEVEL, (byte) 1); /** * Represents scaling with scaling factor 1 for float values. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5FloatStorageFeatures FLOAT_SCALING1_DELETE = new HDF5FloatStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, NO_DEFLATION_LEVEL, (byte) 1); /** * Represents scaling with scaling factor 1 for float values combined with deflation using the * default deflation level. */ public static final HDF5FloatStorageFeatures FLOAT_SCALING1_DEFLATE = new HDF5FloatStorageFeatures(null, DEFAULT_DEFLATION_LEVEL, (byte) 1); /** * Represents scaling with scaling factor 1 for float values combined with deflation using the * default deflation level. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5FloatStorageFeatures FLOAT_SCALING1_DEFLATE_KEEP = new HDF5FloatStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, DEFAULT_DEFLATION_LEVEL, (byte) 1); /** * Represents scaling with scaling factor 1 for float values combined with deflation using the * default deflation level. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5FloatStorageFeatures FLOAT_SCALING1_DEFLATE_DELETE = new HDF5FloatStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, DEFAULT_DEFLATION_LEVEL, (byte) 1); /** * Represents scaling with scaling factor 2 for float values. */ public static final HDF5FloatStorageFeatures FLOAT_SCALING2 = new HDF5FloatStorageFeatures( null, NO_DEFLATION_LEVEL, (byte) 2); /** * Represents scaling with scaling factor 2 for float values. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5FloatStorageFeatures FLOAT_SCALING2_KEEP = new HDF5FloatStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, NO_DEFLATION_LEVEL, (byte) 2); /** * Represents scaling with scaling factor 2 for float values. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5FloatStorageFeatures FLOAT_SCALING2_DELETE = new HDF5FloatStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, NO_DEFLATION_LEVEL, (byte) 2); /** * Represents scaling with scaling factor 2 for float values combined with deflation using the * default deflation level. */ public static final HDF5FloatStorageFeatures FLOAT_SCALING2_DEFLATE = new HDF5FloatStorageFeatures(null, DEFAULT_DEFLATION_LEVEL, (byte) 2); /** * Represents scaling with scaling factor 2 for float values combined with deflation using the * default deflation level. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5FloatStorageFeatures FLOAT_SCALING2_DEFLATE_KEEP = new HDF5FloatStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, DEFAULT_DEFLATION_LEVEL, (byte) 2); /** * Represents scaling with scaling factor 2 for float values combined with deflation using the * default deflation level. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5FloatStorageFeatures FLOAT_SCALING2_DEFLATE_DELETE = new HDF5FloatStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, DEFAULT_DEFLATION_LEVEL, (byte) 2); /** * Represents scaling with scaling factor 3 for float values. */ public static final HDF5FloatStorageFeatures FLOAT_SCALING3 = new HDF5FloatStorageFeatures( null, NO_DEFLATION_LEVEL, (byte) 3); /** * Represents scaling with scaling factor 3 for float values. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5FloatStorageFeatures FLOAT_SCALING3_KEEP = new HDF5FloatStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, NO_DEFLATION_LEVEL, (byte) 3); /** * Represents scaling with scaling factor 3 for float values. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5FloatStorageFeatures FLOAT_SCALING3_DELETE = new HDF5FloatStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, true, NO_DEFLATION_LEVEL, (byte) 3); /** * Represents scaling with scaling factor 3 for float values combined with deflation using the * default deflation level. */ public static final HDF5FloatStorageFeatures FLOAT_SCALING3_DEFLATE = new HDF5FloatStorageFeatures(null, DEFAULT_DEFLATION_LEVEL, (byte) 3); /** * Represents scaling with scaling factor 3 for float values combined with deflation using the * default deflation level. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5FloatStorageFeatures FLOAT_SCALING3_DEFLATE_KEEP = new HDF5FloatStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, DEFAULT_DEFLATION_LEVEL, (byte) 3); /** * Represents scaling with scaling factor 3 for float values combined with deflation using the * default deflation level. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5FloatStorageFeatures FLOAT_SCALING3_DEFLATE_DELETE = new HDF5FloatStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, DEFAULT_DEFLATION_LEVEL, (byte) 3); /** * A builder for storage features. */ public static final class HDF5FloatStorageFeatureBuilder extends HDF5AbstractStorageFeatureBuilder { public HDF5FloatStorageFeatureBuilder() { } public HDF5FloatStorageFeatureBuilder(HDF5AbstractStorageFeatures template) { super(template); } /** * Compresses the dataset with default deflation level, if compress==true, do * not compress if compress==false. * * @return This builder. */ @Override public HDF5FloatStorageFeatureBuilder compress(boolean compress) { super.compress(compress); return this; } /** * Compress the dataset with default deflation level. * * @return This builder. */ @Override public HDF5FloatStorageFeatureBuilder compress() { super.compress(); return this; } /** * Compresses this dataset with the given deflateLevel. * {@link #NO_DEFLATION_LEVEL} means: do not compress. A good default value is * {@link #DEFAULT_DEFLATION_LEVEL}, the maximum value supported is * {@link #MAX_DEFLATION_LEVEL}. * * @return This builder. */ @Override public HDF5FloatStorageFeatureBuilder deflateLevel(byte deflateLevel) { super.deflateLevel(deflateLevel); return this; } /** * Sets the scaling factor for an integer scaling pre-filter. * * @return This builder. */ @Override public HDF5FloatStorageFeatureBuilder scalingFactor(byte scalingFactor) { super.scalingFactor(scalingFactor); return this; } /** * Disables the scaling pre-filter. * * @return This builder. */ @Override public HDF5FloatStorageFeatureBuilder noScaling() { super.noScaling(); return this; } /** * Sets a shuffling pre-filter for deflation if shuffleBeforeDeflate==true and * disables it if shuffleBeforeDeflate==false. Theshuffling pre-filter may * improve the compression level but may also increase the compression time. *

* Only takes effect if compression is switched on. * * @return This builder. */ @Override public HDF5FloatStorageFeatureBuilder shuffleBeforeDeflate(boolean shuffleBeforeDeflate) { super.shuffleBeforeDeflate(shuffleBeforeDeflate); return this; } /** * Sets a shuffling pre-filter for deflation. This may improve the compression level but may * also increase the compression time. *

* Only takes effect if compression is switched on. * * @see #compress() * @see #deflateLevel(byte) * @return This builder. */ @Override public HDF5AbstractStorageFeatureBuilder shuffleBeforeDeflate() { super.shuffleBeforeDeflate(); return this; } /** * Set the layout for the dataset. * * @return This builder. */ @Override public HDF5FloatStorageFeatureBuilder storageLayout(HDF5StorageLayout proposedLayout) { super.storageLayout(proposedLayout); return this; } /** * Set a compact layout for the dataset. * * @return This builder. */ @Override public HDF5AbstractStorageFeatureBuilder compactStorageLayout() { super.compactStorageLayout(); return this; } /** * Set a contiguous layout for the dataset. * * @return This builder. */ @Override public HDF5AbstractStorageFeatureBuilder contiguousStorageLayout() { super.contiguousStorageLayout(); return this; } /** * Set a chunked layout for the dataset. * * @return This builder. */ @Override public HDF5AbstractStorageFeatureBuilder chunkedStorageLayout() { super.chunkedStorageLayout(); return this; } /** * Let a heuristic choose the right layout for the dataset. * * @return This builder. */ @Override public HDF5AbstractStorageFeatureBuilder defaultStorageLayout() { this.defaultStorageLayout(); return this; } /** * Set the dataset replacement policy for existing datasets. * * @return This builder. */ @Override public HDF5FloatStorageFeatureBuilder datasetReplacementPolicy( DataSetReplacementPolicy datasetReplacementPolicy) { super.datasetReplacementPolicy(datasetReplacementPolicy); return this; } /** * Set the dataset replacement policy for existing datasets to * {@link ch.systemsx.cisd.hdf5.HDF5AbstractStorageFeatures.DataSetReplacementPolicy#USE_WRITER_DEFAULT} * . * * @return This builder. */ @Override public HDF5FloatStorageFeatureBuilder datasetReplacementUseWriterDefault() { super.datasetReplacementUseWriterDefault(); return this; } /** * Set the dataset replacement policy for existing datasets to * {@link ch.systemsx.cisd.hdf5.HDF5AbstractStorageFeatures.DataSetReplacementPolicy#ENFORCE_KEEP_EXISTING} * . * * @return This builder. */ @Override public HDF5FloatStorageFeatureBuilder datasetReplacementEnforceKeepExisting() { super.datasetReplacementEnforceKeepExisting(); return this; } /** * Set the dataset replacement policy for existing datasets to * {@link ch.systemsx.cisd.hdf5.HDF5AbstractStorageFeatures.DataSetReplacementPolicy#ENFORCE_REPLACE_WITH_NEW} * . * * @return This builder. */ @Override public HDF5FloatStorageFeatureBuilder datasetReplacementEnforceReplaceWithNew() { super.datasetReplacementEnforceReplaceWithNew(); return this; } /** * Returns the storage features corresponding to this builder's values. */ @Override public HDF5FloatStorageFeatures features() { return new HDF5FloatStorageFeatures(this); } } /** * Returns a new storage feature builder. */ public static HDF5FloatStorageFeatureBuilder build() { return new HDF5FloatStorageFeatureBuilder(); } /** * Returns a new storage feature builder, initializing from template. */ public static HDF5FloatStorageFeatureBuilder build(HDF5AbstractStorageFeatures template) { return new HDF5FloatStorageFeatureBuilder(template); } /** * Create a corresponding {@link HDF5FloatStorageFeatures} for the given * {@link HDF5GenericStorageFeatures}. */ public static HDF5FloatStorageFeatures createFromGeneric( HDF5GenericStorageFeatures storageFeatures) { if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_CHUNKED) { return HDF5FloatStorageFeatures.FLOAT_CHUNKED; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_CHUNKED_DELETE) { return HDF5FloatStorageFeatures.FLOAT_CHUNKED_DELETE; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_CHUNKED_KEEP) { return HDF5FloatStorageFeatures.FLOAT_CHUNKED_KEEP; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_COMPACT) { return HDF5FloatStorageFeatures.FLOAT_COMPACT; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_COMPACT_DELETE) { return HDF5FloatStorageFeatures.FLOAT_COMPACT_DELETE; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_COMPACT_KEEP) { return HDF5FloatStorageFeatures.FLOAT_COMPACT_KEEP; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_CONTIGUOUS) { return HDF5FloatStorageFeatures.FLOAT_CONTIGUOUS; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_CONTIGUOUS_DELETE) { return HDF5FloatStorageFeatures.FLOAT_CONTIGUOUS_DELETE; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_CONTIGUOUS_KEEP) { return HDF5FloatStorageFeatures.FLOAT_CONTIGUOUS_KEEP; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION) { return HDF5FloatStorageFeatures.FLOAT_NO_COMPRESSION; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION_DELETE) { return HDF5FloatStorageFeatures.FLOAT_NO_COMPRESSION_DELETE; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION_KEEP) { return HDF5FloatStorageFeatures.FLOAT_NO_COMPRESSION_KEEP; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_DEFLATE) { return HDF5FloatStorageFeatures.FLOAT_DEFLATE; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_DEFLATE_DELETE) { return HDF5FloatStorageFeatures.FLOAT_DEFLATE_DELETE; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_DEFLATE_KEEP) { return HDF5FloatStorageFeatures.FLOAT_DEFLATE_KEEP; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_DEFLATE_MAX) { return HDF5FloatStorageFeatures.FLOAT_DEFLATE_MAX; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_DEFLATE_MAX_DELETE) { return HDF5FloatStorageFeatures.FLOAT_DEFLATE_MAX_DELETE; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_DEFLATE_MAX_KEEP) { return HDF5FloatStorageFeatures.FLOAT_DEFLATE_MAX_KEEP; } else { return new HDF5FloatStorageFeatures(storageFeatures.tryGetProposedLayout(), storageFeatures.getDatasetReplacementPolicy(), storageFeatures.getDeflateLevel(), NO_SCALING_FACTOR); } } /** * Creates a {@link HDF5FloatStorageFeatures} object that represents deflation with the given * deflationLevel. */ public static HDF5FloatStorageFeatures createDeflation(int deflationLevel) { return createDeflation(deflationLevel, DataSetReplacementPolicy.USE_WRITER_DEFAULT); } /** * Creates a {@link HDF5FloatStorageFeatures} object that represents deflation with the given * deflationLevel. *

* Keep existing data set and apply only if a new data set has to be created. */ public static HDF5FloatStorageFeatures createDeflationKeep(int deflationLevel) { return createDeflation(deflationLevel, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING); } /** * Creates a {@link HDF5FloatStorageFeatures} object that represents deflation with the given * deflationLevel. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static HDF5FloatStorageFeatures createDeflationDelete(int deflationLevel) { return createDeflation(deflationLevel, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW); } /** * Creates a {@link HDF5FloatStorageFeatures} object that represents deflation with the given * deflationLevel. */ private static HDF5FloatStorageFeatures createDeflation(int deflationLevel, DataSetReplacementPolicy dataSetReplacementPolicy) { return new HDF5FloatStorageFeatures(null, dataSetReplacementPolicy, toByte(deflationLevel), NO_SCALING_FACTOR); } /** * Creates a {@link HDF5FloatStorageFeatures} object that represents float scaling with the * given scalingFactor. */ public static HDF5FloatStorageFeatures createFloatScaling(int scalingFactor) { return new HDF5FloatStorageFeatures(null, NO_DEFLATION_LEVEL, toByte(scalingFactor)); } /** * Creates a {@link HDF5FloatStorageFeatures} object that represents float scaling with the * given scalingFactor. *

* Keep existing data set and apply only if a new data set has to be created. */ public static HDF5FloatStorageFeatures createFloatScalingKeep(int scalingFactor) { return new HDF5FloatStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, NO_DEFLATION_LEVEL, toByte(scalingFactor)); } /** * Creates a {@link HDF5FloatStorageFeatures} object that represents deflation with the default * deflation level and float scaling with the given scalingFactor. */ public static HDF5FloatStorageFeatures createDeflateAndFloatScaling(int scalingFactor) { return new HDF5FloatStorageFeatures(null, DEFAULT_DEFLATION_LEVEL, toByte(scalingFactor)); } /** * Creates a {@link HDF5FloatStorageFeatures} object that represents deflation with the default * deflation level and float scaling with the given scalingFactor. *

* Keep existing data set and apply only if a new data set has to be created. */ public static HDF5FloatStorageFeatures createDeflateAndFloatScalingKeep(int scalingFactor) { return new HDF5FloatStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, DEFAULT_DEFLATION_LEVEL, toByte(scalingFactor)); } /** * Creates a {@link HDF5FloatStorageFeatures} object that represents deflation with the given * deflateLevel and float scaling with the given scalingFactor. */ public static HDF5FloatStorageFeatures createDeflateAndFloatScaling(int deflateLevel, int scalingFactor) { return new HDF5FloatStorageFeatures(null, toByte(deflateLevel), toByte(scalingFactor)); } /** * Creates a {@link HDF5FloatStorageFeatures} object that represents deflation with the given * deflateLevel and float scaling with the given scalingFactor. *

* Keep existing data set and apply only if a new data set has to be created. */ public static HDF5FloatStorageFeatures createDeflateAndFloatScalingKeep(int deflateLevel, int scalingFactor) { return new HDF5FloatStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, toByte(deflateLevel), toByte(scalingFactor)); } HDF5FloatStorageFeatures(HDF5StorageLayout proposedLayoutOrNull, byte deflateLevel, byte scalingFactor) { this(proposedLayoutOrNull, DataSetReplacementPolicy.USE_WRITER_DEFAULT, deflateLevel, scalingFactor); } HDF5FloatStorageFeatures(HDF5StorageLayout proposedLayoutOrNull, DataSetReplacementPolicy dataSetReplacementPolicy, byte deflateLevel, byte scalingFactor) { super(proposedLayoutOrNull, dataSetReplacementPolicy, deflateLevel, scalingFactor); } HDF5FloatStorageFeatures(HDF5FloatStorageFeatureBuilder builder) { super(builder.getStorageLayout(), builder.getDatasetReplacementPolicy(), builder .isShuffleBeforeDeflate(), builder.getDeflateLevel(), builder.getScalingFactor()); } HDF5FloatStorageFeatures(HDF5StorageLayout proposedLayoutOrNull, DataSetReplacementPolicy dataSetReplacementPolicy, boolean shuffleBeforeDeflate, byte deflateLevel, byte scalingFactor) { super(proposedLayoutOrNull, dataSetReplacementPolicy, shuffleBeforeDeflate, deflateLevel, scalingFactor); } /** * Returns true, if this compression setting can be applied on the given dataClassId. */ @Override boolean isCompatibleWithDataClass(int dataClassId) { return (dataClassId == H5T_FLOAT); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5FloatWriter.java000066400000000000000000000661651256564762100271140ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.HDF5FloatStorageFeatures.FLOAT_NO_COMPRESSION; import static ch.systemsx.cisd.hdf5.hdf5lib.H5D.H5Dwrite; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_ALL; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_FLOAT; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_IEEE_F32LE; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDFloatArray; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; /** * The implementation of {@link IHDF5FloatWriter}. * * @author Bernd Rinn */ class HDF5FloatWriter extends HDF5FloatReader implements IHDF5FloatWriter { private final HDF5BaseWriter baseWriter; HDF5FloatWriter(HDF5BaseWriter baseWriter) { super(baseWriter); assert baseWriter != null; this.baseWriter = baseWriter; } // ///////////////////// // Attributes // ///////////////////// @Override public void setAttr(final String objectPath, final String name, final float value) { assert objectPath != null; assert name != null; baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { 1 }, registry); baseWriter.setAttribute(objectPath, name, H5T_IEEE_F32LE, H5T_NATIVE_FLOAT, dataSpaceId, new float[] { value }, registry); } else { baseWriter.setAttribute(objectPath, name, H5T_IEEE_F32LE, H5T_NATIVE_FLOAT, -1, new float[] { value }, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void setArrayAttr(final String objectPath, final String name, final float[] value) { assert objectPath != null; assert name != null; assert value != null; baseWriter.checkOpen(); final ICallableWithCleanUp setAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { value.length }, registry); baseWriter.setAttribute(objectPath, name, H5T_IEEE_F32LE, H5T_NATIVE_FLOAT, dataSpaceId, value, registry); } else { final int memoryTypeId = baseWriter.h5.createArrayType(H5T_NATIVE_FLOAT, value.length, registry); final int storageTypeId = baseWriter.h5.createArrayType(H5T_IEEE_F32LE, value.length, registry); baseWriter.setAttribute(objectPath, name, storageTypeId, memoryTypeId, -1, value, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(setAttributeRunnable); } @Override public void setMDArrayAttr(final String objectPath, final String name, final MDFloatArray value) { assert objectPath != null; assert name != null; assert value != null; baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(value.longDimensions(), registry); baseWriter.setAttribute(objectPath, name, H5T_IEEE_F32LE, H5T_NATIVE_FLOAT, dataSpaceId, value.getAsFlatArray(), registry); } else { final int memoryTypeId = baseWriter.h5.createArrayType(H5T_NATIVE_FLOAT, value.dimensions(), registry); final int storageTypeId = baseWriter.h5.createArrayType(H5T_IEEE_F32LE, value.dimensions(), registry); baseWriter.setAttribute(objectPath, name, storageTypeId, memoryTypeId, -1, value.getAsFlatArray(), registry); } return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void setMatrixAttr(final String objectPath, final String name, final float[][] value) { setMDArrayAttr(objectPath, name, new MDFloatArray(value)); } // ///////////////////// // Data Sets // ///////////////////// @Override public void write(final String objectPath, final float value) { assert objectPath != null; baseWriter.checkOpen(); baseWriter.writeScalar(objectPath, H5T_IEEE_F32LE, H5T_NATIVE_FLOAT, value); } @Override public void writeArray(final String objectPath, final float[] data) { writeArray(objectPath, data, FLOAT_NO_COMPRESSION); } @Override public void writeArray(final String objectPath, final float[] data, final HDF5FloatStorageFeatures features) { assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, H5T_IEEE_F32LE, new long[] { data.length }, 4, features, registry); H5Dwrite(dataSetId, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createArray(final String objectPath, final int size) { createArray(objectPath, size, FLOAT_NO_COMPRESSION); } @Override public void createArray(final String objectPath, final long size, final int blockSize) { createArray(objectPath, size, blockSize, FLOAT_NO_COMPRESSION); } @Override public void createArray(final String objectPath, final int size, final HDF5FloatStorageFeatures features) { assert objectPath != null; assert size >= 0; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (features.requiresChunking()) { baseWriter.createDataSet(objectPath, H5T_IEEE_F32LE, features, new long[] { 0 }, new long[] { size }, 4, registry); } else { baseWriter.createDataSet(objectPath, H5T_IEEE_F32LE, features, new long[] { size }, null, 4, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void createArray(final String objectPath, final long size, final int blockSize, final HDF5FloatStorageFeatures features) { assert objectPath != null; assert size >= 0; assert blockSize >= 0 && (blockSize <= size || size == 0); baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { baseWriter.createDataSet(objectPath, H5T_IEEE_F32LE, features, new long[] { size }, new long[] { blockSize }, 4, registry); return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void writeArrayBlock(final String objectPath, final float[] data, final long blockNumber) { writeArrayBlockWithOffset(objectPath, data, data.length, data.length * blockNumber); } @Override public void writeArrayBlockWithOffset(final String objectPath, final float[] data, final int dataSize, final long offset) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] blockDimensions = new long[] { dataSize }; final long[] slabStartOrNull = new long[] { offset }; final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, new long[] { offset + dataSize }, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, slabStartOrNull, blockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(blockDimensions, registry); H5Dwrite(dataSetId, H5T_NATIVE_FLOAT, memorySpaceId, dataSpaceId, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } /** * Writes out a float matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ @Override public void writeMatrix(final String objectPath, final float[][] data) { writeMatrix(objectPath, data, FLOAT_NO_COMPRESSION); } @Override public void writeMatrix(final String objectPath, final float[][] data, final HDF5FloatStorageFeatures features) { assert objectPath != null; assert data != null; assert HDF5Utils.areMatrixDimensionsConsistent(data); writeMDArray(objectPath, new MDFloatArray(data), features); } @Override public void createMatrix(final String objectPath, final int sizeX, final int sizeY) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; createMDArray(objectPath, new int[] { sizeX, sizeY }); } @Override public void createMatrix(final String objectPath, final int sizeX, final int sizeY, final HDF5FloatStorageFeatures features) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; createMDArray(objectPath, new int[] { sizeX, sizeY }, features); } @Override public void createMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; assert blockSizeX >= 0 && (blockSizeX <= sizeX || sizeX == 0); assert blockSizeY >= 0 && (blockSizeY <= sizeY || sizeY == 0); createMDArray(objectPath, new long[] { sizeX, sizeY }, new int[] { blockSizeX, blockSizeY }); } @Override public void createMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY, final HDF5FloatStorageFeatures features) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; assert blockSizeX >= 0 && (blockSizeX <= sizeX || sizeX == 0); assert blockSizeY >= 0 && (blockSizeY <= sizeY || sizeY == 0); createMDArray(objectPath, new long[] { sizeX, sizeY }, new int[] { blockSizeX, blockSizeY }, features); } @Override public void writeMatrixBlock(final String objectPath, final float[][] data, final long blockNumberX, final long blockNumberY) { assert objectPath != null; assert data != null; writeMDArrayBlock(objectPath, new MDFloatArray(data), new long[] { blockNumberX, blockNumberY }); } @Override public void writeMatrixBlockWithOffset(final String objectPath, final float[][] data, final long offsetX, final long offsetY) { assert objectPath != null; assert data != null; writeMDArrayBlockWithOffset(objectPath, new MDFloatArray(data, new int[] { data.length, data[0].length }), new long[] { offsetX, offsetY }); } @Override public void writeMatrixBlockWithOffset(final String objectPath, final float[][] data, final int dataSizeX, final int dataSizeY, final long offsetX, final long offsetY) { assert objectPath != null; assert data != null; writeMDArrayBlockWithOffset(objectPath, new MDFloatArray(data, new int[] { dataSizeX, dataSizeY }), new long[] { offsetX, offsetY }); } @Override public void writeMDArray(final String objectPath, final MDFloatArray data) { writeMDArray(objectPath, data, FLOAT_NO_COMPRESSION); } @Override public void writeMDArraySlice(String objectPath, MDFloatArray data, IndexMap boundIndices) { baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), null, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDFloatArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArraySlice(String objectPath, MDFloatArray data, long[] boundIndices) { baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), null, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDFloatArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArray(final String objectPath, final MDFloatArray data, final HDF5FloatStorageFeatures features) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, H5T_IEEE_F32LE, data.longDimensions(), 4, features, registry); H5Dwrite(dataSetId, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createMDArray(final String objectPath, final int[] dimensions) { createMDArray(objectPath, dimensions, FLOAT_NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions) { createMDArray(objectPath, dimensions, blockDimensions, FLOAT_NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final int[] dimensions, final HDF5FloatStorageFeatures features) { assert objectPath != null; assert dimensions != null; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (features.requiresChunking()) { final long[] nullDimensions = new long[dimensions.length]; baseWriter.createDataSet(objectPath, H5T_IEEE_F32LE, features, nullDimensions, MDArray.toLong(dimensions), 4, registry); } else { baseWriter.createDataSet(objectPath, H5T_IEEE_F32LE, features, MDArray.toLong(dimensions), null, 4, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void createMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions, final HDF5FloatStorageFeatures features) { assert objectPath != null; assert dimensions != null; assert blockDimensions != null; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { baseWriter.createDataSet(objectPath, H5T_IEEE_F32LE, features, dimensions, MDArray.toLong(blockDimensions), 4, registry); return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void writeMDArrayBlock(final String objectPath, final MDFloatArray data, final long[] blockNumber) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeMDArrayBlockWithOffset(objectPath, data, offset); } @Override public void writeSlicedMDArrayBlock(final String objectPath, final MDFloatArray data, final long[] blockNumber, IndexMap boundIndices) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeSlicedMDArrayBlockWithOffset(objectPath, data, offset, boundIndices); } @Override public void writeSlicedMDArrayBlock(String objectPath, MDFloatArray data, long[] blockNumber, long[] boundIndices) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeSlicedMDArrayBlockWithOffset(objectPath, data, offset, boundIndices); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final MDFloatArray data, final long[] offset) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] dimensions = data.longDimensions(); assert dimensions.length == offset.length; final long[] dataSetDimensions = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + dimensions[i]; } final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, dimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(dimensions, registry); H5Dwrite(dataSetId, H5T_NATIVE_FLOAT, memorySpaceId, dataSpaceId, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeSlicedMDArrayBlockWithOffset(String objectPath, MDFloatArray data, long[] offset, IndexMap boundIndices) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), offset, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDFloatArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeSlicedMDArrayBlockWithOffset(String objectPath, MDFloatArray data, long[] offset, long[] boundIndices) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), offset, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDFloatArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final MDFloatArray data, final int[] blockDimensions, final long[] offset, final int[] memoryOffset) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] memoryDimensions = data.longDimensions(); assert memoryDimensions.length == offset.length; final long[] longBlockDimensions = MDArray.toLong(blockDimensions); assert longBlockDimensions.length == offset.length; final long[] dataSetDimensions = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + blockDimensions[i]; } final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, longBlockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(memoryDimensions, registry); baseWriter.h5.setHyperslabBlock(memorySpaceId, MDArray.toLong(memoryOffset), longBlockDimensions); H5Dwrite(dataSetId, H5T_NATIVE_FLOAT, memorySpaceId, dataSpaceId, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5GenericStorageFeatures.java000066400000000000000000000501751256564762100312440ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; /** * An object representing the storage features that are to be used for a data set. *

* The ..._KEEP variants denote that the specified storage features should only be * applied if a new data set has to be created. If the data set already exists, it will be kept with * whatever storage features it has. * Note that this may lead to an exception if the existing data set is non-extendable and the * dimensions of the new data set differ from the dimensions of the existing data set. *

* The ..._DELETE variants denote that the specified storage features should always be * applied. If the data set already exists, it will be deleted before the new data set is written. * This is the default behavior. However, if the * {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} setting is given, the * ..._DELETE variant can be used to override this setting on a case-by-case basis. *

* The available storage layouts are {@link HDF5StorageLayout#COMPACT}, * {@link HDF5StorageLayout#CONTIGUOUS} or {@link HDF5StorageLayout#CHUNKED} can be chosen. Only * {@link HDF5StorageLayout#CHUNKED} is extendable and can be compressed. *

* For generic (that is non-integer and non-float) data sets only one type of compression is * supported, which is deflation, the method used by gzip. The deflation level * can be chosen to get the right balance between speed of compression and compression ratio. Often * the {@link #DEFAULT_DEFLATION_LEVEL} will be the right choice. * * @author Bernd Rinn */ public final class HDF5GenericStorageFeatures extends HDF5AbstractStorageFeatures { /** * Represents 'no compression'. */ public static final HDF5GenericStorageFeatures GENERIC_NO_COMPRESSION = new HDF5GenericStorageFeatures(null, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents 'no compression'. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5GenericStorageFeatures GENERIC_NO_COMPRESSION_KEEP = new HDF5GenericStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents 'no compression'. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5GenericStorageFeatures GENERIC_NO_COMPRESSION_DELETE = new HDF5GenericStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents a compact storage layout. */ public static final HDF5GenericStorageFeatures GENERIC_COMPACT = new HDF5GenericStorageFeatures(HDF5StorageLayout.COMPACT, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents a compact storage layout. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5GenericStorageFeatures GENERIC_COMPACT_KEEP = new HDF5GenericStorageFeatures(HDF5StorageLayout.COMPACT, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents a compact storage layout. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5GenericStorageFeatures GENERIC_COMPACT_DELETE = new HDF5GenericStorageFeatures(HDF5StorageLayout.COMPACT, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents a contiguous storage layout. */ public static final HDF5GenericStorageFeatures GENERIC_CONTIGUOUS = new HDF5GenericStorageFeatures(HDF5StorageLayout.CONTIGUOUS, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents a contiguous storage layout. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5GenericStorageFeatures GENERIC_CONTIGUOUS_KEEP = new HDF5GenericStorageFeatures(HDF5StorageLayout.CONTIGUOUS, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents a contiguous storage layout. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5GenericStorageFeatures GENERIC_CONTIGUOUS_DELETE = new HDF5GenericStorageFeatures(HDF5StorageLayout.CONTIGUOUS, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents a chunked storage layout. */ public static final HDF5GenericStorageFeatures GENERIC_CHUNKED = new HDF5GenericStorageFeatures(HDF5StorageLayout.CHUNKED, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents a chunked storage layout. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5GenericStorageFeatures GENERIC_CHUNKED_KEEP = new HDF5GenericStorageFeatures(HDF5StorageLayout.CHUNKED, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents a chunked storage layout. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5GenericStorageFeatures GENERIC_CHUNKED_DELETE = new HDF5GenericStorageFeatures(HDF5StorageLayout.CHUNKED, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents 'standard compression', that is deflation with the default deflation level. */ public static final HDF5GenericStorageFeatures GENERIC_DEFLATE = new HDF5GenericStorageFeatures(null, DEFAULT_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents 'standard compression' with a pre-filter shuffle, that is deflation with the * default deflation level. */ public static final HDF5GenericStorageFeatures GENERIC_SHUFFLE_DEFLATE = new HDF5GenericStorageFeatures(null, DataSetReplacementPolicy.USE_WRITER_DEFAULT, true, DEFAULT_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents 'standard compression', that is deflation with the default deflation level. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5GenericStorageFeatures GENERIC_DEFLATE_KEEP = new HDF5GenericStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, DEFAULT_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents 'standard compression', that is deflation with the default deflation level. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5GenericStorageFeatures GENERIC_DEFLATE_DELETE = new HDF5GenericStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, DEFAULT_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents 'maximal compression', that is deflation with the maximal deflation level. */ public static final HDF5GenericStorageFeatures GENERIC_DEFLATE_MAX = new HDF5GenericStorageFeatures(null, MAX_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents 'maximal compression' with a pre-filter shuffle, that is deflation with the * default deflation level. */ public static final HDF5GenericStorageFeatures GENERIC_SHUFFLE_DEFLATE_MAX = new HDF5GenericStorageFeatures(null, DataSetReplacementPolicy.USE_WRITER_DEFAULT, true, MAX_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents 'maximal compression', that is deflation with the maximal deflation level. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5GenericStorageFeatures GENERIC_DEFLATE_MAX_KEEP = new HDF5GenericStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, MAX_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Represents 'maximal compression', that is deflation with the maximal deflation level. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5GenericStorageFeatures GENERIC_DEFLATE_MAX_DELETE = new HDF5GenericStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, MAX_DEFLATION_LEVEL, NO_SCALING_FACTOR); /** * Creates a {@link HDF5GenericStorageFeatures} object that represents deflation with the given * deflationLevel. */ public static HDF5GenericStorageFeatures createDeflation(int deflationLevel) { return createDeflation(deflationLevel, false); } /** * Creates a {@link HDF5GenericStorageFeatures} object that represents deflation with the given * deflationLevel. *

* Keep existing data set and apply only if a new data set has to be created. */ public static HDF5GenericStorageFeatures createDeflationKeep(int deflationLevel) { return createDeflation(deflationLevel, true); } /** * Creates a {@link HDF5GenericStorageFeatures} object that represents deflation with the given * deflationLevel. */ private static HDF5GenericStorageFeatures createDeflation(int deflationLevel, boolean keepDataSetIfExists) { if (deflationLevel == NO_DEFLATION_LEVEL) { return GENERIC_NO_COMPRESSION; } else if (deflationLevel == DEFAULT_DEFLATION_LEVEL) { return GENERIC_DEFLATE; } else if (deflationLevel == MAX_DEFLATION_LEVEL) { return GENERIC_DEFLATE_MAX; } else { return new HDF5GenericStorageFeatures(null, getDataSetReplacementPolicy( keepDataSetIfExists, false), toByte(deflationLevel), NO_SCALING_FACTOR); } } /** * Legacy method for specifying the compression as a boolean value. */ static HDF5GenericStorageFeatures getCompression(boolean deflate) { return deflate ? GENERIC_DEFLATE : GENERIC_NO_COMPRESSION; } /** * A builder for storage features. */ public static final class HDF5GenericStorageFeatureBuilder extends HDF5AbstractStorageFeatureBuilder { public HDF5GenericStorageFeatureBuilder() { } public HDF5GenericStorageFeatureBuilder(HDF5AbstractStorageFeatures template) { super(template); noScaling(); } /** * Compresses the dataset with default deflation level, if compress==true, do * not compress if compress==false. * * @return This builder. */ @Override public HDF5GenericStorageFeatureBuilder compress(boolean compress) { super.compress(compress); return this; } /** * Compress the dataset with default deflation level. * * @return This builder. */ @Override public HDF5GenericStorageFeatureBuilder compress() { super.compress(); return this; } /** * Compresses this dataset with the given deflateLevel. * {@link #NO_DEFLATION_LEVEL} means: do not compress. A good default value is * {@link #DEFAULT_DEFLATION_LEVEL}, the maximum value supported is * {@link #MAX_DEFLATION_LEVEL}. * * @return This builder. */ @Override public HDF5GenericStorageFeatureBuilder deflateLevel(byte deflateLevel) { super.deflateLevel(deflateLevel); return this; } /** * Sets a shuffling pre-filter for deflation if shuffleBeforeDeflate==true and * disables it if shuffleBeforeDeflate==false. The shuffling pre-filter may * improve the compression level but may also increase the compression time. *

* Only takes effect if compression is switched on. * * @return This builder. */ @Override public HDF5GenericStorageFeatureBuilder shuffleBeforeDeflate(boolean shuffleBeforeDeflate) { super.shuffleBeforeDeflate(shuffleBeforeDeflate); return this; } /** * Sets a shuffling pre-filter for deflation. This may improve the compression level but may * also increase the compression time. *

* Only takes effect if compression is switched on. * * @see #compress() * @see #deflateLevel(byte) * @return This builder. */ @Override public HDF5AbstractStorageFeatureBuilder shuffleBeforeDeflate() { super.shuffleBeforeDeflate(); return this; } /** * Set the layout for the dataset. * * @return This builder. */ @Override public HDF5GenericStorageFeatureBuilder storageLayout(HDF5StorageLayout proposedLayout) { super.storageLayout(proposedLayout); return this; } /** * Set a compact layout for the dataset. * * @return This builder. */ @Override public HDF5AbstractStorageFeatureBuilder compactStorageLayout() { super.compactStorageLayout(); return this; } /** * Set a contiguous layout for the dataset. * * @return This builder. */ @Override public HDF5AbstractStorageFeatureBuilder contiguousStorageLayout() { super.contiguousStorageLayout(); return this; } /** * Set a chunked layout for the dataset. * * @return This builder. */ @Override public HDF5AbstractStorageFeatureBuilder chunkedStorageLayout() { super.chunkedStorageLayout(); return this; } /** * Let a heuristic choose the right layout for the dataset. * * @return This builder. */ @Override public HDF5AbstractStorageFeatureBuilder defaultStorageLayout() { this.defaultStorageLayout(); return this; } /** * Set the dataset replacement policy for existing datasets. * * @return This builder. */ @Override public HDF5GenericStorageFeatureBuilder datasetReplacementPolicy( DataSetReplacementPolicy datasetReplacementPolicy) { super.datasetReplacementPolicy(datasetReplacementPolicy); return this; } /** * Set the dataset replacement policy for existing datasets to * {@link ch.systemsx.cisd.hdf5.HDF5AbstractStorageFeatures.DataSetReplacementPolicy#USE_WRITER_DEFAULT} * . * * @return This builder. */ @Override public HDF5GenericStorageFeatureBuilder datasetReplacementUseWriterDefault() { super.datasetReplacementUseWriterDefault(); return this; } /** * Set the dataset replacement policy for existing datasets to * {@link ch.systemsx.cisd.hdf5.HDF5AbstractStorageFeatures.DataSetReplacementPolicy#ENFORCE_KEEP_EXISTING} * . * * @return This builder. */ @Override public HDF5GenericStorageFeatureBuilder datasetReplacementEnforceKeepExisting() { super.datasetReplacementEnforceKeepExisting(); return this; } /** * Set the dataset replacement policy for existing datasets to * {@link ch.systemsx.cisd.hdf5.HDF5AbstractStorageFeatures.DataSetReplacementPolicy#ENFORCE_REPLACE_WITH_NEW} * . * * @return This builder. */ @Override public HDF5GenericStorageFeatureBuilder datasetReplacementEnforceReplaceWithNew() { super.datasetReplacementEnforceReplaceWithNew(); return this; } /** * Returns the storage features corresponding to this builder's values. */ @Override public HDF5GenericStorageFeatures features() { return new HDF5GenericStorageFeatures(this); } } /** * Returns a new storage feature builder. */ public static HDF5GenericStorageFeatureBuilder build() { return new HDF5GenericStorageFeatureBuilder(); } /** * Returns a new storage feature builder, initializing from template. */ public static HDF5GenericStorageFeatureBuilder build(HDF5AbstractStorageFeatures template) { return new HDF5GenericStorageFeatureBuilder(template); } HDF5GenericStorageFeatures(HDF5GenericStorageFeatureBuilder builder) { super(builder.getStorageLayout(), builder.getDatasetReplacementPolicy(), builder .isShuffleBeforeDeflate(), builder.getDeflateLevel(), builder.getScalingFactor()); } HDF5GenericStorageFeatures(HDF5StorageLayout proposedLayoutOrNull, byte deflateLevel, byte scalingFactor) { this(proposedLayoutOrNull, DataSetReplacementPolicy.USE_WRITER_DEFAULT, deflateLevel, scalingFactor); } HDF5GenericStorageFeatures(HDF5StorageLayout proposedLayoutOrNull, DataSetReplacementPolicy dataSetReplacementPolicy, byte deflateLevel, byte scalingFactor) { super(proposedLayoutOrNull, dataSetReplacementPolicy, deflateLevel, scalingFactor); } HDF5GenericStorageFeatures(HDF5StorageLayout proposedLayoutOrNull, DataSetReplacementPolicy dataSetReplacementPolicy, boolean shuffleBeforeDeflate, byte deflateLevel, byte scalingFactor) { super(proposedLayoutOrNull, dataSetReplacementPolicy, shuffleBeforeDeflate, deflateLevel, scalingFactor); } /** * Returns true, if this compression setting can be applied on the given dataClassId. */ @Override boolean isCompatibleWithDataClass(int dataClassId) { return true; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5IntReader.java000066400000000000000000001016651256564762100265220ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.MatrixUtils.cardinalityBoundIndices; import static ch.systemsx.cisd.hdf5.MatrixUtils.checkBoundIndices; import static ch.systemsx.cisd.hdf5.MatrixUtils.createFullBlockDimensionsAndOffset; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_ARRAY; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_INT32; import java.util.Arrays; import java.util.Iterator; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import ncsa.hdf.hdf5lib.exceptions.HDF5SpaceRankMismatch; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDIntArray; import ch.systemsx.cisd.hdf5.HDF5BaseReader.DataSpaceParameters; import ch.systemsx.cisd.hdf5.HDF5DataTypeInformation.DataTypeInfoOptions; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; import ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants; /** * The implementation of {@link IHDF5IntReader}. * * @author Bernd Rinn */ class HDF5IntReader implements IHDF5IntReader { private final HDF5BaseReader baseReader; HDF5IntReader(HDF5BaseReader baseReader) { assert baseReader != null; this.baseReader = baseReader; } // For Unit tests only. HDF5BaseReader getBaseReader() { return baseReader; } // ///////////////////// // Attributes // ///////////////////// @Override public int getAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public Integer call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int[] data = baseReader.h5.readAttributeAsIntArray(attributeId, H5T_NATIVE_INT32, 1); return data[0]; } }; return baseReader.runner.call(getAttributeRunnable); } @Override public int[] getArrayAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); return getIntArrayAttribute(objectId, attributeName, registry); } }; return baseReader.runner.call(getAttributeRunnable); } @Override public MDIntArray getMDArrayAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public MDIntArray call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); return getIntMDArrayAttribute(objectId, attributeName, registry); } }; return baseReader.runner.call(getAttributeRunnable); } @Override public int[][] getMatrixAttr(final String objectPath, final String attributeName) throws HDF5JavaException { final MDIntArray array = getMDArrayAttr(objectPath, attributeName); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } // ///////////////////// // Data Sets // ///////////////////// @Override public int read(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public Integer call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final int[] data = new int[1]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_INT32, data); return data[0]; } }; return baseReader.runner.call(readCallable); } @Override public int[] readArray(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); return readIntArray(dataSetId, registry); } }; return baseReader.runner.call(readCallable); } private int[] readIntArray(int dataSetId, ICleanUpRegistry registry) { try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); final int[] data = new int[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_INT32, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return data; } catch (HDF5LibraryException ex) { if (ex.getMajorErrorNumber() == HDF5Constants.H5E_DATATYPE && ex.getMinorErrorNumber() == HDF5Constants.H5E_CANTINIT) { // Check whether it is an array data type. final int dataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); if (baseReader.h5.getClassType(dataTypeId) == HDF5Constants.H5T_ARRAY) { return readIntArrayFromArrayType(dataSetId, dataTypeId, registry); } } throw ex; } } private int[] readIntArrayFromArrayType(int dataSetId, final int dataTypeId, ICleanUpRegistry registry) { final int spaceId = baseReader.h5.createScalarDataSpace(); final int[] dimensions = baseReader.h5.getArrayDimensions(dataTypeId); final int[] data = new int[HDF5Utils.getOneDimensionalArraySize(dimensions)]; final int memoryDataTypeId = baseReader.h5.createArrayType(H5T_NATIVE_INT32, data.length, registry); baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceId, spaceId, data); return data; } @Override public int[] readToMDArrayWithOffset(final String objectPath, final MDIntArray array, final int[] memoryOffset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getBlockSpaceParameters(dataSetId, memoryOffset, array .dimensions(), registry); final int nativeDataTypeId = baseReader.getNativeDataTypeId(dataSetId, H5T_NATIVE_INT32, registry); baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, array. getAsFlatArray()); return MDArray.toInt(spaceParams.dimensions); } }; return baseReader.runner.call(readCallable); } @Override public int[] readToMDArrayBlockWithOffset(final String objectPath, final MDIntArray array, final int[] blockDimensions, final long[] offset, final int[] memoryOffset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getBlockSpaceParameters(dataSetId, memoryOffset, array .dimensions(), offset, blockDimensions, registry); final int nativeDataTypeId = baseReader.getNativeDataTypeId(dataSetId, H5T_NATIVE_INT32, registry); baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, array .getAsFlatArray()); return MDArray.toInt(spaceParams.dimensions); } }; return baseReader.runner.call(readCallable); } @Override public int[] readArrayBlock(final String objectPath, final int blockSize, final long blockNumber) { return readArrayBlockWithOffset(objectPath, blockSize, blockNumber * blockSize); } @Override public int[] readArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockSize, registry); final int[] data = new int[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_INT32, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return data; } }; return baseReader.runner.call(readCallable); } @Override public int[][] readMatrix(final String objectPath) throws HDF5JavaException { final MDIntArray array = readMDArray(objectPath); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public int[][] readMatrixBlock(final String objectPath, final int blockSizeX, final int blockSizeY, final long blockNumberX, final long blockNumberY) throws HDF5JavaException { final MDIntArray array = readMDArrayBlock(objectPath, new int[] { blockSizeX, blockSizeY }, new long[] { blockNumberX, blockNumberY }); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public int[][] readMatrixBlockWithOffset(final String objectPath, final int blockSizeX, final int blockSizeY, final long offsetX, final long offsetY) throws HDF5JavaException { final MDIntArray array = readMDArrayBlockWithOffset(objectPath, new int[] { blockSizeX, blockSizeY }, new long[] { offsetX, offsetY }); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public MDIntArray readMDArraySlice(String objectPath, IndexMap boundIndices) { baseReader.checkOpen(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; final int cardBoundIndices = cardinalityBoundIndices(boundIndices); checkBoundIndices(objectPath, fullDimensions, cardBoundIndices); final int[] effectiveBlockDimensions = new int[fullBlockDimensions.length - cardBoundIndices]; Arrays.fill(effectiveBlockDimensions, -1); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, null, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDIntArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); if (fullBlockDimensions.length == cardBoundIndices) // no free indices { return new MDIntArray(result.getAsFlatArray(), new int[] { 1 }); } else { return new MDIntArray(result.getAsFlatArray(), effectiveBlockDimensions); } } @Override public MDIntArray readMDArraySlice(String objectPath, long[] boundIndices) { baseReader.checkOpen(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; final int cardBoundIndices = cardinalityBoundIndices(boundIndices); checkBoundIndices(objectPath, fullDimensions, boundIndices); final int[] effectiveBlockDimensions = new int[fullBlockDimensions.length - cardBoundIndices]; Arrays.fill(effectiveBlockDimensions, -1); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, null, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDIntArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); if (fullBlockDimensions.length == cardBoundIndices) // no free indices { return new MDIntArray(result.getAsFlatArray(), new int[] { 1 }); } else { return new MDIntArray(result.getAsFlatArray(), effectiveBlockDimensions); } } @Override public MDIntArray readMDArray(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public MDIntArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); return readIntMDArray(dataSetId, registry); } }; return baseReader.runner.call(readCallable); } MDIntArray readIntMDArray(int dataSetId, ICleanUpRegistry registry) { try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); final int[] data = new int[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_INT32, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return new MDIntArray(data, spaceParams.dimensions); } catch (HDF5LibraryException ex) { if (ex.getMajorErrorNumber() == HDF5Constants.H5E_DATATYPE && ex.getMinorErrorNumber() == HDF5Constants.H5E_CANTINIT) { // Check whether it is an array data type. final int dataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); if (baseReader.h5.getClassType(dataTypeId) == HDF5Constants.H5T_ARRAY) { return readIntMDArrayFromArrayType(dataSetId, dataTypeId, registry); } } throw ex; } } private MDIntArray readIntMDArrayFromArrayType(int dataSetId, final int dataTypeId, ICleanUpRegistry registry) { final int[] arrayDimensions = baseReader.h5.getArrayDimensions(dataTypeId); final int memoryDataTypeId = baseReader.h5.createArrayType(H5T_NATIVE_INT32, arrayDimensions, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); if (spaceParams.blockSize == 0) { final int spaceId = baseReader.h5.createScalarDataSpace(); final int[] data = new int[MDArray.getLength(arrayDimensions)]; baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceId, spaceId, data); return new MDIntArray(data, arrayDimensions); } else { final int[] data = new int[MDArray.getLength(arrayDimensions) * spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return new MDIntArray(data, MatrixUtils.concat(MDArray.toInt(spaceParams.dimensions), arrayDimensions)); } } @Override public MDIntArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, IndexMap boundIndices) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readSlicedMDArrayBlockWithOffset(objectPath, blockDimensions, offset, boundIndices); } @Override public MDIntArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, long[] boundIndices) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readSlicedMDArrayBlockWithOffset(objectPath, blockDimensions, offset, boundIndices); } @Override public MDIntArray readMDArrayBlock(final String objectPath, final int[] blockDimensions, final long[] blockNumber) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readMDArrayBlockWithOffset(objectPath, blockDimensions, offset); } @Override public MDIntArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, IndexMap boundIndices) { baseReader.checkOpen(); final int[] effectiveBlockDimensions = blockDimensions.clone(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; checkBoundIndices(objectPath, fullDimensions, blockDimensions, cardinalityBoundIndices(boundIndices)); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, offset, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDIntArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); return new MDIntArray(result.getAsFlatArray(), effectiveBlockDimensions); } @Override public MDIntArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, long[] boundIndices) { baseReader.checkOpen(); final int[] effectiveBlockDimensions = blockDimensions.clone(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; checkBoundIndices(objectPath, fullDimensions, blockDimensions, cardinalityBoundIndices(boundIndices)); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, offset, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDIntArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); return new MDIntArray(result.getAsFlatArray(), effectiveBlockDimensions); } @Override public MDIntArray readMDArrayBlockWithOffset(final String objectPath, final int[] blockDimensions, final long[] offset) { assert objectPath != null; assert blockDimensions != null; assert offset != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public MDIntArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockDimensions, registry); final int[] dataBlock = new int[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_INT32, spaceParams.memorySpaceId, spaceParams.dataSpaceId, dataBlock); return new MDIntArray(dataBlock, spaceParams.dimensions); } catch (HDF5SpaceRankMismatch ex) { final HDF5DataSetInformation info = baseReader.getDataSetInformation(objectPath, DataTypeInfoOptions.MINIMAL, false); if (ex.getSpaceRankExpected() - ex.getSpaceRankFound() == info .getTypeInformation().getRank()) { return readMDArrayBlockOfArrays(dataSetId, blockDimensions, offset, info, ex.getSpaceRankFound(), registry); } else { throw ex; } } } }; return baseReader.runner.call(readCallable); } private MDIntArray readMDArrayBlockOfArrays(final int dataSetId, final int[] blockDimensions, final long[] offset, final HDF5DataSetInformation info, final int spaceRank, final ICleanUpRegistry registry) { final int[] arrayDimensions = info.getTypeInformation().getDimensions(); int[] effectiveBlockDimensions = blockDimensions; // We do not support block-wise reading of array types, check // that we do not have to and bail out otherwise. for (int i = 0; i < arrayDimensions.length; ++i) { final int j = spaceRank + i; if (effectiveBlockDimensions[j] < 0) { if (effectiveBlockDimensions == blockDimensions) { effectiveBlockDimensions = blockDimensions.clone(); } effectiveBlockDimensions[j] = arrayDimensions[i]; } if (effectiveBlockDimensions[j] != arrayDimensions[i]) { throw new HDF5JavaException( "Block-wise reading of array type data sets is not supported."); } } final int[] spaceBlockDimensions = Arrays.copyOfRange(effectiveBlockDimensions, 0, spaceRank); final long[] spaceOfs = Arrays.copyOfRange(offset, 0, spaceRank); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, spaceOfs, spaceBlockDimensions, registry); final int[] dataBlock = new int[spaceParams.blockSize * info.getTypeInformation().getNumberOfElements()]; final int memoryDataTypeId = baseReader.h5.createArrayType(H5T_NATIVE_INT32, info.getTypeInformation() .getDimensions(), registry); baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, dataBlock); return new MDIntArray(dataBlock, effectiveBlockDimensions); } @Override public Iterable> getArrayNaturalBlocks(final String dataSetPath) throws HDF5JavaException { baseReader.checkOpen(); final HDF5NaturalBlock1DParameters params = new HDF5NaturalBlock1DParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlock1DParameters.HDF5NaturalBlock1DIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5DataBlock next() { final long offset = index.computeOffsetAndSizeGetOffset(); final int[] block = readArrayBlockWithOffset(dataSetPath, index .getBlockSize(), offset); return new HDF5DataBlock(block, index.getAndIncIndex(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } @Override public Iterable> getMDArrayNaturalBlocks(final String dataSetPath) { baseReader.checkOpen(); final HDF5NaturalBlockMDParameters params = new HDF5NaturalBlockMDParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlockMDParameters.HDF5NaturalBlockMDIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5MDDataBlock next() { final long[] offset = index.computeOffsetAndSizeGetOffsetClone(); final MDIntArray data = readMDArrayBlockWithOffset(dataSetPath, index .getBlockSize(), offset); return new HDF5MDDataBlock(data, index .getIndexClone(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } int[] getIntArrayAttribute(final int objectId, final String attributeName, ICleanUpRegistry registry) { final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, registry); final int memoryTypeId; final int len; if (baseReader.h5.getClassType(attributeTypeId) == H5T_ARRAY) { final int[] arrayDimensions = baseReader.h5.getArrayDimensions(attributeTypeId); if (arrayDimensions.length != 1) { throw new HDF5JavaException( "Array needs to be of rank 1, but is of rank " + arrayDimensions.length); } len = arrayDimensions[0]; memoryTypeId = baseReader.h5.createArrayType(H5T_NATIVE_INT32, len, registry); } else { final long[] arrayDimensions = baseReader.h5.getDataDimensionsForAttribute(attributeId, registry); memoryTypeId = H5T_NATIVE_INT32; len = HDF5Utils.getOneDimensionalArraySize(arrayDimensions); } final int[] data = baseReader.h5.readAttributeAsIntArray(attributeId, memoryTypeId, len); return data; } MDIntArray getIntMDArrayAttribute(final int objectId, final String attributeName, ICleanUpRegistry registry) { try { final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, registry); final int memoryTypeId; final int[] arrayDimensions; if (baseReader.h5.getClassType(attributeTypeId) == H5T_ARRAY) { arrayDimensions = baseReader.h5.getArrayDimensions(attributeTypeId); memoryTypeId = baseReader.h5.createArrayType(H5T_NATIVE_INT32, arrayDimensions, registry); } else { arrayDimensions = MDArray.toInt(baseReader.h5.getDataDimensionsForAttribute( attributeId, registry)); memoryTypeId = H5T_NATIVE_INT32; } final int len = MDArray.getLength(arrayDimensions); final int[] data = baseReader.h5.readAttributeAsIntArray(attributeId, memoryTypeId, len); return new MDIntArray(data, arrayDimensions); } catch (IllegalArgumentException ex) { throw new HDF5JavaException(ex.getMessage()); } } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5IntStorageFeatures.java000066400000000000000000001447331256564762100304260ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_INTEGER; /** * An object representing the storage features that are to be used for an integer data set. *

* The ..._KEEP variants denote that the specified storage features should only be * applied if a new data set has to be created. If the data set already exists, it will be kept with * whatever storage features it has. * Note that this may lead to an exception if the existing data set is non-extendable and the * dimensions of the new data set differ from the dimensions of the existing data set. *

* The ..._DELETE variants denote that the specified storage features should always be * applied. If the data set already exists, it will be deleted before the new data set is written. * This is the default behavior. However, if the * {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} setting is given, the * ..._DELETE variant can be used to override this setting on a case-by-case basis. *

* The available storage layouts are {@link HDF5StorageLayout#COMPACT}, * {@link HDF5StorageLayout#CONTIGUOUS} or {@link HDF5StorageLayout#CHUNKED} can be chosen. Only * {@link HDF5StorageLayout#CHUNKED} is extendable and can be compressed. *

* Two types of compressions are supported: deflation (the method used by gzip) * and scaling, which can be used if the accuracy of the values are smaller than what the * atomic data type can store. Note that scaling can be a lossy compression while * deflation is always lossless. Scaling compression is only available with HDF5 1.8 * and newer. Trying to use scaling in strict HDF5 1.6 compatibility mode will throw an * {@link IllegalStateException}. *

* For deflation the deflation level can be chosen to get the right balance between speed of * compression and compression ratio. Often the {@link #DEFAULT_DEFLATION_LEVEL} will be the right * choice. *

* For scaling, the scaling factor can be chosen that determines the accuracy of the values * saved. For float values, the scaling factor determines the number of significant digits of the * numbers. The algorithm used for scale compression is: *

    *
  1. Calculate the minimum value of all values
    2. *
  2. Subtract the minimum value from all values
    3. *
  3. Store the number of bits specified as scalingFactor
    4. *
* Note that this compression is lossless if * {@literal scalineFactor >= ceil(log2(max(values) - min(values) + 1)}. This in made * sure when using {@link #INT_AUTO_SCALING}, thus {@link #INT_AUTO_SCALING} is always losless. *

* Contrary to float scaling compression, a lossy integer scaling compression is usually an error * as the most significant bits are chopped of! The option to specify the scaling factor is * meant to give you a way to use that you know the span of the values * {@literal max(values) - min(values)} rather than asking the library to waste time on * computing it for you. * * @author Bernd Rinn */ public final class HDF5IntStorageFeatures extends HDF5AbstractStorageFeatures { /** * Perform an automatic scaling on integer data. */ private final static byte INTEGER_AUTO_SCALING_FACTOR = 0; /** * Represents 'no compression', signed integers, use default storage layout. */ public static final HDF5IntStorageFeatures INT_NO_COMPRESSION = new HDF5IntStorageFeatures( null, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR, true); /** * Represents 'no compression', unsigned integers, use default storage layout. */ public static final HDF5IntStorageFeatures INT_NO_COMPRESSION_UNSIGNED = new HDF5IntStorageFeatures(null, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR, false); /** * Represents 'no compression', use default storage layout. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5IntStorageFeatures INT_NO_COMPRESSION_KEEP = new HDF5IntStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR, true); /** * Represents 'no compression', unsigned integers, use default storage layout. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5IntStorageFeatures INT_NO_COMPRESSION_UNSIGNED_KEEP = new HDF5IntStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR, false); /** * Represents 'no compression', use default storage layout. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5IntStorageFeatures INT_NO_COMPRESSION_DELETE = new HDF5IntStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR, true); /** * Represents 'no compression', unsigned integers, use default storage layout. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5IntStorageFeatures INT_NO_COMPRESSION_UNSIGNED_DELETE = new HDF5IntStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR, false); /** * Represents a compact storage layout. */ public static final HDF5IntStorageFeatures INT_COMPACT = new HDF5IntStorageFeatures( HDF5StorageLayout.COMPACT, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR, true); /** * Represents a compact storage layout with unsigned integers. */ public static final HDF5IntStorageFeatures INT_COMPACT_UNSIGNED = new HDF5IntStorageFeatures( HDF5StorageLayout.COMPACT, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR, false); /** * Represents a compact storage layout. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5IntStorageFeatures INT_COMPACT_KEEP = new HDF5IntStorageFeatures( HDF5StorageLayout.COMPACT, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR, true); /** * Represents a compact storage layout with unsigned integers. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5IntStorageFeatures INT_COMPACT_UNSIGNED_KEEP = new HDF5IntStorageFeatures(HDF5StorageLayout.COMPACT, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR, false); /** * Represents a compact storage layout. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5IntStorageFeatures INT_COMPACT_DELETE = new HDF5IntStorageFeatures( HDF5StorageLayout.COMPACT, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR, true); /** * Represents a compact storage layout with unsigned integers. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5IntStorageFeatures INT_COMPACT_UNSIGNED_DELETE = new HDF5IntStorageFeatures(HDF5StorageLayout.COMPACT, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR, false); /** * Represents a contiguous storage layout. */ public static final HDF5IntStorageFeatures INT_CONTIGUOUS = new HDF5IntStorageFeatures( HDF5StorageLayout.CONTIGUOUS, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR, true); /** * Represents a contiguous storage layout with unsigned integers. */ public static final HDF5IntStorageFeatures INT_CONTIGUOUS_UNSIGNED = new HDF5IntStorageFeatures(HDF5StorageLayout.CONTIGUOUS, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR, false); /** * Represents a contiguous storage layout. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5IntStorageFeatures INT_CONTIGUOUS_KEEP = new HDF5IntStorageFeatures( HDF5StorageLayout.CONTIGUOUS, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR, true); /** * Represents a contiguous storage layout with unsigned integers. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5IntStorageFeatures INT_CONTIGUOUS_UNSIGNED_KEEP = new HDF5IntStorageFeatures(HDF5StorageLayout.CONTIGUOUS, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR, false); /** * Represents a contiguous storage layout. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5IntStorageFeatures INT_CONTIGUOUS_DELETE = new HDF5IntStorageFeatures( HDF5StorageLayout.CONTIGUOUS, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR, true); /** * Represents a contiguous storage layout with unsigned integers. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5IntStorageFeatures INT_CONTIGUOUS_UNSIGNED_DELETE = new HDF5IntStorageFeatures(HDF5StorageLayout.CONTIGUOUS, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR, false); /** * Represents a chunked (extendable) storage layout. */ public static final HDF5IntStorageFeatures INT_CHUNKED = new HDF5IntStorageFeatures( HDF5StorageLayout.CHUNKED, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR, true); /** * Represents a chunked (extendable) storage layout with unsigned integers. */ public static final HDF5IntStorageFeatures INT_CHUNKED_UNSIGNED = new HDF5IntStorageFeatures( HDF5StorageLayout.CHUNKED, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR, false); /** * Represents a chunked (extendable) storage layout. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5IntStorageFeatures INT_CHUNKED_KEEP = new HDF5IntStorageFeatures( HDF5StorageLayout.CHUNKED, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR, true); /** * Represents a chunked (extendable) storage layout with unsigned integers. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5IntStorageFeatures INT_CHUNKED_UNSIGNED_KEEP = new HDF5IntStorageFeatures(HDF5StorageLayout.CHUNKED, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR, false); /** * Represents a chunked (extendable) storage layout. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5IntStorageFeatures INT_CHUNKED_DELETE = new HDF5IntStorageFeatures( HDF5StorageLayout.CHUNKED, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR, true); /** * Represents a chunked (extendable) storage layout with unsigned integers. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5IntStorageFeatures INT_CHUNKED_UNSIGNED_DELETE = new HDF5IntStorageFeatures(HDF5StorageLayout.CHUNKED, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, NO_DEFLATION_LEVEL, NO_SCALING_FACTOR, false); /** * Represents 'standard compression', that is deflation with the default deflation level. */ public static final HDF5IntStorageFeatures INT_DEFLATE = new HDF5IntStorageFeatures(null, DEFAULT_DEFLATION_LEVEL, NO_SCALING_FACTOR, true); /** * Represents 'standard compression' with a pre-filter shuffle, that is deflation with the * default deflation level. */ public static final HDF5IntStorageFeatures INT_SHUFFLE_DEFLATE = new HDF5IntStorageFeatures( null, DataSetReplacementPolicy.USE_WRITER_DEFAULT, true, DEFAULT_DEFLATION_LEVEL, NO_SCALING_FACTOR, true); /** * Represents 'standard compression' with unsigned integers, that is deflation with the default * deflation level. */ public static final HDF5IntStorageFeatures INT_DEFLATE_UNSIGNED = new HDF5IntStorageFeatures( null, DEFAULT_DEFLATION_LEVEL, NO_SCALING_FACTOR, false); /** * Represents 'standard compression', that is deflation with the default deflation level. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5IntStorageFeatures INT_DEFLATE_KEEP = new HDF5IntStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, DEFAULT_DEFLATION_LEVEL, NO_SCALING_FACTOR, true); /** * Represents 'standard compression' with unsigned integers, that is deflation with the default * deflation level. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5IntStorageFeatures INT_DEFLATE_UNSIGNED_KEEP = new HDF5IntStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, DEFAULT_DEFLATION_LEVEL, NO_SCALING_FACTOR, false); /** * Represents 'standard compression', that is deflation with the default deflation level. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5IntStorageFeatures INT_DEFLATE_DELETE = new HDF5IntStorageFeatures( null, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, DEFAULT_DEFLATION_LEVEL, NO_SCALING_FACTOR, true); /** * Represents 'standard compression' with unsigned integers, that is deflation with the default * deflation level. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5IntStorageFeatures INT_DEFLATE_UNSIGNED_DELETE = new HDF5IntStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, DEFAULT_DEFLATION_LEVEL, NO_SCALING_FACTOR, false); /** * Represents 'maximal compression', that is deflation with the maximal deflation level. */ public static final HDF5IntStorageFeatures INT_DEFLATE_MAX = new HDF5IntStorageFeatures(null, MAX_DEFLATION_LEVEL, NO_SCALING_FACTOR, true); /** * Represents 'maximal compression' with unsigned integers, that is deflation with the maximal * deflation level. */ public static final HDF5IntStorageFeatures INT_DEFLATE_MAX_UNSIGNED = new HDF5IntStorageFeatures(null, MAX_DEFLATION_LEVEL, NO_SCALING_FACTOR, false); /** * Represents 'maximal compression', that is deflation with the maximal deflation level. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5IntStorageFeatures INT_DEFLATE_MAX_KEEP = new HDF5IntStorageFeatures( null, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, MAX_DEFLATION_LEVEL, NO_SCALING_FACTOR, true); /** * Represents 'maximal compression' with unsigned integers, that is deflation with the maximal * deflation level. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5IntStorageFeatures INT_DEFLATE_MAX_UNSIGNED_KEEP = new HDF5IntStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, MAX_DEFLATION_LEVEL, NO_SCALING_FACTOR, false); /** * Represents 'maximal compression', that is deflation with the maximal deflation level. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5IntStorageFeatures INT_DEFLATE_MAX_DELETE = new HDF5IntStorageFeatures( null, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, MAX_DEFLATION_LEVEL, NO_SCALING_FACTOR, true); /** * Represents 'maximal compression' with unsigned integers, that is deflation with the maximal * deflation level. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5IntStorageFeatures INT_DEFLATE_MAX_UNSIGNED_DELETE = new HDF5IntStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, MAX_DEFLATION_LEVEL, NO_SCALING_FACTOR, false); /** * Represents automatic scaling for integer values. */ public static final HDF5IntStorageFeatures INT_AUTO_SCALING = new HDF5IntStorageFeatures(null, NO_DEFLATION_LEVEL, INTEGER_AUTO_SCALING_FACTOR, true); /** * Represents automatic scaling for integer values with unsigned integers. */ public static final HDF5IntStorageFeatures INT_AUTO_SCALING_UNSIGNED = new HDF5IntStorageFeatures(null, NO_DEFLATION_LEVEL, INTEGER_AUTO_SCALING_FACTOR, false); /** * Represents automatic scaling for integer values. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5IntStorageFeatures INT_AUTO_SCALING_KEEP = new HDF5IntStorageFeatures( null, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, NO_DEFLATION_LEVEL, INTEGER_AUTO_SCALING_FACTOR, true); /** * Represents automatic scaling for integer values with unsigned integers. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5IntStorageFeatures INT_AUTO_SCALING_UNSIGNED_KEEP = new HDF5IntStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, NO_DEFLATION_LEVEL, INTEGER_AUTO_SCALING_FACTOR, false); /** * Represents automatic scaling for integer values. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5IntStorageFeatures INT_AUTO_SCALING_DELETE = new HDF5IntStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, NO_DEFLATION_LEVEL, INTEGER_AUTO_SCALING_FACTOR, true); /** * Represents automatic scaling for integer values with unsigned integers. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5IntStorageFeatures INT_AUTO_SCALING_UNSIGNED_DELETE = new HDF5IntStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, NO_DEFLATION_LEVEL, INTEGER_AUTO_SCALING_FACTOR, false); /** * Represents automatic scaling for integer values combined with deflation with the default * deflation level. */ public static final HDF5IntStorageFeatures INT_AUTO_SCALING_DEFLATE = new HDF5IntStorageFeatures(null, DEFAULT_DEFLATION_LEVEL, INTEGER_AUTO_SCALING_FACTOR, true); /** * Represents automatic scaling for integer values combined with deflation with the default * deflation level, using unsigned integers. */ public static final HDF5IntStorageFeatures INT_AUTO_SCALING_DEFLATE_UNSIGNED = new HDF5IntStorageFeatures(null, DEFAULT_DEFLATION_LEVEL, INTEGER_AUTO_SCALING_FACTOR, false); /** * Represents automatic scaling for integer values combined with deflation with the default * deflation level. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5IntStorageFeatures INT_AUTO_SCALING_DEFLATE_KEEP = new HDF5IntStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, DEFAULT_DEFLATION_LEVEL, INTEGER_AUTO_SCALING_FACTOR, true); /** * Represents automatic scaling for integer values combined with deflation with the default * deflation level, using unsigned integers. *

* Keep existing data set and apply only if a new data set has to be created. */ public static final HDF5IntStorageFeatures INT_AUTO_SCALING_DEFLATE_UNSIGNED_KEEP = new HDF5IntStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, DEFAULT_DEFLATION_LEVEL, INTEGER_AUTO_SCALING_FACTOR, false); /** * Represents automatic scaling for integer values combined with deflation with the default * deflation level. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5IntStorageFeatures INT_AUTO_SCALING_DEFLATE_DELETE = new HDF5IntStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, DEFAULT_DEFLATION_LEVEL, INTEGER_AUTO_SCALING_FACTOR, true); /** * Represents automatic scaling for integer values combined with deflation with the default * deflation level, using unsigned integers. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static final HDF5IntStorageFeatures INT_AUTO_SCALING_DEFLATE_UNSIGNED_DELETE = new HDF5IntStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_REPLACE_WITH_NEW, DEFAULT_DEFLATION_LEVEL, INTEGER_AUTO_SCALING_FACTOR, false); /** * A builder for storage features. */ public static final class HDF5IntStorageFeatureBuilder extends HDF5AbstractStorageFeatureBuilder { private boolean signed = true; public HDF5IntStorageFeatureBuilder() { } public HDF5IntStorageFeatureBuilder(HDF5AbstractStorageFeatures template) { super(template); if (template instanceof HDF5IntStorageFeatures) { signed(((HDF5IntStorageFeatures) template).isSigned()); } } boolean isSigned() { return signed; } /** * Sets that the integer values should be stored as signed integers if * signed==true and as unsigned integers if signed==false. */ public HDF5IntStorageFeatureBuilder signed(@SuppressWarnings("hiding") boolean signed) { this.signed = signed; return this; } /** * Sets that the integer values should be stored as unsigned integers. */ public HDF5IntStorageFeatureBuilder unsigned() { this.signed = false; return this; } /** * Compresses the dataset with default deflation level, if compress==true, do * not compress if compress==false. * * @return This builder. */ @Override public HDF5IntStorageFeatureBuilder compress(boolean compress) { super.compress(compress); return this; } /** * Compress the dataset with default deflation level. * * @return This builder. */ @Override public HDF5IntStorageFeatureBuilder compress() { super.compress(); return this; } /** * Compresses this dataset with the given deflateLevel. * {@link #NO_DEFLATION_LEVEL} means: do not compress. A good default value is * {@link #DEFAULT_DEFLATION_LEVEL}, the maximum value supported is * {@link #MAX_DEFLATION_LEVEL}. * * @return This builder. */ @Override public HDF5IntStorageFeatureBuilder deflateLevel(byte deflateLevel) { super.deflateLevel(deflateLevel); return this; } /** * Sets the scaling factor for an integer scaling pre-filter. * * @return This builder. */ @Override public HDF5IntStorageFeatureBuilder scalingFactor(byte scalingFactor) { super.scalingFactor(scalingFactor); return this; } /** * Disables the scaling pre-filter. * * @return This builder. */ @Override public HDF5IntStorageFeatureBuilder noScaling() { super.noScaling(); return this; } /** * Sets a shuffling pre-filter for deflation if shuffleBeforeDeflate==true and * disables it if shuffleBeforeDeflate==false. Theshuffling pre-filter may * improve the compression level but may also increase the compression time. *

* Only takes effect if compression is switched on. * * @return This builder. */ @Override public HDF5IntStorageFeatureBuilder shuffleBeforeDeflate(boolean shuffleBeforeDeflate) { super.shuffleBeforeDeflate(shuffleBeforeDeflate); return this; } /** * Sets a shuffling pre-filter for deflation. This may improve the compression level but may * also increase the compression time. *

* Only takes effect if compression is switched on. * * @see #compress() * @see #deflateLevel(byte) * @return This builder. */ @Override public HDF5AbstractStorageFeatureBuilder shuffleBeforeDeflate() { super.shuffleBeforeDeflate(); return this; } /** * Set the layout for the dataset. * * @return This builder. */ @Override public HDF5IntStorageFeatureBuilder storageLayout(HDF5StorageLayout proposedLayout) { super.storageLayout(proposedLayout); return this; } /** * Set a compact layout for the dataset. * * @return This builder. */ @Override public HDF5AbstractStorageFeatureBuilder compactStorageLayout() { super.compactStorageLayout(); return this; } /** * Set a contiguous layout for the dataset. * * @return This builder. */ @Override public HDF5AbstractStorageFeatureBuilder contiguousStorageLayout() { super.contiguousStorageLayout(); return this; } /** * Set a chunked layout for the dataset. * * @return This builder. */ @Override public HDF5AbstractStorageFeatureBuilder chunkedStorageLayout() { super.chunkedStorageLayout(); return this; } /** * Let a heuristic choose the right layout for the dataset. * * @return This builder. */ @Override public HDF5AbstractStorageFeatureBuilder defaultStorageLayout() { this.defaultStorageLayout(); return this; } /** * Set the dataset replacement policy for existing datasets. * * @return This builder. */ @Override public HDF5IntStorageFeatureBuilder datasetReplacementPolicy( DataSetReplacementPolicy datasetReplacementPolicy) { super.datasetReplacementPolicy(datasetReplacementPolicy); return this; } /** * Set the dataset replacement policy for existing datasets to * {@link ch.systemsx.cisd.hdf5.HDF5AbstractStorageFeatures.DataSetReplacementPolicy#USE_WRITER_DEFAULT} * . * * @return This builder. */ @Override public HDF5IntStorageFeatureBuilder datasetReplacementUseWriterDefault() { super.datasetReplacementUseWriterDefault(); return this; } /** * Set the dataset replacement policy for existing datasets to * {@link ch.systemsx.cisd.hdf5.HDF5AbstractStorageFeatures.DataSetReplacementPolicy#ENFORCE_KEEP_EXISTING} * . * * @return This builder. */ @Override public HDF5IntStorageFeatureBuilder datasetReplacementEnforceKeepExisting() { super.datasetReplacementEnforceKeepExisting(); return this; } /** * Set the dataset replacement policy for existing datasets to * {@link ch.systemsx.cisd.hdf5.HDF5AbstractStorageFeatures.DataSetReplacementPolicy#ENFORCE_REPLACE_WITH_NEW} * . * * @return This builder. */ @Override public HDF5IntStorageFeatureBuilder datasetReplacementEnforceReplaceWithNew() { super.datasetReplacementEnforceReplaceWithNew(); return this; } /** * Returns the storage features corresponding to this builder's values. */ @Override public HDF5IntStorageFeatures features() { return new HDF5IntStorageFeatures(this); } } /** * Returns a new storage feature builder. */ public static HDF5IntStorageFeatureBuilder build() { return new HDF5IntStorageFeatureBuilder(); } /** * Returns a new storage feature builder, initializing from template. */ public static HDF5IntStorageFeatureBuilder build(HDF5AbstractStorageFeatures template) { return new HDF5IntStorageFeatureBuilder(template); } /** * Create a corresponding {@link HDF5IntStorageFeatures} for the given * {@link HDF5GenericStorageFeatures}. */ public static HDF5IntStorageFeatures createFromGeneric( HDF5GenericStorageFeatures storageFeatures) { if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_CHUNKED) { return HDF5IntStorageFeatures.INT_CHUNKED; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_CHUNKED_DELETE) { return HDF5IntStorageFeatures.INT_CHUNKED_DELETE; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_CHUNKED_KEEP) { return HDF5IntStorageFeatures.INT_CHUNKED_KEEP; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_COMPACT) { return HDF5IntStorageFeatures.INT_COMPACT; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_COMPACT_DELETE) { return HDF5IntStorageFeatures.INT_COMPACT_DELETE; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_COMPACT_KEEP) { return HDF5IntStorageFeatures.INT_COMPACT_KEEP; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_CONTIGUOUS) { return HDF5IntStorageFeatures.INT_CONTIGUOUS; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_CONTIGUOUS_DELETE) { return HDF5IntStorageFeatures.INT_CONTIGUOUS_DELETE; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_CONTIGUOUS_KEEP) { return HDF5IntStorageFeatures.INT_CONTIGUOUS_KEEP; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION) { return HDF5IntStorageFeatures.INT_NO_COMPRESSION; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION_DELETE) { return HDF5IntStorageFeatures.INT_NO_COMPRESSION_DELETE; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION_KEEP) { return HDF5IntStorageFeatures.INT_NO_COMPRESSION_KEEP; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_DEFLATE) { return HDF5IntStorageFeatures.INT_DEFLATE; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_DEFLATE_DELETE) { return HDF5IntStorageFeatures.INT_DEFLATE_DELETE; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_DEFLATE_KEEP) { return HDF5IntStorageFeatures.INT_DEFLATE_KEEP; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_DEFLATE_MAX) { return HDF5IntStorageFeatures.INT_DEFLATE_MAX; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_DEFLATE_MAX_DELETE) { return HDF5IntStorageFeatures.INT_DEFLATE_MAX_DELETE; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_DEFLATE_MAX_KEEP) { return HDF5IntStorageFeatures.INT_DEFLATE_MAX_KEEP; } else { return new HDF5IntStorageFeatures(storageFeatures.tryGetProposedLayout(), storageFeatures.getDatasetReplacementPolicy(), storageFeatures.getDeflateLevel(), NO_SCALING_FACTOR, true); } } /** * Create a corresponding {@link HDF5IntStorageFeatures} for the given * {@link HDF5GenericStorageFeatures}. */ public static HDF5IntStorageFeatures createUnsignedFromGeneric( HDF5GenericStorageFeatures storageFeatures) { if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_CHUNKED) { return HDF5IntStorageFeatures.INT_CHUNKED_UNSIGNED; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_CHUNKED_DELETE) { return HDF5IntStorageFeatures.INT_CHUNKED_UNSIGNED_DELETE; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_CHUNKED_KEEP) { return HDF5IntStorageFeatures.INT_CHUNKED_UNSIGNED_KEEP; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_COMPACT) { return HDF5IntStorageFeatures.INT_COMPACT_UNSIGNED; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_COMPACT_DELETE) { return HDF5IntStorageFeatures.INT_COMPACT_UNSIGNED_DELETE; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_COMPACT_KEEP) { return HDF5IntStorageFeatures.INT_COMPACT_UNSIGNED_KEEP; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_CONTIGUOUS) { return HDF5IntStorageFeatures.INT_CONTIGUOUS_UNSIGNED; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_CONTIGUOUS_DELETE) { return HDF5IntStorageFeatures.INT_CONTIGUOUS_UNSIGNED_DELETE; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_CONTIGUOUS_KEEP) { return HDF5IntStorageFeatures.INT_CONTIGUOUS_UNSIGNED_KEEP; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION) { return HDF5IntStorageFeatures.INT_NO_COMPRESSION_UNSIGNED; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION_DELETE) { return HDF5IntStorageFeatures.INT_NO_COMPRESSION_UNSIGNED_DELETE; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION_KEEP) { return HDF5IntStorageFeatures.INT_NO_COMPRESSION_UNSIGNED_KEEP; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_DEFLATE) { return HDF5IntStorageFeatures.INT_DEFLATE_UNSIGNED; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_DEFLATE_DELETE) { return HDF5IntStorageFeatures.INT_DEFLATE_UNSIGNED_DELETE; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_DEFLATE_KEEP) { return HDF5IntStorageFeatures.INT_DEFLATE_UNSIGNED_KEEP; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_DEFLATE_MAX) { return HDF5IntStorageFeatures.INT_DEFLATE_MAX_UNSIGNED; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_DEFLATE_MAX_DELETE) { return HDF5IntStorageFeatures.INT_DEFLATE_MAX_UNSIGNED_DELETE; } else if (storageFeatures == HDF5GenericStorageFeatures.GENERIC_DEFLATE_MAX_KEEP) { return HDF5IntStorageFeatures.INT_DEFLATE_MAX_UNSIGNED_KEEP; } else { return new HDF5IntStorageFeatures(storageFeatures.tryGetProposedLayout(), storageFeatures.getDatasetReplacementPolicy(), storageFeatures.getDeflateLevel(), NO_SCALING_FACTOR, true); } } /** * Creates a {@link HDF5IntStorageFeatures} object that represents deflation with the given * deflationLevel. */ public static HDF5IntStorageFeatures createDeflation(int deflationLevel) { return createDeflation(deflationLevel, false, false, true); } /** * Creates a {@link HDF5IntStorageFeatures} object that represents deflation with the given * deflationLevel. *

* Keep existing data set and apply only if a new data set has to be created. */ public static HDF5IntStorageFeatures createDeflationKeep(int deflationLevel) { return createDeflation(deflationLevel, true, false, true); } /** * Creates a {@link HDF5IntStorageFeatures} object that represents deflation with the given * deflationLevel. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static HDF5IntStorageFeatures createDeflationDelete(int deflationLevel) { return createDeflation(deflationLevel, false, true, true); } /** * Creates a {@link HDF5IntStorageFeatures} object that represents deflation with the given * deflationLevel. */ public static HDF5IntStorageFeatures createDeflationUnsigned(int deflationLevel) { return createDeflation(deflationLevel, false, false, false); } /** * Creates a {@link HDF5IntStorageFeatures} object that represents deflation with the given * deflationLevel for unsigned integers. *

* Keep existing data set and apply only if a new data set has to be created. */ public static HDF5IntStorageFeatures createDeflationUnsignedKeep(int deflationLevel) { return createDeflation(deflationLevel, true, false, false); } /** * Creates a {@link HDF5IntStorageFeatures} object that represents deflation with the given * deflationLevel for unsigned integers. *

* Delete an existing data set before writing the new one. Always apply the chosen settings. * This allows to overwrite the {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} * setting. */ public static HDF5IntStorageFeatures createDeflationUnsignedDelete(int deflationLevel) { return createDeflation(deflationLevel, false, true, false); } /** * Creates a {@link HDF5IntStorageFeatures} object that represents deflation with the given * deflationLevel for unsigned integers. */ private static HDF5IntStorageFeatures createDeflation(int deflationLevel, boolean keepDataSetIfExists, boolean deleteDataSetIfExists, boolean signed) { if (signed) { return new HDF5IntStorageFeatures(null, getDataSetReplacementPolicy( keepDataSetIfExists, deleteDataSetIfExists), toByte(deflationLevel), NO_SCALING_FACTOR, true); } else { return new HDF5IntStorageFeatures(null, getDataSetReplacementPolicy( keepDataSetIfExists, deleteDataSetIfExists), toByte(deflationLevel), NO_SCALING_FACTOR, false); } } /** * Creates a {@link HDF5IntStorageFeatures} object that represents integer scaling with the * given scalingFactor. */ public static HDF5IntStorageFeatures createIntegerScaling(int scalingFactor) { return createIntegerScaling(scalingFactor, false, true); } /** * Creates a {@link HDF5IntStorageFeatures} object that represents integer scaling with the * given scalingFactor. *

* Keep existing data set and apply only if a new data set has to be created. */ public static HDF5IntStorageFeatures createIntegerScalingKeep(int scalingFactor) { return createIntegerScaling(scalingFactor, true, true); } /** * Creates a {@link HDF5IntStorageFeatures} object that represents integer scaling with the * given scalingFactor. */ public static HDF5IntStorageFeatures createIntegerScalingUnsigned(int scalingFactor) { return createIntegerScaling(scalingFactor, false, false); } /** * Creates a {@link HDF5IntStorageFeatures} object that represents integer scaling with the * given scalingFactor. *

* Keep existing data set and apply only if a new data set has to be created. */ public static HDF5IntStorageFeatures createIntegerScalingUnsigedKeep(int scalingFactor) { return createIntegerScaling(scalingFactor, true, false); } /** * Creates a {@link HDF5IntStorageFeatures} object that represents integer scaling with the * given scalingFactor. */ private static HDF5IntStorageFeatures createIntegerScaling(int scalingFactor, boolean keepExistingDataSetIfExists, boolean signed) { if (signed) { if (scalingFactor == INTEGER_AUTO_SCALING_FACTOR) { return keepExistingDataSetIfExists ? INT_AUTO_SCALING_DEFLATE_KEEP : INT_AUTO_SCALING_DEFLATE; } else { return new HDF5IntStorageFeatures(null, NO_DEFLATION_LEVEL, toByte(scalingFactor), true); } } else { if (scalingFactor == INTEGER_AUTO_SCALING_FACTOR) { return keepExistingDataSetIfExists ? INT_AUTO_SCALING_DEFLATE_UNSIGNED_KEEP : INT_AUTO_SCALING_DEFLATE_UNSIGNED; } else { return new HDF5IntStorageFeatures(null, NO_DEFLATION_LEVEL, toByte(scalingFactor), false); } } } /** * Creates a {@link HDF5IntStorageFeatures} object that represents deflation with the default * deflation level and integer scaling with the given scalingFactor. */ public static HDF5IntStorageFeatures createDeflateAndIntegerScaling(int scalingFactor) { return new HDF5IntStorageFeatures(null, DEFAULT_DEFLATION_LEVEL, toByte(scalingFactor), true); } /** * Creates a {@link HDF5IntStorageFeatures} object that represents deflation with the default * deflation level and integer scaling with the given scalingFactor. *

* Keep existing data set and apply only if a new data set has to be created. */ public static HDF5IntStorageFeatures createDeflateAndIntegerScalingKeep(int scalingFactor) { return new HDF5IntStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, DEFAULT_DEFLATION_LEVEL, toByte(scalingFactor), true); } /** * Creates a {@link HDF5IntStorageFeatures} object that represents deflation with the given * deflateLevel and integer scaling with the given scalingFactor. */ public static HDF5IntStorageFeatures createDeflateAndIntegerScaling(int deflateLevel, byte scalingFactor) { return new HDF5IntStorageFeatures(null, toByte(deflateLevel), scalingFactor, true); } /** * Creates a {@link HDF5IntStorageFeatures} object that represents deflation with the given * deflateLevel and integer scaling with the given scalingFactor. */ public static HDF5IntStorageFeatures createDeflateAndIntegerScalingUnsigned(int deflateLevel, byte scalingFactor) { return new HDF5IntStorageFeatures(null, toByte(deflateLevel), scalingFactor, false); } /** * Creates a {@link HDF5IntStorageFeatures} object that represents deflation with the given * deflateLevel and integer scaling with the given scalingFactor. */ public static HDF5IntStorageFeatures createDeflateAndIntegerScaling(int deflateLevel, byte scalingFactor, boolean keepDataSetIfExists) { return new HDF5IntStorageFeatures(null, getDataSetReplacementPolicy(keepDataSetIfExists, false), toByte(deflateLevel), scalingFactor, true); } /** * Creates a {@link HDF5IntStorageFeatures} object that represents deflation with the given * deflateLevel and integer scaling with the given scalingFactor. */ public static HDF5IntStorageFeatures createDeflateAndIntegerScalingUnsigned(int deflateLevel, byte scalingFactor, boolean keepDataSetIfExists) { return new HDF5IntStorageFeatures(null, getDataSetReplacementPolicy(keepDataSetIfExists, false), toByte(deflateLevel), scalingFactor, false); } /** * Creates a {@link HDF5IntStorageFeatures} object that represents deflation with the given * deflateLevel and integer scaling with the given scalingFactor. *

* Keep existing data set and apply only if a new data set has to be created. */ public static HDF5IntStorageFeatures createDeflateAndIntegerScalingKeep(int deflateLevel, byte scalingFactor) { return new HDF5IntStorageFeatures(null, DataSetReplacementPolicy.ENFORCE_KEEP_EXISTING, toByte(deflateLevel), scalingFactor, true); } private final boolean signed; HDF5IntStorageFeatures(HDF5IntStorageFeatureBuilder builder) { super(builder.getStorageLayout(), builder.getDatasetReplacementPolicy(), builder .isShuffleBeforeDeflate(), builder.getDeflateLevel(), builder.getScalingFactor()); this.signed = builder.isSigned(); } HDF5IntStorageFeatures(HDF5StorageLayout proposedLayoutOrNull, byte deflateLevel, byte scalingFactor, boolean signed) { this(proposedLayoutOrNull, DataSetReplacementPolicy.USE_WRITER_DEFAULT, deflateLevel, scalingFactor, signed); } HDF5IntStorageFeatures(HDF5StorageLayout proposedLayoutOrNull, DataSetReplacementPolicy dataSetReplacementPolicy, byte deflateLevel, byte scalingFactor, boolean signed) { super(proposedLayoutOrNull, dataSetReplacementPolicy, deflateLevel, scalingFactor); this.signed = signed; } HDF5IntStorageFeatures(HDF5StorageLayout proposedLayoutOrNull, DataSetReplacementPolicy dataSetReplacementPolicy, boolean shuffleBeforeDeflate, byte deflateLevel, byte scalingFactor, boolean signed) { super(proposedLayoutOrNull, dataSetReplacementPolicy, shuffleBeforeDeflate, deflateLevel, scalingFactor); this.signed = signed; } /** * Returns true if signed integers should be stored, false otherwise. */ public boolean isSigned() { return signed; } /** * Returns true, if this compression setting can be applied on the given dataClassId. */ @Override boolean isCompatibleWithDataClass(int dataClassId) { return (dataClassId == H5T_INTEGER); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5IntWriter.java000066400000000000000000000665441256564762100266020ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.HDF5IntStorageFeatures.INT_NO_COMPRESSION; import static ch.systemsx.cisd.hdf5.hdf5lib.H5D.H5Dwrite; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_ALL; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_INT32; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_I32LE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_U32LE; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDIntArray; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; /** * The implementation of {@link IHDF5IntWriter}. * * @author Bernd Rinn */ class HDF5IntWriter extends HDF5IntReader implements IHDF5IntWriter { private final HDF5BaseWriter baseWriter; HDF5IntWriter(HDF5BaseWriter baseWriter) { super(baseWriter); assert baseWriter != null; this.baseWriter = baseWriter; } // ///////////////////// // Attributes // ///////////////////// @Override public void setAttr(final String objectPath, final String name, final int value) { assert objectPath != null; assert name != null; baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { 1 }, registry); baseWriter.setAttribute(objectPath, name, H5T_STD_I32LE, H5T_NATIVE_INT32, dataSpaceId, new int[] { value }, registry); } else { baseWriter.setAttribute(objectPath, name, H5T_STD_I32LE, H5T_NATIVE_INT32, -1, new int[] { value }, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void setArrayAttr(final String objectPath, final String name, final int[] value) { assert objectPath != null; assert name != null; assert value != null; baseWriter.checkOpen(); final ICallableWithCleanUp setAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { value.length }, registry); baseWriter.setAttribute(objectPath, name, H5T_STD_I32LE, H5T_NATIVE_INT32, dataSpaceId, value, registry); } else { final int memoryTypeId = baseWriter.h5.createArrayType(H5T_NATIVE_INT32, value.length, registry); final int storageTypeId = baseWriter.h5.createArrayType(H5T_STD_I32LE, value.length, registry); baseWriter.setAttribute(objectPath, name, storageTypeId, memoryTypeId, -1, value, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(setAttributeRunnable); } @Override public void setMDArrayAttr(final String objectPath, final String name, final MDIntArray value) { assert objectPath != null; assert name != null; assert value != null; baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(value.longDimensions(), registry); baseWriter.setAttribute(objectPath, name, H5T_STD_I32LE, H5T_NATIVE_INT32, dataSpaceId, value.getAsFlatArray(), registry); } else { final int memoryTypeId = baseWriter.h5.createArrayType(H5T_NATIVE_INT32, value.dimensions(), registry); final int storageTypeId = baseWriter.h5.createArrayType(H5T_STD_I32LE, value.dimensions(), registry); baseWriter.setAttribute(objectPath, name, storageTypeId, memoryTypeId, -1, value.getAsFlatArray(), registry); } return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void setMatrixAttr(final String objectPath, final String name, final int[][] value) { setMDArrayAttr(objectPath, name, new MDIntArray(value)); } // ///////////////////// // Data Sets // ///////////////////// @Override public void write(final String objectPath, final int value) { assert objectPath != null; baseWriter.checkOpen(); baseWriter.writeScalar(objectPath, H5T_STD_I32LE, H5T_NATIVE_INT32, value); } @Override public void writeArray(final String objectPath, final int[] data) { writeArray(objectPath, data, INT_NO_COMPRESSION); } @Override public void writeArray(final String objectPath, final int[] data, final HDF5IntStorageFeatures features) { assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, features.isSigned() ? H5T_STD_I32LE : H5T_STD_U32LE, new long[] { data.length }, 4, features, registry); H5Dwrite(dataSetId, H5T_NATIVE_INT32, H5S_ALL, H5S_ALL, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createArray(final String objectPath, final int size) { createArray(objectPath, size, INT_NO_COMPRESSION); } @Override public void createArray(final String objectPath, final long size, final int blockSize) { createArray(objectPath, size, blockSize, INT_NO_COMPRESSION); } @Override public void createArray(final String objectPath, final int size, final HDF5IntStorageFeatures features) { assert objectPath != null; assert size >= 0; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (features.requiresChunking()) { baseWriter.createDataSet(objectPath, features.isSigned() ? H5T_STD_I32LE : H5T_STD_U32LE, features, new long[] { 0 }, new long[] { size }, 4, registry); } else { baseWriter.createDataSet(objectPath, features.isSigned() ? H5T_STD_I32LE : H5T_STD_U32LE, features, new long[] { size }, null, 4, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void createArray(final String objectPath, final long size, final int blockSize, final HDF5IntStorageFeatures features) { assert objectPath != null; assert size >= 0; assert blockSize >= 0 && (blockSize <= size || size == 0); baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { baseWriter.createDataSet(objectPath, features.isSigned() ? H5T_STD_I32LE : H5T_STD_U32LE, features, new long[] { size }, new long[] { blockSize }, 4, registry); return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void writeArrayBlock(final String objectPath, final int[] data, final long blockNumber) { writeArrayBlockWithOffset(objectPath, data, data.length, data.length * blockNumber); } @Override public void writeArrayBlockWithOffset(final String objectPath, final int[] data, final int dataSize, final long offset) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] blockDimensions = new long[] { dataSize }; final long[] slabStartOrNull = new long[] { offset }; final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, new long[] { offset + dataSize }, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, slabStartOrNull, blockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(blockDimensions, registry); H5Dwrite(dataSetId, H5T_NATIVE_INT32, memorySpaceId, dataSpaceId, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } /** * Writes out a int matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ @Override public void writeMatrix(final String objectPath, final int[][] data) { writeMatrix(objectPath, data, INT_NO_COMPRESSION); } @Override public void writeMatrix(final String objectPath, final int[][] data, final HDF5IntStorageFeatures features) { assert objectPath != null; assert data != null; assert HDF5Utils.areMatrixDimensionsConsistent(data); writeMDArray(objectPath, new MDIntArray(data), features); } @Override public void createMatrix(final String objectPath, final int sizeX, final int sizeY) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; createMDArray(objectPath, new int[] { sizeX, sizeY }); } @Override public void createMatrix(final String objectPath, final int sizeX, final int sizeY, final HDF5IntStorageFeatures features) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; createMDArray(objectPath, new int[] { sizeX, sizeY }, features); } @Override public void createMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; assert blockSizeX >= 0 && (blockSizeX <= sizeX || sizeX == 0); assert blockSizeY >= 0 && (blockSizeY <= sizeY || sizeY == 0); createMDArray(objectPath, new long[] { sizeX, sizeY }, new int[] { blockSizeX, blockSizeY }); } @Override public void createMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY, final HDF5IntStorageFeatures features) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; assert blockSizeX >= 0 && (blockSizeX <= sizeX || sizeX == 0); assert blockSizeY >= 0 && (blockSizeY <= sizeY || sizeY == 0); createMDArray(objectPath, new long[] { sizeX, sizeY }, new int[] { blockSizeX, blockSizeY }, features); } @Override public void writeMatrixBlock(final String objectPath, final int[][] data, final long blockNumberX, final long blockNumberY) { assert objectPath != null; assert data != null; writeMDArrayBlock(objectPath, new MDIntArray(data), new long[] { blockNumberX, blockNumberY }); } @Override public void writeMatrixBlockWithOffset(final String objectPath, final int[][] data, final long offsetX, final long offsetY) { assert objectPath != null; assert data != null; writeMDArrayBlockWithOffset(objectPath, new MDIntArray(data, new int[] { data.length, data[0].length }), new long[] { offsetX, offsetY }); } @Override public void writeMatrixBlockWithOffset(final String objectPath, final int[][] data, final int dataSizeX, final int dataSizeY, final long offsetX, final long offsetY) { assert objectPath != null; assert data != null; writeMDArrayBlockWithOffset(objectPath, new MDIntArray(data, new int[] { dataSizeX, dataSizeY }), new long[] { offsetX, offsetY }); } @Override public void writeMDArray(final String objectPath, final MDIntArray data) { writeMDArray(objectPath, data, INT_NO_COMPRESSION); } @Override public void writeMDArraySlice(String objectPath, MDIntArray data, IndexMap boundIndices) { baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), null, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDIntArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArraySlice(String objectPath, MDIntArray data, long[] boundIndices) { baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), null, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDIntArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArray(final String objectPath, final MDIntArray data, final HDF5IntStorageFeatures features) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, features.isSigned() ? H5T_STD_I32LE : H5T_STD_U32LE, data.longDimensions(), 4, features, registry); H5Dwrite(dataSetId, H5T_NATIVE_INT32, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createMDArray(final String objectPath, final int[] dimensions) { createMDArray(objectPath, dimensions, INT_NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions) { createMDArray(objectPath, dimensions, blockDimensions, INT_NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final int[] dimensions, final HDF5IntStorageFeatures features) { assert objectPath != null; assert dimensions != null; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (features.requiresChunking()) { final long[] nullDimensions = new long[dimensions.length]; baseWriter.createDataSet(objectPath, features.isSigned() ? H5T_STD_I32LE : H5T_STD_U32LE, features, nullDimensions, MDArray.toLong(dimensions), 4, registry); } else { baseWriter.createDataSet(objectPath, features.isSigned() ? H5T_STD_I32LE : H5T_STD_U32LE, features, MDArray.toLong(dimensions), null, 4, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void createMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions, final HDF5IntStorageFeatures features) { assert objectPath != null; assert dimensions != null; assert blockDimensions != null; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { baseWriter.createDataSet(objectPath, features.isSigned() ? H5T_STD_I32LE : H5T_STD_U32LE, features, dimensions, MDArray.toLong(blockDimensions), 4, registry); return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void writeMDArrayBlock(final String objectPath, final MDIntArray data, final long[] blockNumber) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeMDArrayBlockWithOffset(objectPath, data, offset); } @Override public void writeSlicedMDArrayBlock(final String objectPath, final MDIntArray data, final long[] blockNumber, IndexMap boundIndices) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeSlicedMDArrayBlockWithOffset(objectPath, data, offset, boundIndices); } @Override public void writeSlicedMDArrayBlock(String objectPath, MDIntArray data, long[] blockNumber, long[] boundIndices) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeSlicedMDArrayBlockWithOffset(objectPath, data, offset, boundIndices); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final MDIntArray data, final long[] offset) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] dimensions = data.longDimensions(); assert dimensions.length == offset.length; final long[] dataSetDimensions = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + dimensions[i]; } final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, dimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(dimensions, registry); H5Dwrite(dataSetId, H5T_NATIVE_INT32, memorySpaceId, dataSpaceId, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeSlicedMDArrayBlockWithOffset(String objectPath, MDIntArray data, long[] offset, IndexMap boundIndices) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), offset, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDIntArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeSlicedMDArrayBlockWithOffset(String objectPath, MDIntArray data, long[] offset, long[] boundIndices) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), offset, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDIntArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final MDIntArray data, final int[] blockDimensions, final long[] offset, final int[] memoryOffset) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] memoryDimensions = data.longDimensions(); assert memoryDimensions.length == offset.length; final long[] longBlockDimensions = MDArray.toLong(blockDimensions); assert longBlockDimensions.length == offset.length; final long[] dataSetDimensions = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + blockDimensions[i]; } final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, longBlockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(memoryDimensions, registry); baseWriter.h5.setHyperslabBlock(memorySpaceId, MDArray.toLong(memoryOffset), longBlockDimensions); H5Dwrite(dataSetId, H5T_NATIVE_INT32, memorySpaceId, dataSpaceId, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5LinkInformation.java000066400000000000000000000066311256564762100277450ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; /** * Information about a link in an HDF5 file. * * @author Bernd Rinn */ public final class HDF5LinkInformation extends HDF5CommonInformation { static final HDF5LinkInformation ROOT_LINK_INFO = new HDF5LinkInformation("/", HDF5ObjectType.GROUP, null); private final String symbolicLinkTargetOrNull; private HDF5LinkInformation(String path, HDF5ObjectType type, String symbolicLinkTargetOrNull) { super(path, type); this.symbolicLinkTargetOrNull = symbolicLinkTargetOrNull; } static HDF5LinkInformation create(String path, int typeId, String symbolicLinkTargetOrNull) { final HDF5ObjectType type = objectTypeIdToObjectType(typeId); return new HDF5LinkInformation(path, type, symbolicLinkTargetOrNull); } /** * Returns the symbolic link target of this link, or null, if this link does not * exist or is not a symbolic link. *

* Note that external links have a special format: They start with a prefix " * EXTERNAL::", then comes the path of the external file (beware that this part * uses the native path separator, i.e. "\" on Windows). Finally, separated by ":: * ", the path of the link in the external file is provided (this part always uses "/" as path * separator). */ public String tryGetSymbolicLinkTarget() { return symbolicLinkTargetOrNull; } /** * Returns true, if the link is a soft link. */ public boolean isSoftLink() { return HDF5ObjectType.isSoftLink(type); } /** * Returns true, if the link is an external link. */ public boolean isExternalLink() { return HDF5ObjectType.isExternalLink(type); } /** * Returns true, if the link is either a soft link or an external link. */ public boolean isSymbolicLink() { return HDF5ObjectType.isSymbolicLink(type); } @Override public int hashCode() { final int prime = 31; int result = 1; result = prime * result + ((path == null) ? 0 : path.hashCode()); return result; } @Override public boolean equals(Object obj) { if (this == obj) { return true; } if (obj == null) { return false; } if (getClass() != obj.getClass()) { return false; } final HDF5LinkInformation other = (HDF5LinkInformation) obj; if (path == null) { if (other.path != null) { return false; } } else if (path.equals(other.path) == false) { return false; } return true; } }libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5LongReader.java000066400000000000000000001020351256564762100266570ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.MatrixUtils.cardinalityBoundIndices; import static ch.systemsx.cisd.hdf5.MatrixUtils.checkBoundIndices; import static ch.systemsx.cisd.hdf5.MatrixUtils.createFullBlockDimensionsAndOffset; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_ARRAY; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_INT64; import java.util.Arrays; import java.util.Iterator; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import ncsa.hdf.hdf5lib.exceptions.HDF5SpaceRankMismatch; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDLongArray; import ch.systemsx.cisd.hdf5.HDF5BaseReader.DataSpaceParameters; import ch.systemsx.cisd.hdf5.HDF5DataTypeInformation.DataTypeInfoOptions; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; import ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants; /** * The implementation of {@link IHDF5LongReader}. * * @author Bernd Rinn */ class HDF5LongReader implements IHDF5LongReader { private final HDF5BaseReader baseReader; HDF5LongReader(HDF5BaseReader baseReader) { assert baseReader != null; this.baseReader = baseReader; } // For Unit tests only. HDF5BaseReader getBaseReader() { return baseReader; } // ///////////////////// // Attributes // ///////////////////// @Override public long getAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public Long call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final long[] data = baseReader.h5.readAttributeAsLongArray(attributeId, H5T_NATIVE_INT64, 1); return data[0]; } }; return baseReader.runner.call(getAttributeRunnable); } @Override public long[] getArrayAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public long[] call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); return getLongArrayAttribute(objectId, attributeName, registry); } }; return baseReader.runner.call(getAttributeRunnable); } @Override public MDLongArray getMDArrayAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public MDLongArray call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); return getLongMDArrayAttribute(objectId, attributeName, registry); } }; return baseReader.runner.call(getAttributeRunnable); } @Override public long[][] getMatrixAttr(final String objectPath, final String attributeName) throws HDF5JavaException { final MDLongArray array = getMDArrayAttr(objectPath, attributeName); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } // ///////////////////// // Data Sets // ///////////////////// @Override public long read(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public Long call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final long[] data = new long[1]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_INT64, data); return data[0]; } }; return baseReader.runner.call(readCallable); } @Override public long[] readArray(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public long[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); return readLongArray(dataSetId, registry); } }; return baseReader.runner.call(readCallable); } private long[] readLongArray(int dataSetId, ICleanUpRegistry registry) { try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); final long[] data = new long[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_INT64, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return data; } catch (HDF5LibraryException ex) { if (ex.getMajorErrorNumber() == HDF5Constants.H5E_DATATYPE && ex.getMinorErrorNumber() == HDF5Constants.H5E_CANTINIT) { // Check whether it is an array data type. final int dataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); if (baseReader.h5.getClassType(dataTypeId) == HDF5Constants.H5T_ARRAY) { return readLongArrayFromArrayType(dataSetId, dataTypeId, registry); } } throw ex; } } private long[] readLongArrayFromArrayType(int dataSetId, final int dataTypeId, ICleanUpRegistry registry) { final int spaceId = baseReader.h5.createScalarDataSpace(); final int[] dimensions = baseReader.h5.getArrayDimensions(dataTypeId); final long[] data = new long[HDF5Utils.getOneDimensionalArraySize(dimensions)]; final int memoryDataTypeId = baseReader.h5.createArrayType(H5T_NATIVE_INT64, data.length, registry); baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceId, spaceId, data); return data; } @Override public int[] readToMDArrayWithOffset(final String objectPath, final MDLongArray array, final int[] memoryOffset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getBlockSpaceParameters(dataSetId, memoryOffset, array .dimensions(), registry); final int nativeDataTypeId = baseReader.getNativeDataTypeId(dataSetId, H5T_NATIVE_INT64, registry); baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, array. getAsFlatArray()); return MDArray.toInt(spaceParams.dimensions); } }; return baseReader.runner.call(readCallable); } @Override public int[] readToMDArrayBlockWithOffset(final String objectPath, final MDLongArray array, final int[] blockDimensions, final long[] offset, final int[] memoryOffset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getBlockSpaceParameters(dataSetId, memoryOffset, array .dimensions(), offset, blockDimensions, registry); final int nativeDataTypeId = baseReader.getNativeDataTypeId(dataSetId, H5T_NATIVE_INT64, registry); baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, array .getAsFlatArray()); return MDArray.toInt(spaceParams.dimensions); } }; return baseReader.runner.call(readCallable); } @Override public long[] readArrayBlock(final String objectPath, final int blockSize, final long blockNumber) { return readArrayBlockWithOffset(objectPath, blockSize, blockNumber * blockSize); } @Override public long[] readArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public long[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockSize, registry); final long[] data = new long[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_INT64, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return data; } }; return baseReader.runner.call(readCallable); } @Override public long[][] readMatrix(final String objectPath) throws HDF5JavaException { final MDLongArray array = readMDArray(objectPath); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public long[][] readMatrixBlock(final String objectPath, final int blockSizeX, final int blockSizeY, final long blockNumberX, final long blockNumberY) throws HDF5JavaException { final MDLongArray array = readMDArrayBlock(objectPath, new int[] { blockSizeX, blockSizeY }, new long[] { blockNumberX, blockNumberY }); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public long[][] readMatrixBlockWithOffset(final String objectPath, final int blockSizeX, final int blockSizeY, final long offsetX, final long offsetY) throws HDF5JavaException { final MDLongArray array = readMDArrayBlockWithOffset(objectPath, new int[] { blockSizeX, blockSizeY }, new long[] { offsetX, offsetY }); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public MDLongArray readMDArraySlice(String objectPath, IndexMap boundIndices) { baseReader.checkOpen(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; final int cardBoundIndices = cardinalityBoundIndices(boundIndices); checkBoundIndices(objectPath, fullDimensions, cardBoundIndices); final int[] effectiveBlockDimensions = new int[fullBlockDimensions.length - cardBoundIndices]; Arrays.fill(effectiveBlockDimensions, -1); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, null, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDLongArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); if (fullBlockDimensions.length == cardBoundIndices) // no free indices { return new MDLongArray(result.getAsFlatArray(), new int[] { 1 }); } else { return new MDLongArray(result.getAsFlatArray(), effectiveBlockDimensions); } } @Override public MDLongArray readMDArraySlice(String objectPath, long[] boundIndices) { baseReader.checkOpen(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; final int cardBoundIndices = cardinalityBoundIndices(boundIndices); checkBoundIndices(objectPath, fullDimensions, boundIndices); final int[] effectiveBlockDimensions = new int[fullBlockDimensions.length - cardBoundIndices]; Arrays.fill(effectiveBlockDimensions, -1); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, null, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDLongArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); if (fullBlockDimensions.length == cardBoundIndices) // no free indices { return new MDLongArray(result.getAsFlatArray(), new int[] { 1 }); } else { return new MDLongArray(result.getAsFlatArray(), effectiveBlockDimensions); } } @Override public MDLongArray readMDArray(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public MDLongArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); return readLongMDArray(dataSetId, registry); } }; return baseReader.runner.call(readCallable); } MDLongArray readLongMDArray(int dataSetId, ICleanUpRegistry registry) { try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); final long[] data = new long[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_INT64, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return new MDLongArray(data, spaceParams.dimensions); } catch (HDF5LibraryException ex) { if (ex.getMajorErrorNumber() == HDF5Constants.H5E_DATATYPE && ex.getMinorErrorNumber() == HDF5Constants.H5E_CANTINIT) { // Check whether it is an array data type. final int dataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); if (baseReader.h5.getClassType(dataTypeId) == HDF5Constants.H5T_ARRAY) { return readLongMDArrayFromArrayType(dataSetId, dataTypeId, registry); } } throw ex; } } private MDLongArray readLongMDArrayFromArrayType(int dataSetId, final int dataTypeId, ICleanUpRegistry registry) { final int[] arrayDimensions = baseReader.h5.getArrayDimensions(dataTypeId); final int memoryDataTypeId = baseReader.h5.createArrayType(H5T_NATIVE_INT64, arrayDimensions, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); if (spaceParams.blockSize == 0) { final int spaceId = baseReader.h5.createScalarDataSpace(); final long[] data = new long[MDArray.getLength(arrayDimensions)]; baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceId, spaceId, data); return new MDLongArray(data, arrayDimensions); } else { final long[] data = new long[MDArray.getLength(arrayDimensions) * spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return new MDLongArray(data, MatrixUtils.concat(MDArray.toInt(spaceParams.dimensions), arrayDimensions)); } } @Override public MDLongArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, IndexMap boundIndices) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readSlicedMDArrayBlockWithOffset(objectPath, blockDimensions, offset, boundIndices); } @Override public MDLongArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, long[] boundIndices) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readSlicedMDArrayBlockWithOffset(objectPath, blockDimensions, offset, boundIndices); } @Override public MDLongArray readMDArrayBlock(final String objectPath, final int[] blockDimensions, final long[] blockNumber) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readMDArrayBlockWithOffset(objectPath, blockDimensions, offset); } @Override public MDLongArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, IndexMap boundIndices) { baseReader.checkOpen(); final int[] effectiveBlockDimensions = blockDimensions.clone(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; checkBoundIndices(objectPath, fullDimensions, blockDimensions, cardinalityBoundIndices(boundIndices)); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, offset, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDLongArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); return new MDLongArray(result.getAsFlatArray(), effectiveBlockDimensions); } @Override public MDLongArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, long[] boundIndices) { baseReader.checkOpen(); final int[] effectiveBlockDimensions = blockDimensions.clone(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; checkBoundIndices(objectPath, fullDimensions, blockDimensions, cardinalityBoundIndices(boundIndices)); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, offset, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDLongArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); return new MDLongArray(result.getAsFlatArray(), effectiveBlockDimensions); } @Override public MDLongArray readMDArrayBlockWithOffset(final String objectPath, final int[] blockDimensions, final long[] offset) { assert objectPath != null; assert blockDimensions != null; assert offset != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public MDLongArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockDimensions, registry); final long[] dataBlock = new long[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_INT64, spaceParams.memorySpaceId, spaceParams.dataSpaceId, dataBlock); return new MDLongArray(dataBlock, spaceParams.dimensions); } catch (HDF5SpaceRankMismatch ex) { final HDF5DataSetInformation info = baseReader.getDataSetInformation(objectPath, DataTypeInfoOptions.MINIMAL, false); if (ex.getSpaceRankExpected() - ex.getSpaceRankFound() == info .getTypeInformation().getRank()) { return readMDArrayBlockOfArrays(dataSetId, blockDimensions, offset, info, ex.getSpaceRankFound(), registry); } else { throw ex; } } } }; return baseReader.runner.call(readCallable); } private MDLongArray readMDArrayBlockOfArrays(final int dataSetId, final int[] blockDimensions, final long[] offset, final HDF5DataSetInformation info, final int spaceRank, final ICleanUpRegistry registry) { final int[] arrayDimensions = info.getTypeInformation().getDimensions(); int[] effectiveBlockDimensions = blockDimensions; // We do not support block-wise reading of array types, check // that we do not have to and bail out otherwise. for (int i = 0; i < arrayDimensions.length; ++i) { final int j = spaceRank + i; if (effectiveBlockDimensions[j] < 0) { if (effectiveBlockDimensions == blockDimensions) { effectiveBlockDimensions = blockDimensions.clone(); } effectiveBlockDimensions[j] = arrayDimensions[i]; } if (effectiveBlockDimensions[j] != arrayDimensions[i]) { throw new HDF5JavaException( "Block-wise reading of array type data sets is not supported."); } } final int[] spaceBlockDimensions = Arrays.copyOfRange(effectiveBlockDimensions, 0, spaceRank); final long[] spaceOfs = Arrays.copyOfRange(offset, 0, spaceRank); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, spaceOfs, spaceBlockDimensions, registry); final long[] dataBlock = new long[spaceParams.blockSize * info.getTypeInformation().getNumberOfElements()]; final int memoryDataTypeId = baseReader.h5.createArrayType(H5T_NATIVE_INT64, info.getTypeInformation() .getDimensions(), registry); baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, dataBlock); return new MDLongArray(dataBlock, effectiveBlockDimensions); } @Override public Iterable> getArrayNaturalBlocks(final String dataSetPath) throws HDF5JavaException { baseReader.checkOpen(); final HDF5NaturalBlock1DParameters params = new HDF5NaturalBlock1DParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlock1DParameters.HDF5NaturalBlock1DIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5DataBlock next() { final long offset = index.computeOffsetAndSizeGetOffset(); final long[] block = readArrayBlockWithOffset(dataSetPath, index .getBlockSize(), offset); return new HDF5DataBlock(block, index.getAndIncIndex(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } @Override public Iterable> getMDArrayNaturalBlocks(final String dataSetPath) { baseReader.checkOpen(); final HDF5NaturalBlockMDParameters params = new HDF5NaturalBlockMDParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlockMDParameters.HDF5NaturalBlockMDIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5MDDataBlock next() { final long[] offset = index.computeOffsetAndSizeGetOffsetClone(); final MDLongArray data = readMDArrayBlockWithOffset(dataSetPath, index .getBlockSize(), offset); return new HDF5MDDataBlock(data, index .getIndexClone(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } long[] getLongArrayAttribute(final int objectId, final String attributeName, ICleanUpRegistry registry) { final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, registry); final int memoryTypeId; final int len; if (baseReader.h5.getClassType(attributeTypeId) == H5T_ARRAY) { final int[] arrayDimensions = baseReader.h5.getArrayDimensions(attributeTypeId); if (arrayDimensions.length != 1) { throw new HDF5JavaException( "Array needs to be of rank 1, but is of rank " + arrayDimensions.length); } len = arrayDimensions[0]; memoryTypeId = baseReader.h5.createArrayType(H5T_NATIVE_INT64, len, registry); } else { final long[] arrayDimensions = baseReader.h5.getDataDimensionsForAttribute(attributeId, registry); memoryTypeId = H5T_NATIVE_INT64; len = HDF5Utils.getOneDimensionalArraySize(arrayDimensions); } final long[] data = baseReader.h5.readAttributeAsLongArray(attributeId, memoryTypeId, len); return data; } MDLongArray getLongMDArrayAttribute(final int objectId, final String attributeName, ICleanUpRegistry registry) { try { final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, registry); final int memoryTypeId; final int[] arrayDimensions; if (baseReader.h5.getClassType(attributeTypeId) == H5T_ARRAY) { arrayDimensions = baseReader.h5.getArrayDimensions(attributeTypeId); memoryTypeId = baseReader.h5.createArrayType(H5T_NATIVE_INT64, arrayDimensions, registry); } else { arrayDimensions = MDArray.toInt(baseReader.h5.getDataDimensionsForAttribute( attributeId, registry)); memoryTypeId = H5T_NATIVE_INT64; } final int len = MDArray.getLength(arrayDimensions); final long[] data = baseReader.h5.readAttributeAsLongArray(attributeId, memoryTypeId, len); return new MDLongArray(data, arrayDimensions); } catch (IllegalArgumentException ex) { throw new HDF5JavaException(ex.getMessage()); } } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5LongWriter.java000066400000000000000000000666171256564762100267500ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.HDF5IntStorageFeatures.INT_NO_COMPRESSION; import static ch.systemsx.cisd.hdf5.hdf5lib.H5D.H5Dwrite; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_ALL; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_INT64; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_I64LE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_U64LE; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDLongArray; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; /** * The implementation of {@link IHDF5LongWriter}. * * @author Bernd Rinn */ class HDF5LongWriter extends HDF5LongReader implements IHDF5LongWriter { private final HDF5BaseWriter baseWriter; HDF5LongWriter(HDF5BaseWriter baseWriter) { super(baseWriter); assert baseWriter != null; this.baseWriter = baseWriter; } // ///////////////////// // Attributes // ///////////////////// @Override public void setAttr(final String objectPath, final String name, final long value) { assert objectPath != null; assert name != null; baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { 1 }, registry); baseWriter.setAttribute(objectPath, name, H5T_STD_I64LE, H5T_NATIVE_INT64, dataSpaceId, new long[] { value }, registry); } else { baseWriter.setAttribute(objectPath, name, H5T_STD_I64LE, H5T_NATIVE_INT64, -1, new long[] { value }, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void setArrayAttr(final String objectPath, final String name, final long[] value) { assert objectPath != null; assert name != null; assert value != null; baseWriter.checkOpen(); final ICallableWithCleanUp setAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { value.length }, registry); baseWriter.setAttribute(objectPath, name, H5T_STD_I64LE, H5T_NATIVE_INT64, dataSpaceId, value, registry); } else { final int memoryTypeId = baseWriter.h5.createArrayType(H5T_NATIVE_INT64, value.length, registry); final int storageTypeId = baseWriter.h5.createArrayType(H5T_STD_I64LE, value.length, registry); baseWriter.setAttribute(objectPath, name, storageTypeId, memoryTypeId, -1, value, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(setAttributeRunnable); } @Override public void setMDArrayAttr(final String objectPath, final String name, final MDLongArray value) { assert objectPath != null; assert name != null; assert value != null; baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(value.longDimensions(), registry); baseWriter.setAttribute(objectPath, name, H5T_STD_I64LE, H5T_NATIVE_INT64, dataSpaceId, value.getAsFlatArray(), registry); } else { final int memoryTypeId = baseWriter.h5.createArrayType(H5T_NATIVE_INT64, value.dimensions(), registry); final int storageTypeId = baseWriter.h5.createArrayType(H5T_STD_I64LE, value.dimensions(), registry); baseWriter.setAttribute(objectPath, name, storageTypeId, memoryTypeId, -1, value.getAsFlatArray(), registry); } return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void setMatrixAttr(final String objectPath, final String name, final long[][] value) { setMDArrayAttr(objectPath, name, new MDLongArray(value)); } // ///////////////////// // Data Sets // ///////////////////// @Override public void write(final String objectPath, final long value) { assert objectPath != null; baseWriter.checkOpen(); baseWriter.writeScalar(objectPath, H5T_STD_I64LE, H5T_NATIVE_INT64, value); } @Override public void writeArray(final String objectPath, final long[] data) { writeArray(objectPath, data, INT_NO_COMPRESSION); } @Override public void writeArray(final String objectPath, final long[] data, final HDF5IntStorageFeatures features) { assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, features.isSigned() ? H5T_STD_I64LE : H5T_STD_U64LE, new long[] { data.length }, 8, features, registry); H5Dwrite(dataSetId, H5T_NATIVE_INT64, H5S_ALL, H5S_ALL, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createArray(final String objectPath, final int size) { createArray(objectPath, size, INT_NO_COMPRESSION); } @Override public void createArray(final String objectPath, final long size, final int blockSize) { createArray(objectPath, size, blockSize, INT_NO_COMPRESSION); } @Override public void createArray(final String objectPath, final int size, final HDF5IntStorageFeatures features) { assert objectPath != null; assert size >= 0; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (features.requiresChunking()) { baseWriter.createDataSet(objectPath, features.isSigned() ? H5T_STD_I64LE : H5T_STD_U64LE, features, new long[] { 0 }, new long[] { size }, 8, registry); } else { baseWriter.createDataSet(objectPath, features.isSigned() ? H5T_STD_I64LE : H5T_STD_U64LE, features, new long[] { size }, null, 8, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void createArray(final String objectPath, final long size, final int blockSize, final HDF5IntStorageFeatures features) { assert objectPath != null; assert size >= 0; assert blockSize >= 0 && (blockSize <= size || size == 0); baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { baseWriter.createDataSet(objectPath, features.isSigned() ? H5T_STD_I64LE : H5T_STD_U64LE, features, new long[] { size }, new long[] { blockSize }, 8, registry); return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void writeArrayBlock(final String objectPath, final long[] data, final long blockNumber) { writeArrayBlockWithOffset(objectPath, data, data.length, data.length * blockNumber); } @Override public void writeArrayBlockWithOffset(final String objectPath, final long[] data, final int dataSize, final long offset) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] blockDimensions = new long[] { dataSize }; final long[] slabStartOrNull = new long[] { offset }; final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, new long[] { offset + dataSize }, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, slabStartOrNull, blockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(blockDimensions, registry); H5Dwrite(dataSetId, H5T_NATIVE_INT64, memorySpaceId, dataSpaceId, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } /** * Writes out a long matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ @Override public void writeMatrix(final String objectPath, final long[][] data) { writeMatrix(objectPath, data, INT_NO_COMPRESSION); } @Override public void writeMatrix(final String objectPath, final long[][] data, final HDF5IntStorageFeatures features) { assert objectPath != null; assert data != null; assert HDF5Utils.areMatrixDimensionsConsistent(data); writeMDArray(objectPath, new MDLongArray(data), features); } @Override public void createMatrix(final String objectPath, final int sizeX, final int sizeY) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; createMDArray(objectPath, new int[] { sizeX, sizeY }); } @Override public void createMatrix(final String objectPath, final int sizeX, final int sizeY, final HDF5IntStorageFeatures features) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; createMDArray(objectPath, new int[] { sizeX, sizeY }, features); } @Override public void createMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; assert blockSizeX >= 0 && (blockSizeX <= sizeX || sizeX == 0); assert blockSizeY >= 0 && (blockSizeY <= sizeY || sizeY == 0); createMDArray(objectPath, new long[] { sizeX, sizeY }, new int[] { blockSizeX, blockSizeY }); } @Override public void createMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY, final HDF5IntStorageFeatures features) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; assert blockSizeX >= 0 && (blockSizeX <= sizeX || sizeX == 0); assert blockSizeY >= 0 && (blockSizeY <= sizeY || sizeY == 0); createMDArray(objectPath, new long[] { sizeX, sizeY }, new int[] { blockSizeX, blockSizeY }, features); } @Override public void writeMatrixBlock(final String objectPath, final long[][] data, final long blockNumberX, final long blockNumberY) { assert objectPath != null; assert data != null; writeMDArrayBlock(objectPath, new MDLongArray(data), new long[] { blockNumberX, blockNumberY }); } @Override public void writeMatrixBlockWithOffset(final String objectPath, final long[][] data, final long offsetX, final long offsetY) { assert objectPath != null; assert data != null; writeMDArrayBlockWithOffset(objectPath, new MDLongArray(data, new int[] { data.length, data[0].length }), new long[] { offsetX, offsetY }); } @Override public void writeMatrixBlockWithOffset(final String objectPath, final long[][] data, final int dataSizeX, final int dataSizeY, final long offsetX, final long offsetY) { assert objectPath != null; assert data != null; writeMDArrayBlockWithOffset(objectPath, new MDLongArray(data, new int[] { dataSizeX, dataSizeY }), new long[] { offsetX, offsetY }); } @Override public void writeMDArray(final String objectPath, final MDLongArray data) { writeMDArray(objectPath, data, INT_NO_COMPRESSION); } @Override public void writeMDArraySlice(String objectPath, MDLongArray data, IndexMap boundIndices) { baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), null, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDLongArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArraySlice(String objectPath, MDLongArray data, long[] boundIndices) { baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), null, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDLongArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArray(final String objectPath, final MDLongArray data, final HDF5IntStorageFeatures features) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, features.isSigned() ? H5T_STD_I64LE : H5T_STD_U64LE, data.longDimensions(), 8, features, registry); H5Dwrite(dataSetId, H5T_NATIVE_INT64, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createMDArray(final String objectPath, final int[] dimensions) { createMDArray(objectPath, dimensions, INT_NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions) { createMDArray(objectPath, dimensions, blockDimensions, INT_NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final int[] dimensions, final HDF5IntStorageFeatures features) { assert objectPath != null; assert dimensions != null; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (features.requiresChunking()) { final long[] nullDimensions = new long[dimensions.length]; baseWriter.createDataSet(objectPath, features.isSigned() ? H5T_STD_I64LE : H5T_STD_U64LE, features, nullDimensions, MDArray.toLong(dimensions), 8, registry); } else { baseWriter.createDataSet(objectPath, features.isSigned() ? H5T_STD_I64LE : H5T_STD_U64LE, features, MDArray.toLong(dimensions), null, 8, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void createMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions, final HDF5IntStorageFeatures features) { assert objectPath != null; assert dimensions != null; assert blockDimensions != null; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { baseWriter.createDataSet(objectPath, features.isSigned() ? H5T_STD_I64LE : H5T_STD_U64LE, features, dimensions, MDArray.toLong(blockDimensions), 8, registry); return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void writeMDArrayBlock(final String objectPath, final MDLongArray data, final long[] blockNumber) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeMDArrayBlockWithOffset(objectPath, data, offset); } @Override public void writeSlicedMDArrayBlock(final String objectPath, final MDLongArray data, final long[] blockNumber, IndexMap boundIndices) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeSlicedMDArrayBlockWithOffset(objectPath, data, offset, boundIndices); } @Override public void writeSlicedMDArrayBlock(String objectPath, MDLongArray data, long[] blockNumber, long[] boundIndices) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeSlicedMDArrayBlockWithOffset(objectPath, data, offset, boundIndices); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final MDLongArray data, final long[] offset) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] dimensions = data.longDimensions(); assert dimensions.length == offset.length; final long[] dataSetDimensions = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + dimensions[i]; } final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, dimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(dimensions, registry); H5Dwrite(dataSetId, H5T_NATIVE_INT64, memorySpaceId, dataSpaceId, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeSlicedMDArrayBlockWithOffset(String objectPath, MDLongArray data, long[] offset, IndexMap boundIndices) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), offset, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDLongArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeSlicedMDArrayBlockWithOffset(String objectPath, MDLongArray data, long[] offset, long[] boundIndices) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), offset, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDLongArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final MDLongArray data, final int[] blockDimensions, final long[] offset, final int[] memoryOffset) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] memoryDimensions = data.longDimensions(); assert memoryDimensions.length == offset.length; final long[] longBlockDimensions = MDArray.toLong(blockDimensions); assert longBlockDimensions.length == offset.length; final long[] dataSetDimensions = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + blockDimensions[i]; } final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, longBlockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(memoryDimensions, registry); baseWriter.h5.setHyperslabBlock(memorySpaceId, MDArray.toLong(memoryOffset), longBlockDimensions); H5Dwrite(dataSetId, H5T_NATIVE_INT64, memorySpaceId, dataSpaceId, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5MDDataBlock.java000066400000000000000000000044111256564762100267010ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ch.systemsx.cisd.base.mdarray.MDAbstractArray; /** * A class that is used for iterating over a data set block by block, using * natural data blocks. The Natural block for chunked data sets is a chunk, for * non-chunked data sets it is the complete array. *

* The pattern for using this class is: * * 

 * for (HDF5DataBlock<MDIntArray> block : reader.getIntMDNaturalBlocks(dsNameMD))
 * {
 *     MDIntArray naturalBlock = block.getData();
 *     ... work on naturalBlock, use block.getIndex() or block.getOffset() where needed ...
 * }
 *
* * The iteration in the multi-dimensional case will be in C-order, that is last-index is iterated * over first. *

* Note: If the size of the data set is not an integer number of blocks, then the last block * will be smaller than the natural block size. * * @author Bernd Rinn */ public class HDF5MDDataBlock> { private final T data; private final long[] offset; private final long[] index; HDF5MDDataBlock(T block, long[] index, long[] offset) { this.data = block; this.index = index; this.offset = offset; } /** * Returns the data block itself. */ public T getData() { return data; } /** * Returns the offset in the data set for the current iteration in each dimension. */ public long[] getOffset() { return offset; } /** * Returns the iteration index of this block, starting with { 0, ..., 0 }. */ public long[] getIndex() { return index; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5MDEnumBlock.java000066400000000000000000000044261256564762100267420ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; /** * A class that is used for iterating over an Enum data set block by block, using * natural data blocks. The Natural block for chunked data sets is a chunk, for * non-chunked data sets it is the complete array. *

* The pattern for using this class is: * * 

 * for (HDF5MDEnumBlock block : reader.getEnumMDNaturalBlocks(dsNameMD))
 * {
 *     HDF5EnumerationValueMDArray naturalBlock = block.getData();
 *     ... work on naturalBlock, use block.getIndex() or block.getOffset() where needed ...
 * }
 *
* * The iteration in the multi-dimensional case will be in C-order, that is last-index is iterated * over first. *

* Note: If the size of the data set is not an integer number of blocks, then the last block * will be smaller than the natural block size. * * @author Bernd Rinn */ public class HDF5MDEnumBlock { private final HDF5EnumerationValueMDArray data; private final long[] offset; private final long[] index; HDF5MDEnumBlock(HDF5EnumerationValueMDArray block, long[] index, long[] offset) { this.data = block; this.index = index; this.offset = offset; } /** * Returns the data block itself. */ public HDF5EnumerationValueMDArray getData() { return data; } /** * Returns the offset in the data set for the current iteration in each dimension. */ public long[] getOffset() { return offset; } /** * Returns the iteration index of this block, starting with { 0, ..., 0 }. */ public long[] getIndex() { return index; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5MemberByteifyer.java000066400000000000000000000125651256564762100277370ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.hdf5lib.H5T.H5Tinsert; import java.lang.reflect.Field; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; import ch.systemsx.cisd.hdf5.hdf5lib.HDFNativeData; /** * A class that byteifies member fields of objects. * * @author Bernd Rinn */ abstract class HDF5MemberByteifyer { private final Field fieldOrNull; private final String memberName; protected final int maxCharacters; protected final int size; protected final int offsetOnDisk; protected final int offsetInMemory; protected final CharacterEncoding encoding; private final HDF5DataTypeVariant typeVariant; private final boolean isVariableLengthType; HDF5MemberByteifyer(Field fieldOrNull, String memberName, int size, int offset, int memOffset, boolean isVariableLengthType, HDF5DataTypeVariant typeVariantOrNull) { this(fieldOrNull, memberName, size, offset, memOffset, CharacterEncoding.ASCII, size, isVariableLengthType, false, typeVariantOrNull); } HDF5MemberByteifyer(Field fieldOrNull, String memberName, int size, int offset, int memOffset, CharacterEncoding encoding, int maxCharacters, boolean isVariableLengthType, boolean isReferenceType) { this(fieldOrNull, memberName, size, offset, memOffset, encoding, maxCharacters, isVariableLengthType, isReferenceType, HDF5DataTypeVariant.NONE); } private HDF5MemberByteifyer(Field fieldOrNull, String memberName, int size, int offset, int memOffset, CharacterEncoding encoding, int maxCharacters, boolean isVariableLengthType, boolean isReferenceType, HDF5DataTypeVariant typeVariantOrNull) { this.isVariableLengthType = isVariableLengthType; this.fieldOrNull = fieldOrNull; this.memberName = memberName; this.maxCharacters = maxCharacters; if (isVariableLengthType) { this.size = HDFNativeData.getMachineWordSize(); } else if (isReferenceType) { this.size = HDF5BaseReader.REFERENCE_SIZE_IN_BYTES; } else { this.size = size; } this.offsetOnDisk = offset; this.offsetInMemory = PaddingUtils.padOffset(memOffset, getElementSize()); this.encoding = encoding; this.typeVariant = HDF5DataTypeVariant.maskNull(typeVariantOrNull); } /** * Returns the size of one element of this data type in bytes. */ abstract int getElementSize(); abstract byte[] byteify(int compoundDataTypeId, Object obj) throws IllegalAccessException; abstract void setFromByteArray(int compoundDataTypeId, Object obj, byte[] byteArr, int arrayOffset) throws IllegalAccessException; abstract int getMemberStorageTypeId(); /** * Returns -1 if the native type id should be inferred from the storage type id */ abstract int getMemberNativeTypeId(); HDF5EnumerationType tryGetEnumType() { return null; } void insertType(int dataTypeId) { H5Tinsert(dataTypeId, memberName, offsetOnDisk, getMemberStorageTypeId()); } void insertNativeType(int dataTypeId, HDF5 h5, ICleanUpRegistry registry) { if (getMemberNativeTypeId() < 0) { H5Tinsert(dataTypeId, memberName, offsetInMemory, h5.getNativeDataType(getMemberStorageTypeId(), registry)); } else { H5Tinsert(dataTypeId, memberName, offsetInMemory, getMemberNativeTypeId()); } } String getMemberName() { return memberName; } Field tryGetField() { return fieldOrNull; } int getMaxCharacters() { return maxCharacters; } int getSize() { return size; } int getOffsetOnDisk() { return offsetOnDisk; } int getTotalSizeOnDisk() { return offsetOnDisk + size; } int getOffsetInMemory() { return offsetInMemory; } int getTotalSizeInMemory() { return offsetInMemory + size; } HDF5DataTypeVariant getTypeVariant() { return typeVariant; } boolean isVariableLengthType() { return isVariableLengthType; } String describe() { if (fieldOrNull != null) { return "field '" + fieldOrNull.getName() + "' of class '" + fieldOrNull.getDeclaringClass().getCanonicalName() + "'"; } else { return "member '" + memberName + "'"; } } boolean isDummy() { return false; } boolean mayBeCut() { return false; } @Override public String toString() { return describe(); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5NaturalBlock1DParameters.java000066400000000000000000000050761256564762100314360ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.util.NoSuchElementException; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; /** * A class for computing the parameters of one-dimensional natural blocks. * * @author Bernd Rinn */ final class HDF5NaturalBlock1DParameters { private final int naturalBlockSize; private final long numberOfBlocks; private final int lastBlockSize; final class HDF5NaturalBlock1DIndex { private long index = 0; private long offset; private int blockSize; boolean hasNext() { return index < numberOfBlocks; } long computeOffsetAndSizeGetOffset() { if (hasNext() == false) { throw new NoSuchElementException(); } offset = naturalBlockSize * index; blockSize = (index == numberOfBlocks - 1) ? lastBlockSize : naturalBlockSize; return offset; } int getBlockSize() { return blockSize; } long getAndIncIndex() { return index++; } } HDF5NaturalBlock1DParameters(final HDF5DataSetInformation info) { if (info.getRank() > 1) { throw new HDF5JavaException("Data Set is expected to be of rank 1 (rank=" + info.getRank() + ")"); } final long size = info.getDimensions()[0]; naturalBlockSize = (info.getStorageLayout() == HDF5StorageLayout.CHUNKED) ? info.tryGetChunkSizes()[0] : (int) size; final int sizeModNaturalBlockSize = (int) (size % naturalBlockSize); numberOfBlocks = (size / naturalBlockSize) + (sizeModNaturalBlockSize != 0 ? 1 : 0); lastBlockSize = (sizeModNaturalBlockSize != 0) ? sizeModNaturalBlockSize : naturalBlockSize; } HDF5NaturalBlock1DIndex getNaturalBlockIndex() { return new HDF5NaturalBlock1DIndex(); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5NaturalBlockMDParameters.java000066400000000000000000000067411256564762100314720ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.util.NoSuchElementException; import ch.systemsx.cisd.base.mdarray.MDAbstractArray; /** * A class for computing the parameters of multi-dimensional natural blocks. * * @author Bernd Rinn */ final class HDF5NaturalBlockMDParameters { private final int rank; private final long[] numberOfBlocks; private final int[] naturalBlockSize; private final int[] lastBlockSize; final class HDF5NaturalBlockMDIndex { private long[] index = new long[rank]; private long[] offset = new long[rank]; private int[] blockSize = naturalBlockSize.clone(); private boolean indexCalculated = true; boolean hasNext() { if (indexCalculated) { return true; } for (int i = index.length - 1; i >= 0; --i) { ++index[i]; if (index[i] < numberOfBlocks[i]) { offset[i] += naturalBlockSize[i]; if (index[i] == numberOfBlocks[i] - 1) { blockSize[i] = lastBlockSize[i]; } indexCalculated = true; break; } else { index[i] = 0; offset[i] = 0; blockSize[i] = naturalBlockSize[i]; } } return indexCalculated; } long[] computeOffsetAndSizeGetOffsetClone() { if (hasNext() == false) { throw new NoSuchElementException(); } indexCalculated = false; return offset.clone(); } int[] getBlockSize() { return blockSize; } long[] getIndexClone() { return index.clone(); } } HDF5NaturalBlockMDParameters(final HDF5DataSetInformation info) { rank = info.getRank(); final long[] dimensions = info.getDimensions(); naturalBlockSize = (info.getStorageLayout() == HDF5StorageLayout.CHUNKED) ? info.tryGetChunkSizes() : MDAbstractArray.toInt(dimensions); numberOfBlocks = new long[rank]; lastBlockSize = new int[rank]; for (int i = 0; i < dimensions.length; ++i) { final int sizeModNaturalBlockSize = (int) (dimensions[i] % naturalBlockSize[i]); numberOfBlocks[i] = (dimensions[i] / naturalBlockSize[i]) + (sizeModNaturalBlockSize != 0 ? 1 : 0); lastBlockSize[i] = (sizeModNaturalBlockSize != 0) ? sizeModNaturalBlockSize : naturalBlockSize[i]; } } HDF5NaturalBlockMDIndex getNaturalBlockIndex() { return new HDF5NaturalBlockMDIndex(); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5ObjectInformation.java000066400000000000000000000064761256564762100302650ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; /** * Information about an object in an HDF5 file. * * @author Bernd Rinn */ public final class HDF5ObjectInformation extends HDF5CommonInformation { private final long fileNumber; private final long address; private final int referenceCount; private final long creationTime; private final long numberOfAttributes; HDF5ObjectInformation(String path, HDF5ObjectType objectType, long[] info) { super(path, objectType); this.fileNumber = info[0]; this.address = info[1]; this.referenceCount = (int) info[2]; this.creationTime = info[3]; this.numberOfAttributes = info[4]; } /** * Returns the file number that the object is in. Can be useful when external links are * involved. */ public long getFileNumber() { return fileNumber; } /** * Returns the address of the object in the file. If the address of two links is the same, then * they point to the same object. Can be used to spot hard or soft links. */ public long getAddress() { return address; } /** * Returns the number of references that point to this object. (Number of hard links that point * to the object). */ public int getReferenceCount() { return referenceCount; } /** * Returns the time of creation of this object (as number of seconds since start of the epoch). * Note that this only works for data set, for groups, this will always return 0. */ public long getCreationTime() { return creationTime; } /** * Returns the number of attributes that is object has. */ public long getNumberOfAttributes() { return numberOfAttributes; } @Override public int hashCode() { final int prime = 31; int result = 1; result = prime * result + ((path == null) ? 0 : path.hashCode()); result = prime * result + ((int) address); return result; } @Override public boolean equals(Object obj) { if (this == obj) { return true; } if (obj == null) { return false; } if (getClass() != obj.getClass()) { return false; } final HDF5ObjectInformation other = (HDF5ObjectInformation) obj; if (path == null) { if (other.path != null) { return false; } } else if (path.equals(other.path) == false) { return false; } if (other.address != address) { return false; } return true; } } HDF5ObjectReadOnlyInfoProviderHandler.java000066400000000000000000000406261256564762100332560ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.HDF5Utils.removeInternalNames; import java.util.List; import ch.systemsx.cisd.base.mdarray.MDAbstractArray; import ch.systemsx.cisd.hdf5.HDF5DataTypeInformation.DataTypeInfoOptions; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; /** * Implementation of {@link IHDF5ObjectReadOnlyInfoProviderHandler} * * @author Bernd Rinn */ class HDF5ObjectReadOnlyInfoProviderHandler implements IHDF5ObjectReadOnlyInfoProviderHandler { private final HDF5BaseReader baseReader; HDF5ObjectReadOnlyInfoProviderHandler(HDF5BaseReader baseReader) { assert baseReader != null; this.baseReader = baseReader; } // ///////////////////// // Objects & Links // ///////////////////// @Override public HDF5LinkInformation getLinkInformation(final String objectPath) { baseReader.checkOpen(); return baseReader.h5.getLinkInfo(baseReader.fileId, objectPath, false); } @Override public HDF5ObjectInformation getObjectInformation(final String objectPath) { baseReader.checkOpen(); return baseReader.h5.getObjectInfo(baseReader.fileId, objectPath, false); } @Override public HDF5ObjectType getObjectType(final String objectPath, boolean followLink) { baseReader.checkOpen(); if (followLink) { return baseReader.h5.getObjectTypeInfo(baseReader.fileId, objectPath, false); } else { return baseReader.h5.getLinkTypeInfo(baseReader.fileId, objectPath, false); } } @Override public HDF5ObjectType getObjectType(final String objectPath) { return getObjectType(objectPath, true); } @Override public boolean exists(final String objectPath, boolean followLink) { if (followLink == false) { // Optimization baseReader.checkOpen(); if ("/".equals(objectPath)) { return true; } return baseReader.h5.exists(baseReader.fileId, objectPath); } else { return exists(objectPath); } } @Override public boolean exists(final String objectPath) { baseReader.checkOpen(); if ("/".equals(objectPath)) { return true; } return baseReader.h5.getObjectTypeId(baseReader.fileId, objectPath, false) >= 0; } @Override public String toHouseKeepingPath(String objectPath) { return HDF5Utils.toHouseKeepingPath(objectPath, baseReader.houseKeepingNameSuffix); } @Override public boolean isHouseKeepingObject(String objectPath) { return HDF5Utils.isInternalName(objectPath, baseReader.houseKeepingNameSuffix); } @Override public boolean isGroup(final String objectPath, boolean followLink) { return HDF5ObjectType.isGroup(getObjectType(objectPath, followLink)); } @Override public boolean isGroup(final String objectPath) { return HDF5ObjectType.isGroup(getObjectType(objectPath)); } @Override public boolean isDataSet(final String objectPath, boolean followLink) { return HDF5ObjectType.isDataSet(getObjectType(objectPath, followLink)); } @Override public boolean isDataSet(final String objectPath) { return HDF5ObjectType.isDataSet(getObjectType(objectPath)); } @Override public boolean isDataType(final String objectPath, boolean followLink) { return HDF5ObjectType.isDataType(getObjectType(objectPath, followLink)); } @Override public boolean isDataType(final String objectPath) { return HDF5ObjectType.isDataType(getObjectType(objectPath)); } @Override public boolean isSoftLink(final String objectPath) { return HDF5ObjectType.isSoftLink(getObjectType(objectPath, false)); } @Override public boolean isExternalLink(final String objectPath) { return HDF5ObjectType.isExternalLink(getObjectType(objectPath, false)); } @Override public boolean isSymbolicLink(final String objectPath) { return HDF5ObjectType.isSymbolicLink(getObjectType(objectPath, false)); } @Override public String tryGetSymbolicLinkTarget(final String objectPath) { return getLinkInformation(objectPath).tryGetSymbolicLinkTarget(); } @Override public String tryGetDataTypePath(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp dataTypeNameCallable = new ICallableWithCleanUp() { @Override public String call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final int dataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); return baseReader.tryGetDataTypePath(dataTypeId); } }; return baseReader.runner.call(dataTypeNameCallable); } @Override public String tryGetDataTypePath(HDF5DataType type) { assert type != null; baseReader.checkOpen(); type.check(baseReader.fileId); return baseReader.tryGetDataTypePath(type.getStorageTypeId()); } @Override public List getAttributeNames(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); return removeInternalNames(getAllAttributeNames(objectPath), baseReader.houseKeepingNameSuffix, "/".equals(objectPath)); } @Override public List getAllAttributeNames(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp> attributeNameReaderRunnable = new ICallableWithCleanUp>() { @Override public List call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); return baseReader.h5.getAttributeNames(objectId, registry); } }; return baseReader.runner.call(attributeNameReaderRunnable); } @Override public HDF5DataTypeInformation getAttributeInformation(final String dataSetPath, final String attributeName) { return getAttributeInformation(dataSetPath, attributeName, DataTypeInfoOptions.DEFAULT); } @Override public HDF5DataTypeInformation getAttributeInformation(final String dataSetPath, final String attributeName, final DataTypeInfoOptions dataTypeInfoOptions) { assert dataSetPath != null; baseReader.checkOpen(); final ICallableWithCleanUp informationDeterminationRunnable = new ICallableWithCleanUp() { @Override public HDF5DataTypeInformation call(ICleanUpRegistry registry) { try { final int objectId = baseReader.h5.openObject(baseReader.fileId, dataSetPath, registry); final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int dataTypeId = baseReader.h5 .getDataTypeForAttribute(attributeId, registry); final HDF5DataTypeInformation dataTypeInformation = baseReader.getDataTypeInformation(dataTypeId, dataTypeInfoOptions, registry); if (dataTypeInformation.isArrayType() == false) { final int[] dimensions = MDAbstractArray.toInt(baseReader.h5 .getDataDimensionsForAttribute(attributeId, registry)); if (dimensions.length > 0) { dataTypeInformation.setDimensions(dimensions); } } return dataTypeInformation; } catch (RuntimeException ex) { throw ex; } } }; return baseReader.runner.call(informationDeterminationRunnable); } @Override public HDF5DataSetInformation getDataSetInformation(final String dataSetPath) { return getDataSetInformation(dataSetPath, DataTypeInfoOptions.DEFAULT); } @Override public HDF5DataSetInformation getDataSetInformation(final String dataSetPath, final DataTypeInfoOptions dataTypeInfoOptions) { return getDataSetInformation(dataSetPath, dataTypeInfoOptions, true); } HDF5DataSetInformation getDataSetInformation(final String dataSetPath, final DataTypeInfoOptions dataTypeInfoOptions, final boolean fillInDimensions) { assert dataSetPath != null; baseReader.checkOpen(); return baseReader.getDataSetInformation(dataSetPath, dataTypeInfoOptions, fillInDimensions); } @Override public long getSize(final String objectPath) { return getDataSetInformation(objectPath, DataTypeInfoOptions.MINIMAL).getSize(); } @Override public long getNumberOfElements(final String objectPath) { return getDataSetInformation(objectPath, DataTypeInfoOptions.MINIMAL).getNumberOfElements(); } @Override public int getElementSize(final String objectPath) { return getDataSetInformation(objectPath, DataTypeInfoOptions.MINIMAL, false) .getTypeInformation().getElementSize(); } @Override public int getSpaceRank(String objectPath) { baseReader.checkOpen(); return baseReader.getSpaceRank(objectPath); } @Override public long[] getSpaceDimensions(String objectPath) { baseReader.checkOpen(); return baseReader.getSpaceDimensions(objectPath); } @Override public int getArrayRank(String objectPath) { final HDF5DataSetInformation info = getDataSetInformation(objectPath, DataTypeInfoOptions.MINIMAL, false); return info.getTypeInformation().getRank(); } @Override public int[] getArrayDimensions(String objectPath) { final HDF5DataSetInformation info = getDataSetInformation(objectPath, DataTypeInfoOptions.MINIMAL, false); return info.getTypeInformation().getDimensions(); } @Override public int getRank(String objectPath) { baseReader.checkOpen(); return baseReader.getRank(objectPath); } @Override public long[] getDimensions(String objectPath) { baseReader.checkOpen(); return baseReader.getDimensions(objectPath); } // ///////////////////// // Copies // ///////////////////// @Override public void copy(final String sourceObject, final IHDF5Writer destinationWriter, final String destinationObject) { baseReader.checkOpen(); final HDF5Writer dwriter = (HDF5Writer) destinationWriter; if (dwriter.object() != this) { dwriter.checkOpen(); } baseReader.copyObject(sourceObject, dwriter.getFileId(), destinationObject); } @Override public void copy(String sourceObject, IHDF5Writer destinationWriter) { copy(sourceObject, destinationWriter, "/"); } @Override public void copyAll(IHDF5Writer destinationWriter) { copy("/", destinationWriter, "/"); } // ///////////////////// // Group // ///////////////////// @Override public List getGroupMembers(final String groupPath) { assert groupPath != null; baseReader.checkOpen(); return baseReader.getGroupMembers(groupPath); } @Override public List getAllGroupMembers(final String groupPath) { assert groupPath != null; baseReader.checkOpen(); return baseReader.getAllGroupMembers(groupPath); } @Override public List getGroupMemberPaths(final String groupPath) { assert groupPath != null; baseReader.checkOpen(); return baseReader.getGroupMemberPaths(groupPath); } @Override public List getGroupMemberInformation(final String groupPath, boolean readLinkTargets) { baseReader.checkOpen(); if (readLinkTargets) { return baseReader.h5.getGroupMemberLinkInfo(baseReader.fileId, groupPath, false, baseReader.houseKeepingNameSuffix); } else { return baseReader.h5.getGroupMemberTypeInfo(baseReader.fileId, groupPath, false, baseReader.houseKeepingNameSuffix); } } @Override public List getAllGroupMemberInformation(final String groupPath, boolean readLinkTargets) { baseReader.checkOpen(); if (readLinkTargets) { return baseReader.h5.getGroupMemberLinkInfo(baseReader.fileId, groupPath, true, baseReader.houseKeepingNameSuffix); } else { return baseReader.h5.getGroupMemberTypeInfo(baseReader.fileId, groupPath, true, baseReader.houseKeepingNameSuffix); } } // ///////////////////// // Types // ///////////////////// @Override public HDF5DataTypeVariant tryGetTypeVariant(final String objectPath) { baseReader.checkOpen(); return baseReader.tryGetTypeVariant(objectPath); } @Override public HDF5DataTypeVariant tryGetTypeVariant(String objectPath, String attributeName) { baseReader.checkOpen(); return baseReader.tryGetTypeVariant(objectPath, attributeName); } // ///////////////////// // Attributes // ///////////////////// @Override public boolean hasAttribute(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Boolean call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); return baseReader.h5.existsAttribute(objectId, attributeName); } }; return baseReader.runner.call(writeRunnable); } } HDF5ObjectReadWriteInfoProviderHandler.java000066400000000000000000000305361256564762100334260ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.HDF5Utils.createAttributeTypeVariantAttributeName; import static ch.systemsx.cisd.hdf5.HDF5Utils.createObjectTypeVariantAttributeName; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; /** * Implementation of {@link HDF5ObjectReadWriteInfoProviderHandler}. * * @author Bernd Rinn */ final class HDF5ObjectReadWriteInfoProviderHandler extends HDF5ObjectReadOnlyInfoProviderHandler implements IHDF5ObjectReadWriteInfoProviderHandler { private final HDF5BaseWriter baseWriter; HDF5ObjectReadWriteInfoProviderHandler(HDF5BaseWriter baseWriter) { super(baseWriter); assert baseWriter != null; this.baseWriter = baseWriter; } @Override public void createHardLink(String currentPath, String newPath) { assert currentPath != null; assert newPath != null; baseWriter.checkOpen(); baseWriter.h5.createHardLink(baseWriter.fileId, currentPath, newPath); } @Override public void createSoftLink(String targetPath, String linkPath) { assert targetPath != null; assert linkPath != null; baseWriter.checkOpen(); baseWriter.h5.createSoftLink(baseWriter.fileId, linkPath, targetPath); } @Override public void createOrUpdateSoftLink(String targetPath, String linkPath) { assert targetPath != null; assert linkPath != null; baseWriter.checkOpen(); if (isSymbolicLink(linkPath)) { delete(linkPath); } baseWriter.h5.createSoftLink(baseWriter.fileId, linkPath, targetPath); } @Override public void createExternalLink(String targetFileName, String targetPath, String linkPath) throws IllegalStateException { assert targetFileName != null; assert targetPath != null; assert linkPath != null; baseWriter.checkOpen(); if (baseWriter.fileFormat.isHDF5_1_8_OK() == false) { throw new IllegalStateException( "External links are not allowed in strict HDF5 1.6.x compatibility mode."); } baseWriter.h5.createExternalLink(baseWriter.fileId, linkPath, targetFileName, targetPath); } @Override public void createOrUpdateExternalLink(String targetFileName, String targetPath, String linkPath) throws IllegalStateException { assert targetFileName != null; assert targetPath != null; assert linkPath != null; baseWriter.checkOpen(); if (baseWriter.fileFormat.isHDF5_1_8_OK() == false) { throw new IllegalStateException( "External links are not allowed in strict HDF5 1.6.x compatibility mode."); } if (isSymbolicLink(linkPath)) { delete(linkPath); } baseWriter.h5.createExternalLink(baseWriter.fileId, linkPath, targetFileName, targetPath); } @Override public void delete(String objectPath) { baseWriter.checkOpen(); if (isGroup(objectPath, false)) { for (String path : getGroupMemberPaths(objectPath)) { delete(path); } } baseWriter.h5.deleteObject(baseWriter.fileId, objectPath); } @Override public void move(String oldLinkPath, String newLinkPath) { baseWriter.checkOpen(); baseWriter.h5.moveLink(baseWriter.fileId, oldLinkPath, newLinkPath); } // ///////////////////// // Group // ///////////////////// @Override public void createGroup(final String groupPath) { baseWriter.checkOpen(); baseWriter.h5.createGroup(baseWriter.fileId, groupPath); } @Override public void createGroup(final String groupPath, final int sizeHint) { baseWriter.checkOpen(); final ICallableWithCleanUp createGroupRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { baseWriter.h5.createOldStyleGroup(baseWriter.fileId, groupPath, sizeHint, registry); return null; // Nothing to return. } }; baseWriter.runner.call(createGroupRunnable); } @Override public void createGroup(final String groupPath, final int maxCompact, final int minDense) { baseWriter.checkOpen(); if (baseWriter.fileFormat.isHDF5_1_8_OK() == false) { throw new IllegalStateException( "New style groups are not allowed in strict HDF5 1.6.x compatibility mode."); } final ICallableWithCleanUp createGroupRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { baseWriter.h5.createNewStyleGroup(baseWriter.fileId, groupPath, maxCompact, minDense, registry); return null; // Nothing to return. } }; baseWriter.runner.call(createGroupRunnable); } // ///////////////////// // Attributes // ///////////////////// @Override public void deleteAttribute(final String objectPath, final String name) { baseWriter.checkOpen(); final ICallableWithCleanUp deleteAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int objectId = baseWriter.h5.openObject(baseWriter.fileId, objectPath, registry); baseWriter.h5.deleteAttribute(objectId, name); return null; // Nothing to return. } }; baseWriter.runner.call(deleteAttributeRunnable); } // ///////////////////// // Data Sets // ///////////////////// @Override public void setDataSetSize(final String objectPath, final long newSize) { setDataSetDimensions(objectPath, new long[] { newSize }); } @Override public void setDataSetDimensions(final String objectPath, final long[] newDimensions) { baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { baseWriter.setDataSetDimensions(objectPath, newDimensions, registry); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } // ///////////////////// // Types // ///////////////////// @Override public void setTypeVariant(final String objectPath, final HDF5DataTypeVariant typeVariant) { baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { 1 }, registry); baseWriter.setAttribute( objectPath, createObjectTypeVariantAttributeName(baseWriter.houseKeepingNameSuffix), baseWriter.typeVariantDataType.getStorageTypeId(), baseWriter.typeVariantDataType.getNativeTypeId(), dataSpaceId, baseWriter.typeVariantDataType.getEnumType().toStorageForm( typeVariant.ordinal()), registry); } else { baseWriter.setAttribute( objectPath, createObjectTypeVariantAttributeName(baseWriter.houseKeepingNameSuffix), baseWriter.typeVariantDataType.getStorageTypeId(), baseWriter.typeVariantDataType.getNativeTypeId(), -1, baseWriter.typeVariantDataType.getEnumType().toStorageForm( typeVariant.ordinal()), registry); } return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void setTypeVariant(final String objectPath, final String attributeName, final HDF5DataTypeVariant typeVariant) { baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { 1 }, registry); baseWriter.setAttribute( objectPath, createAttributeTypeVariantAttributeName(attributeName, baseWriter.houseKeepingNameSuffix), baseWriter.typeVariantDataType.getStorageTypeId(), baseWriter.typeVariantDataType.getNativeTypeId(), dataSpaceId, baseWriter.typeVariantDataType.getEnumType() .toStorageForm(typeVariant.ordinal()), registry); } else { baseWriter.setAttribute( objectPath, createAttributeTypeVariantAttributeName(attributeName, baseWriter.houseKeepingNameSuffix), baseWriter.typeVariantDataType.getStorageTypeId(), baseWriter.typeVariantDataType.getNativeTypeId(), -1, baseWriter.typeVariantDataType.getEnumType().toStorageForm( typeVariant.ordinal()), registry); } return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void deleteTypeVariant(String objectPath) { deleteAttribute(objectPath, createObjectTypeVariantAttributeName(baseWriter.houseKeepingNameSuffix)); } @Override public void deleteTypeVariant(String objectPath, String attributeName) { deleteAttribute( objectPath, createAttributeTypeVariantAttributeName(attributeName, baseWriter.houseKeepingNameSuffix)); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5ObjectType.java000066400000000000000000000063341256564762100267120ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; /** * An enumeration that represents the basic HDF5 object types. * * @author Bernd Rinn */ public enum HDF5ObjectType { DATASET, DATATYPE, GROUP, SOFT_LINK, EXTERNAL_LINK, OTHER, NONEXISTENT; /** * Returns false, if the objectTypeOrNull is equal to * {@link #NONEXISTENT} and true otherwise. * * @param objectType The object type to check. */ public static boolean exists(HDF5ObjectType objectType) { return (objectType != NONEXISTENT); } /** * Returns true, if the objectTypeOrNull is equal to {@link #GROUP} and * false otherwise. * * @param objectType The object type to check. */ public static boolean isGroup(HDF5ObjectType objectType) { return (objectType == GROUP); } /** * Returns true, if the objectTypeOrNull is equal to {@link #DATASET} * and false otherwise. * * @param objectType The object type to check. */ public static boolean isDataSet(HDF5ObjectType objectType) { return (objectType == DATASET); } /** * Returns true, if the objectTypeOrNull is equal to {@link #DATATYPE} * and false otherwise. * * @param objectType The object type to check. */ public static boolean isDataType(HDF5ObjectType objectType) { return (objectType == DATATYPE); } /** * Returns true, if the objectTypeOrNull is equal to {@link #SOFT_LINK} * and false otherwise. * * @param objectType The object type to check. */ public static boolean isSoftLink(HDF5ObjectType objectType) { return (objectType == SOFT_LINK); } /** * Returns true, if the objectTypeOrNull is equal to * {@link #EXTERNAL_LINK} and false otherwise. * * @param objectType The object type to check (can be null). */ public static boolean isExternalLink(HDF5ObjectType objectType) { return (objectType == EXTERNAL_LINK); } /** * Returns true, if the objectTypeOrNull is equal to either * {@link #SOFT_LINK} or {@link #EXTERNAL_LINK}. and false otherwise. * * @param objectType The object type to check. */ public static boolean isSymbolicLink(HDF5ObjectType objectType) { return (objectType == SOFT_LINK) || (objectType == EXTERNAL_LINK); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5OpaqueReader.java000066400000000000000000000322761256564762100272230ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STRING; import java.io.UnsupportedEncodingException; import java.util.Iterator; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.hdf5.HDF5BaseReader.DataSpaceParameters; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; /** * Implementation of {@link IHDF5OpaqueReader} * * @author Bernd Rinn */ public class HDF5OpaqueReader implements IHDF5OpaqueReader { private final HDF5BaseReader baseReader; HDF5OpaqueReader(HDF5BaseReader baseReader) { assert baseReader != null; this.baseReader = baseReader; } @Override public String tryGetOpaqueTag(final String objectPath) { baseReader.checkOpen(); final ICallableWithCleanUp readTagCallable = new ICallableWithCleanUp() { @Override public String call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final int dataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); return baseReader.h5.tryGetOpaqueTag(dataTypeId); } }; return baseReader.runner.call(readTagCallable); } @Override public HDF5OpaqueType tryGetOpaqueType(final String objectPath) { baseReader.checkOpen(); final ICallableWithCleanUp readTagCallable = new ICallableWithCleanUp() { @Override public HDF5OpaqueType call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final int dataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, baseReader.fileRegistry); final String opaqueTagOrNull = baseReader.h5.tryGetOpaqueTag(dataTypeId); if (opaqueTagOrNull == null) { return null; } else { return new HDF5OpaqueType(baseReader.fileId, dataTypeId, opaqueTagOrNull, baseReader); } } }; return baseReader.runner.call(readTagCallable); } @Override public byte[] readArray(final String objectPath) { baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public byte[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); final int nativeDataTypeId = baseReader.h5.getNativeDataTypeForDataSet(dataSetId, registry); final boolean isString = (baseReader.h5.getClassType(nativeDataTypeId) == H5T_STRING); byte[] data; if (isString) { if (baseReader.h5.isVariableLengthString(nativeDataTypeId)) { String[] value = new String[1]; baseReader.h5.readDataSetVL(dataSetId, nativeDataTypeId, value); try { data = value[0].getBytes(CharacterEncoding.ASCII.getCharSetName()); } catch (UnsupportedEncodingException ex) { data = value[0].getBytes(); } } else { final int size = baseReader.h5.getDataTypeSize(nativeDataTypeId); data = new byte[size]; baseReader.h5.readDataSetNonNumeric(dataSetId, nativeDataTypeId, data); } } else { final int elementSize = baseReader.h5.getDataTypeSize(nativeDataTypeId); data = new byte[spaceParams.blockSize * elementSize]; baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); } return data; } }; return baseReader.runner.call(readCallable); } @Override public byte[] getArrayAttr(final String objectPath, final String attributeName) { baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public byte[] call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); return baseReader.getAttributeAsByteArray(objectId, attributeName, registry); } }; return baseReader.runner.call(readCallable); } @Override public byte[] readArrayBlock(final String objectPath, final int blockSize, final long blockNumber) throws HDF5JavaException { baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public byte[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, blockNumber * blockSize, blockSize, registry); final int nativeDataTypeId = baseReader.h5.getNativeDataTypeForDataSet(dataSetId, registry); checkNotAString(objectPath, nativeDataTypeId); final int elementSize = baseReader.h5.getDataTypeSize(nativeDataTypeId); final byte[] data = new byte[elementSize * spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return data; } }; return baseReader.runner.call(readCallable); } @Override public byte[] readArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset) throws HDF5JavaException { baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public byte[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockSize, registry); final int nativeDataTypeId = baseReader.h5.getNativeDataTypeForDataSet(dataSetId, registry); checkNotAString(objectPath, nativeDataTypeId); final int elementSize = baseReader.h5.getDataTypeSize(nativeDataTypeId); final byte[] data = new byte[elementSize * spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return data; } }; return baseReader.runner.call(readCallable); } @Override public int readArrayToBlockWithOffset(final String objectPath, final byte[] buffer, final int blockSize, final long offset, final int memoryOffset) throws HDF5JavaException { if (blockSize + memoryOffset > buffer.length) { throw new HDF5JavaException("Buffer not large enough for blockSize and memoryOffset"); } baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public Integer call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, memoryOffset, offset, blockSize, registry); final int nativeDataTypeId = baseReader.h5.getNativeDataTypeForDataSet(dataSetId, registry); checkNotAString(objectPath, nativeDataTypeId); final int elementSize = baseReader.h5.getDataTypeSize(nativeDataTypeId); if ((blockSize + memoryOffset) * elementSize > buffer.length) { throw new HDF5JavaException( "Buffer not large enough for blockSize and memoryOffset"); } baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, buffer); return spaceParams.blockSize; } }; return baseReader.runner.call(readCallable); } @Override public Iterable> getArrayNaturalBlocks(final String dataSetPath) throws HDF5JavaException { final HDF5NaturalBlock1DParameters params = new HDF5NaturalBlock1DParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlock1DParameters.HDF5NaturalBlock1DIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5DataBlock next() { final long offset = index.computeOffsetAndSizeGetOffset(); final byte[] block = readArrayBlockWithOffset(dataSetPath, index.getBlockSize(), offset); return new HDF5DataBlock(block, index.getAndIncIndex(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } private void checkNotAString(final String objectPath, final int nativeDataTypeId) { final boolean isString = (baseReader.h5.getClassType(nativeDataTypeId) == H5T_STRING); if (isString) { throw new HDF5JavaException(objectPath + " cannot be a String."); } } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5OpaqueType.java000066400000000000000000000023601256564762100267310ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; /** * A class that represents an opaque data type for a given HDF5 file and tag. * * @author Bernd Rinn */ public final class HDF5OpaqueType extends HDF5DataType { private final String tag; HDF5OpaqueType(int fileId, int typeId, String tag, HDF5BaseReader baseReader) { super(fileId, typeId, typeId, baseReader); assert tag != null; this.tag = tag; } /** * Returns the tag of this opaque type. */ public String getTag() { return tag; } @Override public String tryGetName() { return tag; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5OpaqueWriter.java000066400000000000000000000224141256564762100272660ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.HDF5Utils.OPAQUE_PREFIX; import static ch.systemsx.cisd.hdf5.HDF5Utils.createDataTypePath; import static ch.systemsx.cisd.hdf5.hdf5lib.H5D.H5Dwrite; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_ALL; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; /** * Implementation of {@link IHDF5OpaqueWriter}. * * @author Bernd Rinn */ public class HDF5OpaqueWriter extends HDF5OpaqueReader implements IHDF5OpaqueWriter { private final HDF5BaseWriter baseWriter; HDF5OpaqueWriter(HDF5BaseWriter baseWriter) { super(baseWriter); assert baseWriter != null; this.baseWriter = baseWriter; } @Override public void writeArray(final String objectPath, final String tag, final byte[] data) { writeArray(objectPath, tag, data, HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION); } @Override public void writeArray(final String objectPath, final String tag, final byte[] data, final HDF5GenericStorageFeatures features) { assert objectPath != null; assert tag != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataTypeId = getOrCreateOpaqueTypeId(tag); final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, dataTypeId, new long[] { data.length }, 1, features, registry); H5Dwrite(dataSetId, dataTypeId, H5S_ALL, H5S_ALL, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public HDF5OpaqueType createArray(String objectPath, String tag, int size) { return createArray(objectPath, tag, size, HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION); } @Override public HDF5OpaqueType createArray(final String objectPath, final String tag, final long size, final int blockSize) { return createArray(objectPath, tag, size, blockSize, HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION); } @Override public HDF5OpaqueType createArray(final String objectPath, final String tag, final int size, final HDF5GenericStorageFeatures features) { assert objectPath != null; assert tag != null; assert size >= 0; baseWriter.checkOpen(); final int dataTypeId = getOrCreateOpaqueTypeId(tag); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (features.requiresChunking()) { baseWriter.createDataSet(objectPath, dataTypeId, features, new long[] { 0 }, new long[] { size }, 1, registry); } else { baseWriter.createDataSet(objectPath, dataTypeId, features, new long[] { size }, null, 1, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); return new HDF5OpaqueType(baseWriter.fileId, dataTypeId, tag, baseWriter); } @Override public HDF5OpaqueType createArray(final String objectPath, final String tag, final long size, final int blockSize, final HDF5GenericStorageFeatures features) { assert objectPath != null; assert tag != null; assert size >= 0; assert blockSize >= 0 && (blockSize <= size || size == 0); baseWriter.checkOpen(); final int dataTypeId = getOrCreateOpaqueTypeId(tag); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { baseWriter.createDataSet(objectPath, dataTypeId, features, new long[] { size }, new long[] { blockSize }, 1, registry); return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); return new HDF5OpaqueType(baseWriter.fileId, dataTypeId, tag, baseWriter); } @Override public void writeArrayBlock(final String objectPath, final HDF5OpaqueType dataType, final byte[] data, final long blockNumber) { assert objectPath != null; assert dataType != null; assert data != null; baseWriter.checkOpen(); dataType.check(baseWriter.fileId); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] blockDimensions = new long[] { data.length }; final long[] slabStartOrNull = new long[] { data.length * blockNumber }; final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, new long[] { data.length * (blockNumber + 1) }, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, slabStartOrNull, blockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(blockDimensions, registry); H5Dwrite(dataSetId, dataType.getNativeTypeId(), memorySpaceId, dataSpaceId, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeArrayBlockWithOffset(final String objectPath, final HDF5OpaqueType dataType, final byte[] data, final int dataSize, final long offset) { assert objectPath != null; assert dataType != null; assert data != null; baseWriter.checkOpen(); dataType.check(baseWriter.fileId); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] blockDimensions = new long[] { dataSize }; final long[] slabStartOrNull = new long[] { offset }; final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, new long[] { offset + dataSize }, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, slabStartOrNull, blockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(blockDimensions, registry); H5Dwrite(dataSetId, dataType.getNativeTypeId(), memorySpaceId, dataSpaceId, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } private int getOrCreateOpaqueTypeId(final String tag) { final String dataTypePath = createDataTypePath(OPAQUE_PREFIX, baseWriter.houseKeepingNameSuffix, tag); int dataTypeId = baseWriter.getDataTypeId(dataTypePath); if (dataTypeId < 0) { dataTypeId = baseWriter.h5.createDataTypeOpaque(1, tag, baseWriter.fileRegistry); baseWriter.commitDataType(dataTypePath, dataTypeId); } return dataTypeId; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5Reader.java000066400000000000000000002121241256564762100260400ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.io.File; import java.util.Arrays; import java.util.BitSet; import java.util.Date; import java.util.List; import ncsa.hdf.hdf5lib.exceptions.HDF5DatatypeInterfaceException; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDByteArray; import ch.systemsx.cisd.base.mdarray.MDDoubleArray; import ch.systemsx.cisd.base.mdarray.MDFloatArray; import ch.systemsx.cisd.base.mdarray.MDIntArray; import ch.systemsx.cisd.base.mdarray.MDLongArray; import ch.systemsx.cisd.base.mdarray.MDShortArray; import ch.systemsx.cisd.hdf5.HDF5DataTypeInformation.DataTypeInfoOptions; import ch.systemsx.cisd.hdf5.IHDF5CompoundInformationRetriever.IByteArrayInspector; /** * A class for reading HDF5 files (HDF5 1.8.x and older). *

* The class focuses on ease of use instead of completeness. As a consequence not all features of a * valid HDF5 files can be read using this class, but only a subset. (All information written by * {@link HDF5Writer} can be read by this class.) *

* Usage: * * 

 * HDF5Reader reader = new HDF5ReaderConfig("test.h5").reader();
 * float[] f = reader.readFloatArray("/some/path/dataset");
 * String s = reader.getAttributeString("/some/path/dataset", "some key");
 * reader.close();
 *
* * @author Bernd Rinn */ class HDF5Reader implements IHDF5Reader { private final HDF5BaseReader baseReader; private final IHDF5FileLevelReadOnlyHandler fileHandler; private final IHDF5ObjectReadOnlyInfoProviderHandler objectHandler; private final IHDF5ByteReader byteReader; private final IHDF5ByteReader ubyteReader; private final IHDF5ShortReader shortReader; private final IHDF5ShortReader ushortReader; private final IHDF5IntReader intReader; private final IHDF5IntReader uintReader; protected final IHDF5LongReader longReader; private final IHDF5LongReader ulongReader; private final IHDF5FloatReader floatReader; private final IHDF5DoubleReader doubleReader; private final IHDF5BooleanReader booleanReader; private final IHDF5StringReader stringReader; private final IHDF5EnumReader enumReader; private final IHDF5CompoundReader compoundReader; private final IHDF5DateTimeReader dateTimeReader; private final HDF5TimeDurationReader timeDurationReader; private final IHDF5ReferenceReader referenceReader; private final IHDF5OpaqueReader opaqueReader; HDF5Reader(final HDF5BaseReader baseReader) { assert baseReader != null; this.baseReader = baseReader; this.fileHandler = new HDF5FileLevelReadOnlyHandler(baseReader); this.objectHandler = new HDF5ObjectReadOnlyInfoProviderHandler(baseReader); this.byteReader = new HDF5ByteReader(baseReader); this.ubyteReader = new HDF5UnsignedByteReader(baseReader); this.shortReader = new HDF5ShortReader(baseReader); this.ushortReader = new HDF5UnsignedShortReader(baseReader); this.intReader = new HDF5IntReader(baseReader); this.uintReader = new HDF5UnsignedIntReader(baseReader); this.longReader = new HDF5LongReader(baseReader); this.ulongReader = new HDF5UnsignedLongReader(baseReader); this.floatReader = new HDF5FloatReader(baseReader); this.doubleReader = new HDF5DoubleReader(baseReader); this.booleanReader = new HDF5BooleanReader(baseReader); this.stringReader = new HDF5StringReader(baseReader); this.enumReader = new HDF5EnumReader(baseReader); this.compoundReader = new HDF5CompoundReader(baseReader, enumReader); this.dateTimeReader = new HDF5DateTimeReader(baseReader, (HDF5LongReader) longReader); this.timeDurationReader = new HDF5TimeDurationReader(baseReader, (HDF5LongReader) longReader); this.referenceReader = new HDF5ReferenceReader(baseReader); this.opaqueReader = new HDF5OpaqueReader(baseReader); } void checkOpen() { baseReader.checkOpen(); } int getFileId() { return baseReader.fileId; } // ///////////////////// // File // ///////////////////// @Override public IHDF5FileLevelReadOnlyHandler file() { return fileHandler; } @Override public boolean isPerformNumericConversions() { return baseReader.performNumericConversions; } @Override public String getHouseKeepingNameSuffix() { return baseReader.houseKeepingNameSuffix; } @Override public File getFile() { return baseReader.hdf5File; } @Override protected void finalize() throws Throwable { super.finalize(); close(); } @Override public void close() { baseReader.close(); } @Override public boolean isClosed() { return baseReader.isClosed(); } // ///////////////////////////////// // Objects, links, groups and types // ///////////////////////////////// @Override public IHDF5ObjectReadOnlyInfoProviderHandler object() { return objectHandler; } @Override public HDF5LinkInformation getLinkInformation(String objectPath) { return objectHandler.getLinkInformation(objectPath); } @Override public HDF5ObjectInformation getObjectInformation(String objectPath) { return objectHandler.getObjectInformation(objectPath); } @Override public HDF5ObjectType getObjectType(String objectPath, boolean followLink) { return objectHandler.getObjectType(objectPath, followLink); } @Override public HDF5ObjectType getObjectType(String objectPath) { return objectHandler.getObjectType(objectPath); } @Override public boolean exists(String objectPath, boolean followLink) { return objectHandler.exists(objectPath, followLink); } @Override public boolean exists(String objectPath) { return objectHandler.exists(objectPath); } @Override public String toHouseKeepingPath(String objectPath) { return objectHandler.toHouseKeepingPath(objectPath); } @Override public boolean isHouseKeepingObject(String objectPath) { return objectHandler.isHouseKeepingObject(objectPath); } @Override public boolean isGroup(String objectPath, boolean followLink) { return objectHandler.isGroup(objectPath, followLink); } @Override public boolean isGroup(String objectPath) { return objectHandler.isGroup(objectPath); } @Override public boolean isDataSet(String objectPath, boolean followLink) { return objectHandler.isDataSet(objectPath, followLink); } @Override public boolean isDataSet(String objectPath) { return objectHandler.isDataSet(objectPath); } @Override public boolean isDataType(String objectPath, boolean followLink) { return objectHandler.isDataType(objectPath, followLink); } @Override public boolean isDataType(String objectPath) { return objectHandler.isDataType(objectPath); } @Override public boolean isSoftLink(String objectPath) { return objectHandler.isSoftLink(objectPath); } @Override public boolean isExternalLink(String objectPath) { return objectHandler.isExternalLink(objectPath); } @Override public boolean isSymbolicLink(String objectPath) { return objectHandler.isSymbolicLink(objectPath); } @Override public String tryGetSymbolicLinkTarget(String objectPath) { return objectHandler.tryGetSymbolicLinkTarget(objectPath); } @Override public boolean hasAttribute(String objectPath, String attributeName) { return objectHandler.hasAttribute(objectPath, attributeName); } @Override public List getAttributeNames(String objectPath) { return objectHandler.getAttributeNames(objectPath); } @Override public List getAllAttributeNames(String objectPath) { return objectHandler.getAllAttributeNames(objectPath); } @Override public HDF5DataTypeInformation getAttributeInformation(String objectPath, String attributeName) { return objectHandler.getAttributeInformation(objectPath, attributeName); } @Override public HDF5DataTypeInformation getAttributeInformation(String objectPath, String attributeName, DataTypeInfoOptions dataTypeInfoOptions) { return objectHandler.getAttributeInformation(objectPath, attributeName, dataTypeInfoOptions); } @Override public HDF5DataSetInformation getDataSetInformation(String dataSetPath) { return objectHandler.getDataSetInformation(dataSetPath); } @Override public HDF5DataSetInformation getDataSetInformation(String dataSetPath, DataTypeInfoOptions dataTypeInfoOptions) { return objectHandler.getDataSetInformation(dataSetPath, dataTypeInfoOptions); } @Override public long getSize(String objectPath) { return objectHandler.getSize(objectPath); } @Override public long getNumberOfElements(String objectPath) { return objectHandler.getNumberOfElements(objectPath); } @Override public void copy(String sourceObject, IHDF5Writer destinationWriter, String destinationObject) { objectHandler.copy(sourceObject, destinationWriter, destinationObject); } @Override public void copy(String sourceObject, IHDF5Writer destinationWriter) { objectHandler.copy(sourceObject, destinationWriter); } @Override public void copyAll(IHDF5Writer destinationWriter) { objectHandler.copyAll(destinationWriter); } @Override public List getGroupMembers(String groupPath) { return objectHandler.getGroupMembers(groupPath); } @Override public List getAllGroupMembers(String groupPath) { return objectHandler.getAllGroupMembers(groupPath); } @Override public List getGroupMemberPaths(String groupPath) { return objectHandler.getGroupMemberPaths(groupPath); } @Override public List getGroupMemberInformation(String groupPath, boolean readLinkTargets) { return objectHandler.getGroupMemberInformation(groupPath, readLinkTargets); } @Override public List getAllGroupMemberInformation(String groupPath, boolean readLinkTargets) { return objectHandler.getAllGroupMemberInformation(groupPath, readLinkTargets); } @Override public HDF5DataTypeVariant tryGetTypeVariant(String objectPath) { return objectHandler.tryGetTypeVariant(objectPath); } @Override public HDF5DataTypeVariant tryGetTypeVariant(String objectPath, String attributeName) { return objectHandler.tryGetTypeVariant(objectPath, attributeName); } @Override public String tryGetDataTypePath(String objectPath) { return objectHandler.tryGetDataTypePath(objectPath); } @Override public String tryGetDataTypePath(HDF5DataType type) { return objectHandler.tryGetDataTypePath(type); } @Override public boolean getBooleanAttribute(String objectPath, String attributeName) throws HDF5JavaException { return booleanReader.getAttr(objectPath, attributeName); } @Override public String getEnumAttributeAsString(final String objectPath, final String attributeName) throws HDF5JavaException { return enumReader.getAttrAsString(objectPath, attributeName); } @Override public HDF5EnumerationValue getEnumAttribute(final String objectPath, final String attributeName) throws HDF5JavaException { return enumReader.getAttr(objectPath, attributeName); } @Override public > T getEnumAttribute(String objectPath, String attributeName, Class enumClass) throws HDF5JavaException { return enumReader.getAttr(objectPath, attributeName, enumClass); } @Override public String[] getEnumArrayAttributeAsString(final String objectPath, final String attributeName) throws HDF5JavaException { return enumReader.getArrayAttr(objectPath, attributeName).toStringArray(); } @Override public HDF5EnumerationValueArray getEnumArrayAttribute(final String objectPath, final String attributeName) throws HDF5JavaException { return enumReader.getArrayAttr(objectPath, attributeName); } @Override public HDF5EnumerationType getEnumType(String dataTypeName) { return enumReader.getType(dataTypeName); } @Override public HDF5EnumerationType getEnumType(String dataTypeName, String[] values) throws HDF5JavaException { return enumReader.getType(dataTypeName, values); } @Override public HDF5EnumerationType getEnumType(String dataTypeName, String[] values, boolean check) throws HDF5JavaException { return enumReader.getType(dataTypeName, values, check); } @Override public HDF5EnumerationType getDataSetEnumType(String dataSetPath) { return enumReader.getDataSetType(dataSetPath); } @Override public HDF5EnumerationType getEnumTypeForObject(String dataSetPath) { return enumReader.getDataSetType(dataSetPath); } // ///////////////////// // Data Sets reading // ///////////////////// // // Opaque // @Override public String tryGetOpaqueTag(String objectPath) { return opaqueReader.tryGetOpaqueTag(objectPath); } @Override public HDF5OpaqueType tryGetOpaqueType(String objectPath) { return opaqueReader.tryGetOpaqueType(objectPath); } @Override public IHDF5OpaqueReader opaque() { return opaqueReader; } @Override public Iterable> getAsByteArrayNaturalBlocks(String dataSetPath) throws HDF5JavaException { return opaqueReader.getArrayNaturalBlocks(dataSetPath); } @Override public byte[] readAsByteArray(String objectPath) { return opaqueReader.readArray(objectPath); } @Override public byte[] getAttributeAsByteArray(String objectPath, String attributeName) { return opaqueReader.getArrayAttr(objectPath, attributeName); } @Override public byte[] readAsByteArrayBlock(String objectPath, int blockSize, long blockNumber) throws HDF5JavaException { return opaqueReader.readArrayBlock(objectPath, blockSize, blockNumber); } @Override public byte[] readAsByteArrayBlockWithOffset(String objectPath, int blockSize, long offset) throws HDF5JavaException { return opaqueReader.readArrayBlockWithOffset(objectPath, blockSize, offset); } @Override public int readAsByteArrayToBlockWithOffset(String objectPath, byte[] buffer, int blockSize, long offset, int memoryOffset) throws HDF5JavaException { return opaqueReader.readArrayToBlockWithOffset(objectPath, buffer, blockSize, offset, memoryOffset); } // // Boolean // @Override public IHDF5BooleanReader bool() { return booleanReader; } @Override public BitSet readBitField(String objectPath) throws HDF5DatatypeInterfaceException { return booleanReader.readBitField(objectPath); } @Override public BitSet readBitFieldBlock(String objectPath, int blockSize, long blockNumber) { return booleanReader.readBitFieldBlock(objectPath, blockSize, blockNumber); } @Override public BitSet readBitFieldBlockWithOffset(String objectPath, int blockSize, long offset) { return booleanReader.readBitFieldBlockWithOffset(objectPath, blockSize, offset); } @Override public boolean isBitSetInBitField(String objectPath, int bitIndex) { return booleanReader.isBitSet(objectPath, bitIndex); } @Override public boolean readBoolean(String objectPath) throws HDF5JavaException { return booleanReader.read(objectPath); } // // Time & date // @Override public IHDF5DateTimeReader time() { return dateTimeReader; } @Override public IHDF5TimeDurationReader duration() { return timeDurationReader; } @Override public long getTimeStampAttribute(String objectPath, String attributeName) { return dateTimeReader.getAttrAsLong(objectPath, attributeName); } @Override public Date getDateAttribute(String objectPath, String attributeName) { return dateTimeReader.getAttr(objectPath, attributeName); } @Override public boolean isTimeStamp(String objectPath, String attributeName) throws HDF5JavaException { return dateTimeReader.isTimeStamp(objectPath, attributeName); } @Override public HDF5TimeDuration getTimeDurationAttribute(String objectPath, String attributeName) { return timeDurationReader.getAttr(objectPath, attributeName); } @Override public boolean isTimeDuration(String objectPath) throws HDF5JavaException { return timeDurationReader.isTimeDuration(objectPath); } @Override public boolean isTimeStamp(String objectPath) throws HDF5JavaException { return dateTimeReader.isTimeStamp(objectPath); } @Override public boolean isTimeDuration(String objectPath, String attributeName) throws HDF5JavaException { return timeDurationReader.isTimeDuration(objectPath, attributeName); } @Override public HDF5TimeUnit tryGetTimeUnit(String objectPath, String attributeName) throws HDF5JavaException { return timeDurationReader.tryGetTimeUnit(objectPath, attributeName); } @Override public long[] getTimeStampArrayAttribute(String objectPath, String attributeName) { return dateTimeReader.getArrayAttrAsLong(objectPath, attributeName); } @Override public Date[] getDateArrayAttribute(String objectPath, String attributeName) { return dateTimeReader.getArrayAttr(objectPath, attributeName); } @Override public HDF5TimeDurationArray getTimeDurationArrayAttribute(String objectPath, String attributeName) { return timeDurationReader.getArrayAttr(objectPath, attributeName); } @Override public HDF5TimeUnit tryGetTimeUnit(String objectPath) throws HDF5JavaException { return timeDurationReader.tryGetTimeUnit(objectPath); } @Override @Deprecated public Iterable> getTimeDurationArrayNaturalBlocks(String dataSetPath, HDF5TimeUnit timeUnit) throws HDF5JavaException { return timeDurationReader.getTimeDurationArrayNaturalBlocks(dataSetPath, timeUnit); } @Override @Deprecated public Iterable> getTimeDurationAndUnitArrayNaturalBlocks( String objectPath) throws HDF5JavaException { return timeDurationReader.getTimeDurationAndUnitArrayNaturalBlocks(objectPath); } @Override public Iterable> getTimeStampArrayNaturalBlocks(String dataSetPath) throws HDF5JavaException { return dateTimeReader.getTimeStampArrayNaturalBlocks(dataSetPath); } @Override public Date readDate(String objectPath) throws HDF5JavaException { return dateTimeReader.readDate(objectPath); } @Override public Date[] readDateArray(String objectPath) throws HDF5JavaException { return dateTimeReader.readDateArray(objectPath); } @Override @Deprecated public long readTimeDuration(String objectPath, HDF5TimeUnit timeUnit) throws HDF5JavaException { return timeDurationReader.readTimeDuration(objectPath, timeUnit); } @Override public HDF5TimeDuration readTimeDuration(String objectPath) throws HDF5JavaException { return timeDurationReader.read(objectPath); } @Override @Deprecated public HDF5TimeDuration readTimeDurationAndUnit(String objectPath) throws HDF5JavaException { return timeDurationReader.readTimeDurationAndUnit(objectPath); } @Override @Deprecated public long[] readTimeDurationArray(String objectPath, HDF5TimeUnit timeUnit) throws HDF5JavaException { return timeDurationReader.readTimeDurationArray(objectPath, timeUnit); } @Override public HDF5TimeDurationArray readTimeDurationArray(String objectPath) throws HDF5JavaException { return timeDurationReader.readArray(objectPath); } @Override @Deprecated public HDF5TimeDuration[] readTimeDurationAndUnitArray(String objectPath) throws HDF5JavaException { return timeDurationReader.readTimeDurationAndUnitArray(objectPath); } @Override @Deprecated public long[] readTimeDurationArrayBlock(String objectPath, int blockSize, long blockNumber, HDF5TimeUnit timeUnit) { return timeDurationReader.readTimeDurationArrayBlock(objectPath, blockSize, blockNumber, timeUnit); } @Override @Deprecated public long[] readTimeDurationArrayBlockWithOffset(String objectPath, int blockSize, long offset, HDF5TimeUnit timeUnit) { return timeDurationReader.readTimeDurationArrayBlockWithOffset(objectPath, blockSize, offset, timeUnit); } @Override @Deprecated public HDF5TimeDuration[] readTimeDurationAndUnitArrayBlock(String objectPath, int blockSize, long blockNumber) throws HDF5JavaException { return timeDurationReader.readTimeDurationAndUnitArrayBlock(objectPath, blockSize, blockNumber); } @Override @Deprecated public HDF5TimeDuration[] readTimeDurationAndUnitArrayBlockWithOffset(String objectPath, int blockSize, long offset) throws HDF5JavaException { return timeDurationReader.readTimeDurationAndUnitArrayBlockWithOffset(objectPath, blockSize, offset); } @Override public long readTimeStamp(String objectPath) throws HDF5JavaException { return dateTimeReader.readTimeStamp(objectPath); } @Override public long[] readTimeStampArray(String objectPath) throws HDF5JavaException { return dateTimeReader.readTimeStampArray(objectPath); } @Override public long[] readTimeStampArrayBlock(String objectPath, int blockSize, long blockNumber) { return dateTimeReader.readTimeStampArrayBlock(objectPath, blockSize, blockNumber); } @Override public long[] readTimeStampArrayBlockWithOffset(String objectPath, int blockSize, long offset) { return dateTimeReader.readTimeStampArrayBlockWithOffset(objectPath, blockSize, offset); } // // Reference // @Override public IHDF5ReferenceReader reference() { return referenceReader; } @Override public String readObjectReference(final String objectPath) { return referenceReader.read(objectPath); } @Override public String readObjectReference(String objectPath, boolean resolveName) { return referenceReader.read(objectPath, resolveName); } @Override public String[] readObjectReferenceArrayBlock(String objectPath, int blockSize, long blockNumber, boolean resolveName) { return referenceReader.readArrayBlock(objectPath, blockSize, blockNumber, resolveName); } @Override public String[] readObjectReferenceArrayBlockWithOffset(String objectPath, int blockSize, long offset, boolean resolveName) { return referenceReader.readArrayBlockWithOffset(objectPath, blockSize, offset, resolveName); } @Override public MDArray readObjectReferenceMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, boolean resolveName) { return referenceReader.readMDArrayBlock(objectPath, blockDimensions, blockNumber, resolveName); } @Override public MDArray readObjectReferenceMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, boolean resolveName) { return referenceReader.readMDArrayBlockWithOffset(objectPath, blockDimensions, offset, resolveName); } @Override public Iterable> getObjectReferenceArrayNaturalBlocks( String dataSetPath, boolean resolveName) { return referenceReader.getArrayNaturalBlocks(dataSetPath, resolveName); } @Override public Iterable>> getObjectReferenceMDArrayNaturalBlocks( String dataSetPath, boolean resolveName) { return referenceReader.getMDArrayNaturalBlocks(dataSetPath, resolveName); } @Override public String[] readObjectReferenceArray(String objectPath) { return referenceReader.readArray(objectPath); } @Override public String[] readObjectReferenceArray(String objectPath, boolean resolveName) { return referenceReader.readArray(objectPath, resolveName); } @Override public MDArray readObjectReferenceMDArray(String objectPath) { return referenceReader.readMDArray(objectPath); } @Override public MDArray readObjectReferenceMDArray(String objectPath, boolean resolveName) { return referenceReader.readMDArray(objectPath, resolveName); } @Override public String getObjectReferenceAttribute(String objectPath, String attributeName, boolean resolveName) { return referenceReader.getAttr(objectPath, attributeName, resolveName); } @Override public String[] getObjectReferenceArrayAttribute(String objectPath, String attributeName, boolean resolveName) { return referenceReader.getArrayAttr(objectPath, attributeName, resolveName); } @Override public MDArray getObjectReferenceMDArrayAttribute(String objectPath, String attributeName, boolean resolveName) { return referenceReader.getMDArrayAttr(objectPath, attributeName, resolveName); } @Override public HDF5TimeDurationArray readTimeDurationArrayBlock(String objectPath, int blockSize, long blockNumber) throws HDF5JavaException { return timeDurationReader.readArrayBlock(objectPath, blockSize, blockNumber); } @Override public HDF5TimeDurationArray readTimeDurationArrayBlockWithOffset(String objectPath, int blockSize, long offset) throws HDF5JavaException { return timeDurationReader.readArrayBlockWithOffset(objectPath, blockSize, offset); } @Override public Iterable> getTimeDurationArrayNaturalBlocks( String objectPath) throws HDF5JavaException { return timeDurationReader.getArrayNaturalBlocks(objectPath); } // // References // @Override public String resolvePath(String reference) throws HDF5JavaException { return referenceReader.resolvePath(reference); } @Override public String getObjectReferenceAttribute(final String objectPath, final String attributeName) { return referenceReader.getAttr(objectPath, attributeName); } @Override public String[] getObjectReferenceArrayAttribute(String objectPath, String attributeName) { return referenceReader.getArrayAttr(objectPath, attributeName); } @Override public MDArray getObjectReferenceMDArrayAttribute(String objectPath, String attributeName) { return referenceReader.getMDArrayAttr(objectPath, attributeName); } @Override public String[] readObjectReferenceArrayBlock(String objectPath, int blockSize, long blockNumber) { return referenceReader.readArrayBlock(objectPath, blockSize, blockNumber); } @Override public String[] readObjectReferenceArrayBlockWithOffset(String objectPath, int blockSize, long offset) { return referenceReader.readArrayBlockWithOffset(objectPath, blockSize, offset); } @Override public MDArray readObjectReferenceMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber) { return referenceReader.readMDArrayBlock(objectPath, blockDimensions, blockNumber); } @Override public MDArray readObjectReferenceMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset) { return referenceReader.readMDArrayBlockWithOffset(objectPath, blockDimensions, offset); } @Override public Iterable> getObjectReferenceArrayNaturalBlocks(String dataSetPath) throws HDF5JavaException { return referenceReader.getArrayNaturalBlocks(dataSetPath); } @Override public Iterable>> getObjectReferenceMDArrayNaturalBlocks( String dataSetPath) { return referenceReader.getMDArrayNaturalBlocks(dataSetPath); } // // String // @Override public IHDF5StringReader string() { return stringReader; } @Override public String getStringAttribute(String objectPath, String attributeName) { return stringReader.getAttr(objectPath, attributeName); } @Override public String[] getStringArrayAttribute(String objectPath, String attributeName) { return stringReader.getArrayAttr(objectPath, attributeName); } @Override public MDArray getStringMDArrayAttribute(String objectPath, String attributeName) { return stringReader.getMDArrayAttr(objectPath, attributeName); } @Override public String readString(String objectPath) throws HDF5JavaException { return stringReader.read(objectPath); } @Override public String[] readStringArray(String objectPath) throws HDF5JavaException { return stringReader.readArray(objectPath); } @Override public String[] readStringArrayBlock(String objectPath, int blockSize, long blockNumber) { return stringReader.readArrayBlock(objectPath, blockSize, blockNumber); } @Override public String[] readStringArrayBlockWithOffset(String objectPath, int blockSize, long offset) { return stringReader.readArrayBlockWithOffset(objectPath, blockSize, offset); } @Override public MDArray readStringMDArray(String objectPath) { return stringReader.readMDArray(objectPath); } @Override public MDArray readStringMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber) { return stringReader.readMDArrayBlock(objectPath, blockDimensions, blockNumber); } @Override public MDArray readStringMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset) { return stringReader.readMDArrayBlockWithOffset(objectPath, blockDimensions, offset); } @Override public Iterable> getStringArrayNaturalBlocks(String objectPath) throws HDF5JavaException { return stringReader.getArrayNaturalBlocks(objectPath); } @Override public Iterable>> getStringMDArrayNaturalBlocks( String objectPath) { return stringReader.getMDArrayNaturalBlocks(objectPath); } // // Enums // @Override public IHDF5EnumReader enums() { return enumReader; } @Override public IHDF5EnumReader enumeration() { return enumReader; } @Override public Iterable> getEnumArrayNaturalBlocks( String objectPath, HDF5EnumerationType enumType) throws HDF5JavaException { return enumReader.getArrayBlocks(objectPath, enumType); } @Override public Iterable> getEnumArrayNaturalBlocks( String objectPath) throws HDF5JavaException { return enumReader.getArrayBlocks(objectPath); } @Override public HDF5EnumerationValue readEnum(String objectPath, HDF5EnumerationType enumType) throws HDF5JavaException { return enumReader.read(objectPath, enumType); } @Override public HDF5EnumerationValue readEnum(String objectPath) throws HDF5JavaException { return enumReader.read(objectPath); } @Override public > T readEnum(String objectPath, Class enumClass) throws HDF5JavaException { return enumReader.read(objectPath, enumClass); } @Override public HDF5EnumerationValueArray readEnumArray(String objectPath, HDF5EnumerationType enumType) throws HDF5JavaException { return enumReader.readArray(objectPath, enumType); } @Override public HDF5EnumerationValueArray readEnumArray(String objectPath) throws HDF5JavaException { return enumReader.readArray(objectPath); } @Override public > T[] readEnumArray(String objectPath, Class enumClass) throws HDF5JavaException { return readEnumArray(objectPath).toEnumArray(enumClass); } @Override public String[] readEnumArrayAsString(String objectPath) throws HDF5JavaException { return enumReader.readArray(objectPath).toStringArray(); } @Override public HDF5EnumerationValueArray readEnumArrayBlock(String objectPath, HDF5EnumerationType enumType, int blockSize, long blockNumber) { return enumReader.readArrayBlock(objectPath, enumType, blockSize, blockNumber); } @Override public HDF5EnumerationValueArray readEnumArrayBlock(String objectPath, int blockSize, long blockNumber) { return enumReader.readArrayBlock(objectPath, blockSize, blockNumber); } @Override public HDF5EnumerationValueArray readEnumArrayBlockWithOffset(String objectPath, HDF5EnumerationType enumType, int blockSize, long offset) { return enumReader.readArrayBlockWithOffset(objectPath, enumType, blockSize, offset); } @Override public HDF5EnumerationValueArray readEnumArrayBlockWithOffset(String objectPath, int blockSize, long offset) { return enumReader.readArrayBlockWithOffset(objectPath, blockSize, offset); } @Override public String readEnumAsString(String objectPath) throws HDF5JavaException { return enumReader.readAsString(objectPath); } // // Compounds // @Override public IHDF5CompoundReader compounds() { return compoundReader; } @Override public IHDF5CompoundReader compound() { return compoundReader; } @Override public Iterable> getCompoundArrayNaturalBlocks(String objectPath, HDF5CompoundType type, IByteArrayInspector inspectorOrNull) throws HDF5JavaException { return compoundReader.getArrayBlocks(objectPath, type, inspectorOrNull); } @Override public Iterable> getCompoundArrayNaturalBlocks(String objectPath, HDF5CompoundType type) throws HDF5JavaException { return compoundReader.getArrayBlocks(objectPath, type); } @Override public Iterable>> getCompoundMDArrayNaturalBlocks( String objectPath, HDF5CompoundType type, IByteArrayInspector inspectorOrNull) throws HDF5JavaException { return compoundReader.getMDArrayBlocks(objectPath, type, inspectorOrNull); } @Override public Iterable>> getCompoundMDArrayNaturalBlocks( String objectPath, HDF5CompoundType type) throws HDF5JavaException { return compoundReader.getMDArrayBlocks(objectPath, type); } @Override public Iterable> getCompoundArrayNaturalBlocks(String objectPath, Class pojoClass) throws HDF5JavaException { return compoundReader.getArrayBlocks(objectPath, pojoClass); } @Override public Iterable>> getCompoundMDArrayNaturalBlocks( String objectPath, Class pojoClass) throws HDF5JavaException { return compoundReader.getMDArrayBlocks(objectPath, pojoClass); } @Override public HDF5CompoundMemberInformation[] getCompoundDataSetInformation(String dataSetPath, boolean sortAlphabetically) throws HDF5JavaException { final HDF5CompoundMemberInformation[] compoundInformation = compoundReader.getDataSetInfo(dataSetPath, DataTypeInfoOptions.DEFAULT); if (sortAlphabetically) { Arrays.sort(compoundInformation); } return compoundInformation; } @Override public HDF5CompoundMemberInformation[] getCompoundDataSetInformation(String dataSetPath) throws HDF5JavaException { return compoundReader.getDataSetInfo(dataSetPath); } @Override public HDF5CompoundMemberInformation[] getCompoundMemberInformation(Class compoundClass) { return compoundReader.getMemberInfo(compoundClass); } @Override public HDF5CompoundMemberInformation[] getCompoundMemberInformation(String dataTypeName) { return compoundReader.getMemberInfo(dataTypeName); } @Override public HDF5CompoundType getCompoundType(Class pojoClass, HDF5CompoundMemberMapping... members) { return compoundReader.getType(pojoClass, members); } @Override public HDF5CompoundType getCompoundType(String name, Class compoundType, HDF5CompoundMemberMapping... members) { return compoundReader.getType(name, compoundType, members); } @Override public HDF5CompoundType getDataSetCompoundType(String objectPath, Class compoundClass) { return compoundReader.getDataSetType(objectPath, compoundClass); } @Override public HDF5CompoundType getAttributeCompoundType(String objectPath, String attributeName, Class pojoClass) { return compoundReader.getAttributeType(objectPath, attributeName, pojoClass); } @Override public HDF5CompoundType getInferredCompoundType(Class pojoClass) { return compoundReader.getInferredType(pojoClass); } @Override public HDF5CompoundType getInferredCompoundType(String name, Class compoundType) { return compoundReader.getInferredType(name, compoundType); } @Override public HDF5CompoundType getInferredCompoundType(String name, T template) { return compoundReader.getInferredType(name, template); } @Override public HDF5CompoundType getInferredCompoundType(T template) { return compoundReader.getInferredType(template); } @Override public HDF5CompoundType getInferredCompoundType(String name, T template, HDF5CompoundMappingHints hints) { return compoundReader.getInferredType(name, template, hints); } @Override public HDF5CompoundType> getInferredCompoundType(String name, List memberNames, List template) { return compoundReader.getInferredType(name, memberNames, template); } @Override public HDF5CompoundType getInferredCompoundType(String name, String[] memberNames, Object[] template) { return compoundReader.getInferredType(name, memberNames, template); } @Override public HDF5CompoundType> getInferredCompoundType(List memberNames, List template) { return compoundReader.getInferredType(memberNames, template); } @Override public HDF5CompoundType getInferredCompoundType(String[] memberNames, Object[] template) { return compoundReader.getInferredType(memberNames, template); } @Override public HDF5CompoundType getNamedCompoundType(Class compoundClass) { return compoundReader.getNamedType(compoundClass); } @Override public HDF5CompoundType getNamedCompoundType(String dataTypeName, Class compoundClass) { return compoundReader.getNamedType(dataTypeName, compoundClass); } @Override public T readCompound(String objectPath, HDF5CompoundType type, IByteArrayInspector inspectorOrNull) throws HDF5JavaException { return compoundReader.read(objectPath, type, inspectorOrNull); } @Override public T readCompound(String objectPath, HDF5CompoundType type) throws HDF5JavaException { return compoundReader.read(objectPath, type); } @Override public T readCompound(String objectPath, Class pojoClass) throws HDF5JavaException { return compoundReader.read(objectPath, pojoClass); } @Override public T[] readCompoundArray(String objectPath, HDF5CompoundType type, IByteArrayInspector inspectorOrNull) throws HDF5JavaException { return compoundReader.readArray(objectPath, type, inspectorOrNull); } @Override public T[] readCompoundArray(String objectPath, HDF5CompoundType type) throws HDF5JavaException { return compoundReader.readArray(objectPath, type); } @Override public T[] readCompoundArray(String objectPath, Class pojoClass) throws HDF5JavaException { return compoundReader.readArray(objectPath, pojoClass); } @Override public T[] readCompoundArrayBlock(String objectPath, HDF5CompoundType type, int blockSize, long blockNumber, IByteArrayInspector inspectorOrNull) throws HDF5JavaException { return compoundReader.readArrayBlock(objectPath, type, blockSize, blockNumber, inspectorOrNull); } @Override public T[] readCompoundArrayBlock(String objectPath, HDF5CompoundType type, int blockSize, long blockNumber) throws HDF5JavaException { return compoundReader.readArrayBlock(objectPath, type, blockSize, blockNumber); } @Override public T[] readCompoundArrayBlockWithOffset(String objectPath, HDF5CompoundType type, int blockSize, long offset, IByteArrayInspector inspectorOrNull) throws HDF5JavaException { return compoundReader.readArrayBlockWithOffset(objectPath, type, blockSize, offset, inspectorOrNull); } @Override public T[] readCompoundArrayBlockWithOffset(String objectPath, HDF5CompoundType type, int blockSize, long offset) throws HDF5JavaException { return compoundReader.readArrayBlockWithOffset(objectPath, type, blockSize, offset); } @Override public MDArray readCompoundMDArray(String objectPath, HDF5CompoundType type, IByteArrayInspector inspectorOrNull) throws HDF5JavaException { return compoundReader.readMDArray(objectPath, type, inspectorOrNull); } @Override public MDArray readCompoundMDArray(String objectPath, HDF5CompoundType type) throws HDF5JavaException { return compoundReader.readMDArray(objectPath, type); } @Override public MDArray readCompoundMDArray(String objectPath, Class pojoClass) throws HDF5JavaException { return compoundReader.readMDArray(objectPath, pojoClass); } @Override public MDArray readCompoundMDArrayBlock(String objectPath, HDF5CompoundType type, int[] blockDimensions, long[] blockNumber, IByteArrayInspector inspectorOrNull) throws HDF5JavaException { return compoundReader.readMDArrayBlock(objectPath, type, blockDimensions, blockNumber, inspectorOrNull); } @Override public MDArray readCompoundMDArrayBlock(String objectPath, HDF5CompoundType type, int[] blockDimensions, long[] blockNumber) throws HDF5JavaException { return compoundReader.readMDArrayBlock(objectPath, type, blockDimensions, blockNumber); } @Override public MDArray readCompoundMDArrayBlockWithOffset(String objectPath, HDF5CompoundType type, int[] blockDimensions, long[] offset, IByteArrayInspector inspectorOrNull) throws HDF5JavaException { return compoundReader.readMDArrayBlockWithOffset(objectPath, type, blockDimensions, offset, inspectorOrNull); } @Override public MDArray readCompoundMDArrayBlockWithOffset(String objectPath, HDF5CompoundType type, int[] blockDimensions, long[] offset) throws HDF5JavaException { return compoundReader.readMDArrayBlockWithOffset(objectPath, type, blockDimensions, offset); } // ------------------------------------------------------------------------------ // Primite types - START // ------------------------------------------------------------------------------ @Override public byte[] getByteArrayAttribute(String objectPath, String attributeName) { return byteReader.getArrayAttr(objectPath, attributeName); } @Override public Iterable> getByteArrayNaturalBlocks(String dataSetPath) throws HDF5JavaException { return byteReader.getArrayNaturalBlocks(dataSetPath); } @Override public byte getByteAttribute(String objectPath, String attributeName) { return byteReader.getAttr(objectPath, attributeName); } @Override public MDByteArray getByteMDArrayAttribute(String objectPath, String attributeName) { return byteReader.getMDArrayAttr(objectPath, attributeName); } @Override public Iterable> getByteMDArrayNaturalBlocks(String dataSetPath) { return byteReader.getMDArrayNaturalBlocks(dataSetPath); } @Override public byte[][] getByteMatrixAttribute(String objectPath, String attributeName) throws HDF5JavaException { return byteReader.getMatrixAttr(objectPath, attributeName); } @Override public byte readByte(String objectPath) { return byteReader.read(objectPath); } @Override public byte[] readByteArray(String objectPath) { return byteReader.readArray(objectPath); } @Override public byte[] readByteArrayBlock(String objectPath, int blockSize, long blockNumber) { return byteReader.readArrayBlock(objectPath, blockSize, blockNumber); } @Override public byte[] readByteArrayBlockWithOffset(String objectPath, int blockSize, long offset) { return byteReader.readArrayBlockWithOffset(objectPath, blockSize, offset); } @Override public MDByteArray readByteMDArray(String objectPath) { return byteReader.readMDArray(objectPath); } @Override public MDByteArray readByteMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber) { return byteReader.readMDArrayBlock(objectPath, blockDimensions, blockNumber); } @Override public MDByteArray readByteMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset) { return byteReader.readMDArrayBlockWithOffset(objectPath, blockDimensions, offset); } @Override public byte[][] readByteMatrix(String objectPath) throws HDF5JavaException { return byteReader.readMatrix(objectPath); } @Override public byte[][] readByteMatrixBlock(String objectPath, int blockSizeX, int blockSizeY, long blockNumberX, long blockNumberY) throws HDF5JavaException { return byteReader.readMatrixBlock(objectPath, blockSizeX, blockSizeY, blockNumberX, blockNumberY); } @Override public byte[][] readByteMatrixBlockWithOffset(String objectPath, int blockSizeX, int blockSizeY, long offsetX, long offsetY) throws HDF5JavaException { return byteReader.readMatrixBlockWithOffset(objectPath, blockSizeX, blockSizeY, offsetX, offsetY); } @Override public int[] readToByteMDArrayBlockWithOffset(String objectPath, MDByteArray array, int[] blockDimensions, long[] offset, int[] memoryOffset) { return byteReader.readToMDArrayBlockWithOffset(objectPath, array, blockDimensions, offset, memoryOffset); } @Override public int[] readToByteMDArrayWithOffset(String objectPath, MDByteArray array, int[] memoryOffset) { return byteReader.readToMDArrayWithOffset(objectPath, array, memoryOffset); } @Override public double[] getDoubleArrayAttribute(String objectPath, String attributeName) { return doubleReader.getArrayAttr(objectPath, attributeName); } @Override public Iterable> getDoubleArrayNaturalBlocks(String dataSetPath) throws HDF5JavaException { return doubleReader.getArrayNaturalBlocks(dataSetPath); } @Override public double getDoubleAttribute(String objectPath, String attributeName) { return doubleReader.getAttr(objectPath, attributeName); } @Override public MDDoubleArray getDoubleMDArrayAttribute(String objectPath, String attributeName) { return doubleReader.getMDArrayAttr(objectPath, attributeName); } @Override public Iterable> getDoubleMDArrayNaturalBlocks(String dataSetPath) { return doubleReader.getMDArrayNaturalBlocks(dataSetPath); } @Override public double[][] getDoubleMatrixAttribute(String objectPath, String attributeName) throws HDF5JavaException { return doubleReader.getMatrixAttr(objectPath, attributeName); } @Override public double readDouble(String objectPath) { return doubleReader.read(objectPath); } @Override public double[] readDoubleArray(String objectPath) { return doubleReader.readArray(objectPath); } @Override public double[] readDoubleArrayBlock(String objectPath, int blockSize, long blockNumber) { return doubleReader.readArrayBlock(objectPath, blockSize, blockNumber); } @Override public double[] readDoubleArrayBlockWithOffset(String objectPath, int blockSize, long offset) { return doubleReader.readArrayBlockWithOffset(objectPath, blockSize, offset); } @Override public MDDoubleArray readDoubleMDArray(String objectPath) { return doubleReader.readMDArray(objectPath); } @Override public MDDoubleArray readDoubleMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber) { return doubleReader.readMDArrayBlock(objectPath, blockDimensions, blockNumber); } @Override public MDDoubleArray readDoubleMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset) { return doubleReader.readMDArrayBlockWithOffset(objectPath, blockDimensions, offset); } @Override public double[][] readDoubleMatrix(String objectPath) throws HDF5JavaException { return doubleReader.readMatrix(objectPath); } @Override public double[][] readDoubleMatrixBlock(String objectPath, int blockSizeX, int blockSizeY, long blockNumberX, long blockNumberY) throws HDF5JavaException { return doubleReader.readMatrixBlock(objectPath, blockSizeX, blockSizeY, blockNumberX, blockNumberY); } @Override public double[][] readDoubleMatrixBlockWithOffset(String objectPath, int blockSizeX, int blockSizeY, long offsetX, long offsetY) throws HDF5JavaException { return doubleReader.readMatrixBlockWithOffset(objectPath, blockSizeX, blockSizeY, offsetX, offsetY); } @Override public int[] readToDoubleMDArrayBlockWithOffset(String objectPath, MDDoubleArray array, int[] blockDimensions, long[] offset, int[] memoryOffset) { return doubleReader.readToMDArrayBlockWithOffset(objectPath, array, blockDimensions, offset, memoryOffset); } @Override public int[] readToDoubleMDArrayWithOffset(String objectPath, MDDoubleArray array, int[] memoryOffset) { return doubleReader.readToMDArrayWithOffset(objectPath, array, memoryOffset); } @Override public float[] getFloatArrayAttribute(String objectPath, String attributeName) { return floatReader.getArrayAttr(objectPath, attributeName); } @Override public Iterable> getFloatArrayNaturalBlocks(String dataSetPath) throws HDF5JavaException { return floatReader.getArrayNaturalBlocks(dataSetPath); } @Override public float getFloatAttribute(String objectPath, String attributeName) { return floatReader.getAttr(objectPath, attributeName); } @Override public MDFloatArray getFloatMDArrayAttribute(String objectPath, String attributeName) { return floatReader.getMDArrayAttr(objectPath, attributeName); } @Override public Iterable> getFloatMDArrayNaturalBlocks(String dataSetPath) { return floatReader.getMDArrayNaturalBlocks(dataSetPath); } @Override public float[][] getFloatMatrixAttribute(String objectPath, String attributeName) throws HDF5JavaException { return floatReader.getMatrixAttr(objectPath, attributeName); } @Override public float readFloat(String objectPath) { return floatReader.read(objectPath); } @Override public float[] readFloatArray(String objectPath) { return floatReader.readArray(objectPath); } @Override public float[] readFloatArrayBlock(String objectPath, int blockSize, long blockNumber) { return floatReader.readArrayBlock(objectPath, blockSize, blockNumber); } @Override public float[] readFloatArrayBlockWithOffset(String objectPath, int blockSize, long offset) { return floatReader.readArrayBlockWithOffset(objectPath, blockSize, offset); } @Override public MDFloatArray readFloatMDArray(String objectPath) { return floatReader.readMDArray(objectPath); } @Override public MDFloatArray readFloatMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber) { return floatReader.readMDArrayBlock(objectPath, blockDimensions, blockNumber); } @Override public MDFloatArray readFloatMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset) { return floatReader.readMDArrayBlockWithOffset(objectPath, blockDimensions, offset); } @Override public float[][] readFloatMatrix(String objectPath) throws HDF5JavaException { return floatReader.readMatrix(objectPath); } @Override public float[][] readFloatMatrixBlock(String objectPath, int blockSizeX, int blockSizeY, long blockNumberX, long blockNumberY) throws HDF5JavaException { return floatReader.readMatrixBlock(objectPath, blockSizeX, blockSizeY, blockNumberX, blockNumberY); } @Override public float[][] readFloatMatrixBlockWithOffset(String objectPath, int blockSizeX, int blockSizeY, long offsetX, long offsetY) throws HDF5JavaException { return floatReader.readMatrixBlockWithOffset(objectPath, blockSizeX, blockSizeY, offsetX, offsetY); } @Override public int[] readToFloatMDArrayBlockWithOffset(String objectPath, MDFloatArray array, int[] blockDimensions, long[] offset, int[] memoryOffset) { return floatReader.readToMDArrayBlockWithOffset(objectPath, array, blockDimensions, offset, memoryOffset); } @Override public int[] readToFloatMDArrayWithOffset(String objectPath, MDFloatArray array, int[] memoryOffset) { return floatReader.readToMDArrayWithOffset(objectPath, array, memoryOffset); } @Override public int[] getIntArrayAttribute(String objectPath, String attributeName) { return intReader.getArrayAttr(objectPath, attributeName); } @Override public Iterable> getIntArrayNaturalBlocks(String dataSetPath) throws HDF5JavaException { return intReader.getArrayNaturalBlocks(dataSetPath); } @Override public int getIntAttribute(String objectPath, String attributeName) { return intReader.getAttr(objectPath, attributeName); } @Override public MDIntArray getIntMDArrayAttribute(String objectPath, String attributeName) { return intReader.getMDArrayAttr(objectPath, attributeName); } @Override public Iterable> getIntMDArrayNaturalBlocks(String dataSetPath) { return intReader.getMDArrayNaturalBlocks(dataSetPath); } @Override public int[][] getIntMatrixAttribute(String objectPath, String attributeName) throws HDF5JavaException { return intReader.getMatrixAttr(objectPath, attributeName); } @Override public int readInt(String objectPath) { return intReader.read(objectPath); } @Override public int[] readIntArray(String objectPath) { return intReader.readArray(objectPath); } @Override public int[] readIntArrayBlock(String objectPath, int blockSize, long blockNumber) { return intReader.readArrayBlock(objectPath, blockSize, blockNumber); } @Override public int[] readIntArrayBlockWithOffset(String objectPath, int blockSize, long offset) { return intReader.readArrayBlockWithOffset(objectPath, blockSize, offset); } @Override public MDIntArray readIntMDArray(String objectPath) { return intReader.readMDArray(objectPath); } @Override public MDIntArray readIntMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber) { return intReader.readMDArrayBlock(objectPath, blockDimensions, blockNumber); } @Override public MDIntArray readIntMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset) { return intReader.readMDArrayBlockWithOffset(objectPath, blockDimensions, offset); } @Override public int[][] readIntMatrix(String objectPath) throws HDF5JavaException { return intReader.readMatrix(objectPath); } @Override public int[][] readIntMatrixBlock(String objectPath, int blockSizeX, int blockSizeY, long blockNumberX, long blockNumberY) throws HDF5JavaException { return intReader.readMatrixBlock(objectPath, blockSizeX, blockSizeY, blockNumberX, blockNumberY); } @Override public int[][] readIntMatrixBlockWithOffset(String objectPath, int blockSizeX, int blockSizeY, long offsetX, long offsetY) throws HDF5JavaException { return intReader.readMatrixBlockWithOffset(objectPath, blockSizeX, blockSizeY, offsetX, offsetY); } @Override public int[] readToIntMDArrayBlockWithOffset(String objectPath, MDIntArray array, int[] blockDimensions, long[] offset, int[] memoryOffset) { return intReader.readToMDArrayBlockWithOffset(objectPath, array, blockDimensions, offset, memoryOffset); } @Override public int[] readToIntMDArrayWithOffset(String objectPath, MDIntArray array, int[] memoryOffset) { return intReader.readToMDArrayWithOffset(objectPath, array, memoryOffset); } @Override public long[] getLongArrayAttribute(String objectPath, String attributeName) { return longReader.getArrayAttr(objectPath, attributeName); } @Override public Iterable> getLongArrayNaturalBlocks(String dataSetPath) throws HDF5JavaException { return longReader.getArrayNaturalBlocks(dataSetPath); } @Override public long getLongAttribute(String objectPath, String attributeName) { return longReader.getAttr(objectPath, attributeName); } @Override public MDLongArray getLongMDArrayAttribute(String objectPath, String attributeName) { return longReader.getMDArrayAttr(objectPath, attributeName); } @Override public Iterable> getLongMDArrayNaturalBlocks(String dataSetPath) { return longReader.getMDArrayNaturalBlocks(dataSetPath); } @Override public long[][] getLongMatrixAttribute(String objectPath, String attributeName) throws HDF5JavaException { return longReader.getMatrixAttr(objectPath, attributeName); } @Override public long readLong(String objectPath) { return longReader.read(objectPath); } @Override public long[] readLongArray(String objectPath) { return longReader.readArray(objectPath); } @Override public long[] readLongArrayBlock(String objectPath, int blockSize, long blockNumber) { return longReader.readArrayBlock(objectPath, blockSize, blockNumber); } @Override public long[] readLongArrayBlockWithOffset(String objectPath, int blockSize, long offset) { return longReader.readArrayBlockWithOffset(objectPath, blockSize, offset); } @Override public MDLongArray readLongMDArray(String objectPath) { return longReader.readMDArray(objectPath); } @Override public MDLongArray readLongMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber) { return longReader.readMDArrayBlock(objectPath, blockDimensions, blockNumber); } @Override public MDLongArray readLongMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset) { return longReader.readMDArrayBlockWithOffset(objectPath, blockDimensions, offset); } @Override public long[][] readLongMatrix(String objectPath) throws HDF5JavaException { return longReader.readMatrix(objectPath); } @Override public long[][] readLongMatrixBlock(String objectPath, int blockSizeX, int blockSizeY, long blockNumberX, long blockNumberY) throws HDF5JavaException { return longReader.readMatrixBlock(objectPath, blockSizeX, blockSizeY, blockNumberX, blockNumberY); } @Override public long[][] readLongMatrixBlockWithOffset(String objectPath, int blockSizeX, int blockSizeY, long offsetX, long offsetY) throws HDF5JavaException { return longReader.readMatrixBlockWithOffset(objectPath, blockSizeX, blockSizeY, offsetX, offsetY); } @Override public int[] readToLongMDArrayBlockWithOffset(String objectPath, MDLongArray array, int[] blockDimensions, long[] offset, int[] memoryOffset) { return longReader.readToMDArrayBlockWithOffset(objectPath, array, blockDimensions, offset, memoryOffset); } @Override public int[] readToLongMDArrayWithOffset(String objectPath, MDLongArray array, int[] memoryOffset) { return longReader.readToMDArrayWithOffset(objectPath, array, memoryOffset); } @Override public short[] getShortArrayAttribute(String objectPath, String attributeName) { return shortReader.getArrayAttr(objectPath, attributeName); } @Override public Iterable> getShortArrayNaturalBlocks(String dataSetPath) throws HDF5JavaException { return shortReader.getArrayNaturalBlocks(dataSetPath); } @Override public short getShortAttribute(String objectPath, String attributeName) { return shortReader.getAttr(objectPath, attributeName); } @Override public MDShortArray getShortMDArrayAttribute(String objectPath, String attributeName) { return shortReader.getMDArrayAttr(objectPath, attributeName); } @Override public Iterable> getShortMDArrayNaturalBlocks(String dataSetPath) { return shortReader.getMDArrayNaturalBlocks(dataSetPath); } @Override public short[][] getShortMatrixAttribute(String objectPath, String attributeName) throws HDF5JavaException { return shortReader.getMatrixAttr(objectPath, attributeName); } @Override public short readShort(String objectPath) { return shortReader.read(objectPath); } @Override public short[] readShortArray(String objectPath) { return shortReader.readArray(objectPath); } @Override public short[] readShortArrayBlock(String objectPath, int blockSize, long blockNumber) { return shortReader.readArrayBlock(objectPath, blockSize, blockNumber); } @Override public short[] readShortArrayBlockWithOffset(String objectPath, int blockSize, long offset) { return shortReader.readArrayBlockWithOffset(objectPath, blockSize, offset); } @Override public MDShortArray readShortMDArray(String objectPath) { return shortReader.readMDArray(objectPath); } @Override public MDShortArray readShortMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber) { return shortReader.readMDArrayBlock(objectPath, blockDimensions, blockNumber); } @Override public MDShortArray readShortMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset) { return shortReader.readMDArrayBlockWithOffset(objectPath, blockDimensions, offset); } @Override public short[][] readShortMatrix(String objectPath) throws HDF5JavaException { return shortReader.readMatrix(objectPath); } @Override public short[][] readShortMatrixBlock(String objectPath, int blockSizeX, int blockSizeY, long blockNumberX, long blockNumberY) throws HDF5JavaException { return shortReader.readMatrixBlock(objectPath, blockSizeX, blockSizeY, blockNumberX, blockNumberY); } @Override public short[][] readShortMatrixBlockWithOffset(String objectPath, int blockSizeX, int blockSizeY, long offsetX, long offsetY) throws HDF5JavaException { return shortReader.readMatrixBlockWithOffset(objectPath, blockSizeX, blockSizeY, offsetX, offsetY); } @Override public int[] readToShortMDArrayBlockWithOffset(String objectPath, MDShortArray array, int[] blockDimensions, long[] offset, int[] memoryOffset) { return shortReader.readToMDArrayBlockWithOffset(objectPath, array, blockDimensions, offset, memoryOffset); } @Override public int[] readToShortMDArrayWithOffset(String objectPath, MDShortArray array, int[] memoryOffset) { return shortReader.readToMDArrayWithOffset(objectPath, array, memoryOffset); } @Override public IHDF5ByteReader int8() { return byteReader; } @Override public IHDF5ByteReader uint8() { return ubyteReader; } @Override public IHDF5ShortReader int16() { return shortReader; } @Override public IHDF5ShortReader uint16() { return ushortReader; } @Override public IHDF5IntReader int32() { return intReader; } @Override public IHDF5IntReader uint32() { return uintReader; } @Override public IHDF5LongReader int64() { return longReader; } @Override public IHDF5LongReader uint64() { return ulongReader; } @Override public IHDF5FloatReader float32() { return floatReader; } @Override public IHDF5DoubleReader float64() { return doubleReader; } // ------------------------------------------------------------------------------ // Primitive types - END // ------------------------------------------------------------------------------ } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5ReaderConfigurator.java000066400000000000000000000045541256564762100304310ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.io.File; /** * If you want the reader to perform numeric conversions, call {@link #performNumericConversions()} * before calling {@link #reader()}. * * @author Bernd Rinn */ class HDF5ReaderConfigurator implements IHDF5ReaderConfigurator { protected final File hdf5File; protected boolean performNumericConversions; protected boolean useUTF8CharEncoding; protected boolean autoDereference = true; protected HDF5Reader readerWriterOrNull; HDF5ReaderConfigurator(File hdf5File) { assert hdf5File != null; this.hdf5File = hdf5File.getAbsoluteFile(); } @Override public boolean platformSupportsNumericConversions() { // Note: code in here any known exceptions of platforms not supporting numeric conversions. return true; } @Override public HDF5ReaderConfigurator performNumericConversions() { if (platformSupportsNumericConversions()) { this.performNumericConversions = true; } return this; } @Override public HDF5ReaderConfigurator useUTF8CharacterEncoding() { this.useUTF8CharEncoding = true; return this; } @Override public HDF5ReaderConfigurator noAutoDereference() { this.autoDereference = false; return this; } @Override public IHDF5Reader reader() { if (readerWriterOrNull == null) { readerWriterOrNull = new HDF5Reader(new HDF5BaseReader(hdf5File, performNumericConversions, autoDereference, IHDF5WriterConfigurator.FileFormat.ALLOW_1_8, false, "")); } return readerWriterOrNull; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5ReferenceReader.java000066400000000000000000000704321256564762100276630ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_ARRAY; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_REFERENCE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_REF_OBJ; import java.util.Iterator; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.base.mdarray.MDAbstractArray; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.hdf5.HDF5BaseReader.DataSpaceParameters; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; import ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants; /** * A reader for HDF5 references. * * @author Bernd Rinn */ public class HDF5ReferenceReader implements IHDF5ReferenceReader { private final HDF5BaseReader baseReader; HDF5ReferenceReader(HDF5BaseReader baseReader) { assert baseReader != null; this.baseReader = baseReader; } // ///////////////////// // Specific // ///////////////////// @Override public String resolvePath(String reference) { assert reference != null; baseReader.checkOpen(); if (reference.charAt(0) != '\0') { throw new HDF5JavaException(String.format("'%s' is not a reference.", reference)); } return baseReader.h5.getReferencedObjectName(baseReader.fileId, Long.parseLong(reference.substring(1))); } private String refToStr(long reference) { return '\0' + Long.toString(reference); } private String[] refToStr(long[] references) { final String[] result = new String[references.length]; for (int i = 0; i < references.length; ++i) { result[i] = '\0' + Long.toString(references[i]); } return result; } private void checkReference(final int dataTypeId, final String objectPath) throws HDF5JavaException { final boolean isReference = (baseReader.h5.getClassType(dataTypeId) == H5T_REFERENCE); if (isReference == false) { throw new HDF5JavaException("Dataset " + objectPath + " is not a reference."); } } private void checkRank1(final int[] arrayDimensions, final String objectPath) { if (arrayDimensions.length != 1) { throw new HDF5JavaException("Dataset " + objectPath + ": array needs to be of rank 1, but is of rank " + arrayDimensions.length); } } private void checkRank1(final long[] arrayDimensions, final String objectPath) { if (arrayDimensions.length != 1) { throw new HDF5JavaException("Dataset " + objectPath + ": array needs to be of rank 1, but is of rank " + arrayDimensions.length); } } // ///////////////////// // Attributes // ///////////////////// @Override public String getAttr(final String objectPath, final String attributeName) { return getAttr(objectPath, attributeName, true); } @Override public String getAttr(final String objectPath, final String attributeName, final boolean resolveName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp readRunnable = new ICallableWithCleanUp() { @Override public String call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int dataTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, registry); checkReference(dataTypeId, objectPath); final long[] reference = baseReader.h5.readAttributeAsLongArray(attributeId, dataTypeId, 1); return resolveName ? baseReader.h5.getReferencedObjectName(attributeId, reference[0]) : refToStr(reference[0]); } }; return baseReader.runner.call(readRunnable); } @Override public String[] getArrayAttr(final String objectPath, final String attributeName) { return getArrayAttr(objectPath, attributeName, true); } @Override public String[] getArrayAttr(final String objectPath, final String attributeName, final boolean resolveName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public String[] call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, registry); final int memoryTypeId; final int len; if (baseReader.h5.getClassType(attributeTypeId) == H5T_ARRAY) { final int baseDataTypeId = baseReader.h5.getBaseDataType(attributeTypeId, registry); checkReference(baseDataTypeId, objectPath); final int[] arrayDimensions = baseReader.h5.getArrayDimensions(attributeTypeId); checkRank1(arrayDimensions, objectPath); len = arrayDimensions[0]; memoryTypeId = baseReader.h5.createArrayType(H5T_STD_REF_OBJ, len, registry); } else { checkReference(attributeTypeId, objectPath); final long[] arrayDimensions = baseReader.h5.getDataDimensionsForAttribute(attributeId, registry); checkRank1(arrayDimensions, objectPath); memoryTypeId = H5T_STD_REF_OBJ; len = HDF5Utils.getOneDimensionalArraySize(arrayDimensions); } final long[] references = baseReader.h5.readAttributeAsLongArray(attributeId, memoryTypeId, len); return resolveName ? baseReader.h5.getReferencedObjectNames( attributeId, references) : refToStr(references); } }; return baseReader.runner.call(getAttributeRunnable); } @Override public MDArray getMDArrayAttr(final String objectPath, final String attributeName) { return getMDArrayAttr(objectPath, attributeName, true); } @Override public MDArray getMDArrayAttr(final String objectPath, final String attributeName, final boolean resolveName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp> getAttributeRunnable = new ICallableWithCleanUp>() { @Override public MDArray call(ICleanUpRegistry registry) { try { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int attributeTypeId = baseReader.h5 .getDataTypeForAttribute(attributeId, registry); final int memoryTypeId; final int[] arrayDimensions; if (baseReader.h5.getClassType(attributeTypeId) == H5T_ARRAY) { final int baseDataTypeId = baseReader.h5 .getBaseDataType(attributeTypeId, registry); checkReference(baseDataTypeId, objectPath); arrayDimensions = baseReader.h5.getArrayDimensions(attributeTypeId); memoryTypeId = baseReader.h5.createArrayType(H5T_STD_REF_OBJ, arrayDimensions, registry); } else { checkReference(attributeTypeId, objectPath); arrayDimensions = MDAbstractArray.toInt(baseReader.h5 .getDataDimensionsForAttribute(attributeId, registry)); memoryTypeId = H5T_STD_REF_OBJ; } final int len; len = MDAbstractArray.getLength(arrayDimensions); final long[] references = baseReader.h5.readAttributeAsLongArray(attributeId, memoryTypeId, len); return new MDArray( resolveName ? baseReader.h5.getReferencedObjectNames( attributeId, references) : refToStr(references), arrayDimensions); } catch (IllegalArgumentException ex) { throw new HDF5JavaException(ex.getMessage()); } } }; return baseReader.runner.call(getAttributeRunnable); } // ///////////////////// // Data Sets // ///////////////////// @Override public String read(final String objectPath) { return read(objectPath, true); } @Override public String read(final String objectPath, final boolean resolveName) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readRunnable = new ICallableWithCleanUp() { @Override public String call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); final int objectReferenceDataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); checkReference(objectReferenceDataTypeId, objectPath); final long[] reference = new long[1]; baseReader.h5.readDataSet(dataSetId, objectReferenceDataTypeId, reference); return resolveName ? baseReader.h5.getReferencedObjectName(dataSetId, reference[0]) : refToStr(reference[0]); } }; return baseReader.runner.call(readRunnable); } @Override public String[] readArray(final String objectPath) { return readArray(objectPath, true); } @Override public String[] readArray(final String objectPath, final boolean resolveName) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public String[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final int dataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); final long[] references; if (baseReader.h5.getClassType(dataTypeId) == H5T_REFERENCE) { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); checkRank1(spaceParams.dimensions, objectPath); references = new long[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, dataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, references); } else if (baseReader.h5.getClassType(dataTypeId) == HDF5Constants.H5T_ARRAY && baseReader.h5.getClassType(baseReader.h5.getBaseDataType(dataTypeId, registry)) == H5T_REFERENCE) { final int spaceId = baseReader.h5.createScalarDataSpace(); final int[] dimensions = baseReader.h5.getArrayDimensions(dataTypeId); checkRank1(dimensions, objectPath); final int len = dimensions[0]; references = new long[len]; final int memoryTypeId = baseReader.h5.createArrayType(H5T_STD_REF_OBJ, len, registry); baseReader.h5.readDataSet(dataSetId, memoryTypeId, spaceId, spaceId, references); } else { throw new HDF5JavaException("Dataset " + objectPath + " is not a reference."); } return resolveName ? baseReader.h5.getReferencedObjectNames(baseReader.fileId, references) : refToStr(references); } }; return baseReader.runner.call(readCallable); } @Override public String[] readArrayBlock(final String objectPath, final int blockSize, final long blockNumber) { return readArrayBlockWithOffset(objectPath, blockSize, blockNumber * blockSize, true); } @Override public String[] readArrayBlock(final String objectPath, final int blockSize, final long blockNumber, final boolean resolveName) { return readArrayBlockWithOffset(objectPath, blockSize, blockNumber * blockSize, resolveName); } @Override public String[] readArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset) { return readArrayBlockWithOffset(objectPath, blockSize, offset, true); } @Override public String[] readArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset, final boolean resolveName) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public String[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockSize, registry); final long[] references = new long[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_STD_REF_OBJ, spaceParams.memorySpaceId, spaceParams.dataSpaceId, references); return resolveName ? baseReader.h5.getReferencedObjectNames(baseReader.fileId, references) : refToStr(references); } }; return baseReader.runner.call(readCallable); } @Override public MDArray readMDArray(final String objectPath) { return readMDArray(objectPath, true); } @Override public MDArray readMDArray(final String objectPath, final boolean resolveName) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp> readCallable = new ICallableWithCleanUp>() { @Override public MDArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final int dataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); final long[] references; final int[] dimensions; if (baseReader.h5.getClassType(dataTypeId) == H5T_REFERENCE) { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); dimensions = MDAbstractArray.toInt(spaceParams.dimensions); references = new long[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, dataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, references); } else if (baseReader.h5.getClassType(dataTypeId) == HDF5Constants.H5T_ARRAY && baseReader.h5.getClassType(baseReader.h5.getBaseDataType( dataTypeId, registry)) == H5T_REFERENCE) { final int spaceId = baseReader.h5.createScalarDataSpace(); dimensions = baseReader.h5.getArrayDimensions(dataTypeId); final int len = MDAbstractArray.getLength(dimensions); references = new long[len]; final int memoryTypeId = baseReader.h5.createArrayType(H5T_STD_REF_OBJ, len, registry); baseReader.h5.readDataSet(dataSetId, memoryTypeId, spaceId, spaceId, references); } else { throw new HDF5JavaException("Dataset " + objectPath + " is not a reference."); } final String[] referencedObjectNames = resolveName ? baseReader.h5.getReferencedObjectNames( baseReader.fileId, references) : refToStr(references); return new MDArray(referencedObjectNames, dimensions); } }; return baseReader.runner.call(readCallable); } @Override public MDArray readMDArrayBlock(final String objectPath, final int[] blockDimensions, final long[] blockNumber) { return readMDArrayBlock(objectPath, blockDimensions, blockNumber, true); } @Override public MDArray readMDArrayBlock(final String objectPath, final int[] blockDimensions, final long[] blockNumber, final boolean resolveName) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readMDArrayBlockWithOffset(objectPath, blockDimensions, offset, resolveName); } @Override public MDArray readMDArrayBlockWithOffset(final String objectPath, final int[] blockDimensions, final long[] offset) { return readMDArrayBlockWithOffset(objectPath, blockDimensions, offset, true); } @Override public MDArray readMDArrayBlockWithOffset(final String objectPath, final int[] blockDimensions, final long[] offset, final boolean resolveName) { assert objectPath != null; assert blockDimensions != null; assert offset != null; baseReader.checkOpen(); final ICallableWithCleanUp> readCallable = new ICallableWithCleanUp>() { @Override public MDArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockDimensions, registry); final long[] referencesBlock = new long[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_STD_REF_OBJ, spaceParams.memorySpaceId, spaceParams.dataSpaceId, referencesBlock); final String[] referencedObjectNamesBlock = resolveName ? baseReader.h5.getReferencedObjectNames( baseReader.fileId, referencesBlock) : refToStr(referencesBlock); return new MDArray(referencedObjectNamesBlock, blockDimensions); } }; return baseReader.runner.call(readCallable); } @Override public Iterable> getArrayNaturalBlocks( final String dataSetPath) throws HDF5JavaException { return getArrayNaturalBlocks(dataSetPath, true); } @Override public Iterable> getArrayNaturalBlocks( final String dataSetPath, final boolean resolveName) throws HDF5JavaException { baseReader.checkOpen(); final HDF5NaturalBlock1DParameters params = new HDF5NaturalBlock1DParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlock1DParameters.HDF5NaturalBlock1DIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5DataBlock next() { final long offset = index.computeOffsetAndSizeGetOffset(); final String[] referencesBlock = readArrayBlockWithOffset(dataSetPath, index.getBlockSize(), offset, resolveName); return new HDF5DataBlock(referencesBlock, index.getAndIncIndex(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } @Override public Iterable>> getMDArrayNaturalBlocks( final String dataSetPath) { return getMDArrayNaturalBlocks(dataSetPath, true); } @Override public Iterable>> getMDArrayNaturalBlocks( final String dataSetPath, final boolean resolveName) { baseReader.checkOpen(); final HDF5NaturalBlockMDParameters params = new HDF5NaturalBlockMDParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>>() { @Override public Iterator>> iterator() { return new Iterator>>() { final HDF5NaturalBlockMDParameters.HDF5NaturalBlockMDIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5MDDataBlock> next() { final long[] offset = index.computeOffsetAndSizeGetOffsetClone(); final MDArray data = readMDArrayBlockWithOffset(dataSetPath, index.getBlockSize(), offset, resolveName); return new HDF5MDDataBlock>(data, index.getIndexClone(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5ReferenceWriter.java000066400000000000000000000526771256564762100277500ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.HDF5BaseReader.REFERENCE_SIZE_IN_BYTES; import static ch.systemsx.cisd.hdf5.HDF5IntStorageFeatures.INT_NO_COMPRESSION; import static ch.systemsx.cisd.hdf5.hdf5lib.H5D.H5Dwrite; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_ALL; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_REF_OBJ; import ch.systemsx.cisd.base.mdarray.MDAbstractArray; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDLongArray; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; /** * The implementation of {@link IHDF5ReferenceWriter}. * * @author Bernd Rinn */ public class HDF5ReferenceWriter extends HDF5ReferenceReader implements IHDF5ReferenceWriter { private final HDF5BaseWriter baseWriter; HDF5ReferenceWriter(HDF5BaseWriter baseWriter) { super(baseWriter); assert baseWriter != null; this.baseWriter = baseWriter; } // ///////////////////// // Attributes // ///////////////////// @Override public void setAttr(final String objectPath, final String name, final String referencedObjectPath) { assert objectPath != null; assert name != null; assert referencedObjectPath != null; baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { final byte[] reference = baseWriter.h5.createObjectReference(baseWriter.fileId, referencedObjectPath); if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { 1 }, registry); baseWriter.setAttribute(objectPath, name, H5T_STD_REF_OBJ, H5T_STD_REF_OBJ, dataSpaceId, reference, registry); } else { baseWriter.setAttribute(objectPath, name, H5T_STD_REF_OBJ, H5T_STD_REF_OBJ, -1, reference, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void setArrayAttr(final String objectPath, final String name, final String[] referencedObjectPaths) { assert objectPath != null; assert name != null; assert referencedObjectPaths != null; baseWriter.checkOpen(); final ICallableWithCleanUp setAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] references = baseWriter.h5.createObjectReferences(baseWriter.fileId, referencedObjectPaths); if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { references.length }, registry); baseWriter.setAttribute(objectPath, name, H5T_STD_REF_OBJ, H5T_STD_REF_OBJ, dataSpaceId, references); } else { final int typeId = baseWriter.h5.createArrayType(H5T_STD_REF_OBJ, referencedObjectPaths.length, registry); baseWriter.setAttribute(objectPath, name, typeId, typeId, -1, references); } return null; // Nothing to return. } }; baseWriter.runner.call(setAttributeRunnable); } @Override public void setMDArrayAttr(final String objectPath, final String name, final MDArray referencedObjectPaths) { assert objectPath != null; assert name != null; assert referencedObjectPaths != null; baseWriter.checkOpen(); final ICallableWithCleanUp setAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] references = baseWriter.h5.createObjectReferences(baseWriter.fileId, referencedObjectPaths.getAsFlatArray()); if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace( referencedObjectPaths.longDimensions(), registry); baseWriter.setAttribute(objectPath, name, H5T_STD_REF_OBJ, H5T_STD_REF_OBJ, dataSpaceId, references); } else { final int typeId = baseWriter.h5.createArrayType(H5T_STD_REF_OBJ, referencedObjectPaths.dimensions(), registry); baseWriter.setAttribute(objectPath, name, typeId, typeId, -1, references); } return null; // Nothing to return. } }; baseWriter.runner.call(setAttributeRunnable); } // ///////////////////// // Data Sets // ///////////////////// @Override public void write(String objectPath, String referencedObjectPath) { assert objectPath != null; assert referencedObjectPath != null; baseWriter.checkOpen(); final byte[] reference = baseWriter.h5.createObjectReference(baseWriter.fileId, referencedObjectPath); baseWriter.writeScalar(objectPath, H5T_STD_REF_OBJ, H5T_STD_REF_OBJ, reference); } @Override public void writeArray(final String objectPath, final String[] referencedObjectPath) { writeArray(objectPath, referencedObjectPath, HDF5IntStorageFeatures.INT_NO_COMPRESSION); } @Override public void writeArray(final String objectPath, final String[] referencedObjectPaths, final HDF5IntStorageFeatures features) { assert referencedObjectPaths != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] references = baseWriter.h5.createObjectReferences(baseWriter.fileId, referencedObjectPaths); final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, H5T_STD_REF_OBJ, new long[] { referencedObjectPaths.length }, REFERENCE_SIZE_IN_BYTES, features, registry); H5Dwrite(dataSetId, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, references); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createArray(final String objectPath, final int size) { createArray(objectPath, size, INT_NO_COMPRESSION); } @Override public void createArray(final String objectPath, final long size, final int blockSize) { createArray(objectPath, size, blockSize, INT_NO_COMPRESSION); } @Override public void createArray(final String objectPath, final int size, final HDF5IntStorageFeatures features) { assert objectPath != null; assert size >= 0; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (features.requiresChunking()) { baseWriter.createDataSet(objectPath, H5T_STD_REF_OBJ, features, new long[] { 0 }, new long[] { size }, REFERENCE_SIZE_IN_BYTES, registry); } else { baseWriter.createDataSet(objectPath, H5T_STD_REF_OBJ, features, new long[] { size }, null, REFERENCE_SIZE_IN_BYTES, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void createArray(final String objectPath, final long size, final int blockSize, final HDF5IntStorageFeatures features) { assert objectPath != null; assert size >= 0; assert blockSize >= 0 && (blockSize <= size || size == 0); baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { baseWriter.createDataSet(objectPath, H5T_STD_REF_OBJ, features, new long[] { size }, new long[] { blockSize }, REFERENCE_SIZE_IN_BYTES, registry); return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void writeArrayBlock(final String objectPath, final String[] referencedObjectPaths, final long blockNumber) { writeArrayBlockWithOffset(objectPath, referencedObjectPaths, referencedObjectPaths.length, referencedObjectPaths.length * blockNumber); } @Override public void writeArrayBlockWithOffset(final String objectPath, final String[] referencedObjectPaths, final int dataSize, final long offset) { assert objectPath != null; assert referencedObjectPaths != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] blockDimensions = new long[] { dataSize }; final long[] slabStartOrNull = new long[] { offset }; final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, new long[] { offset + dataSize }, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, slabStartOrNull, blockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(blockDimensions, registry); final long[] references = baseWriter.h5.createObjectReferences(baseWriter.fileId, referencedObjectPaths); H5Dwrite(dataSetId, H5T_STD_REF_OBJ, memorySpaceId, dataSpaceId, H5P_DEFAULT, references); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeMDArray(final String objectPath, final MDArray referencedObjectPaths) { writeMDArray(objectPath, referencedObjectPaths, HDF5IntStorageFeatures.INT_NO_COMPRESSION); } @Override public void writeMDArray(final String objectPath, final MDArray referencedObjectPaths, final HDF5IntStorageFeatures features) { assert referencedObjectPaths != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] references = baseWriter.h5.createObjectReferences(baseWriter.fileId, referencedObjectPaths.getAsFlatArray()); final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, H5T_STD_REF_OBJ, referencedObjectPaths.longDimensions(), REFERENCE_SIZE_IN_BYTES, features, registry); H5Dwrite(dataSetId, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, references); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createMDArray(final String objectPath, final int[] dimensions) { createMDArray(objectPath, dimensions, INT_NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions) { createMDArray(objectPath, dimensions, blockDimensions, INT_NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final int[] dimensions, final HDF5IntStorageFeatures features) { assert objectPath != null; assert dimensions != null; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (features.requiresChunking()) { final long[] nullDimensions = new long[dimensions.length]; baseWriter.createDataSet(objectPath, H5T_STD_REF_OBJ, features, nullDimensions, MDAbstractArray.toLong(dimensions), REFERENCE_SIZE_IN_BYTES, registry); } else { baseWriter.createDataSet(objectPath, H5T_STD_REF_OBJ, features, MDAbstractArray.toLong(dimensions), null, REFERENCE_SIZE_IN_BYTES, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void createMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions, final HDF5IntStorageFeatures features) { assert objectPath != null; assert dimensions != null; assert blockDimensions != null; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { baseWriter.createDataSet(objectPath, H5T_STD_REF_OBJ, features, dimensions, MDAbstractArray.toLong(blockDimensions), REFERENCE_SIZE_IN_BYTES, registry); return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void writeMDArrayBlock(final String objectPath, final MDArray referencedObjectPaths, final long[] blockNumber) { assert blockNumber != null; final long[] dimensions = referencedObjectPaths.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeMDArrayBlockWithOffset(objectPath, referencedObjectPaths, offset); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final MDArray referencedObjectPaths, final long[] offset) { assert objectPath != null; assert referencedObjectPaths != null; assert offset != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] dimensions = referencedObjectPaths.longDimensions(); assert dimensions.length == offset.length; final long[] dataSetDimensions = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + dimensions[i]; } final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, dimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(dimensions, registry); final long[] references = baseWriter.h5.createObjectReferences(baseWriter.fileId, referencedObjectPaths.getAsFlatArray()); H5Dwrite(dataSetId, H5T_STD_REF_OBJ, memorySpaceId, dataSpaceId, H5P_DEFAULT, references); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final MDLongArray data, final int[] blockDimensions, final long[] offset, final int[] memoryOffset) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] memoryDimensions = data.longDimensions(); assert memoryDimensions.length == offset.length; final long[] longBlockDimensions = MDAbstractArray.toLong(blockDimensions); assert longBlockDimensions.length == offset.length; final long[] dataSetDimensions = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + blockDimensions[i]; } final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, longBlockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(memoryDimensions, registry); baseWriter.h5.setHyperslabBlock(memorySpaceId, MDAbstractArray.toLong(memoryOffset), longBlockDimensions); H5Dwrite(dataSetId, H5T_STD_REF_OBJ, memorySpaceId, dataSpaceId, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5ShortReader.java000066400000000000000000001022351256564762100270610ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.MatrixUtils.cardinalityBoundIndices; import static ch.systemsx.cisd.hdf5.MatrixUtils.checkBoundIndices; import static ch.systemsx.cisd.hdf5.MatrixUtils.createFullBlockDimensionsAndOffset; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_ARRAY; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_INT16; import java.util.Arrays; import java.util.Iterator; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import ncsa.hdf.hdf5lib.exceptions.HDF5SpaceRankMismatch; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDShortArray; import ch.systemsx.cisd.hdf5.HDF5BaseReader.DataSpaceParameters; import ch.systemsx.cisd.hdf5.HDF5DataTypeInformation.DataTypeInfoOptions; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; import ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants; /** * The implementation of {@link IHDF5ShortReader}. * * @author Bernd Rinn */ class HDF5ShortReader implements IHDF5ShortReader { private final HDF5BaseReader baseReader; HDF5ShortReader(HDF5BaseReader baseReader) { assert baseReader != null; this.baseReader = baseReader; } // For Unit tests only. HDF5BaseReader getBaseReader() { return baseReader; } // ///////////////////// // Attributes // ///////////////////// @Override public short getAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public Short call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final short[] data = baseReader.h5.readAttributeAsShortArray(attributeId, H5T_NATIVE_INT16, 1); return data[0]; } }; return baseReader.runner.call(getAttributeRunnable); } @Override public short[] getArrayAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public short[] call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); return getShortArrayAttribute(objectId, attributeName, registry); } }; return baseReader.runner.call(getAttributeRunnable); } @Override public MDShortArray getMDArrayAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public MDShortArray call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); return getShortMDArrayAttribute(objectId, attributeName, registry); } }; return baseReader.runner.call(getAttributeRunnable); } @Override public short[][] getMatrixAttr(final String objectPath, final String attributeName) throws HDF5JavaException { final MDShortArray array = getMDArrayAttr(objectPath, attributeName); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } // ///////////////////// // Data Sets // ///////////////////// @Override public short read(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public Short call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final short[] data = new short[1]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_INT16, data); return data[0]; } }; return baseReader.runner.call(readCallable); } @Override public short[] readArray(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public short[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); return readShortArray(dataSetId, registry); } }; return baseReader.runner.call(readCallable); } private short[] readShortArray(int dataSetId, ICleanUpRegistry registry) { try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); final short[] data = new short[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_INT16, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return data; } catch (HDF5LibraryException ex) { if (ex.getMajorErrorNumber() == HDF5Constants.H5E_DATATYPE && ex.getMinorErrorNumber() == HDF5Constants.H5E_CANTINIT) { // Check whether it is an array data type. final int dataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); if (baseReader.h5.getClassType(dataTypeId) == HDF5Constants.H5T_ARRAY) { return readShortArrayFromArrayType(dataSetId, dataTypeId, registry); } } throw ex; } } private short[] readShortArrayFromArrayType(int dataSetId, final int dataTypeId, ICleanUpRegistry registry) { final int spaceId = baseReader.h5.createScalarDataSpace(); final int[] dimensions = baseReader.h5.getArrayDimensions(dataTypeId); final short[] data = new short[HDF5Utils.getOneDimensionalArraySize(dimensions)]; final int memoryDataTypeId = baseReader.h5.createArrayType(H5T_NATIVE_INT16, data.length, registry); baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceId, spaceId, data); return data; } @Override public int[] readToMDArrayWithOffset(final String objectPath, final MDShortArray array, final int[] memoryOffset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getBlockSpaceParameters(dataSetId, memoryOffset, array .dimensions(), registry); final int nativeDataTypeId = baseReader.getNativeDataTypeId(dataSetId, H5T_NATIVE_INT16, registry); baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, array. getAsFlatArray()); return MDArray.toInt(spaceParams.dimensions); } }; return baseReader.runner.call(readCallable); } @Override public int[] readToMDArrayBlockWithOffset(final String objectPath, final MDShortArray array, final int[] blockDimensions, final long[] offset, final int[] memoryOffset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getBlockSpaceParameters(dataSetId, memoryOffset, array .dimensions(), offset, blockDimensions, registry); final int nativeDataTypeId = baseReader.getNativeDataTypeId(dataSetId, H5T_NATIVE_INT16, registry); baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, array .getAsFlatArray()); return MDArray.toInt(spaceParams.dimensions); } }; return baseReader.runner.call(readCallable); } @Override public short[] readArrayBlock(final String objectPath, final int blockSize, final long blockNumber) { return readArrayBlockWithOffset(objectPath, blockSize, blockNumber * blockSize); } @Override public short[] readArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public short[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockSize, registry); final short[] data = new short[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_INT16, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return data; } }; return baseReader.runner.call(readCallable); } @Override public short[][] readMatrix(final String objectPath) throws HDF5JavaException { final MDShortArray array = readMDArray(objectPath); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public short[][] readMatrixBlock(final String objectPath, final int blockSizeX, final int blockSizeY, final long blockNumberX, final long blockNumberY) throws HDF5JavaException { final MDShortArray array = readMDArrayBlock(objectPath, new int[] { blockSizeX, blockSizeY }, new long[] { blockNumberX, blockNumberY }); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public short[][] readMatrixBlockWithOffset(final String objectPath, final int blockSizeX, final int blockSizeY, final long offsetX, final long offsetY) throws HDF5JavaException { final MDShortArray array = readMDArrayBlockWithOffset(objectPath, new int[] { blockSizeX, blockSizeY }, new long[] { offsetX, offsetY }); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public MDShortArray readMDArraySlice(String objectPath, IndexMap boundIndices) { baseReader.checkOpen(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; final int cardBoundIndices = cardinalityBoundIndices(boundIndices); checkBoundIndices(objectPath, fullDimensions, cardBoundIndices); final int[] effectiveBlockDimensions = new int[fullBlockDimensions.length - cardBoundIndices]; Arrays.fill(effectiveBlockDimensions, -1); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, null, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDShortArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); if (fullBlockDimensions.length == cardBoundIndices) // no free indices { return new MDShortArray(result.getAsFlatArray(), new int[] { 1 }); } else { return new MDShortArray(result.getAsFlatArray(), effectiveBlockDimensions); } } @Override public MDShortArray readMDArraySlice(String objectPath, long[] boundIndices) { baseReader.checkOpen(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; final int cardBoundIndices = cardinalityBoundIndices(boundIndices); checkBoundIndices(objectPath, fullDimensions, boundIndices); final int[] effectiveBlockDimensions = new int[fullBlockDimensions.length - cardBoundIndices]; Arrays.fill(effectiveBlockDimensions, -1); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, null, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDShortArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); if (fullBlockDimensions.length == cardBoundIndices) // no free indices { return new MDShortArray(result.getAsFlatArray(), new int[] { 1 }); } else { return new MDShortArray(result.getAsFlatArray(), effectiveBlockDimensions); } } @Override public MDShortArray readMDArray(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public MDShortArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); return readShortMDArray(dataSetId, registry); } }; return baseReader.runner.call(readCallable); } MDShortArray readShortMDArray(int dataSetId, ICleanUpRegistry registry) { try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); final short[] data = new short[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_INT16, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return new MDShortArray(data, spaceParams.dimensions); } catch (HDF5LibraryException ex) { if (ex.getMajorErrorNumber() == HDF5Constants.H5E_DATATYPE && ex.getMinorErrorNumber() == HDF5Constants.H5E_CANTINIT) { // Check whether it is an array data type. final int dataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); if (baseReader.h5.getClassType(dataTypeId) == HDF5Constants.H5T_ARRAY) { return readShortMDArrayFromArrayType(dataSetId, dataTypeId, registry); } } throw ex; } } private MDShortArray readShortMDArrayFromArrayType(int dataSetId, final int dataTypeId, ICleanUpRegistry registry) { final int[] arrayDimensions = baseReader.h5.getArrayDimensions(dataTypeId); final int memoryDataTypeId = baseReader.h5.createArrayType(H5T_NATIVE_INT16, arrayDimensions, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); if (spaceParams.blockSize == 0) { final int spaceId = baseReader.h5.createScalarDataSpace(); final short[] data = new short[MDArray.getLength(arrayDimensions)]; baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceId, spaceId, data); return new MDShortArray(data, arrayDimensions); } else { final short[] data = new short[MDArray.getLength(arrayDimensions) * spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return new MDShortArray(data, MatrixUtils.concat(MDArray.toInt(spaceParams.dimensions), arrayDimensions)); } } @Override public MDShortArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, IndexMap boundIndices) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readSlicedMDArrayBlockWithOffset(objectPath, blockDimensions, offset, boundIndices); } @Override public MDShortArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, long[] boundIndices) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readSlicedMDArrayBlockWithOffset(objectPath, blockDimensions, offset, boundIndices); } @Override public MDShortArray readMDArrayBlock(final String objectPath, final int[] blockDimensions, final long[] blockNumber) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readMDArrayBlockWithOffset(objectPath, blockDimensions, offset); } @Override public MDShortArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, IndexMap boundIndices) { baseReader.checkOpen(); final int[] effectiveBlockDimensions = blockDimensions.clone(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; checkBoundIndices(objectPath, fullDimensions, blockDimensions, cardinalityBoundIndices(boundIndices)); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, offset, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDShortArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); return new MDShortArray(result.getAsFlatArray(), effectiveBlockDimensions); } @Override public MDShortArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, long[] boundIndices) { baseReader.checkOpen(); final int[] effectiveBlockDimensions = blockDimensions.clone(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; checkBoundIndices(objectPath, fullDimensions, blockDimensions, cardinalityBoundIndices(boundIndices)); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, offset, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDShortArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); return new MDShortArray(result.getAsFlatArray(), effectiveBlockDimensions); } @Override public MDShortArray readMDArrayBlockWithOffset(final String objectPath, final int[] blockDimensions, final long[] offset) { assert objectPath != null; assert blockDimensions != null; assert offset != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public MDShortArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockDimensions, registry); final short[] dataBlock = new short[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_INT16, spaceParams.memorySpaceId, spaceParams.dataSpaceId, dataBlock); return new MDShortArray(dataBlock, spaceParams.dimensions); } catch (HDF5SpaceRankMismatch ex) { final HDF5DataSetInformation info = baseReader.getDataSetInformation(objectPath, DataTypeInfoOptions.MINIMAL, false); if (ex.getSpaceRankExpected() - ex.getSpaceRankFound() == info .getTypeInformation().getRank()) { return readMDArrayBlockOfArrays(dataSetId, blockDimensions, offset, info, ex.getSpaceRankFound(), registry); } else { throw ex; } } } }; return baseReader.runner.call(readCallable); } private MDShortArray readMDArrayBlockOfArrays(final int dataSetId, final int[] blockDimensions, final long[] offset, final HDF5DataSetInformation info, final int spaceRank, final ICleanUpRegistry registry) { final int[] arrayDimensions = info.getTypeInformation().getDimensions(); int[] effectiveBlockDimensions = blockDimensions; // We do not support block-wise reading of array types, check // that we do not have to and bail out otherwise. for (int i = 0; i < arrayDimensions.length; ++i) { final int j = spaceRank + i; if (effectiveBlockDimensions[j] < 0) { if (effectiveBlockDimensions == blockDimensions) { effectiveBlockDimensions = blockDimensions.clone(); } effectiveBlockDimensions[j] = arrayDimensions[i]; } if (effectiveBlockDimensions[j] != arrayDimensions[i]) { throw new HDF5JavaException( "Block-wise reading of array type data sets is not supported."); } } final int[] spaceBlockDimensions = Arrays.copyOfRange(effectiveBlockDimensions, 0, spaceRank); final long[] spaceOfs = Arrays.copyOfRange(offset, 0, spaceRank); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, spaceOfs, spaceBlockDimensions, registry); final short[] dataBlock = new short[spaceParams.blockSize * info.getTypeInformation().getNumberOfElements()]; final int memoryDataTypeId = baseReader.h5.createArrayType(H5T_NATIVE_INT16, info.getTypeInformation() .getDimensions(), registry); baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, dataBlock); return new MDShortArray(dataBlock, effectiveBlockDimensions); } @Override public Iterable> getArrayNaturalBlocks(final String dataSetPath) throws HDF5JavaException { baseReader.checkOpen(); final HDF5NaturalBlock1DParameters params = new HDF5NaturalBlock1DParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlock1DParameters.HDF5NaturalBlock1DIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5DataBlock next() { final long offset = index.computeOffsetAndSizeGetOffset(); final short[] block = readArrayBlockWithOffset(dataSetPath, index .getBlockSize(), offset); return new HDF5DataBlock(block, index.getAndIncIndex(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } @Override public Iterable> getMDArrayNaturalBlocks(final String dataSetPath) { baseReader.checkOpen(); final HDF5NaturalBlockMDParameters params = new HDF5NaturalBlockMDParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlockMDParameters.HDF5NaturalBlockMDIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5MDDataBlock next() { final long[] offset = index.computeOffsetAndSizeGetOffsetClone(); final MDShortArray data = readMDArrayBlockWithOffset(dataSetPath, index .getBlockSize(), offset); return new HDF5MDDataBlock(data, index .getIndexClone(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } short[] getShortArrayAttribute(final int objectId, final String attributeName, ICleanUpRegistry registry) { final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, registry); final int memoryTypeId; final int len; if (baseReader.h5.getClassType(attributeTypeId) == H5T_ARRAY) { final int[] arrayDimensions = baseReader.h5.getArrayDimensions(attributeTypeId); if (arrayDimensions.length != 1) { throw new HDF5JavaException( "Array needs to be of rank 1, but is of rank " + arrayDimensions.length); } len = arrayDimensions[0]; memoryTypeId = baseReader.h5.createArrayType(H5T_NATIVE_INT16, len, registry); } else { final long[] arrayDimensions = baseReader.h5.getDataDimensionsForAttribute(attributeId, registry); memoryTypeId = H5T_NATIVE_INT16; len = HDF5Utils.getOneDimensionalArraySize(arrayDimensions); } final short[] data = baseReader.h5.readAttributeAsShortArray(attributeId, memoryTypeId, len); return data; } MDShortArray getShortMDArrayAttribute(final int objectId, final String attributeName, ICleanUpRegistry registry) { try { final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, registry); final int memoryTypeId; final int[] arrayDimensions; if (baseReader.h5.getClassType(attributeTypeId) == H5T_ARRAY) { arrayDimensions = baseReader.h5.getArrayDimensions(attributeTypeId); memoryTypeId = baseReader.h5.createArrayType(H5T_NATIVE_INT16, arrayDimensions, registry); } else { arrayDimensions = MDArray.toInt(baseReader.h5.getDataDimensionsForAttribute( attributeId, registry)); memoryTypeId = H5T_NATIVE_INT16; } final int len = MDArray.getLength(arrayDimensions); final short[] data = baseReader.h5.readAttributeAsShortArray(attributeId, memoryTypeId, len); return new MDShortArray(data, arrayDimensions); } catch (IllegalArgumentException ex) { throw new HDF5JavaException(ex.getMessage()); } } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5ShortWriter.java000066400000000000000000000666721256564762100271510ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.HDF5IntStorageFeatures.INT_NO_COMPRESSION; import static ch.systemsx.cisd.hdf5.hdf5lib.H5D.H5Dwrite; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_ALL; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_INT16; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_I16LE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_U16LE; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDShortArray; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; /** * The implementation of {@link IHDF5ShortWriter}. * * @author Bernd Rinn */ class HDF5ShortWriter extends HDF5ShortReader implements IHDF5ShortWriter { private final HDF5BaseWriter baseWriter; HDF5ShortWriter(HDF5BaseWriter baseWriter) { super(baseWriter); assert baseWriter != null; this.baseWriter = baseWriter; } // ///////////////////// // Attributes // ///////////////////// @Override public void setAttr(final String objectPath, final String name, final short value) { assert objectPath != null; assert name != null; baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { 1 }, registry); baseWriter.setAttribute(objectPath, name, H5T_STD_I16LE, H5T_NATIVE_INT16, dataSpaceId, new short[] { value }, registry); } else { baseWriter.setAttribute(objectPath, name, H5T_STD_I16LE, H5T_NATIVE_INT16, -1, new short[] { value }, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void setArrayAttr(final String objectPath, final String name, final short[] value) { assert objectPath != null; assert name != null; assert value != null; baseWriter.checkOpen(); final ICallableWithCleanUp setAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { value.length }, registry); baseWriter.setAttribute(objectPath, name, H5T_STD_I16LE, H5T_NATIVE_INT16, dataSpaceId, value, registry); } else { final int memoryTypeId = baseWriter.h5.createArrayType(H5T_NATIVE_INT16, value.length, registry); final int storageTypeId = baseWriter.h5.createArrayType(H5T_STD_I16LE, value.length, registry); baseWriter.setAttribute(objectPath, name, storageTypeId, memoryTypeId, -1, value, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(setAttributeRunnable); } @Override public void setMDArrayAttr(final String objectPath, final String name, final MDShortArray value) { assert objectPath != null; assert name != null; assert value != null; baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(value.longDimensions(), registry); baseWriter.setAttribute(objectPath, name, H5T_STD_I16LE, H5T_NATIVE_INT16, dataSpaceId, value.getAsFlatArray(), registry); } else { final int memoryTypeId = baseWriter.h5.createArrayType(H5T_NATIVE_INT16, value.dimensions(), registry); final int storageTypeId = baseWriter.h5.createArrayType(H5T_STD_I16LE, value.dimensions(), registry); baseWriter.setAttribute(objectPath, name, storageTypeId, memoryTypeId, -1, value.getAsFlatArray(), registry); } return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void setMatrixAttr(final String objectPath, final String name, final short[][] value) { setMDArrayAttr(objectPath, name, new MDShortArray(value)); } // ///////////////////// // Data Sets // ///////////////////// @Override public void write(final String objectPath, final short value) { assert objectPath != null; baseWriter.checkOpen(); baseWriter.writeScalar(objectPath, H5T_STD_I16LE, H5T_NATIVE_INT16, value); } @Override public void writeArray(final String objectPath, final short[] data) { writeArray(objectPath, data, INT_NO_COMPRESSION); } @Override public void writeArray(final String objectPath, final short[] data, final HDF5IntStorageFeatures features) { assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, features.isSigned() ? H5T_STD_I16LE : H5T_STD_U16LE, new long[] { data.length }, 2, features, registry); H5Dwrite(dataSetId, H5T_NATIVE_INT16, H5S_ALL, H5S_ALL, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createArray(final String objectPath, final int size) { createArray(objectPath, size, INT_NO_COMPRESSION); } @Override public void createArray(final String objectPath, final long size, final int blockSize) { createArray(objectPath, size, blockSize, INT_NO_COMPRESSION); } @Override public void createArray(final String objectPath, final int size, final HDF5IntStorageFeatures features) { assert objectPath != null; assert size >= 0; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (features.requiresChunking()) { baseWriter.createDataSet(objectPath, features.isSigned() ? H5T_STD_I16LE : H5T_STD_U16LE, features, new long[] { 0 }, new long[] { size }, 2, registry); } else { baseWriter.createDataSet(objectPath, features.isSigned() ? H5T_STD_I16LE : H5T_STD_U16LE, features, new long[] { size }, null, 2, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void createArray(final String objectPath, final long size, final int blockSize, final HDF5IntStorageFeatures features) { assert objectPath != null; assert size >= 0; assert blockSize >= 0 && (blockSize <= size || size == 0); baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { baseWriter.createDataSet(objectPath, features.isSigned() ? H5T_STD_I16LE : H5T_STD_U16LE, features, new long[] { size }, new long[] { blockSize }, 2, registry); return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void writeArrayBlock(final String objectPath, final short[] data, final long blockNumber) { writeArrayBlockWithOffset(objectPath, data, data.length, data.length * blockNumber); } @Override public void writeArrayBlockWithOffset(final String objectPath, final short[] data, final int dataSize, final long offset) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] blockDimensions = new long[] { dataSize }; final long[] slabStartOrNull = new long[] { offset }; final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, new long[] { offset + dataSize }, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, slabStartOrNull, blockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(blockDimensions, registry); H5Dwrite(dataSetId, H5T_NATIVE_INT16, memorySpaceId, dataSpaceId, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } /** * Writes out a short matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ @Override public void writeMatrix(final String objectPath, final short[][] data) { writeMatrix(objectPath, data, INT_NO_COMPRESSION); } @Override public void writeMatrix(final String objectPath, final short[][] data, final HDF5IntStorageFeatures features) { assert objectPath != null; assert data != null; assert HDF5Utils.areMatrixDimensionsConsistent(data); writeMDArray(objectPath, new MDShortArray(data), features); } @Override public void createMatrix(final String objectPath, final int sizeX, final int sizeY) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; createMDArray(objectPath, new int[] { sizeX, sizeY }); } @Override public void createMatrix(final String objectPath, final int sizeX, final int sizeY, final HDF5IntStorageFeatures features) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; createMDArray(objectPath, new int[] { sizeX, sizeY }, features); } @Override public void createMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; assert blockSizeX >= 0 && (blockSizeX <= sizeX || sizeX == 0); assert blockSizeY >= 0 && (blockSizeY <= sizeY || sizeY == 0); createMDArray(objectPath, new long[] { sizeX, sizeY }, new int[] { blockSizeX, blockSizeY }); } @Override public void createMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY, final HDF5IntStorageFeatures features) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; assert blockSizeX >= 0 && (blockSizeX <= sizeX || sizeX == 0); assert blockSizeY >= 0 && (blockSizeY <= sizeY || sizeY == 0); createMDArray(objectPath, new long[] { sizeX, sizeY }, new int[] { blockSizeX, blockSizeY }, features); } @Override public void writeMatrixBlock(final String objectPath, final short[][] data, final long blockNumberX, final long blockNumberY) { assert objectPath != null; assert data != null; writeMDArrayBlock(objectPath, new MDShortArray(data), new long[] { blockNumberX, blockNumberY }); } @Override public void writeMatrixBlockWithOffset(final String objectPath, final short[][] data, final long offsetX, final long offsetY) { assert objectPath != null; assert data != null; writeMDArrayBlockWithOffset(objectPath, new MDShortArray(data, new int[] { data.length, data[0].length }), new long[] { offsetX, offsetY }); } @Override public void writeMatrixBlockWithOffset(final String objectPath, final short[][] data, final int dataSizeX, final int dataSizeY, final long offsetX, final long offsetY) { assert objectPath != null; assert data != null; writeMDArrayBlockWithOffset(objectPath, new MDShortArray(data, new int[] { dataSizeX, dataSizeY }), new long[] { offsetX, offsetY }); } @Override public void writeMDArray(final String objectPath, final MDShortArray data) { writeMDArray(objectPath, data, INT_NO_COMPRESSION); } @Override public void writeMDArraySlice(String objectPath, MDShortArray data, IndexMap boundIndices) { baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), null, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDShortArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArraySlice(String objectPath, MDShortArray data, long[] boundIndices) { baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), null, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDShortArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArray(final String objectPath, final MDShortArray data, final HDF5IntStorageFeatures features) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, features.isSigned() ? H5T_STD_I16LE : H5T_STD_U16LE, data.longDimensions(), 2, features, registry); H5Dwrite(dataSetId, H5T_NATIVE_INT16, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createMDArray(final String objectPath, final int[] dimensions) { createMDArray(objectPath, dimensions, INT_NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions) { createMDArray(objectPath, dimensions, blockDimensions, INT_NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final int[] dimensions, final HDF5IntStorageFeatures features) { assert objectPath != null; assert dimensions != null; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (features.requiresChunking()) { final long[] nullDimensions = new long[dimensions.length]; baseWriter.createDataSet(objectPath, features.isSigned() ? H5T_STD_I16LE : H5T_STD_U16LE, features, nullDimensions, MDArray.toLong(dimensions), 2, registry); } else { baseWriter.createDataSet(objectPath, features.isSigned() ? H5T_STD_I16LE : H5T_STD_U16LE, features, MDArray.toLong(dimensions), null, 2, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void createMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions, final HDF5IntStorageFeatures features) { assert objectPath != null; assert dimensions != null; assert blockDimensions != null; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { baseWriter.createDataSet(objectPath, features.isSigned() ? H5T_STD_I16LE : H5T_STD_U16LE, features, dimensions, MDArray.toLong(blockDimensions), 2, registry); return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void writeMDArrayBlock(final String objectPath, final MDShortArray data, final long[] blockNumber) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeMDArrayBlockWithOffset(objectPath, data, offset); } @Override public void writeSlicedMDArrayBlock(final String objectPath, final MDShortArray data, final long[] blockNumber, IndexMap boundIndices) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeSlicedMDArrayBlockWithOffset(objectPath, data, offset, boundIndices); } @Override public void writeSlicedMDArrayBlock(String objectPath, MDShortArray data, long[] blockNumber, long[] boundIndices) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeSlicedMDArrayBlockWithOffset(objectPath, data, offset, boundIndices); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final MDShortArray data, final long[] offset) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] dimensions = data.longDimensions(); assert dimensions.length == offset.length; final long[] dataSetDimensions = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + dimensions[i]; } final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, dimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(dimensions, registry); H5Dwrite(dataSetId, H5T_NATIVE_INT16, memorySpaceId, dataSpaceId, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeSlicedMDArrayBlockWithOffset(String objectPath, MDShortArray data, long[] offset, IndexMap boundIndices) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), offset, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDShortArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeSlicedMDArrayBlockWithOffset(String objectPath, MDShortArray data, long[] offset, long[] boundIndices) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), offset, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDShortArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final MDShortArray data, final int[] blockDimensions, final long[] offset, final int[] memoryOffset) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] memoryDimensions = data.longDimensions(); assert memoryDimensions.length == offset.length; final long[] longBlockDimensions = MDArray.toLong(blockDimensions); assert longBlockDimensions.length == offset.length; final long[] dataSetDimensions = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + blockDimensions[i]; } final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, longBlockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(memoryDimensions, registry); baseWriter.h5.setHyperslabBlock(memorySpaceId, MDArray.toLong(memoryOffset), longBlockDimensions); H5Dwrite(dataSetId, H5T_NATIVE_INT16, memorySpaceId, dataSpaceId, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5StorageLayout.java000066400000000000000000000014441256564762100274410ustar00rootroot00000000000000package ch.systemsx.cisd.hdf5; import ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants; /** * The storage layout of a data set in the HDF5 file. Not applicable for attributes. * * @author Bernd Rinn */ public enum HDF5StorageLayout { COMPACT(HDF5Constants.H5D_COMPACT), CONTIGUOUS(HDF5Constants.H5D_CONTIGUOUS), CHUNKED( HDF5Constants.H5D_CHUNKED), NOT_APPLICABLE(-1); private int id; private HDF5StorageLayout(int id) { this.id = id; } static HDF5StorageLayout fromId(int id) throws IllegalArgumentException { for (HDF5StorageLayout layout : values()) { if (layout.id == id) { return layout; } } throw new IllegalArgumentException("Illegal layout id " + id); } }libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5StringReader.java000066400000000000000000000706401256564762100272340ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.HDF5Utils.getOneDimensionalArraySize; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STRING; import java.util.Iterator; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.hdf5.HDF5BaseReader.DataSpaceParameters; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; /** * The implementation of {@link IHDF5StringReader}. * * @author Bernd Rinn */ public class HDF5StringReader implements IHDF5StringReader { private final HDF5BaseReader baseReader; HDF5StringReader(HDF5BaseReader baseReader) { assert baseReader != null; this.baseReader = baseReader; } // // Attributes // @Override public String getAttr(final String objectPath, final String attributeName) { return getStringAttribute(objectPath, attributeName, false); } @Override public String getAttrRaw(final String objectPath, final String attributeName) { return getStringAttribute(objectPath, attributeName, true); } String getStringAttribute(final String objectPath, final String attributeName, final boolean readRaw) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp readRunnable = new ICallableWithCleanUp() { @Override public String call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); return baseReader.getStringAttribute(objectId, objectPath, attributeName, readRaw, registry); } }; return baseReader.runner.call(readRunnable); } @Override public String[] getArrayAttr(final String objectPath, final String attributeName) { return getStringArrayAttribute(objectPath, attributeName, false); } @Override public String[] getArrayAttrRaw(final String objectPath, final String attributeName) { return getStringArrayAttribute(objectPath, attributeName, true); } String[] getStringArrayAttribute(final String objectPath, final String attributeName, final boolean readRaw) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp readRunnable = new ICallableWithCleanUp() { @Override public String[] call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); return baseReader.getStringArrayAttribute(objectId, objectPath, attributeName, readRaw, registry); } }; return baseReader.runner.call(readRunnable); } @Override public MDArray getMDArrayAttr(final String objectPath, final String attributeName) { return getStringMDArrayAttribute(objectPath, attributeName, false); } @Override public MDArray getMDArrayAttrRaw(final String objectPath, final String attributeName) { return getStringMDArrayAttribute(objectPath, attributeName, true); } MDArray getStringMDArrayAttribute(final String objectPath, final String attributeName, final boolean readRaw) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp> readRunnable = new ICallableWithCleanUp>() { @Override public MDArray call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); return baseReader.getStringMDArrayAttribute(objectId, objectPath, attributeName, readRaw, registry); } }; return baseReader.runner.call(readRunnable); } // // Data Sets // @Override public String read(final String objectPath) throws HDF5JavaException { return readString(objectPath, false); } @Override public String readRaw(String objectPath) throws HDF5JavaException { return readString(objectPath, true); } String readString(final String objectPath, final boolean readRaw) throws HDF5JavaException { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public String call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final int dataTypeId = baseReader.h5.getNativeDataTypeForDataSet(dataSetId, registry); final boolean isString = (baseReader.h5.getClassType(dataTypeId) == H5T_STRING); if (isString == false) { throw new HDF5JavaException(objectPath + " needs to be a String."); } if (baseReader.h5.isVariableLengthString(dataTypeId)) { String[] data = new String[1]; baseReader.h5.readDataSetVL(dataSetId, dataTypeId, data); return data[0]; } else { final int size = baseReader.h5.getDataTypeSize(dataTypeId); final CharacterEncoding encoding = baseReader.h5.getCharacterEncoding(dataTypeId); byte[] data = new byte[size]; baseReader.h5.readDataSetNonNumeric(dataSetId, dataTypeId, data); return readRaw ? StringUtils.fromBytes(data, encoding) : StringUtils .fromBytes0Term(data, encoding); } } }; return baseReader.runner.call(writeRunnable); } @Override public String[] readArrayRaw(final String objectPath) throws HDF5JavaException { return readStringArray(objectPath, true); } @Override public String[] readArray(final String objectPath) throws HDF5JavaException { return readStringArray(objectPath, false); } String[] readStringArray(final String objectPath, final boolean readRaw) throws HDF5JavaException { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public String[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final long[] dimensions = baseReader.h5.getDataDimensions(dataSetId, registry); final int oneDimSize = getOneDimensionalArraySize(dimensions); final String[] data = new String[oneDimSize]; final int dataTypeId = baseReader.h5.getNativeDataTypeForDataSet(dataSetId, registry); if (baseReader.h5.isVariableLengthString(dataTypeId)) { baseReader.h5.readDataSetVL(dataSetId, dataTypeId, data); } else { final boolean isString = (baseReader.h5.getClassType(dataTypeId) == H5T_STRING); if (isString == false) { throw new HDF5JavaException(objectPath + " needs to be a String."); } final int strLength; final byte[] bdata; if (readRaw) { strLength = baseReader.h5.getDataTypeSize(dataTypeId); bdata = new byte[oneDimSize * strLength]; baseReader.h5.readDataSetNonNumeric(dataSetId, dataTypeId, bdata); } else { strLength = -1; bdata = null; baseReader.h5.readDataSetString(dataSetId, dataTypeId, data); } if (bdata != null && readRaw) { final CharacterEncoding encoding = baseReader.h5.getCharacterEncoding(dataTypeId); for (int i = 0, startIdx = 0; i < oneDimSize; ++i, startIdx += strLength) { data[i] = StringUtils.fromBytes(bdata, startIdx, startIdx + strLength, encoding); } } } return data; } }; return baseReader.runner.call(writeRunnable); } @Override public String[] readArrayBlock(final String objectPath, final int blockSize, final long blockNumber) { return readArrayBlockWithOffset(objectPath, blockSize, blockSize * blockNumber); } @Override public String[] readArrayBlockRaw(String objectPath, int blockSize, long blockNumber) { return readArrayBlockWithOffsetRaw(objectPath, blockSize, blockSize * blockNumber); } String[] readArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset, final boolean readRaw) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public String[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockSize, registry); final String[] data = new String[spaceParams.blockSize]; final int dataTypeId = baseReader.h5.getNativeDataTypeForDataSet(dataSetId, registry); if (baseReader.h5.isVariableLengthString(dataTypeId)) { baseReader.h5.readDataSetVL(dataSetId, dataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); } else { final boolean isString = (baseReader.h5.getClassType(dataTypeId) == H5T_STRING); if (isString == false) { throw new HDF5JavaException(objectPath + " needs to be a String."); } final int strLength; final byte[] bdata; if (readRaw) { strLength = baseReader.h5.getDataTypeSize(dataTypeId); bdata = new byte[spaceParams.blockSize * strLength]; baseReader.h5.readDataSetNonNumeric(dataSetId, dataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, bdata); } else { strLength = -1; bdata = null; baseReader.h5.readDataSetString(dataSetId, dataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); } if (bdata != null && readRaw) { final CharacterEncoding encoding = baseReader.h5.getCharacterEncoding(dataTypeId); for (int i = 0, startIdx = 0; i < spaceParams.blockSize; ++i, startIdx += strLength) { data[i] = StringUtils.fromBytes(bdata, startIdx, startIdx + strLength, encoding); } } } return data; } }; return baseReader.runner.call(readCallable); } @Override public String[] readArrayBlockWithOffset(String objectPath, int blockSize, long offset) { return readArrayBlockWithOffset(objectPath, blockSize, offset, false); } @Override public String[] readArrayBlockWithOffsetRaw(String objectPath, int blockSize, long offset) { return readArrayBlockWithOffset(objectPath, blockSize, offset, true); } @Override public MDArray readMDArray(final String objectPath) { return readStringMDArray(objectPath, false); } @Override public MDArray readMDArrayRaw(final String objectPath) { return readStringMDArray(objectPath, true); } MDArray readStringMDArray(final String objectPath, final boolean readRaw) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp> readCallable = new ICallableWithCleanUp>() { @Override public MDArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); final String[] data = new String[spaceParams.blockSize]; final int dataTypeId = baseReader.h5.getNativeDataTypeForDataSet(dataSetId, registry); if (baseReader.h5.isVariableLengthString(dataTypeId)) { baseReader.h5.readDataSetVL(dataSetId, dataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); } else { final boolean isString = (baseReader.h5.getClassType(dataTypeId) == H5T_STRING); if (isString == false) { throw new HDF5JavaException(objectPath + " needs to be a String."); } final int strLength; final byte[] bdata; if (readRaw) { strLength = baseReader.h5.getDataTypeSize(dataTypeId); bdata = new byte[spaceParams.blockSize * strLength]; baseReader.h5.readDataSetNonNumeric(dataSetId, dataTypeId, bdata); } else { strLength = -1; bdata = null; baseReader.h5.readDataSetString(dataSetId, dataTypeId, data); } if (bdata != null && readRaw) { final CharacterEncoding encoding = baseReader.h5.getCharacterEncoding(dataTypeId); for (int i = 0, startIdx = 0; i < spaceParams.blockSize; ++i, startIdx += strLength) { data[i] = StringUtils.fromBytes(bdata, startIdx, startIdx + strLength, encoding); } } } return new MDArray(data, spaceParams.dimensions); } }; return baseReader.runner.call(readCallable); } MDArray readMDArrayBlockWithOffset(final String objectPath, final int[] blockDimensions, final long[] offset, final boolean readRaw) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp> readCallable = new ICallableWithCleanUp>() { @Override public MDArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockDimensions, registry); final String[] dataBlock = new String[spaceParams.blockSize]; final int dataTypeId = baseReader.h5.getNativeDataTypeForDataSet(dataSetId, registry); if (baseReader.h5.isVariableLengthString(dataTypeId)) { baseReader.h5.readDataSetVL(dataSetId, dataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, dataBlock); } else { final boolean isString = (baseReader.h5.getClassType(dataTypeId) == H5T_STRING); if (isString == false) { throw new HDF5JavaException(objectPath + " needs to be a String."); } final int strLength; byte[] bdata = null; if (readRaw) { strLength = baseReader.h5.getDataTypeSize(dataTypeId); bdata = new byte[spaceParams.blockSize * strLength]; baseReader.h5.readDataSetNonNumeric(dataSetId, dataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, bdata); } else { strLength = -1; baseReader.h5.readDataSetString(dataSetId, dataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, dataBlock); } if (bdata != null && readRaw) { final CharacterEncoding encoding = baseReader.h5.getCharacterEncoding(dataTypeId); for (int i = 0, startIdx = 0; i < spaceParams.blockSize; ++i, startIdx += strLength) { dataBlock[i] = StringUtils.fromBytes(bdata, startIdx, startIdx + strLength, encoding); } } } return new MDArray(dataBlock, blockDimensions); } }; return baseReader.runner.call(readCallable); } @Override public MDArray readMDArrayBlockWithOffset(final String objectPath, final int[] blockDimensions, final long[] offset) { return readMDArrayBlockWithOffset(objectPath, blockDimensions, offset, false); } @Override public MDArray readMDArrayBlockWithOffsetRaw(String objectPath, int[] blockDimensions, long[] offset) { return readMDArrayBlockWithOffset(objectPath, blockDimensions, offset, true); } @Override public MDArray readMDArrayBlock(final String objectPath, final int[] blockDimensions, final long[] blockNumber) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readMDArrayBlockWithOffset(objectPath, blockDimensions, offset); } @Override public MDArray readMDArrayBlockRaw(String objectPath, int[] blockDimensions, long[] blockNumber) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readMDArrayBlockWithOffsetRaw(objectPath, blockDimensions, offset); } Iterable> getArrayNaturalBlocks(final String dataSetPath, final boolean readRaw) throws HDF5JavaException { baseReader.checkOpen(); final HDF5NaturalBlock1DParameters params = new HDF5NaturalBlock1DParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlock1DParameters.HDF5NaturalBlock1DIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5DataBlock next() { final long offset = index.computeOffsetAndSizeGetOffset(); final String[] block = readRaw ? readArrayBlockWithOffsetRaw(dataSetPath, index.getBlockSize(), offset) : readArrayBlockWithOffset(dataSetPath, index.getBlockSize(), offset); return new HDF5DataBlock(block, index.getAndIncIndex(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } @Override public Iterable> getArrayNaturalBlocks(final String dataSetPath) throws HDF5JavaException { return getArrayNaturalBlocks(dataSetPath, false); } @Override public Iterable> getArrayNaturalBlocksRaw(String dataSetPath) throws HDF5JavaException { return getArrayNaturalBlocks(dataSetPath, true); } Iterable>> getMDArrayNaturalBlocks(final String objectPath, final boolean readRaw) { baseReader.checkOpen(); final HDF5NaturalBlockMDParameters params = new HDF5NaturalBlockMDParameters(baseReader.getDataSetInformation(objectPath)); return new Iterable>>() { @Override public Iterator>> iterator() { return new Iterator>>() { final HDF5NaturalBlockMDParameters.HDF5NaturalBlockMDIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5MDDataBlock> next() { final long[] offset = index.computeOffsetAndSizeGetOffsetClone(); final MDArray data = readRaw ? readMDArrayBlockWithOffsetRaw(objectPath, index.getBlockSize(), offset) : readMDArrayBlockWithOffset(objectPath, index.getBlockSize(), offset); return new HDF5MDDataBlock>(data, index.getIndexClone(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } @Override public Iterable>> getMDArrayNaturalBlocks( final String objectPath) { return getMDArrayNaturalBlocks(objectPath, false); } @Override public Iterable>> getMDArrayNaturalBlocksRaw(String objectPath) { return getMDArrayNaturalBlocks(objectPath, true); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5StringWriter.java000066400000000000000000001156211256564762100273050ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION; import static ch.systemsx.cisd.hdf5.hdf5lib.H5D.H5Dwrite; import static ch.systemsx.cisd.hdf5.hdf5lib.H5D.H5DwriteString; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_ALL; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_SCALAR; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import ch.systemsx.cisd.base.mdarray.MDAbstractArray; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.hdf5.HDF5BaseWriter.StringArrayBuffer; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; /** * The implementation of {@link IHDF5StringWriter}. * * @author Bernd Rinn */ public class HDF5StringWriter extends HDF5StringReader implements IHDF5StringWriter { private static final int MAX_COMPACT_SIZE = 64 * 1024 - 12; private final HDF5BaseWriter baseWriter; HDF5StringWriter(HDF5BaseWriter baseWriter) { super(baseWriter); assert baseWriter != null; this.baseWriter = baseWriter; } // ///////////////////// // Attributes // ///////////////////// @Override public void setAttrVL(final String objectPath, final String name, final String value) { assert name != null; assert value != null; baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { final int objectId = baseWriter.h5.openObject(baseWriter.fileId, objectPath, registry); baseWriter.setStringAttributeVariableLength(objectId, name, value, registry); return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void setAttr(final String objectPath, final String name, final String value) { setStringAttribute(objectPath, name, value, value.length(), true); } @Override public void setAttr(final String objectPath, final String name, final String value, final int maxLength) { setStringAttribute(objectPath, name, value, maxLength, false); } void setStringAttribute(final String objectPath, final String name, final String value, final int maxLength, final boolean lengthFitsValue) { assert objectPath != null; assert name != null; assert value != null; baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { final int objectId = baseWriter.h5.openObject(baseWriter.fileId, objectPath, registry); baseWriter.setStringAttribute(objectId, name, value, maxLength, lengthFitsValue, registry); return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void setArrayAttr(final String objectPath, final String name, final String[] value) { setStringArrayAttribute(objectPath, name, value, -1, true); } @Override public void setArrayAttr(final String objectPath, final String name, final String[] value, final int maxLength) { setStringArrayAttribute(objectPath, name, value, maxLength, false); } void setStringArrayAttribute(final String objectPath, final String name, final String[] value, final int maxLength, final boolean lengthFitsValue) { assert objectPath != null; assert name != null; assert value != null; baseWriter.checkOpen(); final ICallableWithCleanUp setAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int objectId = baseWriter.h5.openObject(baseWriter.fileId, objectPath, registry); baseWriter.setStringArrayAttribute(objectId, name, value, maxLength, lengthFitsValue, registry); return null; // Nothing to return. } }; baseWriter.runner.call(setAttributeRunnable); } @Override public void setMDArrayAttr(final String objectPath, final String name, final MDArray value) { setStringMDArrayAttribute(objectPath, name, value, -1, true); } @Override public void setMDArrayAttr(final String objectPath, final String name, final MDArray value, final int maxLength) { setStringMDArrayAttribute(objectPath, name, value, maxLength, false); } void setStringMDArrayAttribute(final String objectPath, final String name, final MDArray value, final int maxLength, final boolean lengthFitsValue) { assert objectPath != null; assert name != null; assert value != null; baseWriter.checkOpen(); final ICallableWithCleanUp setAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int objectId = baseWriter.h5.openObject(baseWriter.fileId, objectPath, registry); baseWriter.setStringArrayAttribute(objectId, name, value, maxLength, lengthFitsValue, registry); return null; // Nothing to return. } }; baseWriter.runner.call(setAttributeRunnable); } // ///////////////////// // Data Sets // ///////////////////// @Override public void write(final String objectPath, final String data, final int maxLength) { writeString(objectPath, data, maxLength, true, HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION); } @Override public void write(final String objectPath, final String data) { writeString(objectPath, data, data.length(), true, HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION); } @Override public void write(final String objectPath, final String data, final HDF5GenericStorageFeatures features) { writeString(objectPath, data, data.length(), true, features); } @Override public void write(final String objectPath, final String data, final int maxLength, final HDF5GenericStorageFeatures features) { writeString(objectPath, data, maxLength, false, features); } // Implementation note: this needs special treatment as we want to create a (possibly chunked) // data set with max dimension 1 instead of infinity. void writeString(final String objectPath, final String data, final int maxLength, final boolean lengthFitsValue, final HDF5GenericStorageFeatures features) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { final byte[] bytes; final int realMaxLengthInBytes; if (lengthFitsValue) { bytes = StringUtils.toBytes0Term(data, baseWriter.encodingForNewDataSets); realMaxLengthInBytes = (bytes.length == 1) ? 1 : bytes.length - 1; } else { bytes = StringUtils.toBytes0Term(data, maxLength, baseWriter.encodingForNewDataSets); realMaxLengthInBytes = baseWriter.encodingForNewDataSets.getMaxBytesPerChar() * ((maxLength == 0) ? 1 : maxLength); } boolean exists = baseWriter.h5.exists(baseWriter.fileId, objectPath); if (exists && baseWriter.keepDataIfExists(features) == false) { baseWriter.h5.deleteObject(baseWriter.fileId, objectPath); exists = false; } final int stringDataTypeId = baseWriter.h5.createDataTypeString(realMaxLengthInBytes, registry); if (features.requiresChunking() == false) { // If we do not want to compress, we can create a scalar dataset. baseWriter.writeScalar(objectPath, stringDataTypeId, stringDataTypeId, bytes, features.allowsCompact() && (realMaxLengthInBytes < MAX_COMPACT_SIZE), baseWriter.keepDataIfExists(features), registry); } else { final long[] chunkSizeOrNull = HDF5Utils.tryGetChunkSizeForString(realMaxLengthInBytes, features.requiresChunking()); final int dataSetId; if (exists) { dataSetId = baseWriter.h5.openDataSet(baseWriter.fileId, objectPath, registry); } else { final HDF5StorageLayout layout = baseWriter.determineLayout(stringDataTypeId, HDF5Utils.SCALAR_DIMENSIONS, chunkSizeOrNull, null); dataSetId = baseWriter.h5.createDataSet(baseWriter.fileId, HDF5Utils.SCALAR_DIMENSIONS, chunkSizeOrNull, stringDataTypeId, features, objectPath, layout, baseWriter.fileFormat, registry); } H5Dwrite(dataSetId, stringDataTypeId, H5S_ALL, H5S_ALL, H5P_DEFAULT, bytes); } return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeArray(final String objectPath, final String[] data, final HDF5GenericStorageFeatures features) { assert objectPath != null; assert data != null; writeStringArray(objectPath, data, getMaxLength(data), true, features, false); } @Override public void writeArray(final String objectPath, final String[] data) { assert objectPath != null; assert data != null; writeStringArray(objectPath, data, getMaxLength(data), true, HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION, false); } @Override public void writeArray(final String objectPath, final String[] data, final int maxLength) { writeStringArray(objectPath, data, maxLength, false, HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION, false); } private static int getMaxLength(String[] data) { int maxLength = 0; for (String s : data) { maxLength = Math.max(maxLength, s.length()); } return maxLength; } @Override public void writeArray(final String objectPath, final String[] data, int maxLength, final HDF5GenericStorageFeatures features) throws HDF5JavaException { assert maxLength >= 0; writeStringArray(objectPath, data, maxLength, false, features, false); } private void writeStringArray(final String objectPath, final String[] data, final int maxLength, final boolean lengthFitsValue, final HDF5GenericStorageFeatures features, final boolean variableLength) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { if (variableLength) { final int elementSize = 8; // 64bit pointers final int stringDataTypeId = baseWriter.variableLengthStringDataTypeId; final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, stringDataTypeId, new long[] { data.length }, elementSize, features, registry); baseWriter.writeStringVL(dataSetId, data); } else { final StringArrayBuffer array = baseWriter.new StringArrayBuffer(maxLength, lengthFitsValue); array.addAll(data); final byte[] arrData = array.toArray(); final int elementSize = array.getMaxLengthInByte(); final int stringDataTypeId = baseWriter.h5.createDataTypeString(elementSize, registry); final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, stringDataTypeId, new long[] { data.length }, elementSize, features, registry); H5Dwrite(dataSetId, stringDataTypeId, H5S_ALL, H5S_ALL, H5P_DEFAULT, arrData); } return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createArray(final String objectPath, final int maxLength, final int size) { createArray(objectPath, maxLength, size, GENERIC_NO_COMPRESSION); } @Override public void createArray(final String objectPath, final int maxLength, final long size, final int blockSize) { createArray(objectPath, maxLength, size, blockSize, GENERIC_NO_COMPRESSION); } @Override public void createArray(final String objectPath, final int maxLength, final int size, final HDF5GenericStorageFeatures features) { assert maxLength > 0; createStringArray(objectPath, maxLength, size, features, false); } private void createStringArray(final String objectPath, final int maxLength, final int size, final HDF5GenericStorageFeatures features, final boolean variableLength) { assert objectPath != null; assert size >= 0; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { final int elementSize; final int stringDataTypeId; if (variableLength) { elementSize = 8; // 64bit pointers stringDataTypeId = baseWriter.variableLengthStringDataTypeId; } else { elementSize = baseWriter.encodingForNewDataSets.getMaxBytesPerChar() * maxLength; stringDataTypeId = baseWriter.h5.createDataTypeString(elementSize, registry); } if (features.requiresChunking()) { baseWriter.createDataSet(objectPath, stringDataTypeId, features, new long[] { 0 }, new long[] { size }, elementSize, registry); } else { baseWriter.createDataSet(objectPath, stringDataTypeId, features, new long[] { size }, null, elementSize, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createArray(final String objectPath, final int maxLength, final long size, final int blockSize, final HDF5GenericStorageFeatures features) { assert maxLength > 0; createStringArray(objectPath, maxLength, size, blockSize, features, false); } private void createStringArray(final String objectPath, final int maxLength, final long size, final int blockSize, final HDF5GenericStorageFeatures features, final boolean variableLength) { assert objectPath != null; assert blockSize > 0; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { final int elementSize; final int stringDataTypeId; if (variableLength) { elementSize = 8; // 64bit pointers stringDataTypeId = baseWriter.variableLengthStringDataTypeId; } else { elementSize = baseWriter.encodingForNewDataSets.getMaxBytesPerChar() * maxLength; stringDataTypeId = baseWriter.h5.createDataTypeString(elementSize, registry); } baseWriter.createDataSet(objectPath, stringDataTypeId, features, new long[] { size }, new long[] { blockSize }, elementSize, registry); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeArrayBlock(final String objectPath, final String[] data, final long blockNumber) { assert data != null; writeArrayBlockWithOffset(objectPath, data, data.length, data.length * blockNumber); } @Override public void writeArrayBlockWithOffset(final String objectPath, final String[] data, final int dataSize, final long offset) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] blockDimensions = new long[] { dataSize }; final long[] slabStartOrNull = new long[] { offset }; final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, new long[] { offset + dataSize }, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, slabStartOrNull, blockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(blockDimensions, registry); final int stringDataTypeId = baseWriter.h5.getDataTypeForDataSet(dataSetId, registry); if (baseWriter.h5.isVariableLengthString(stringDataTypeId)) { baseWriter.writeStringVL(dataSetId, memorySpaceId, dataSpaceId, data); } else { final int maxLength = baseWriter.h5.getDataTypeSize(stringDataTypeId); writeStringArray(dataSetId, stringDataTypeId, memorySpaceId, dataSpaceId, H5P_DEFAULT, data, maxLength); } return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeMDArray(final String objectPath, final MDArray data) throws HDF5JavaException { writeStringMDArray(objectPath, data, getMaxLength(data.getAsFlatArray()), true, HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION, false); } @Override public void writeMDArray(final String objectPath, final MDArray data, final HDF5GenericStorageFeatures features) throws HDF5JavaException { writeStringMDArray(objectPath, data, getMaxLength(data.getAsFlatArray()), true, features, false); } @Override public void writeMDArray(final String objectPath, final MDArray data, final int maxLength) throws HDF5JavaException { writeMDArray(objectPath, data, maxLength, HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION); } @Override public void writeMDArray(final String objectPath, final MDArray data, final int maxLength, final HDF5GenericStorageFeatures features) throws HDF5JavaException { writeStringMDArray(objectPath, data, maxLength, false, features, false); } private void writeStringMDArray(final String objectPath, final MDArray data, final int maxLength, final boolean lengthFitsValue, final HDF5GenericStorageFeatures features, final boolean variableLength) { assert objectPath != null; assert data != null; assert maxLength >= 0; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { if (variableLength) { final int elementSize = 8; // 64bit pointers final int stringDataTypeId = baseWriter.variableLengthStringDataTypeId; final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, stringDataTypeId, data.longDimensions(), elementSize, features, registry); baseWriter.writeStringVL(dataSetId, data.getAsFlatArray()); } else { final StringArrayBuffer array = baseWriter.new StringArrayBuffer(maxLength, lengthFitsValue); array.addAll(data.getAsFlatArray()); final byte[] arrData = array.toArray(); final int elementSize = array.getMaxLengthInByte(); final int stringDataTypeId = baseWriter.h5.createDataTypeString(elementSize, registry); final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, stringDataTypeId, data.longDimensions(), elementSize, features, registry); H5Dwrite(dataSetId, stringDataTypeId, H5S_ALL, H5S_ALL, H5P_DEFAULT, arrData); } return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createMDArray(final String objectPath, final int maxLength, final int[] dimensions) { createMDArray(objectPath, maxLength, dimensions, GENERIC_NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final int maxLength, final long[] dimensions, final int[] blockSize) { createMDArray(objectPath, maxLength, dimensions, blockSize, GENERIC_NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final int maxLength, final int[] dimensions, final HDF5GenericStorageFeatures features) { assert maxLength > 0; createStringMDArray(objectPath, maxLength, dimensions, features, false); } private void createStringMDArray(final String objectPath, final int maxLength, final int[] dimensions, final HDF5GenericStorageFeatures features, final boolean variableLength) { assert objectPath != null; assert dimensions != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { final int elementSize; final int stringDataTypeId; if (variableLength) { elementSize = 8; // 64bit pointers stringDataTypeId = baseWriter.variableLengthStringDataTypeId; } else { elementSize = baseWriter.encodingForNewDataSets.getMaxBytesPerChar() * maxLength; stringDataTypeId = baseWriter.h5.createDataTypeString(elementSize, registry); } if (features.requiresChunking()) { baseWriter.createDataSet(objectPath, stringDataTypeId, features, new long[] { 0 }, MDAbstractArray.toLong(dimensions), maxLength, registry); } else { baseWriter.createDataSet(objectPath, stringDataTypeId, features, MDAbstractArray.toLong(dimensions), null, maxLength, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createMDArray(final String objectPath, final int maxLength, final long[] dimensions, final int[] blockSize, final HDF5GenericStorageFeatures features) { assert maxLength > 0; createStringMDArray(objectPath, maxLength, dimensions, blockSize, features, false); } private void createStringMDArray(final String objectPath, final int maxLength, final long[] dimensions, final int[] blockSize, final HDF5GenericStorageFeatures features, final boolean variableLength) { assert objectPath != null; assert dimensions != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { final int elementSize; final int stringDataTypeId; if (variableLength) { elementSize = 8; // 64bit pointers stringDataTypeId = baseWriter.variableLengthStringDataTypeId; } else { elementSize = baseWriter.encodingForNewDataSets.getMaxBytesPerChar() * maxLength; stringDataTypeId = baseWriter.h5.createDataTypeString(elementSize, registry); } baseWriter.createDataSet(objectPath, stringDataTypeId, features, dimensions, MDAbstractArray.toLong(blockSize), elementSize, registry); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeMDArrayBlock(final String objectPath, final MDArray data, final long[] blockNumber) { assert data != null; assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeMDArrayBlockWithOffset(objectPath, data, offset); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final MDArray data, final long[] offset) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] dimensions = data.longDimensions(); assert dimensions.length == offset.length; final long[] dataSetDimensions = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + dimensions[i]; } final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, dimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(dimensions, registry); final int stringDataTypeId = baseWriter.h5.getDataTypeForDataSet(dataSetId, registry); if (baseWriter.h5.isVariableLengthString(stringDataTypeId)) { baseWriter.writeStringVL(dataSetId, memorySpaceId, dataSpaceId, data.getAsFlatArray()); } else { final int maxLength = baseWriter.h5.getDataTypeSize(stringDataTypeId); writeStringArray(dataSetId, stringDataTypeId, memorySpaceId, dataSpaceId, H5P_DEFAULT, data.getAsFlatArray(), maxLength); } return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeVL(final String objectPath, final String data) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { final int dataSetId; if (baseWriter.h5.exists(baseWriter.fileId, objectPath)) { dataSetId = baseWriter.h5.openObject(baseWriter.fileId, objectPath, registry); } else { dataSetId = baseWriter.h5.createScalarDataSet(baseWriter.fileId, baseWriter.variableLengthStringDataTypeId, objectPath, true, registry); } H5DwriteString(dataSetId, baseWriter.variableLengthStringDataTypeId, H5S_SCALAR, H5S_SCALAR, H5P_DEFAULT, new String[] { data }); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeArrayVL(final String objectPath, final String[] data) { writeArrayVL(objectPath, data, GENERIC_NO_COMPRESSION); } @Override public void writeArrayVL(final String objectPath, final String[] data, final HDF5GenericStorageFeatures features) { writeStringArray(objectPath, data, -1, false, features, true); } @Override public void createArrayVL(final String objectPath, final int size) { createArrayVL(objectPath, size, HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION); } @Override public void createArrayVL(final String objectPath, final long size, final int blockSize) throws HDF5JavaException { createArrayVL(objectPath, size, blockSize, HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION); } @Override public void createArrayVL(final String objectPath, final long size, final int blockSize, final HDF5GenericStorageFeatures features) { createStringArray(objectPath, -1, size, blockSize, features, true); } @Override public void createArrayVL(final String objectPath, final int size, final HDF5GenericStorageFeatures features) { createStringArray(objectPath, -1, size, features, true); } @Override public void createMDArrayVL(final String objectPath, final int[] dimensions, final HDF5GenericStorageFeatures features) { createStringMDArray(objectPath, -1, dimensions, features, true); } @Override public void createMDArrayVL(final String objectPath, final int[] dimensions) { createStringMDArray(objectPath, -1, dimensions, GENERIC_NO_COMPRESSION, true); } @Override public void createMDArrayVL(final String objectPath, final long[] dimensions, final int[] blockSize, final HDF5GenericStorageFeatures features) { createStringMDArray(objectPath, -1, dimensions, blockSize, features, true); } @Override public void createMDArrayVL(final String objectPath, final long[] dimensions, final int[] blockSize) { createStringMDArray(objectPath, -1, dimensions, blockSize, GENERIC_NO_COMPRESSION, true); } @Override public void writeMDArrayVL(final String objectPath, final MDArray data, final HDF5GenericStorageFeatures features) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { final int pointerSize = 8; // 64bit pointers final int stringDataTypeId = baseWriter.variableLengthStringDataTypeId; final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, stringDataTypeId, MDAbstractArray.toLong(data.dimensions()), pointerSize, features, registry); baseWriter.writeStringVL(dataSetId, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeMDArrayVL(final String objectPath, final MDArray data) { writeMDArrayVL(objectPath, data, GENERIC_NO_COMPRESSION); } /** * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the * application memory data object into the file. * * @param dataset_id Identifier of the dataset read from. * @param mem_type_id Identifier of the memory datatype. * @param mem_space_id Identifier of the memory dataspace. * @param file_space_id Identifier of the dataset's dataspace in the file. * @param xfer_plist_id Identifier of a transfer property list for this I/O operation. * @param obj String array with data to be written to the file. * @param maxLength The maximal length of one String in the array. * @return a non-negative value if successful * @exception HDF5Exception - Failure in the data conversion. * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - data object is null. */ private int writeStringArray(final int dataset_id, final int mem_type_id, final int mem_space_id, final int file_space_id, final int xfer_plist_id, final String[] obj, final int maxLength) throws HDF5Exception, HDF5LibraryException, NullPointerException { final byte[] buf = StringUtils.toBytes(obj, maxLength, baseWriter.encodingForNewDataSets); /* will raise exception on error */ final int status = H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf); return status; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5TimeDuration.java000066400000000000000000000053161256564762100272450ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; /** * An object to store a time duration. * * @author Bernd Rinn */ public class HDF5TimeDuration { private final long duration; private final HDF5TimeUnit timeUnit; public HDF5TimeDuration(long duration, HDF5TimeUnit timeUnit) { this.duration = duration; this.timeUnit = timeUnit; } /** * The time duration, see {@link #getUnit()} for the time unit. */ public long getValue() { return duration; } /** * The time duration in the given targetUnit. */ public long getValue(HDF5TimeUnit targetUnit) { return (targetUnit == timeUnit) ? duration : targetUnit.convert(duration, timeUnit); } /** * The time unit of the duration. */ public HDF5TimeUnit getUnit() { return timeUnit; } /** * Returns true, if that represents the same time duration. */ public boolean isEquivalent(HDF5TimeDuration that) { if (this.timeUnit == that.timeUnit) { return this.duration == that.duration; } else { return this.timeUnit.convert(that) == this.duration; } } // // Object // @Override public int hashCode() { final int prime = 31; int result = 1; result = prime * result + (int) (duration ^ (duration >>> 32)); result = prime * result + ((timeUnit == null) ? 0 : timeUnit.hashCode()); return result; } @Override public boolean equals(Object obj) { if (this == obj) return true; if (obj == null) return false; if (getClass() != obj.getClass()) return false; HDF5TimeDuration other = (HDF5TimeDuration) obj; if (duration != other.duration) return false; if (timeUnit != other.timeUnit) return false; return true; } @Override public String toString() { return Long.toString(duration) + " " + timeUnit.toString(); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5TimeDurationArray.java000066400000000000000000000135651256564762100302510ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.util.Arrays; /** * An array of time durations. * * @author Bernd Rinn */ public class HDF5TimeDurationArray { final long[] timeDurations; final HDF5TimeUnit timeUnit; /** * Creates an array of timeDurations using a common timeUnit. */ public HDF5TimeDurationArray(long[] timeDurations, HDF5TimeUnit timeUnit) { this.timeDurations = timeDurations; this.timeUnit = timeUnit; } /** * Creates a {@link HDF5TimeDurationArray} from the array of given durationValues * with the given timeUnit. */ public static HDF5TimeDurationArray create(HDF5TimeUnit timeUnit, long... durationValues) { if (durationValues.length == 0) { return new HDF5TimeDurationArray(new long[0], timeUnit); } return new HDF5TimeDurationArray(durationValues, timeUnit); } /** * Creates a {@link HDF5TimeDurationArray} from the given timeDurations. Converts all * values to the smallest time unit found in timeDurations. */ public static HDF5TimeDurationArray create(HDF5TimeDuration... timeDurations) { if (timeDurations.length == 0) { return new HDF5TimeDurationArray(new long[0], HDF5TimeUnit.SECONDS); } HDF5TimeUnit unit = timeDurations[0].getUnit(); boolean needsConversion = false; for (int i = 1; i < timeDurations.length; ++i) { final HDF5TimeUnit u = timeDurations[i].getUnit(); if (u != unit) { if (u.ordinal() < unit.ordinal()) { unit = u; } needsConversion = true; } } final long[] durations = new long[timeDurations.length]; if (needsConversion) { for (int i = 0; i < timeDurations.length; ++i) { durations[i] = unit.convert(timeDurations[i]); } } else { for (int i = 0; i < timeDurations.length; ++i) { durations[i] = timeDurations[i].getValue(); } } return new HDF5TimeDurationArray(durations, unit); } /** * Returns the time unit. */ public HDF5TimeUnit getUnit() { return timeUnit; } /** * Returns the time duration values. */ public long[] getValues() { return timeDurations; } /** * Returns the number of elements. */ public int getLength() { return timeDurations.length; } /** * Returns the time duration values in the given targetUnit. */ public long[] getValues(HDF5TimeUnit targetUnit) { if (targetUnit == timeUnit) { return timeDurations; } final long[] targetDurations = new long[timeDurations.length]; for (int i = 0; i < targetDurations.length; ++i) { targetDurations[i] = targetUnit.convert(timeDurations[i], timeUnit); } return targetDurations; } /** * Returns the element index. */ public HDF5TimeDuration get(int index) { return new HDF5TimeDuration(timeDurations[index], timeUnit); } /** * Returns the element index in the given targetUnit. */ public HDF5TimeDuration get(int index, HDF5TimeUnit targetUnit) { if (targetUnit == timeUnit) { return new HDF5TimeDuration(timeDurations[index], timeUnit); } else { return new HDF5TimeDuration(targetUnit.convert(timeDurations[index], timeUnit), targetUnit); } } /** * Returns the value element index. */ public long getValue(int index) { return timeDurations[index]; } /** * Returns the value element index in the given targetUnit. */ public long getValue(int index, HDF5TimeUnit targetUnit) { return (targetUnit == timeUnit) ? timeDurations[index] : targetUnit.convert( timeDurations[index], timeUnit); } @Override public int hashCode() { final int prime = 31; int result = 1; result = prime * result + Arrays.hashCode(timeDurations); result = prime * result + ((timeUnit == null) ? 0 : timeUnit.hashCode()); return result; } @Override public boolean equals(Object obj) { if (this == obj) { return true; } if (obj == null) { return false; } if (getClass() != obj.getClass()) { return false; } final HDF5TimeDurationArray other = (HDF5TimeDurationArray) obj; if (Arrays.equals(timeDurations, other.timeDurations) == false) { return false; } if (timeUnit != other.timeUnit) { return false; } return true; } @Override public String toString() { return "HDF5TimeDurationArray [timeDurations=" + Arrays.toString(timeDurations) + ", timeUnit=" + timeUnit + "]"; } }libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5TimeDurationMDArray.java000066400000000000000000000365031256564762100304670ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.util.Iterator; import ch.systemsx.cisd.base.mdarray.MDAbstractArray; import ch.systemsx.cisd.base.mdarray.MDLongArray; /** * A multi-dimensional array of time durations. * * @author Bernd Rinn */ public class HDF5TimeDurationMDArray extends MDAbstractArray { private static final long serialVersionUID = 1L; final MDLongArray timeDurations; final HDF5TimeUnit timeUnit; /** * Creates an array of timeDurations using a common timeUnit. */ public HDF5TimeDurationMDArray(MDLongArray timeDurations, HDF5TimeUnit timeUnit) { super(timeDurations.dimensions(), timeDurations.getAsFlatArray().length, 0); this.timeDurations = timeDurations; this.timeUnit = timeUnit; } /** * Creates an array of timeDurations using a common timeUnit. */ public HDF5TimeDurationMDArray(long[] timeDurations, int[] dimensions, HDF5TimeUnit timeUnit) { super(dimensions, timeDurations.length, 0); this.timeDurations = new MDLongArray(timeDurations, dimensions, true); this.timeUnit = timeUnit; } /** * Creates an array of dimension dimensions with timeUnit. */ public HDF5TimeDurationMDArray(int[] dimensions, HDF5TimeUnit timeUnit) { this(new long[getLength(dimensions, 0)], dimensions, timeUnit); } /** * Creates an array of timeDurations using a common timeUnit. */ public HDF5TimeDurationMDArray(HDF5TimeDuration[] timeDurations, int[] dimensions, HDF5TimeUnit timeUnit) { super(dimensions, timeDurations.length, 0); HDF5TimeUnit smallestTimeUnit = getSmallestUnit(timeDurations); final long[] durations = new long[timeDurations.length]; if (timeUnit != smallestTimeUnit) { for (int i = 0; i < timeDurations.length; ++i) { durations[i] = timeUnit.convert(timeDurations[i]); } } else { for (int i = 0; i < timeDurations.length; ++i) { durations[i] = timeDurations[i].getValue(); } } this.timeDurations = new MDLongArray(durations, dimensions, true); this.timeUnit = timeUnit; } /** * Creates an array of timeDurations using the smallest time unit. */ public HDF5TimeDurationMDArray(HDF5TimeDuration[] timeDurations, int[] dimensions) { super(dimensions, timeDurations.length, 0); HDF5TimeUnit smallestTimeUnit = getSmallestUnit(timeDurations); final long[] durations = new long[timeDurations.length]; for (int i = 0; i < timeDurations.length; ++i) { durations[i] = smallestTimeUnit.convert(timeDurations[i]); } this.timeDurations = new MDLongArray(durations, dimensions, true); this.timeUnit = smallestTimeUnit; } private static HDF5TimeUnit getSmallestUnit(HDF5TimeDuration[] timeDurations) { HDF5TimeUnit unit = timeDurations[0].getUnit(); for (int i = 1; i < timeDurations.length; ++i) { final HDF5TimeUnit u = timeDurations[i].getUnit(); if (u != unit) { if (u.ordinal() < unit.ordinal()) { unit = u; } } } return unit; } /** * Returns the time unit. */ public HDF5TimeUnit getUnit() { return timeUnit; } /** * Returns the time duration values as a flat array. */ @Override public long[] getAsFlatArray() { return timeDurations.getAsFlatArray(); } /** * Returns the number of elements. */ @Override public int[] dimensions() { return timeDurations.dimensions(); } /** * Returns the number of elements. */ @Override public long[] longDimensions() { return timeDurations.longDimensions(); } /** * Returns the number of elements. */ public int getLength() { return timeDurations.size(); } /** * Returns the time duration values. */ public MDLongArray getValues() { return timeDurations; } /** * Returns the time duration values in the given targetUnit. */ public MDLongArray getValues(HDF5TimeUnit targetUnit) { if (targetUnit == timeUnit) { return timeDurations; } final long[] sourceDurations = timeDurations.getAsFlatArray(); final long[] targetDurations = new long[sourceDurations.length]; for (int i = 0; i < targetDurations.length; ++i) { targetDurations[i] = targetUnit.convert(sourceDurations[i], timeUnit); } return new MDLongArray(targetDurations, timeDurations.dimensions()); } /** * Returns the time duration values as a flat array in the given targetUnit. */ public long[] getAsFlatArray(HDF5TimeUnit targetUnit) { return getValues(targetUnit).getAsFlatArray(); } /** * Returns the value of a one-dimensional array at the position defined by index in * the given targetUnit. *

* Do not call for arrays other than one-dimensional! */ public HDF5TimeDuration get(HDF5TimeUnit targetUnit, int index) { if (targetUnit == timeUnit) { return new HDF5TimeDuration(timeDurations.get(index), timeUnit); } else { return new HDF5TimeDuration(targetUnit.convert(timeDurations.get(index), timeUnit), targetUnit); } } /** * Returns the value of a two-dimensional array at the position defined by indexX and * indexY in the given targetUnit. *

* Do not call for arrays other than two-dimensional! */ public HDF5TimeDuration get(HDF5TimeUnit targetUnit, int indexX, int indexY) { if (targetUnit == timeUnit) { return new HDF5TimeDuration(timeDurations.get(indexX, indexY), timeUnit); } else { return new HDF5TimeDuration(targetUnit.convert(timeDurations.get(indexX, indexY), timeUnit), targetUnit); } } /** * Returns the value of a three-dimensional array at the position defined by indexX, * indexY and indexZ in the given targetUnit. *

* Do not call for arrays other than three-dimensional! */ public HDF5TimeDuration get(HDF5TimeUnit targetUnit, int indexX, int indexY, int indexZ) { if (targetUnit == timeUnit) { return new HDF5TimeDuration(timeDurations.get(indexX, indexY, indexZ), timeUnit); } else { return new HDF5TimeDuration(targetUnit.convert( timeDurations.get(indexX, indexY, indexZ), timeUnit), targetUnit); } } /** * Returns the value of array at the position defined by indices in the given * targetUnit. */ public HDF5TimeDuration get(HDF5TimeUnit targetUnit, int... indices) { if (targetUnit == timeUnit) { return new HDF5TimeDuration(timeDurations.get(indices), timeUnit); } else { return new HDF5TimeDuration(targetUnit.convert(timeDurations.get(indices), timeUnit), targetUnit); } } /** * Returns the value element index. *

* Do not call for arrays other than one-dimensional! */ public long getValue(int index) { return timeDurations.get(index); } /** * Returns the value element (indexX,indexY). *

* Do not call for arrays other than two-dimensional! */ public long getValue(int indexX, int indexY) { return timeDurations.get(indexX, indexY); } /** * Returns the value element (indexX,indexY,indexZ). *

* Do not call for arrays other than three-dimensional! */ public long getValue(int indexX, int indexY, int indexZ) { return timeDurations.get(indexX, indexY, indexZ); } /** * Returns the value element indices. */ public long getValue(int... indices) { return timeDurations.get(indices); } /** * Returns the value element index in the given targetUnit. *

* Do not call for arrays other than one-dimensional! */ public long getValue(HDF5TimeUnit targetUnit, int index) { return (targetUnit == timeUnit) ? timeDurations.get(index) : targetUnit.convert( timeDurations.get(index), timeUnit); } /** * Returns the value element index in the given targetUnit. *

* Do not call for arrays other than one-dimensional! */ public long getValue(HDF5TimeUnit targetUnit, int indexX, int indexY) { return (targetUnit == timeUnit) ? timeDurations.get(indexX, indexY) : targetUnit.convert( timeDurations.get(indexX, indexY), timeUnit); } /** * Returns the value element index in the given targetUnit. *

* Do not call for arrays other than one-dimensional! */ public long getValue(HDF5TimeUnit targetUnit, int indexX, int indexY, int indexZ) { return (targetUnit == timeUnit) ? timeDurations.get(indexX, indexY, indexZ) : targetUnit .convert(timeDurations.get(indexX, indexY, indexZ), timeUnit); } /** * Returns the value element index in the given targetUnit. *

* Do not call for arrays other than one-dimensional! */ public long getValue(HDF5TimeUnit targetUnit, int... indices) { return (targetUnit == timeUnit) ? timeDurations.get(indices) : targetUnit.convert( timeDurations.get(indices), timeUnit); } @Override public int hashCode() { final int prime = 31; int result = 1; result = prime * result + timeDurations.hashCode(); result = prime * result + ((timeUnit == null) ? 0 : timeUnit.hashCode()); return result; } @Override public boolean equals(Object obj) { if (this == obj) { return true; } if (obj == null) { return false; } if (getClass() != obj.getClass()) { return false; } final HDF5TimeDurationMDArray other = (HDF5TimeDurationMDArray) obj; if (timeDurations.equals(other.timeDurations) == false) { return false; } if (timeUnit != other.timeUnit) { return false; } return true; } @Override public String toString() { return "HDF5TimeDurationArray [timeDurations=" + timeDurations.toString() + ", timeUnit=" + timeUnit + "]"; } @Override public Long getAsObject(int linearIndex) { return timeDurations.getAsObject(linearIndex); } @Override public Long getAsObject(int... indices) { return timeDurations.getAsObject(indices); } @Override public void setToObject(Long value, int... indices) { timeDurations.setToObject(value, indices); } @Override public void setToObject(Long value, int linearIndex) { timeDurations.setToObject(value, linearIndex); } @Override public long[] getCopyAsFlatArray() { return timeDurations.getCopyAsFlatArray(); } @Override protected void adaptCapacityHyperRows() { // Noop } @Override public int capacity() { return timeDurations.capacity(); } @Override public int incNumberOfHyperRows(int count) { return timeDurations.incNumberOfHyperRows(count); } @Override public int rank() { return timeDurations.rank(); } @Override public int size(int dim) { return timeDurations.size(dim); } @Override public int size() { return timeDurations.size(); } @Override public int numberOfHyperRows() { return timeDurations.numberOfHyperRows(); } @Override public int decNumberOfHyperRows(int count) { return timeDurations.decNumberOfHyperRows(count); } @Override public int computeIndex(int... indices) { return timeDurations.computeIndex(indices); } @Override public int[] computeReverseIndex(int linearIndex) { return timeDurations.computeReverseIndex(linearIndex); } @Override public int computeIndex(int indexX, int indexY) { return timeDurations.computeIndex(indexX, indexY); } @Override public int computeIndex(int indexX, int indexY, int indexZ) { return timeDurations.computeIndex(indexX, indexY, indexZ); } @Override public Iterator.ArrayEntry> iterator() { return timeDurations.iterator(); } /** * @see MDLongArray#get(int) */ public long get(int index) { return timeDurations.get(index); } /** * @see MDLongArray#get(int, int) */ public long get(int indexX, int indexY) { return timeDurations.get(indexX, indexY); } /** * @see MDLongArray#get(int, int, int) */ public long get(int indexX, int indexY, int indexZ) { return timeDurations.get(indexX, indexY, indexZ); } /** * @see MDLongArray#get(int[]) */ public long get(int... indices) { return timeDurations.get(indices); } /** * @see MDLongArray#set(long, int) */ public void set(long value, int index) { timeDurations.set(value, index); } /** * @see MDLongArray#set(long, int, int) */ public void set(long value, int indexX, int indexY) { timeDurations.set(value, indexX, indexY); } /** * @see MDLongArray#set(long, int, int, int) */ public void set(long value, int indexX, int indexY, int indexZ) { timeDurations.set(value, indexX, indexY, indexZ); } /** * @see MDLongArray#set(long, int[]) */ public void set(long value, int... indices) { timeDurations.set(value, indices); } /** * @see MDLongArray#toMatrix() */ public long[][] toMatrix() { return timeDurations.toMatrix(); } }libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5TimeDurationReader.java000066400000000000000000000711061256564762100303700ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_INT64; import java.util.Iterator; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDLongArray; import ch.systemsx.cisd.hdf5.HDF5BaseReader.DataSpaceParameters; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; /** * Implementation of {@Link IHDF5TimeDurationReader}. * * @author Bernd Rinn */ class HDF5TimeDurationReader implements IHDF5TimeDurationReader { private final HDF5BaseReader baseReader; private final HDF5LongReader longReader; HDF5TimeDurationReader(HDF5BaseReader baseReader, HDF5LongReader longReader) { assert baseReader != null; assert longReader != null; this.baseReader = baseReader; this.longReader = longReader; } @Override public HDF5TimeDuration getAttr(final String objectPath, final String attributeName) { baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public HDF5TimeDuration call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final HDF5TimeUnit unit = baseReader.checkIsTimeDuration(objectPath, attributeName, objectId, registry); final long[] data = baseReader.h5.readAttributeAsLongArray(attributeId, H5T_NATIVE_INT64, 1); return new HDF5TimeDuration(data[0], unit); } }; return baseReader.runner.call(getAttributeRunnable); } @Override public boolean isTimeDuration(String objectPath, String attributeName) throws HDF5JavaException { final HDF5DataTypeVariant typeVariantOrNull = baseReader.tryGetTypeVariant(objectPath, attributeName); return typeVariantOrNull != null && typeVariantOrNull.isTimeDuration(); } @Override public HDF5TimeUnit tryGetTimeUnit(String objectPath, String attributeName) throws HDF5JavaException { final HDF5DataTypeVariant typeVariantOrNull = baseReader.tryGetTypeVariant(objectPath, attributeName); return (typeVariantOrNull != null) ? typeVariantOrNull.tryGetTimeUnit() : null; } @Override public HDF5TimeDurationArray getArrayAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public HDF5TimeDurationArray call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); final HDF5TimeUnit storedUnit = baseReader.checkIsTimeDuration(objectPath, attributeName, objectId, registry); final long[] data = longReader.getArrayAttr(objectPath, attributeName); return new HDF5TimeDurationArray(data, storedUnit); } }; return baseReader.runner.call(getAttributeRunnable); } @Override public HDF5TimeDurationMDArray getMDArrayAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public HDF5TimeDurationMDArray call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); final HDF5TimeUnit storedUnit = baseReader.checkIsTimeDuration(objectPath, attributeName, objectId, registry); final MDLongArray data = longReader.getMDArrayAttr(objectPath, attributeName); return new HDF5TimeDurationMDArray(data, storedUnit); } }; return baseReader.runner.call(getAttributeRunnable); } @Override public boolean isTimeDuration(final String objectPath) throws HDF5JavaException { final HDF5DataTypeVariant typeVariantOrNull = baseReader.tryGetTypeVariant(objectPath); return typeVariantOrNull != null && typeVariantOrNull.isTimeDuration(); } @Override public HDF5TimeUnit tryGetTimeUnit(final String objectPath) throws HDF5JavaException { final HDF5DataTypeVariant typeVariantOrNull = baseReader.tryGetTypeVariant(objectPath); return (typeVariantOrNull != null) ? typeVariantOrNull.tryGetTimeUnit() : null; } @Override public HDF5TimeDuration read(final String objectPath) throws HDF5JavaException { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public HDF5TimeDuration call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final HDF5TimeUnit storedUnit = baseReader.checkIsTimeDuration(objectPath, dataSetId, registry); final long[] data = new long[1]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_INT64, data); return new HDF5TimeDuration(data[0], storedUnit); } }; return baseReader.runner.call(readCallable); } public long readTimeDuration(final String objectPath, final HDF5TimeUnit timeUnit) throws HDF5JavaException { return timeUnit.convert(read(objectPath)); } public HDF5TimeDuration readTimeDurationAndUnit(final String objectPath) throws HDF5JavaException { return read(objectPath); } @Override public HDF5TimeDurationArray readArray(final String objectPath) throws HDF5JavaException { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public HDF5TimeDurationArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final HDF5TimeUnit storedUnit = baseReader.checkIsTimeDuration(objectPath, dataSetId, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); final long[] data = new long[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_INT64, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return new HDF5TimeDurationArray(data, storedUnit); } }; return baseReader.runner.call(readCallable); } public long[] readTimeDurationArray(final String objectPath, final HDF5TimeUnit timeUnit) throws HDF5JavaException { return timeUnit.convert(readArray(objectPath)); } public HDF5TimeDuration[] readTimeDurationAndUnitArray(final String objectPath) throws HDF5JavaException { final HDF5TimeDurationArray durations = readArray(objectPath); return convertTimeDurations(durations.timeUnit, durations.timeDurations); } public long[] readTimeDurationArrayBlock(final String objectPath, final int blockSize, final long blockNumber, final HDF5TimeUnit timeUnit) { return timeUnit.convert(readArrayBlock(objectPath, blockSize, blockNumber)); } @Override public HDF5TimeDurationArray readArrayBlock(final String objectPath, final int blockSize, final long blockNumber) { return readArrayBlockWithOffset(objectPath, blockSize, blockNumber * blockSize); } @Override public HDF5TimeDurationArray readArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public HDF5TimeDurationArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final HDF5TimeUnit storedUnit = baseReader.checkIsTimeDuration(objectPath, dataSetId, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockSize, registry); final long[] data = new long[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_INT64, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return new HDF5TimeDurationArray(data, storedUnit); } }; return baseReader.runner.call(readCallable); } public long[] readTimeDurationArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset, final HDF5TimeUnit timeUnit) { return timeUnit.convert(readArrayBlockWithOffset(objectPath, blockSize, offset)); } public HDF5TimeDuration[] readTimeDurationAndUnitArrayBlock(final String objectPath, final int blockSize, final long blockNumber) throws HDF5JavaException { return readTimeDurationAndUnitArrayBlockWithOffset(objectPath, blockSize, blockSize * blockNumber); } public HDF5TimeDuration[] readTimeDurationAndUnitArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset) throws HDF5JavaException { final HDF5TimeDurationArray durations = readArrayBlockWithOffset(objectPath, blockSize, offset); return convertTimeDurations(durations.timeUnit, durations.timeDurations); } public Iterable> getTimeDurationAndUnitArrayNaturalBlocks( final String objectPath) throws HDF5JavaException { final HDF5NaturalBlock1DParameters params = new HDF5NaturalBlock1DParameters(baseReader.getDataSetInformation(objectPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlock1DParameters.HDF5NaturalBlock1DIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5DataBlock next() { final long offset = index.computeOffsetAndSizeGetOffset(); final HDF5TimeDuration[] block = readTimeDurationAndUnitArrayBlockWithOffset(objectPath, index.getBlockSize(), offset); return new HDF5DataBlock(block, index.getAndIncIndex(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } @Override public HDF5TimeDurationMDArray readMDArray(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public HDF5TimeDurationMDArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final HDF5TimeUnit storedUnit = baseReader.checkIsTimeDuration(objectPath, dataSetId, registry); return new HDF5TimeDurationMDArray(longReader.readLongMDArray( dataSetId, registry), storedUnit); } }; return baseReader.runner.call(readCallable); } @Override public HDF5TimeDurationMDArray readMDArrayBlock(final String objectPath, final int[] blockDimensions, final long[] blockNumber) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readMDArrayBlockWithOffset(objectPath, blockDimensions, offset); } @Override public HDF5TimeDurationMDArray readMDArrayBlockWithOffset(final String objectPath, final int[] blockDimensions, final long[] offset) { assert objectPath != null; assert blockDimensions != null; assert offset != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public HDF5TimeDurationMDArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final HDF5TimeUnit storedUnit = baseReader.checkIsTimeDuration(objectPath, dataSetId, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockDimensions, registry); final long[] dataBlock = new long[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_INT64, spaceParams.memorySpaceId, spaceParams.dataSpaceId, dataBlock); return new HDF5TimeDurationMDArray(new MDLongArray(dataBlock, blockDimensions), storedUnit); } }; return baseReader.runner.call(readCallable); } @Override public int[] readToMDArrayWithOffset(final String objectPath, final HDF5TimeDurationMDArray array, final int[] memoryOffset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final HDF5TimeUnit storedUnit = baseReader.checkIsTimeDuration(objectPath, dataSetId, registry); final DataSpaceParameters spaceParams = baseReader.getBlockSpaceParameters(dataSetId, memoryOffset, array.dimensions(), registry); final int nativeDataTypeId = baseReader.getNativeDataTypeId(dataSetId, H5T_NATIVE_INT64, registry); baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, array.getAsFlatArray()); final int[] effectiveBlockDims = MDArray.toInt(spaceParams.dimensions); if (array.getUnit() != storedUnit) { convertUnit(array.getValues(), storedUnit, array.getUnit(), effectiveBlockDims, memoryOffset); } return effectiveBlockDims; } }; return baseReader.runner.call(readCallable); } @Override public int[] readToMDArrayBlockWithOffset(final String objectPath, final HDF5TimeDurationMDArray array, final int[] blockDimensions, final long[] offset, final int[] memoryOffset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final HDF5TimeUnit storedUnit = baseReader.checkIsTimeDuration(objectPath, dataSetId, registry); final DataSpaceParameters spaceParams = baseReader.getBlockSpaceParameters(dataSetId, memoryOffset, array.dimensions(), offset, blockDimensions, registry); final int nativeDataTypeId = baseReader.getNativeDataTypeId(dataSetId, H5T_NATIVE_INT64, registry); baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, array.getAsFlatArray()); final int[] effectiveBlockDims = MDArray.toInt(spaceParams.dimensions); if (array.getUnit() != storedUnit) { convertUnit(array.getValues(), storedUnit, array.getUnit(), effectiveBlockDims, memoryOffset); } return effectiveBlockDims; } }; return baseReader.runner.call(readCallable); } static void convertUnit(MDLongArray array, HDF5TimeUnit fromUnit, HDF5TimeUnit toUnit, int[] dims, int[] offset) { final long[] flatArray = array.getAsFlatArray(); final int[] idx = offset.clone(); System.arraycopy(offset, 0, idx, 0, idx.length); while (true) { final int linIdx = array.computeIndex(idx); flatArray[linIdx] = toUnit.convert(flatArray[linIdx], fromUnit); if (MatrixUtils.incrementIdx(idx, dims, offset) == false) { break; } } } @Override public Iterable> getArrayNaturalBlocks( final String objectPath) throws HDF5JavaException { final HDF5NaturalBlock1DParameters params = new HDF5NaturalBlock1DParameters(baseReader.getDataSetInformation(objectPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlock1DParameters.HDF5NaturalBlock1DIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5DataBlock next() { final long offset = index.computeOffsetAndSizeGetOffset(); final HDF5TimeDurationArray block = readArrayBlockWithOffset(objectPath, index.getBlockSize(), offset); return new HDF5DataBlock(block, index.getAndIncIndex(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } public Iterable> getTimeDurationArrayNaturalBlocks( final String objectPath, final HDF5TimeUnit timeUnit) throws HDF5JavaException { final HDF5NaturalBlock1DParameters params = new HDF5NaturalBlock1DParameters(baseReader.getDataSetInformation(objectPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlock1DParameters.HDF5NaturalBlock1DIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5DataBlock next() { final long offset = index.computeOffsetAndSizeGetOffset(); final long[] block = readTimeDurationArrayBlockWithOffset(objectPath, index.getBlockSize(), offset, timeUnit); return new HDF5DataBlock(block, index.getAndIncIndex(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } @Override public Iterable> getMDArrayNaturalBlocks( final String dataSetPath) { baseReader.checkOpen(); final HDF5NaturalBlockMDParameters params = new HDF5NaturalBlockMDParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlockMDParameters.HDF5NaturalBlockMDIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5MDDataBlock next() { final long[] offset = index.computeOffsetAndSizeGetOffsetClone(); final HDF5TimeDurationMDArray data = readMDArrayBlockWithOffset(dataSetPath, index.getBlockSize(), offset); return new HDF5MDDataBlock(data, index.getIndexClone(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } static void convertTimeDurations(final HDF5TimeUnit toTimeUnit, final HDF5TimeUnit fromTimeUnit, final long[] data) { if (toTimeUnit != fromTimeUnit) { for (int i = 0; i < data.length; ++i) { data[i] = toTimeUnit.convert(data[i], fromTimeUnit); } } } static HDF5TimeDuration[] convertTimeDurations(final HDF5TimeUnit timeUnit, final long[] data) { final HDF5TimeDuration[] durations = new HDF5TimeDuration[data.length]; for (int i = 0; i < data.length; ++i) { durations[i] = new HDF5TimeDuration(data[i], timeUnit); } return durations; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5TimeDurationWriter.java000066400000000000000000000650001256564762100304360ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.HDF5IntStorageFeatures.INT_NO_COMPRESSION; import static ch.systemsx.cisd.hdf5.hdf5lib.H5D.H5Dwrite; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_ALL; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_INT64; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_I64LE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_U64LE; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; import ch.systemsx.cisd.hdf5.hdf5lib.HDFNativeData; /** * Implementation of {@link IHDF5TimeDurationWriter}. * * @author Bernd Rinn */ public class HDF5TimeDurationWriter extends HDF5TimeDurationReader implements IHDF5TimeDurationWriter { private final HDF5BaseWriter baseWriter; HDF5TimeDurationWriter(HDF5BaseWriter baseWriter, HDF5LongReader longReader) { super(baseWriter, longReader); assert baseWriter != null; this.baseWriter = baseWriter; } @Override public void setAttr(final String objectPath, final String name, final long timeDuration, final HDF5TimeUnit timeUnit) { baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { 1 }, registry); baseWriter.setAttribute(objectPath, name, timeUnit.getTypeVariant(), H5T_STD_I64LE, H5T_NATIVE_INT64, dataSpaceId, new long[] { timeDuration }, registry); } else { baseWriter.setAttribute(objectPath, name, timeUnit.getTypeVariant(), H5T_STD_I64LE, H5T_NATIVE_INT64, -1, new long[] { timeDuration }, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void setAttr(String objectPath, String name, HDF5TimeDuration timeDuration) { setAttr(objectPath, name, timeDuration.getValue(), timeDuration.getUnit()); } @Override public void setArrayAttr(final String objectPath, final String name, final HDF5TimeDurationArray timeDurations) { assert objectPath != null; assert name != null; assert timeDurations != null; baseWriter.checkOpen(); final ICallableWithCleanUp setAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { timeDurations.timeDurations.length }, registry); baseWriter.setAttribute(objectPath, name, timeDurations.timeUnit.getTypeVariant(), H5T_STD_I64LE, H5T_NATIVE_INT64, dataSpaceId, timeDurations.timeDurations, registry); } else { final int memoryTypeId = baseWriter.h5.createArrayType(H5T_NATIVE_INT64, timeDurations.timeDurations.length, registry); final int storageTypeId = baseWriter.h5.createArrayType(H5T_STD_I64LE, timeDurations.timeDurations.length, registry); baseWriter.setAttribute(objectPath, name, timeDurations.timeUnit.getTypeVariant(), storageTypeId, memoryTypeId, -1, timeDurations.timeDurations, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(setAttributeRunnable); } @Override public void setMDArrayAttr(final String objectPath, final String attributeName, final HDF5TimeDurationMDArray timeDurations) { assert objectPath != null; assert attributeName != null; assert timeDurations != null; baseWriter.checkOpen(); final ICallableWithCleanUp setAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace( timeDurations.timeDurations.longDimensions(), registry); baseWriter.setAttribute(objectPath, attributeName, timeDurations.timeUnit.getTypeVariant(), H5T_STD_I64LE, H5T_NATIVE_INT64, dataSpaceId, timeDurations.timeDurations.getAsFlatArray(), registry); } else { final int memoryTypeId = baseWriter.h5.createArrayType(H5T_NATIVE_INT64, timeDurations.timeDurations.dimensions(), registry); final int storageTypeId = baseWriter.h5.createArrayType(H5T_STD_I64LE, timeDurations.timeDurations.dimensions(), registry); baseWriter.setAttribute(objectPath, attributeName, timeDurations.timeUnit.getTypeVariant(), storageTypeId, memoryTypeId, -1, timeDurations.timeDurations.getAsFlatArray(), registry); } return null; // Nothing to return. } }; baseWriter.runner.call(setAttributeRunnable); } public void writeTimeDuration(final String objectPath, final long timeDuration) { write(objectPath, timeDuration, HDF5TimeUnit.SECONDS); } @Override public void write(final String objectPath, final long timeDuration, final HDF5TimeUnit timeUnit) { assert objectPath != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeScalarRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.writeScalar(objectPath, H5T_STD_I64LE, H5T_NATIVE_INT64, HDFNativeData.longToByte(timeDuration), true, true, registry); baseWriter.setTypeVariant(dataSetId, timeUnit.getTypeVariant(), registry); return null; // Nothing to return. } }; baseWriter.runner.call(writeScalarRunnable); } @Override public void write(String objectPath, HDF5TimeDuration timeDuration) { write(objectPath, timeDuration.getValue(), timeDuration.getUnit()); } @Override public void createArray(String objectPath, int size, HDF5TimeUnit timeUnit) { createArray(objectPath, size, timeUnit, HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION); } @Override public void createArray(final String objectPath, final long size, final int blockSize, final HDF5TimeUnit timeUnit) { createArray(objectPath, size, blockSize, timeUnit, HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION); } @Override public void createArray(final String objectPath, final int size, final HDF5TimeUnit timeUnit, final HDF5GenericStorageFeatures features) { assert objectPath != null; assert size >= 0; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int longBytes = 8; final int dataSetId; if (features.requiresChunking()) { dataSetId = baseWriter.createDataSet(objectPath, H5T_STD_I64LE, features, new long[] { 0 }, new long[] { size }, longBytes, registry); } else { dataSetId = baseWriter.createDataSet(objectPath, H5T_STD_I64LE, features, new long[] { size }, null, longBytes, registry); } baseWriter.setTypeVariant(dataSetId, timeUnit.getTypeVariant(), registry); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createArray(final String objectPath, final long size, final int blockSize, final HDF5TimeUnit timeUnit, final HDF5GenericStorageFeatures features) { assert objectPath != null; assert size >= 0; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int longBytes = 8; final int dataSetId = baseWriter.createDataSet(objectPath, H5T_STD_I64LE, features, new long[] { size }, new long[] { blockSize }, longBytes, registry); baseWriter.setTypeVariant(dataSetId, timeUnit.getTypeVariant(), registry); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } public void writeTimeDurationArray(final String objectPath, final long[] timeDurations) { writeTimeDurationArray(objectPath, timeDurations, HDF5TimeUnit.SECONDS, HDF5IntStorageFeatures.INT_NO_COMPRESSION); } @Override public void writeArray(String objectPath, HDF5TimeDurationArray timeDurations) { writeArray(objectPath, timeDurations, HDF5IntStorageFeatures.INT_NO_COMPRESSION); } @Override public void writeArray(final String objectPath, final HDF5TimeDurationArray timeDurations, final HDF5IntStorageFeatures features) { assert objectPath != null; assert timeDurations != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int longBytes = 8; final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, H5T_STD_I64LE, new long[] { timeDurations.timeDurations.length }, longBytes, features, registry); H5Dwrite(dataSetId, H5T_NATIVE_INT64, H5S_ALL, H5S_ALL, H5P_DEFAULT, timeDurations.timeDurations); baseWriter.setTypeVariant(dataSetId, timeDurations.timeUnit.getTypeVariant(), registry); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } public void writeTimeDurationArray(final String objectPath, final long[] timeDurations, final HDF5TimeUnit timeUnit) { writeTimeDurationArray(objectPath, timeDurations, timeUnit, HDF5IntStorageFeatures.INT_NO_COMPRESSION); } public void writeTimeDurationArray(final String objectPath, final long[] timeDurations, final HDF5TimeUnit timeUnit, final HDF5IntStorageFeatures features) { writeArray(objectPath, new HDF5TimeDurationArray(timeDurations, timeUnit)); } public void writeTimeDurationArray(final String objectPath, final HDF5TimeDuration[] timeDurations) { writeTimeDurationArray(objectPath, timeDurations, HDF5IntStorageFeatures.INT_NO_COMPRESSION); } public void writeTimeDurationArray(final String objectPath, final HDF5TimeDuration[] timeDurations, final HDF5IntStorageFeatures features) { assert objectPath != null; assert timeDurations != null; if (timeDurations.length == 0) { return; } final HDF5TimeDurationArray durations = HDF5TimeDurationArray.create(timeDurations); writeArray(objectPath, durations); } @Override public void writeArrayBlock(String objectPath, HDF5TimeDurationArray data, long blockNumber) { writeArrayBlockWithOffset(objectPath, data, data.getLength(), data.getLength() * blockNumber); } @Override public void writeArrayBlockWithOffset(final String objectPath, final HDF5TimeDurationArray data, final int dataSize, final long offset) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] blockDimensions = new long[] { dataSize }; final long[] slabStartOrNull = new long[] { offset }; final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, new long[] { offset + dataSize }, -1, registry); final HDF5TimeUnit storedUnit = baseWriter.checkIsTimeDuration(objectPath, dataSetId, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, slabStartOrNull, blockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(blockDimensions, registry); H5Dwrite(dataSetId, H5T_NATIVE_INT64, memorySpaceId, dataSpaceId, H5P_DEFAULT, storedUnit.convert(data)); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } public void writeTimeDurationArrayBlock(final String objectPath, final long[] data, final long blockNumber, final HDF5TimeUnit timeUnit) { writeTimeDurationArrayBlockWithOffset(objectPath, data, data.length, data.length * blockNumber, timeUnit); } public void writeTimeDurationArrayBlockWithOffset(final String objectPath, final long[] data, final int dataSize, final long offset, final HDF5TimeUnit timeUnit) { writeArrayBlockWithOffset(objectPath, new HDF5TimeDurationArray(data, timeUnit), dataSize, offset); } public void writeTimeDurationArrayBlock(final String objectPath, final HDF5TimeDuration[] data, final long blockNumber) { writeTimeDurationArrayBlockWithOffset(objectPath, data, data.length, data.length * blockNumber); } public void writeTimeDurationArrayBlockWithOffset(final String objectPath, final HDF5TimeDuration[] data, final int dataSize, final long offset) { writeArrayBlockWithOffset(objectPath, HDF5TimeDurationArray.create(data), dataSize, offset); } @Override public void writeMDArray(final String objectPath, final HDF5TimeDurationMDArray data, final HDF5IntStorageFeatures features) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, features.isSigned() ? H5T_STD_I64LE : H5T_STD_U64LE, data.longDimensions(), 8, features, registry); H5Dwrite(dataSetId, H5T_NATIVE_INT64, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.getAsFlatArray()); baseWriter.setTypeVariant(dataSetId, data.timeUnit.getTypeVariant(), registry); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeMDArray(final String objectPath, final HDF5TimeDurationMDArray data) { writeMDArray(objectPath, data, HDF5IntStorageFeatures.INT_NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final int[] dimensions, final HDF5TimeUnit timeUnit) { createMDArray(objectPath, dimensions, timeUnit, INT_NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions, final HDF5TimeUnit timeUnit) { createMDArray(objectPath, dimensions, blockDimensions, timeUnit, INT_NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final int[] dimensions, final HDF5TimeUnit timeUnit, final HDF5IntStorageFeatures features) { assert objectPath != null; assert dimensions != null; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId; if (features.requiresChunking()) { final long[] nullDimensions = new long[dimensions.length]; dataSetId = baseWriter.createDataSet(objectPath, features.isSigned() ? H5T_STD_I64LE : H5T_STD_U64LE, features, nullDimensions, MDArray.toLong(dimensions), 8, registry); } else { dataSetId = baseWriter.createDataSet(objectPath, features.isSigned() ? H5T_STD_I64LE : H5T_STD_U64LE, features, MDArray.toLong(dimensions), null, 8, registry); } baseWriter.setTypeVariant(dataSetId, timeUnit.getTypeVariant(), registry); return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void createMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions, final HDF5TimeUnit timeUnit, final HDF5IntStorageFeatures features) { assert objectPath != null; assert dimensions != null; assert blockDimensions != null; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.createDataSet(objectPath, features.isSigned() ? H5T_STD_I64LE : H5T_STD_U64LE, features, dimensions, MDArray.toLong(blockDimensions), 8, registry); baseWriter.setTypeVariant(dataSetId, timeUnit.getTypeVariant(), registry); return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void writeMDArrayBlock(final String objectPath, final HDF5TimeDurationMDArray data, final long[] blockNumber) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeMDArrayBlockWithOffset(objectPath, data, offset); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final HDF5TimeDurationMDArray data, final long[] offset) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] dimensions = data.longDimensions(); assert dimensions.length == offset.length; final long[] dataSetDimensions = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + dimensions[i]; } final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final HDF5TimeUnit storedUnit = baseWriter.checkIsTimeDuration(objectPath, dataSetId, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, dimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(dimensions, registry); H5Dwrite(dataSetId, H5T_NATIVE_INT64, memorySpaceId, dataSpaceId, H5P_DEFAULT, data.getAsFlatArray(storedUnit)); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final HDF5TimeDurationMDArray data, final int[] blockDimensions, final long[] offset, final int[] memoryOffset) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] memoryDimensions = data.longDimensions(); assert memoryDimensions.length == offset.length; final long[] longBlockDimensions = MDArray.toLong(blockDimensions); assert longBlockDimensions.length == offset.length; final long[] dataSetDimensions = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + blockDimensions[i]; } final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); final HDF5TimeUnit storedUnit = baseWriter.checkIsTimeDuration(objectPath, dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, longBlockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(memoryDimensions, registry); baseWriter.h5.setHyperslabBlock(memorySpaceId, MDArray.toLong(memoryOffset), longBlockDimensions); H5Dwrite(dataSetId, H5T_NATIVE_INT64, memorySpaceId, dataSpaceId, H5P_DEFAULT, data.getAsFlatArray(storedUnit)); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5TimeUnit.java000066400000000000000000000260121256564762100263730ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; /** * A TimeUnit represents a unit of a time duration. Each unit corresponds to one time * duration {@link HDF5DataTypeVariant}. *

* The conversion of time durations is heavily inspired by Doug Lea's class in the Java runtime * library. * * @author Bernd Rinn */ public enum HDF5TimeUnit { MICROSECONDS, MILLISECONDS, SECONDS, MINUTES, HOURS, DAYS; /** Lookup table for type variants. */ private static final HDF5DataTypeVariant[] typeVariants = { HDF5DataTypeVariant.TIME_DURATION_MICROSECONDS, HDF5DataTypeVariant.TIME_DURATION_MILLISECONDS, HDF5DataTypeVariant.TIME_DURATION_SECONDS, HDF5DataTypeVariant.TIME_DURATION_MINUTES, HDF5DataTypeVariant.TIME_DURATION_HOURS, HDF5DataTypeVariant.TIME_DURATION_DAYS }; /** Lookup table for conversion factors (to smaller units). */ private static final long[][] multipliers = { // first dimension is the start unit, second is the delta // micro seconds { 1L }, // milli seconds { 1L, 1000L }, // seconds { 1L, 1000L, 1000L * 1000 }, // minutes { 1L, 60L, 60L * 1000, 60L * 1000 * 1000 }, // hours { 1L, 60L, 60L * 60, 60L * 60 * 1000, 60L * 60 * 1000 * 1000 }, // days { 1L, 24L, 24L * 60, 24L * 60 * 60, 24L * 60 * 60 * 1000L, 24L * 60 * 60 * 1000 * 1000 } }; /** Lookup table for conversion factors (to larger units). */ private static final double[][] divisors = { // first dimension is the start unit, second is the delta // micro seconds { 1.0, 1000.0, 1000.0 * 1000, 1000.0 * 1000 * 60, 1000.0 * 1000 * 60 * 60, 1000.0 * 1000 * 60 * 60 * 24 }, // millis seconds { 1.0, 1000.0, 1000.0 * 60, 1000.0 * 60 * 60, 1000.0 * 60 * 60 * 24 }, // seconds { 1.0, 60.0, 60.0 * 60, 60 * 60 * 24 }, // minutes { 1.0, 60.0, 60.0 * 24 }, // hours { 1.0, 24.0 }, // days { 1.0 } }; /** * Lookup table to check saturation. Note that because we are dividing these down, we don't have * to deal with asymmetry of MIN/MAX values. */ private static final long[][] overflows = { // first dimension is the start unit, second is the delta // micro seconds { -1 }, // milli seconds { -1, Long.MAX_VALUE / 1000L }, // seconds { -1, Long.MAX_VALUE / 1000L, Long.MAX_VALUE / (1000L * 1000) }, // minutes { -1, Long.MAX_VALUE / 60L, Long.MAX_VALUE / (60L * 1000), Long.MAX_VALUE / (60L * 1000 * 1000) }, // hours { -1, Long.MAX_VALUE / 60L, Long.MAX_VALUE / (60L * 60), Long.MAX_VALUE / (60L * 60 * 1000), Long.MAX_VALUE / (60L * 60 * 1000 * 1000) }, // days { -1, Long.MAX_VALUE / 24L, Long.MAX_VALUE / (24L * 60), Long.MAX_VALUE / (24L * 60 * 60), Long.MAX_VALUE / (24L * 60 * 60 * 1000), Long.MAX_VALUE / (24L * 60 * 60 * 1000 * 1000) } }; private static long doConvert(int ordinal, int delta, long duration) { if (delta == 0) { return duration; } if (delta < 0) { return Math.round(duration / divisors[ordinal][-delta]); } final long overflow = overflows[ordinal][delta]; if (duration > overflow) { return Long.MAX_VALUE; } if (duration < -overflow) { return Long.MIN_VALUE; } return duration * multipliers[ordinal][delta]; } /** * Returns the type variant corresponding to this unit. */ public HDF5DataTypeVariant getTypeVariant() { return typeVariants[ordinal()]; } /** * Convert the given time duration in the given unit to this unit. Conversions from smaller to * larger units perform rounding, so they lose precision. Conversions from larger to smaller * units with arguments that would numerically overflow saturate to Long.MIN_VALUE * if negative or Long.MAX_VALUE if positive. * * @param duration The time duration in the given unit. * @param unit The unit of the duration argument. * @return The converted duration in this unit, or Long.MIN_VALUE if conversion * would negatively overflow, or Long.MAX_VALUE if it would positively * overflow. */ public long convert(long duration, HDF5TimeUnit unit) { final int currentUnitOrdinal = unit.ordinal(); return doConvert(currentUnitOrdinal, currentUnitOrdinal - ordinal(), duration); } /** * Convert the given time durations in the given time unit to this unit. * Conversions from smaller to larger units perform rounding, so they lose precision. * Conversions from larger to smaller units with arguments that would numerically overflow * saturate to Long.MIN_VALUE if negative or Long.MAX_VALUE if * positive. * * @param durations The time durations. * @return The converted duration in this unit, or Long.MIN_VALUE if conversion * would negatively overflow, or Long.MAX_VALUE if it would positively * overflow. */ public long[] convert(final HDF5TimeDurationArray durations) { if (this != durations.timeUnit) { final long[] convertedData = new long[durations.timeDurations.length]; for (int i = 0; i < durations.timeDurations.length; ++i) { convertedData[i] = this.convert(durations.timeDurations[i], durations.timeUnit); } return convertedData; } else { return durations.timeDurations; } } /** * Convert the given time durations in the given time unit to this unit. * Conversions from smaller to larger units perform rounding, so they lose precision. * Conversions from larger to smaller units with arguments that would numerically overflow * saturate to Long.MIN_VALUE if negative or Long.MAX_VALUE if * positive. * * @param durations The time durations. * @return The converted duration in this unit, or Long.MIN_VALUE if conversion * would negatively overflow, or Long.MAX_VALUE if it would positively * overflow. */ public HDF5TimeDurationMDArray convert(final HDF5TimeDurationMDArray durations) { if (this != durations.timeUnit) { final long[] originalData = durations.getAsFlatArray(); final long[] convertedData = new long[originalData.length]; for (int i = 0; i < originalData.length; ++i) { convertedData[i] = this.convert(originalData[i], durations.timeUnit); } return new HDF5TimeDurationMDArray(convertedData, durations.dimensions(), this); } else { return durations; } } /** * Convert the given time durations in the given time unit to this unit. * Conversions from smaller to larger units perform rounding, so they lose precision. * Conversions from larger to smaller units with arguments that would numerically overflow * saturate to Long.MIN_VALUE if negative or Long.MAX_VALUE if * positive. * * @param durations The time duration in the given unit. * @param unit The unit of the duration argument. * @return The converted duration in this unit, or Long.MIN_VALUE if conversion * would negatively overflow, or Long.MAX_VALUE if it would positively * overflow. */ public long[] convert(final long[] durations, final HDF5TimeUnit unit) { if (this != unit) { final long[] convertedData = new long[durations.length]; for (int i = 0; i < durations.length; ++i) { convertedData[i] = this.convert(durations[i], unit); } return convertedData; } else { return durations; } } /** * Convert the given time duration in the given unit to this unit. Conversions from smaller to * larger units perform rounding, so they lose precision. Conversions from larger to smaller * units with arguments that would numerically overflow saturate to Long.MIN_VALUE * if negative or Long.MAX_VALUE if positive. * * @param duration The time duration and its unit. * @return The converted duration in this unit, or Long.MIN_VALUE if conversion * would negatively overflow, or Long.MAX_VALUE if it would positively * overflow. */ public long convert(HDF5TimeDuration duration) { return convert(duration.getValue(), duration.getUnit()); } /** * Convert the given time durations to this unit. Conversions from smaller to larger * units perform rounding, so they lose precision. Conversions from larger to smaller units with * arguments that would numerically overflow saturate to Long.MIN_VALUE if negative * or Long.MAX_VALUE if positive. * * @return The converted durations in this unit, or Long.MIN_VALUE if conversion * would negatively overflow, or Long.MAX_VALUE if it would positively * overflow. */ public long[] convert(final HDF5TimeDuration[] durations) { final long[] convertedData = new long[durations.length]; for (int i = 0; i < durations.length; ++i) { convertedData[i] = this.convert(durations[i]); } return convertedData; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5UnsignedByteReader.java000066400000000000000000001020711256564762100303600ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.MatrixUtils.cardinalityBoundIndices; import static ch.systemsx.cisd.hdf5.MatrixUtils.checkBoundIndices; import static ch.systemsx.cisd.hdf5.MatrixUtils.createFullBlockDimensionsAndOffset; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_ARRAY; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_UINT8; import java.util.Arrays; import java.util.Iterator; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import ncsa.hdf.hdf5lib.exceptions.HDF5SpaceRankMismatch; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDByteArray; import ch.systemsx.cisd.hdf5.HDF5BaseReader.DataSpaceParameters; import ch.systemsx.cisd.hdf5.HDF5DataTypeInformation.DataTypeInfoOptions; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; import ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants; /** * The implementation of {@link IHDF5ByteReader}. * * @author Bernd Rinn */ class HDF5UnsignedByteReader implements IHDF5ByteReader { private final HDF5BaseReader baseReader; HDF5UnsignedByteReader(HDF5BaseReader baseReader) { assert baseReader != null; this.baseReader = baseReader; } // For Unit tests only. HDF5BaseReader getBaseReader() { return baseReader; } // ///////////////////// // Attributes // ///////////////////// @Override public byte getAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public Byte call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final byte[] data = baseReader.h5.readAttributeAsByteArray(attributeId, H5T_NATIVE_UINT8, 1); return data[0]; } }; return baseReader.runner.call(getAttributeRunnable); } @Override public byte[] getArrayAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public byte[] call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); return getByteArrayAttribute(objectId, attributeName, registry); } }; return baseReader.runner.call(getAttributeRunnable); } @Override public MDByteArray getMDArrayAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public MDByteArray call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); return getByteMDArrayAttribute(objectId, attributeName, registry); } }; return baseReader.runner.call(getAttributeRunnable); } @Override public byte[][] getMatrixAttr(final String objectPath, final String attributeName) throws HDF5JavaException { final MDByteArray array = getMDArrayAttr(objectPath, attributeName); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } // ///////////////////// // Data Sets // ///////////////////// @Override public byte read(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public Byte call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final byte[] data = new byte[1]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_UINT8, data); return data[0]; } }; return baseReader.runner.call(readCallable); } @Override public byte[] readArray(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public byte[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); return readByteArray(dataSetId, registry); } }; return baseReader.runner.call(readCallable); } private byte[] readByteArray(int dataSetId, ICleanUpRegistry registry) { try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); final byte[] data = new byte[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_UINT8, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return data; } catch (HDF5LibraryException ex) { if (ex.getMajorErrorNumber() == HDF5Constants.H5E_DATATYPE && ex.getMinorErrorNumber() == HDF5Constants.H5E_CANTINIT) { // Check whether it is an array data type. final int dataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); if (baseReader.h5.getClassType(dataTypeId) == HDF5Constants.H5T_ARRAY) { return readByteArrayFromArrayType(dataSetId, dataTypeId, registry); } } throw ex; } } private byte[] readByteArrayFromArrayType(int dataSetId, final int dataTypeId, ICleanUpRegistry registry) { final int spaceId = baseReader.h5.createScalarDataSpace(); final int[] dimensions = baseReader.h5.getArrayDimensions(dataTypeId); final byte[] data = new byte[HDF5Utils.getOneDimensionalArraySize(dimensions)]; final int memoryDataTypeId = baseReader.h5.createArrayType(H5T_NATIVE_UINT8, data.length, registry); baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceId, spaceId, data); return data; } @Override public int[] readToMDArrayWithOffset(final String objectPath, final MDByteArray array, final int[] memoryOffset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getBlockSpaceParameters(dataSetId, memoryOffset, array .dimensions(), registry); final int nativeDataTypeId = baseReader.getNativeDataTypeId(dataSetId, H5T_NATIVE_UINT8, registry); baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, array. getAsFlatArray()); return MDArray.toInt(spaceParams.dimensions); } }; return baseReader.runner.call(readCallable); } @Override public int[] readToMDArrayBlockWithOffset(final String objectPath, final MDByteArray array, final int[] blockDimensions, final long[] offset, final int[] memoryOffset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getBlockSpaceParameters(dataSetId, memoryOffset, array .dimensions(), offset, blockDimensions, registry); final int nativeDataTypeId = baseReader.getNativeDataTypeId(dataSetId, H5T_NATIVE_UINT8, registry); baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, array .getAsFlatArray()); return MDArray.toInt(spaceParams.dimensions); } }; return baseReader.runner.call(readCallable); } @Override public byte[] readArrayBlock(final String objectPath, final int blockSize, final long blockNumber) { return readArrayBlockWithOffset(objectPath, blockSize, blockNumber * blockSize); } @Override public byte[] readArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public byte[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockSize, registry); final byte[] data = new byte[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_UINT8, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return data; } }; return baseReader.runner.call(readCallable); } @Override public byte[][] readMatrix(final String objectPath) throws HDF5JavaException { final MDByteArray array = readMDArray(objectPath); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public byte[][] readMatrixBlock(final String objectPath, final int blockSizeX, final int blockSizeY, final long blockNumberX, final long blockNumberY) throws HDF5JavaException { final MDByteArray array = readMDArrayBlock(objectPath, new int[] { blockSizeX, blockSizeY }, new long[] { blockNumberX, blockNumberY }); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public byte[][] readMatrixBlockWithOffset(final String objectPath, final int blockSizeX, final int blockSizeY, final long offsetX, final long offsetY) throws HDF5JavaException { final MDByteArray array = readMDArrayBlockWithOffset(objectPath, new int[] { blockSizeX, blockSizeY }, new long[] { offsetX, offsetY }); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public MDByteArray readMDArraySlice(String objectPath, IndexMap boundIndices) { baseReader.checkOpen(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; final int cardBoundIndices = cardinalityBoundIndices(boundIndices); checkBoundIndices(objectPath, fullDimensions, cardBoundIndices); final int[] effectiveBlockDimensions = new int[fullBlockDimensions.length - cardBoundIndices]; Arrays.fill(effectiveBlockDimensions, -1); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, null, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDByteArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); if (fullBlockDimensions.length == cardBoundIndices) // no free indices { return new MDByteArray(result.getAsFlatArray(), new int[] { 1 }); } else { return new MDByteArray(result.getAsFlatArray(), effectiveBlockDimensions); } } @Override public MDByteArray readMDArraySlice(String objectPath, long[] boundIndices) { baseReader.checkOpen(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; final int cardBoundIndices = cardinalityBoundIndices(boundIndices); checkBoundIndices(objectPath, fullDimensions, boundIndices); final int[] effectiveBlockDimensions = new int[fullBlockDimensions.length - cardBoundIndices]; Arrays.fill(effectiveBlockDimensions, -1); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, null, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDByteArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); if (fullBlockDimensions.length == cardBoundIndices) // no free indices { return new MDByteArray(result.getAsFlatArray(), new int[] { 1 }); } else { return new MDByteArray(result.getAsFlatArray(), effectiveBlockDimensions); } } @Override public MDByteArray readMDArray(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public MDByteArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); return readByteMDArray(dataSetId, registry); } }; return baseReader.runner.call(readCallable); } MDByteArray readByteMDArray(int dataSetId, ICleanUpRegistry registry) { try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); final byte[] data = new byte[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_UINT8, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return new MDByteArray(data, spaceParams.dimensions); } catch (HDF5LibraryException ex) { if (ex.getMajorErrorNumber() == HDF5Constants.H5E_DATATYPE && ex.getMinorErrorNumber() == HDF5Constants.H5E_CANTINIT) { // Check whether it is an array data type. final int dataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); if (baseReader.h5.getClassType(dataTypeId) == HDF5Constants.H5T_ARRAY) { return readByteMDArrayFromArrayType(dataSetId, dataTypeId, registry); } } throw ex; } } private MDByteArray readByteMDArrayFromArrayType(int dataSetId, final int dataTypeId, ICleanUpRegistry registry) { final int[] arrayDimensions = baseReader.h5.getArrayDimensions(dataTypeId); final int memoryDataTypeId = baseReader.h5.createArrayType(H5T_NATIVE_UINT8, arrayDimensions, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); if (spaceParams.blockSize == 0) { final int spaceId = baseReader.h5.createScalarDataSpace(); final byte[] data = new byte[MDArray.getLength(arrayDimensions)]; baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceId, spaceId, data); return new MDByteArray(data, arrayDimensions); } else { final byte[] data = new byte[MDArray.getLength(arrayDimensions) * spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return new MDByteArray(data, MatrixUtils.concat(MDArray.toInt(spaceParams.dimensions), arrayDimensions)); } } @Override public MDByteArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, IndexMap boundIndices) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readSlicedMDArrayBlockWithOffset(objectPath, blockDimensions, offset, boundIndices); } @Override public MDByteArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, long[] boundIndices) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readSlicedMDArrayBlockWithOffset(objectPath, blockDimensions, offset, boundIndices); } @Override public MDByteArray readMDArrayBlock(final String objectPath, final int[] blockDimensions, final long[] blockNumber) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readMDArrayBlockWithOffset(objectPath, blockDimensions, offset); } @Override public MDByteArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, IndexMap boundIndices) { baseReader.checkOpen(); final int[] effectiveBlockDimensions = blockDimensions.clone(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; checkBoundIndices(objectPath, fullDimensions, blockDimensions, cardinalityBoundIndices(boundIndices)); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, offset, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDByteArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); return new MDByteArray(result.getAsFlatArray(), effectiveBlockDimensions); } @Override public MDByteArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, long[] boundIndices) { baseReader.checkOpen(); final int[] effectiveBlockDimensions = blockDimensions.clone(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; checkBoundIndices(objectPath, fullDimensions, blockDimensions, cardinalityBoundIndices(boundIndices)); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, offset, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDByteArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); return new MDByteArray(result.getAsFlatArray(), effectiveBlockDimensions); } @Override public MDByteArray readMDArrayBlockWithOffset(final String objectPath, final int[] blockDimensions, final long[] offset) { assert objectPath != null; assert blockDimensions != null; assert offset != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public MDByteArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockDimensions, registry); final byte[] dataBlock = new byte[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_UINT8, spaceParams.memorySpaceId, spaceParams.dataSpaceId, dataBlock); return new MDByteArray(dataBlock, spaceParams.dimensions); } catch (HDF5SpaceRankMismatch ex) { final HDF5DataSetInformation info = baseReader.getDataSetInformation(objectPath, DataTypeInfoOptions.MINIMAL, false); if (ex.getSpaceRankExpected() - ex.getSpaceRankFound() == info .getTypeInformation().getRank()) { return readMDArrayBlockOfArrays(dataSetId, blockDimensions, offset, info, ex.getSpaceRankFound(), registry); } else { throw ex; } } } }; return baseReader.runner.call(readCallable); } private MDByteArray readMDArrayBlockOfArrays(final int dataSetId, final int[] blockDimensions, final long[] offset, final HDF5DataSetInformation info, final int spaceRank, final ICleanUpRegistry registry) { final int[] arrayDimensions = info.getTypeInformation().getDimensions(); int[] effectiveBlockDimensions = blockDimensions; // We do not support block-wise reading of array types, check // that we do not have to and bail out otherwise. for (int i = 0; i < arrayDimensions.length; ++i) { final int j = spaceRank + i; if (effectiveBlockDimensions[j] < 0) { if (effectiveBlockDimensions == blockDimensions) { effectiveBlockDimensions = blockDimensions.clone(); } effectiveBlockDimensions[j] = arrayDimensions[i]; } if (effectiveBlockDimensions[j] != arrayDimensions[i]) { throw new HDF5JavaException( "Block-wise reading of array type data sets is not supported."); } } final int[] spaceBlockDimensions = Arrays.copyOfRange(effectiveBlockDimensions, 0, spaceRank); final long[] spaceOfs = Arrays.copyOfRange(offset, 0, spaceRank); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, spaceOfs, spaceBlockDimensions, registry); final byte[] dataBlock = new byte[spaceParams.blockSize * info.getTypeInformation().getNumberOfElements()]; final int memoryDataTypeId = baseReader.h5.createArrayType(H5T_NATIVE_UINT8, info.getTypeInformation() .getDimensions(), registry); baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, dataBlock); return new MDByteArray(dataBlock, effectiveBlockDimensions); } @Override public Iterable> getArrayNaturalBlocks(final String dataSetPath) throws HDF5JavaException { baseReader.checkOpen(); final HDF5NaturalBlock1DParameters params = new HDF5NaturalBlock1DParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlock1DParameters.HDF5NaturalBlock1DIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5DataBlock next() { final long offset = index.computeOffsetAndSizeGetOffset(); final byte[] block = readArrayBlockWithOffset(dataSetPath, index .getBlockSize(), offset); return new HDF5DataBlock(block, index.getAndIncIndex(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } @Override public Iterable> getMDArrayNaturalBlocks(final String dataSetPath) { baseReader.checkOpen(); final HDF5NaturalBlockMDParameters params = new HDF5NaturalBlockMDParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlockMDParameters.HDF5NaturalBlockMDIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5MDDataBlock next() { final long[] offset = index.computeOffsetAndSizeGetOffsetClone(); final MDByteArray data = readMDArrayBlockWithOffset(dataSetPath, index .getBlockSize(), offset); return new HDF5MDDataBlock(data, index .getIndexClone(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } byte[] getByteArrayAttribute(final int objectId, final String attributeName, ICleanUpRegistry registry) { final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, registry); final int memoryTypeId; final int len; if (baseReader.h5.getClassType(attributeTypeId) == H5T_ARRAY) { final int[] arrayDimensions = baseReader.h5.getArrayDimensions(attributeTypeId); if (arrayDimensions.length != 1) { throw new HDF5JavaException( "Array needs to be of rank 1, but is of rank " + arrayDimensions.length); } len = arrayDimensions[0]; memoryTypeId = baseReader.h5.createArrayType(H5T_NATIVE_UINT8, len, registry); } else { final long[] arrayDimensions = baseReader.h5.getDataDimensionsForAttribute(attributeId, registry); memoryTypeId = H5T_NATIVE_UINT8; len = HDF5Utils.getOneDimensionalArraySize(arrayDimensions); } final byte[] data = baseReader.h5.readAttributeAsByteArray(attributeId, memoryTypeId, len); return data; } MDByteArray getByteMDArrayAttribute(final int objectId, final String attributeName, ICleanUpRegistry registry) { try { final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, registry); final int memoryTypeId; final int[] arrayDimensions; if (baseReader.h5.getClassType(attributeTypeId) == H5T_ARRAY) { arrayDimensions = baseReader.h5.getArrayDimensions(attributeTypeId); memoryTypeId = baseReader.h5.createArrayType(H5T_NATIVE_UINT8, arrayDimensions, registry); } else { arrayDimensions = MDArray.toInt(baseReader.h5.getDataDimensionsForAttribute( attributeId, registry)); memoryTypeId = H5T_NATIVE_UINT8; } final int len = MDArray.getLength(arrayDimensions); final byte[] data = baseReader.h5.readAttributeAsByteArray(attributeId, memoryTypeId, len); return new MDByteArray(data, arrayDimensions); } catch (IllegalArgumentException ex) { throw new HDF5JavaException(ex.getMessage()); } } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5UnsignedByteWriter.java000066400000000000000000000660361256564762100304440ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.HDF5IntStorageFeatures.INT_NO_COMPRESSION; import static ch.systemsx.cisd.hdf5.hdf5lib.H5D.H5Dwrite; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_ALL; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_UINT8; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_U8LE; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDByteArray; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; /** * The implementation of {@link IHDF5ByteWriter}. * * @author Bernd Rinn */ class HDF5UnsignedByteWriter extends HDF5UnsignedByteReader implements IHDF5ByteWriter { private final HDF5BaseWriter baseWriter; HDF5UnsignedByteWriter(HDF5BaseWriter baseWriter) { super(baseWriter); assert baseWriter != null; this.baseWriter = baseWriter; } // ///////////////////// // Attributes // ///////////////////// @Override public void setAttr(final String objectPath, final String name, final byte value) { assert objectPath != null; assert name != null; baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { 1 }, registry); baseWriter.setAttribute(objectPath, name, H5T_STD_U8LE, H5T_NATIVE_UINT8, dataSpaceId, new byte[] { value }, registry); } else { baseWriter.setAttribute(objectPath, name, H5T_STD_U8LE, H5T_NATIVE_UINT8, -1, new byte[] { value }, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void setArrayAttr(final String objectPath, final String name, final byte[] value) { assert objectPath != null; assert name != null; assert value != null; baseWriter.checkOpen(); final ICallableWithCleanUp setAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { value.length }, registry); baseWriter.setAttribute(objectPath, name, H5T_STD_U8LE, H5T_NATIVE_UINT8, dataSpaceId, value, registry); } else { final int memoryTypeId = baseWriter.h5.createArrayType(H5T_NATIVE_UINT8, value.length, registry); final int storageTypeId = baseWriter.h5.createArrayType(H5T_STD_U8LE, value.length, registry); baseWriter.setAttribute(objectPath, name, storageTypeId, memoryTypeId, -1, value, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(setAttributeRunnable); } @Override public void setMDArrayAttr(final String objectPath, final String name, final MDByteArray value) { assert objectPath != null; assert name != null; assert value != null; baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(value.longDimensions(), registry); baseWriter.setAttribute(objectPath, name, H5T_STD_U8LE, H5T_NATIVE_UINT8, dataSpaceId, value.getAsFlatArray(), registry); } else { final int memoryTypeId = baseWriter.h5.createArrayType(H5T_NATIVE_UINT8, value.dimensions(), registry); final int storageTypeId = baseWriter.h5.createArrayType(H5T_STD_U8LE, value.dimensions(), registry); baseWriter.setAttribute(objectPath, name, storageTypeId, memoryTypeId, -1, value.getAsFlatArray(), registry); } return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void setMatrixAttr(final String objectPath, final String name, final byte[][] value) { setMDArrayAttr(objectPath, name, new MDByteArray(value)); } // ///////////////////// // Data Sets // ///////////////////// @Override public void write(final String objectPath, final byte value) { assert objectPath != null; baseWriter.checkOpen(); baseWriter.writeScalar(objectPath, H5T_STD_U8LE, H5T_NATIVE_UINT8, value); } @Override public void writeArray(final String objectPath, final byte[] data) { writeArray(objectPath, data, INT_NO_COMPRESSION); } @Override public void writeArray(final String objectPath, final byte[] data, final HDF5IntStorageFeatures features) { assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, H5T_STD_U8LE, new long[] { data.length }, 1, features, registry); H5Dwrite(dataSetId, H5T_NATIVE_UINT8, H5S_ALL, H5S_ALL, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createArray(final String objectPath, final int size) { createArray(objectPath, size, INT_NO_COMPRESSION); } @Override public void createArray(final String objectPath, final long size, final int blockSize) { createArray(objectPath, size, blockSize, INT_NO_COMPRESSION); } @Override public void createArray(final String objectPath, final int size, final HDF5IntStorageFeatures features) { assert objectPath != null; assert size >= 0; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (features.requiresChunking()) { baseWriter.createDataSet(objectPath, H5T_STD_U8LE, features, new long[] { 0 }, new long[] { size }, 1, registry); } else { baseWriter.createDataSet(objectPath, H5T_STD_U8LE, features, new long[] { size }, null, 1, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void createArray(final String objectPath, final long size, final int blockSize, final HDF5IntStorageFeatures features) { assert objectPath != null; assert size >= 0; assert blockSize >= 0 && (blockSize <= size || size == 0); baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { baseWriter.createDataSet(objectPath, H5T_STD_U8LE, features, new long[] { size }, new long[] { blockSize }, 1, registry); return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void writeArrayBlock(final String objectPath, final byte[] data, final long blockNumber) { writeArrayBlockWithOffset(objectPath, data, data.length, data.length * blockNumber); } @Override public void writeArrayBlockWithOffset(final String objectPath, final byte[] data, final int dataSize, final long offset) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] blockDimensions = new long[] { dataSize }; final long[] slabStartOrNull = new long[] { offset }; final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, new long[] { offset + dataSize }, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, slabStartOrNull, blockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(blockDimensions, registry); H5Dwrite(dataSetId, H5T_NATIVE_UINT8, memorySpaceId, dataSpaceId, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } /** * Writes out a byte matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ @Override public void writeMatrix(final String objectPath, final byte[][] data) { writeMatrix(objectPath, data, INT_NO_COMPRESSION); } @Override public void writeMatrix(final String objectPath, final byte[][] data, final HDF5IntStorageFeatures features) { assert objectPath != null; assert data != null; assert HDF5Utils.areMatrixDimensionsConsistent(data); writeMDArray(objectPath, new MDByteArray(data), features); } @Override public void createMatrix(final String objectPath, final int sizeX, final int sizeY) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; createMDArray(objectPath, new int[] { sizeX, sizeY }); } @Override public void createMatrix(final String objectPath, final int sizeX, final int sizeY, final HDF5IntStorageFeatures features) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; createMDArray(objectPath, new int[] { sizeX, sizeY }, features); } @Override public void createMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; assert blockSizeX >= 0 && (blockSizeX <= sizeX || sizeX == 0); assert blockSizeY >= 0 && (blockSizeY <= sizeY || sizeY == 0); createMDArray(objectPath, new long[] { sizeX, sizeY }, new int[] { blockSizeX, blockSizeY }); } @Override public void createMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY, final HDF5IntStorageFeatures features) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; assert blockSizeX >= 0 && (blockSizeX <= sizeX || sizeX == 0); assert blockSizeY >= 0 && (blockSizeY <= sizeY || sizeY == 0); createMDArray(objectPath, new long[] { sizeX, sizeY }, new int[] { blockSizeX, blockSizeY }, features); } @Override public void writeMatrixBlock(final String objectPath, final byte[][] data, final long blockNumberX, final long blockNumberY) { assert objectPath != null; assert data != null; writeMDArrayBlock(objectPath, new MDByteArray(data), new long[] { blockNumberX, blockNumberY }); } @Override public void writeMatrixBlockWithOffset(final String objectPath, final byte[][] data, final long offsetX, final long offsetY) { assert objectPath != null; assert data != null; writeMDArrayBlockWithOffset(objectPath, new MDByteArray(data, new int[] { data.length, data[0].length }), new long[] { offsetX, offsetY }); } @Override public void writeMatrixBlockWithOffset(final String objectPath, final byte[][] data, final int dataSizeX, final int dataSizeY, final long offsetX, final long offsetY) { assert objectPath != null; assert data != null; writeMDArrayBlockWithOffset(objectPath, new MDByteArray(data, new int[] { dataSizeX, dataSizeY }), new long[] { offsetX, offsetY }); } @Override public void writeMDArray(final String objectPath, final MDByteArray data) { writeMDArray(objectPath, data, INT_NO_COMPRESSION); } @Override public void writeMDArraySlice(String objectPath, MDByteArray data, IndexMap boundIndices) { baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), null, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDByteArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArraySlice(String objectPath, MDByteArray data, long[] boundIndices) { baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), null, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDByteArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArray(final String objectPath, final MDByteArray data, final HDF5IntStorageFeatures features) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, H5T_STD_U8LE, data.longDimensions(), 1, features, registry); H5Dwrite(dataSetId, H5T_NATIVE_UINT8, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createMDArray(final String objectPath, final int[] dimensions) { createMDArray(objectPath, dimensions, INT_NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions) { createMDArray(objectPath, dimensions, blockDimensions, INT_NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final int[] dimensions, final HDF5IntStorageFeatures features) { assert objectPath != null; assert dimensions != null; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (features.requiresChunking()) { final long[] nullDimensions = new long[dimensions.length]; baseWriter.createDataSet(objectPath, H5T_STD_U8LE, features, nullDimensions, MDArray.toLong(dimensions), 1, registry); } else { baseWriter.createDataSet(objectPath, H5T_STD_U8LE, features, MDArray.toLong(dimensions), null, 1, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void createMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions, final HDF5IntStorageFeatures features) { assert objectPath != null; assert dimensions != null; assert blockDimensions != null; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { baseWriter.createDataSet(objectPath, H5T_STD_U8LE, features, dimensions, MDArray.toLong(blockDimensions), 1, registry); return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void writeMDArrayBlock(final String objectPath, final MDByteArray data, final long[] blockNumber) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeMDArrayBlockWithOffset(objectPath, data, offset); } @Override public void writeSlicedMDArrayBlock(final String objectPath, final MDByteArray data, final long[] blockNumber, IndexMap boundIndices) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeSlicedMDArrayBlockWithOffset(objectPath, data, offset, boundIndices); } @Override public void writeSlicedMDArrayBlock(String objectPath, MDByteArray data, long[] blockNumber, long[] boundIndices) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeSlicedMDArrayBlockWithOffset(objectPath, data, offset, boundIndices); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final MDByteArray data, final long[] offset) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] dimensions = data.longDimensions(); assert dimensions.length == offset.length; final long[] dataSetDimensions = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + dimensions[i]; } final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, dimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(dimensions, registry); H5Dwrite(dataSetId, H5T_NATIVE_UINT8, memorySpaceId, dataSpaceId, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeSlicedMDArrayBlockWithOffset(String objectPath, MDByteArray data, long[] offset, IndexMap boundIndices) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), offset, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDByteArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeSlicedMDArrayBlockWithOffset(String objectPath, MDByteArray data, long[] offset, long[] boundIndices) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), offset, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDByteArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final MDByteArray data, final int[] blockDimensions, final long[] offset, final int[] memoryOffset) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] memoryDimensions = data.longDimensions(); assert memoryDimensions.length == offset.length; final long[] longBlockDimensions = MDArray.toLong(blockDimensions); assert longBlockDimensions.length == offset.length; final long[] dataSetDimensions = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + blockDimensions[i]; } final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, longBlockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(memoryDimensions, registry); baseWriter.h5.setHyperslabBlock(memorySpaceId, MDArray.toLong(memoryOffset), longBlockDimensions); H5Dwrite(dataSetId, H5T_NATIVE_UINT8, memorySpaceId, dataSpaceId, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5UnsignedIntReader.java000066400000000000000000001017411256564762100302120ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.MatrixUtils.cardinalityBoundIndices; import static ch.systemsx.cisd.hdf5.MatrixUtils.checkBoundIndices; import static ch.systemsx.cisd.hdf5.MatrixUtils.createFullBlockDimensionsAndOffset; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_ARRAY; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_UINT32; import java.util.Arrays; import java.util.Iterator; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import ncsa.hdf.hdf5lib.exceptions.HDF5SpaceRankMismatch; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDIntArray; import ch.systemsx.cisd.hdf5.HDF5BaseReader.DataSpaceParameters; import ch.systemsx.cisd.hdf5.HDF5DataTypeInformation.DataTypeInfoOptions; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; import ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants; /** * The implementation of {@link IHDF5IntReader}. * * @author Bernd Rinn */ class HDF5UnsignedIntReader implements IHDF5IntReader { private final HDF5BaseReader baseReader; HDF5UnsignedIntReader(HDF5BaseReader baseReader) { assert baseReader != null; this.baseReader = baseReader; } // For Unit tests only. HDF5BaseReader getBaseReader() { return baseReader; } // ///////////////////// // Attributes // ///////////////////// @Override public int getAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public Integer call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int[] data = baseReader.h5.readAttributeAsIntArray(attributeId, H5T_NATIVE_UINT32, 1); return data[0]; } }; return baseReader.runner.call(getAttributeRunnable); } @Override public int[] getArrayAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); return getIntArrayAttribute(objectId, attributeName, registry); } }; return baseReader.runner.call(getAttributeRunnable); } @Override public MDIntArray getMDArrayAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public MDIntArray call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); return getIntMDArrayAttribute(objectId, attributeName, registry); } }; return baseReader.runner.call(getAttributeRunnable); } @Override public int[][] getMatrixAttr(final String objectPath, final String attributeName) throws HDF5JavaException { final MDIntArray array = getMDArrayAttr(objectPath, attributeName); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } // ///////////////////// // Data Sets // ///////////////////// @Override public int read(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public Integer call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final int[] data = new int[1]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_UINT32, data); return data[0]; } }; return baseReader.runner.call(readCallable); } @Override public int[] readArray(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); return readIntArray(dataSetId, registry); } }; return baseReader.runner.call(readCallable); } private int[] readIntArray(int dataSetId, ICleanUpRegistry registry) { try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); final int[] data = new int[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_UINT32, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return data; } catch (HDF5LibraryException ex) { if (ex.getMajorErrorNumber() == HDF5Constants.H5E_DATATYPE && ex.getMinorErrorNumber() == HDF5Constants.H5E_CANTINIT) { // Check whether it is an array data type. final int dataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); if (baseReader.h5.getClassType(dataTypeId) == HDF5Constants.H5T_ARRAY) { return readIntArrayFromArrayType(dataSetId, dataTypeId, registry); } } throw ex; } } private int[] readIntArrayFromArrayType(int dataSetId, final int dataTypeId, ICleanUpRegistry registry) { final int spaceId = baseReader.h5.createScalarDataSpace(); final int[] dimensions = baseReader.h5.getArrayDimensions(dataTypeId); final int[] data = new int[HDF5Utils.getOneDimensionalArraySize(dimensions)]; final int memoryDataTypeId = baseReader.h5.createArrayType(H5T_NATIVE_UINT32, data.length, registry); baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceId, spaceId, data); return data; } @Override public int[] readToMDArrayWithOffset(final String objectPath, final MDIntArray array, final int[] memoryOffset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getBlockSpaceParameters(dataSetId, memoryOffset, array .dimensions(), registry); final int nativeDataTypeId = baseReader.getNativeDataTypeId(dataSetId, H5T_NATIVE_UINT32, registry); baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, array. getAsFlatArray()); return MDArray.toInt(spaceParams.dimensions); } }; return baseReader.runner.call(readCallable); } @Override public int[] readToMDArrayBlockWithOffset(final String objectPath, final MDIntArray array, final int[] blockDimensions, final long[] offset, final int[] memoryOffset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getBlockSpaceParameters(dataSetId, memoryOffset, array .dimensions(), offset, blockDimensions, registry); final int nativeDataTypeId = baseReader.getNativeDataTypeId(dataSetId, H5T_NATIVE_UINT32, registry); baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, array .getAsFlatArray()); return MDArray.toInt(spaceParams.dimensions); } }; return baseReader.runner.call(readCallable); } @Override public int[] readArrayBlock(final String objectPath, final int blockSize, final long blockNumber) { return readArrayBlockWithOffset(objectPath, blockSize, blockNumber * blockSize); } @Override public int[] readArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockSize, registry); final int[] data = new int[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_UINT32, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return data; } }; return baseReader.runner.call(readCallable); } @Override public int[][] readMatrix(final String objectPath) throws HDF5JavaException { final MDIntArray array = readMDArray(objectPath); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public int[][] readMatrixBlock(final String objectPath, final int blockSizeX, final int blockSizeY, final long blockNumberX, final long blockNumberY) throws HDF5JavaException { final MDIntArray array = readMDArrayBlock(objectPath, new int[] { blockSizeX, blockSizeY }, new long[] { blockNumberX, blockNumberY }); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public int[][] readMatrixBlockWithOffset(final String objectPath, final int blockSizeX, final int blockSizeY, final long offsetX, final long offsetY) throws HDF5JavaException { final MDIntArray array = readMDArrayBlockWithOffset(objectPath, new int[] { blockSizeX, blockSizeY }, new long[] { offsetX, offsetY }); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public MDIntArray readMDArraySlice(String objectPath, IndexMap boundIndices) { baseReader.checkOpen(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; final int cardBoundIndices = cardinalityBoundIndices(boundIndices); checkBoundIndices(objectPath, fullDimensions, cardBoundIndices); final int[] effectiveBlockDimensions = new int[fullBlockDimensions.length - cardBoundIndices]; Arrays.fill(effectiveBlockDimensions, -1); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, null, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDIntArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); if (fullBlockDimensions.length == cardBoundIndices) // no free indices { return new MDIntArray(result.getAsFlatArray(), new int[] { 1 }); } else { return new MDIntArray(result.getAsFlatArray(), effectiveBlockDimensions); } } @Override public MDIntArray readMDArraySlice(String objectPath, long[] boundIndices) { baseReader.checkOpen(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; final int cardBoundIndices = cardinalityBoundIndices(boundIndices); checkBoundIndices(objectPath, fullDimensions, boundIndices); final int[] effectiveBlockDimensions = new int[fullBlockDimensions.length - cardBoundIndices]; Arrays.fill(effectiveBlockDimensions, -1); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, null, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDIntArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); if (fullBlockDimensions.length == cardBoundIndices) // no free indices { return new MDIntArray(result.getAsFlatArray(), new int[] { 1 }); } else { return new MDIntArray(result.getAsFlatArray(), effectiveBlockDimensions); } } @Override public MDIntArray readMDArray(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public MDIntArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); return readIntMDArray(dataSetId, registry); } }; return baseReader.runner.call(readCallable); } MDIntArray readIntMDArray(int dataSetId, ICleanUpRegistry registry) { try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); final int[] data = new int[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_UINT32, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return new MDIntArray(data, spaceParams.dimensions); } catch (HDF5LibraryException ex) { if (ex.getMajorErrorNumber() == HDF5Constants.H5E_DATATYPE && ex.getMinorErrorNumber() == HDF5Constants.H5E_CANTINIT) { // Check whether it is an array data type. final int dataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); if (baseReader.h5.getClassType(dataTypeId) == HDF5Constants.H5T_ARRAY) { return readIntMDArrayFromArrayType(dataSetId, dataTypeId, registry); } } throw ex; } } private MDIntArray readIntMDArrayFromArrayType(int dataSetId, final int dataTypeId, ICleanUpRegistry registry) { final int[] arrayDimensions = baseReader.h5.getArrayDimensions(dataTypeId); final int memoryDataTypeId = baseReader.h5.createArrayType(H5T_NATIVE_UINT32, arrayDimensions, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); if (spaceParams.blockSize == 0) { final int spaceId = baseReader.h5.createScalarDataSpace(); final int[] data = new int[MDArray.getLength(arrayDimensions)]; baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceId, spaceId, data); return new MDIntArray(data, arrayDimensions); } else { final int[] data = new int[MDArray.getLength(arrayDimensions) * spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return new MDIntArray(data, MatrixUtils.concat(MDArray.toInt(spaceParams.dimensions), arrayDimensions)); } } @Override public MDIntArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, IndexMap boundIndices) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readSlicedMDArrayBlockWithOffset(objectPath, blockDimensions, offset, boundIndices); } @Override public MDIntArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, long[] boundIndices) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readSlicedMDArrayBlockWithOffset(objectPath, blockDimensions, offset, boundIndices); } @Override public MDIntArray readMDArrayBlock(final String objectPath, final int[] blockDimensions, final long[] blockNumber) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readMDArrayBlockWithOffset(objectPath, blockDimensions, offset); } @Override public MDIntArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, IndexMap boundIndices) { baseReader.checkOpen(); final int[] effectiveBlockDimensions = blockDimensions.clone(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; checkBoundIndices(objectPath, fullDimensions, blockDimensions, cardinalityBoundIndices(boundIndices)); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, offset, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDIntArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); return new MDIntArray(result.getAsFlatArray(), effectiveBlockDimensions); } @Override public MDIntArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, long[] boundIndices) { baseReader.checkOpen(); final int[] effectiveBlockDimensions = blockDimensions.clone(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; checkBoundIndices(objectPath, fullDimensions, blockDimensions, cardinalityBoundIndices(boundIndices)); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, offset, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDIntArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); return new MDIntArray(result.getAsFlatArray(), effectiveBlockDimensions); } @Override public MDIntArray readMDArrayBlockWithOffset(final String objectPath, final int[] blockDimensions, final long[] offset) { assert objectPath != null; assert blockDimensions != null; assert offset != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public MDIntArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockDimensions, registry); final int[] dataBlock = new int[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_UINT32, spaceParams.memorySpaceId, spaceParams.dataSpaceId, dataBlock); return new MDIntArray(dataBlock, spaceParams.dimensions); } catch (HDF5SpaceRankMismatch ex) { final HDF5DataSetInformation info = baseReader.getDataSetInformation(objectPath, DataTypeInfoOptions.MINIMAL, false); if (ex.getSpaceRankExpected() - ex.getSpaceRankFound() == info .getTypeInformation().getRank()) { return readMDArrayBlockOfArrays(dataSetId, blockDimensions, offset, info, ex.getSpaceRankFound(), registry); } else { throw ex; } } } }; return baseReader.runner.call(readCallable); } private MDIntArray readMDArrayBlockOfArrays(final int dataSetId, final int[] blockDimensions, final long[] offset, final HDF5DataSetInformation info, final int spaceRank, final ICleanUpRegistry registry) { final int[] arrayDimensions = info.getTypeInformation().getDimensions(); int[] effectiveBlockDimensions = blockDimensions; // We do not support block-wise reading of array types, check // that we do not have to and bail out otherwise. for (int i = 0; i < arrayDimensions.length; ++i) { final int j = spaceRank + i; if (effectiveBlockDimensions[j] < 0) { if (effectiveBlockDimensions == blockDimensions) { effectiveBlockDimensions = blockDimensions.clone(); } effectiveBlockDimensions[j] = arrayDimensions[i]; } if (effectiveBlockDimensions[j] != arrayDimensions[i]) { throw new HDF5JavaException( "Block-wise reading of array type data sets is not supported."); } } final int[] spaceBlockDimensions = Arrays.copyOfRange(effectiveBlockDimensions, 0, spaceRank); final long[] spaceOfs = Arrays.copyOfRange(offset, 0, spaceRank); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, spaceOfs, spaceBlockDimensions, registry); final int[] dataBlock = new int[spaceParams.blockSize * info.getTypeInformation().getNumberOfElements()]; final int memoryDataTypeId = baseReader.h5.createArrayType(H5T_NATIVE_UINT32, info.getTypeInformation() .getDimensions(), registry); baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, dataBlock); return new MDIntArray(dataBlock, effectiveBlockDimensions); } @Override public Iterable> getArrayNaturalBlocks(final String dataSetPath) throws HDF5JavaException { baseReader.checkOpen(); final HDF5NaturalBlock1DParameters params = new HDF5NaturalBlock1DParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlock1DParameters.HDF5NaturalBlock1DIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5DataBlock next() { final long offset = index.computeOffsetAndSizeGetOffset(); final int[] block = readArrayBlockWithOffset(dataSetPath, index .getBlockSize(), offset); return new HDF5DataBlock(block, index.getAndIncIndex(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } @Override public Iterable> getMDArrayNaturalBlocks(final String dataSetPath) { baseReader.checkOpen(); final HDF5NaturalBlockMDParameters params = new HDF5NaturalBlockMDParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlockMDParameters.HDF5NaturalBlockMDIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5MDDataBlock next() { final long[] offset = index.computeOffsetAndSizeGetOffsetClone(); final MDIntArray data = readMDArrayBlockWithOffset(dataSetPath, index .getBlockSize(), offset); return new HDF5MDDataBlock(data, index .getIndexClone(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } int[] getIntArrayAttribute(final int objectId, final String attributeName, ICleanUpRegistry registry) { final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, registry); final int memoryTypeId; final int len; if (baseReader.h5.getClassType(attributeTypeId) == H5T_ARRAY) { final int[] arrayDimensions = baseReader.h5.getArrayDimensions(attributeTypeId); if (arrayDimensions.length != 1) { throw new HDF5JavaException( "Array needs to be of rank 1, but is of rank " + arrayDimensions.length); } len = arrayDimensions[0]; memoryTypeId = baseReader.h5.createArrayType(H5T_NATIVE_UINT32, len, registry); } else { final long[] arrayDimensions = baseReader.h5.getDataDimensionsForAttribute(attributeId, registry); memoryTypeId = H5T_NATIVE_UINT32; len = HDF5Utils.getOneDimensionalArraySize(arrayDimensions); } final int[] data = baseReader.h5.readAttributeAsIntArray(attributeId, memoryTypeId, len); return data; } MDIntArray getIntMDArrayAttribute(final int objectId, final String attributeName, ICleanUpRegistry registry) { try { final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, registry); final int memoryTypeId; final int[] arrayDimensions; if (baseReader.h5.getClassType(attributeTypeId) == H5T_ARRAY) { arrayDimensions = baseReader.h5.getArrayDimensions(attributeTypeId); memoryTypeId = baseReader.h5.createArrayType(H5T_NATIVE_UINT32, arrayDimensions, registry); } else { arrayDimensions = MDArray.toInt(baseReader.h5.getDataDimensionsForAttribute( attributeId, registry)); memoryTypeId = H5T_NATIVE_UINT32; } final int len = MDArray.getLength(arrayDimensions); final int[] data = baseReader.h5.readAttributeAsIntArray(attributeId, memoryTypeId, len); return new MDIntArray(data, arrayDimensions); } catch (IllegalArgumentException ex) { throw new HDF5JavaException(ex.getMessage()); } } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5UnsignedIntWriter.java000066400000000000000000000660201256564762100302640ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.HDF5IntStorageFeatures.INT_NO_COMPRESSION; import static ch.systemsx.cisd.hdf5.hdf5lib.H5D.H5Dwrite; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_ALL; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_UINT32; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_U32LE; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDIntArray; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; /** * The implementation of {@link IHDF5IntWriter}. * * @author Bernd Rinn */ class HDF5UnsignedIntWriter extends HDF5UnsignedIntReader implements IHDF5IntWriter { private final HDF5BaseWriter baseWriter; HDF5UnsignedIntWriter(HDF5BaseWriter baseWriter) { super(baseWriter); assert baseWriter != null; this.baseWriter = baseWriter; } // ///////////////////// // Attributes // ///////////////////// @Override public void setAttr(final String objectPath, final String name, final int value) { assert objectPath != null; assert name != null; baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { 1 }, registry); baseWriter.setAttribute(objectPath, name, H5T_STD_U32LE, H5T_NATIVE_UINT32, dataSpaceId, new int[] { value }, registry); } else { baseWriter.setAttribute(objectPath, name, H5T_STD_U32LE, H5T_NATIVE_UINT32, -1, new int[] { value }, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void setArrayAttr(final String objectPath, final String name, final int[] value) { assert objectPath != null; assert name != null; assert value != null; baseWriter.checkOpen(); final ICallableWithCleanUp setAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { value.length }, registry); baseWriter.setAttribute(objectPath, name, H5T_STD_U32LE, H5T_NATIVE_UINT32, dataSpaceId, value, registry); } else { final int memoryTypeId = baseWriter.h5.createArrayType(H5T_NATIVE_UINT32, value.length, registry); final int storageTypeId = baseWriter.h5.createArrayType(H5T_STD_U32LE, value.length, registry); baseWriter.setAttribute(objectPath, name, storageTypeId, memoryTypeId, -1, value, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(setAttributeRunnable); } @Override public void setMDArrayAttr(final String objectPath, final String name, final MDIntArray value) { assert objectPath != null; assert name != null; assert value != null; baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(value.longDimensions(), registry); baseWriter.setAttribute(objectPath, name, H5T_STD_U32LE, H5T_NATIVE_UINT32, dataSpaceId, value.getAsFlatArray(), registry); } else { final int memoryTypeId = baseWriter.h5.createArrayType(H5T_NATIVE_UINT32, value.dimensions(), registry); final int storageTypeId = baseWriter.h5.createArrayType(H5T_STD_U32LE, value.dimensions(), registry); baseWriter.setAttribute(objectPath, name, storageTypeId, memoryTypeId, -1, value.getAsFlatArray(), registry); } return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void setMatrixAttr(final String objectPath, final String name, final int[][] value) { setMDArrayAttr(objectPath, name, new MDIntArray(value)); } // ///////////////////// // Data Sets // ///////////////////// @Override public void write(final String objectPath, final int value) { assert objectPath != null; baseWriter.checkOpen(); baseWriter.writeScalar(objectPath, H5T_STD_U32LE, H5T_NATIVE_UINT32, value); } @Override public void writeArray(final String objectPath, final int[] data) { writeArray(objectPath, data, INT_NO_COMPRESSION); } @Override public void writeArray(final String objectPath, final int[] data, final HDF5IntStorageFeatures features) { assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, H5T_STD_U32LE, new long[] { data.length }, 4, features, registry); H5Dwrite(dataSetId, H5T_NATIVE_UINT32, H5S_ALL, H5S_ALL, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createArray(final String objectPath, final int size) { createArray(objectPath, size, INT_NO_COMPRESSION); } @Override public void createArray(final String objectPath, final long size, final int blockSize) { createArray(objectPath, size, blockSize, INT_NO_COMPRESSION); } @Override public void createArray(final String objectPath, final int size, final HDF5IntStorageFeatures features) { assert objectPath != null; assert size >= 0; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (features.requiresChunking()) { baseWriter.createDataSet(objectPath, H5T_STD_U32LE, features, new long[] { 0 }, new long[] { size }, 4, registry); } else { baseWriter.createDataSet(objectPath, H5T_STD_U32LE, features, new long[] { size }, null, 4, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void createArray(final String objectPath, final long size, final int blockSize, final HDF5IntStorageFeatures features) { assert objectPath != null; assert size >= 0; assert blockSize >= 0 && (blockSize <= size || size == 0); baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { baseWriter.createDataSet(objectPath, H5T_STD_U32LE, features, new long[] { size }, new long[] { blockSize }, 4, registry); return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void writeArrayBlock(final String objectPath, final int[] data, final long blockNumber) { writeArrayBlockWithOffset(objectPath, data, data.length, data.length * blockNumber); } @Override public void writeArrayBlockWithOffset(final String objectPath, final int[] data, final int dataSize, final long offset) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] blockDimensions = new long[] { dataSize }; final long[] slabStartOrNull = new long[] { offset }; final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, new long[] { offset + dataSize }, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, slabStartOrNull, blockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(blockDimensions, registry); H5Dwrite(dataSetId, H5T_NATIVE_UINT32, memorySpaceId, dataSpaceId, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } /** * Writes out a int matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ @Override public void writeMatrix(final String objectPath, final int[][] data) { writeMatrix(objectPath, data, INT_NO_COMPRESSION); } @Override public void writeMatrix(final String objectPath, final int[][] data, final HDF5IntStorageFeatures features) { assert objectPath != null; assert data != null; assert HDF5Utils.areMatrixDimensionsConsistent(data); writeMDArray(objectPath, new MDIntArray(data), features); } @Override public void createMatrix(final String objectPath, final int sizeX, final int sizeY) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; createMDArray(objectPath, new int[] { sizeX, sizeY }); } @Override public void createMatrix(final String objectPath, final int sizeX, final int sizeY, final HDF5IntStorageFeatures features) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; createMDArray(objectPath, new int[] { sizeX, sizeY }, features); } @Override public void createMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; assert blockSizeX >= 0 && (blockSizeX <= sizeX || sizeX == 0); assert blockSizeY >= 0 && (blockSizeY <= sizeY || sizeY == 0); createMDArray(objectPath, new long[] { sizeX, sizeY }, new int[] { blockSizeX, blockSizeY }); } @Override public void createMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY, final HDF5IntStorageFeatures features) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; assert blockSizeX >= 0 && (blockSizeX <= sizeX || sizeX == 0); assert blockSizeY >= 0 && (blockSizeY <= sizeY || sizeY == 0); createMDArray(objectPath, new long[] { sizeX, sizeY }, new int[] { blockSizeX, blockSizeY }, features); } @Override public void writeMatrixBlock(final String objectPath, final int[][] data, final long blockNumberX, final long blockNumberY) { assert objectPath != null; assert data != null; writeMDArrayBlock(objectPath, new MDIntArray(data), new long[] { blockNumberX, blockNumberY }); } @Override public void writeMatrixBlockWithOffset(final String objectPath, final int[][] data, final long offsetX, final long offsetY) { assert objectPath != null; assert data != null; writeMDArrayBlockWithOffset(objectPath, new MDIntArray(data, new int[] { data.length, data[0].length }), new long[] { offsetX, offsetY }); } @Override public void writeMatrixBlockWithOffset(final String objectPath, final int[][] data, final int dataSizeX, final int dataSizeY, final long offsetX, final long offsetY) { assert objectPath != null; assert data != null; writeMDArrayBlockWithOffset(objectPath, new MDIntArray(data, new int[] { dataSizeX, dataSizeY }), new long[] { offsetX, offsetY }); } @Override public void writeMDArray(final String objectPath, final MDIntArray data) { writeMDArray(objectPath, data, INT_NO_COMPRESSION); } @Override public void writeMDArraySlice(String objectPath, MDIntArray data, IndexMap boundIndices) { baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), null, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDIntArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArraySlice(String objectPath, MDIntArray data, long[] boundIndices) { baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), null, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDIntArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArray(final String objectPath, final MDIntArray data, final HDF5IntStorageFeatures features) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, H5T_STD_U32LE, data.longDimensions(), 4, features, registry); H5Dwrite(dataSetId, H5T_NATIVE_UINT32, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createMDArray(final String objectPath, final int[] dimensions) { createMDArray(objectPath, dimensions, INT_NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions) { createMDArray(objectPath, dimensions, blockDimensions, INT_NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final int[] dimensions, final HDF5IntStorageFeatures features) { assert objectPath != null; assert dimensions != null; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (features.requiresChunking()) { final long[] nullDimensions = new long[dimensions.length]; baseWriter.createDataSet(objectPath, H5T_STD_U32LE, features, nullDimensions, MDArray.toLong(dimensions), 4, registry); } else { baseWriter.createDataSet(objectPath, H5T_STD_U32LE, features, MDArray.toLong(dimensions), null, 4, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void createMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions, final HDF5IntStorageFeatures features) { assert objectPath != null; assert dimensions != null; assert blockDimensions != null; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { baseWriter.createDataSet(objectPath, H5T_STD_U32LE, features, dimensions, MDArray.toLong(blockDimensions), 4, registry); return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void writeMDArrayBlock(final String objectPath, final MDIntArray data, final long[] blockNumber) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeMDArrayBlockWithOffset(objectPath, data, offset); } @Override public void writeSlicedMDArrayBlock(final String objectPath, final MDIntArray data, final long[] blockNumber, IndexMap boundIndices) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeSlicedMDArrayBlockWithOffset(objectPath, data, offset, boundIndices); } @Override public void writeSlicedMDArrayBlock(String objectPath, MDIntArray data, long[] blockNumber, long[] boundIndices) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeSlicedMDArrayBlockWithOffset(objectPath, data, offset, boundIndices); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final MDIntArray data, final long[] offset) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] dimensions = data.longDimensions(); assert dimensions.length == offset.length; final long[] dataSetDimensions = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + dimensions[i]; } final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, dimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(dimensions, registry); H5Dwrite(dataSetId, H5T_NATIVE_UINT32, memorySpaceId, dataSpaceId, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeSlicedMDArrayBlockWithOffset(String objectPath, MDIntArray data, long[] offset, IndexMap boundIndices) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), offset, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDIntArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeSlicedMDArrayBlockWithOffset(String objectPath, MDIntArray data, long[] offset, long[] boundIndices) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), offset, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDIntArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final MDIntArray data, final int[] blockDimensions, final long[] offset, final int[] memoryOffset) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] memoryDimensions = data.longDimensions(); assert memoryDimensions.length == offset.length; final long[] longBlockDimensions = MDArray.toLong(blockDimensions); assert longBlockDimensions.length == offset.length; final long[] dataSetDimensions = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + blockDimensions[i]; } final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, longBlockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(memoryDimensions, registry); baseWriter.h5.setHyperslabBlock(memorySpaceId, MDArray.toLong(memoryOffset), longBlockDimensions); H5Dwrite(dataSetId, H5T_NATIVE_UINT32, memorySpaceId, dataSpaceId, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5UnsignedLongReader.java000066400000000000000000001021111256564762100303470ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.MatrixUtils.cardinalityBoundIndices; import static ch.systemsx.cisd.hdf5.MatrixUtils.checkBoundIndices; import static ch.systemsx.cisd.hdf5.MatrixUtils.createFullBlockDimensionsAndOffset; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_ARRAY; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_UINT64; import java.util.Arrays; import java.util.Iterator; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import ncsa.hdf.hdf5lib.exceptions.HDF5SpaceRankMismatch; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDLongArray; import ch.systemsx.cisd.hdf5.HDF5BaseReader.DataSpaceParameters; import ch.systemsx.cisd.hdf5.HDF5DataTypeInformation.DataTypeInfoOptions; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; import ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants; /** * The implementation of {@link IHDF5LongReader}. * * @author Bernd Rinn */ class HDF5UnsignedLongReader implements IHDF5LongReader { private final HDF5BaseReader baseReader; HDF5UnsignedLongReader(HDF5BaseReader baseReader) { assert baseReader != null; this.baseReader = baseReader; } // For Unit tests only. HDF5BaseReader getBaseReader() { return baseReader; } // ///////////////////// // Attributes // ///////////////////// @Override public long getAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public Long call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final long[] data = baseReader.h5.readAttributeAsLongArray(attributeId, H5T_NATIVE_UINT64, 1); return data[0]; } }; return baseReader.runner.call(getAttributeRunnable); } @Override public long[] getArrayAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public long[] call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); return getLongArrayAttribute(objectId, attributeName, registry); } }; return baseReader.runner.call(getAttributeRunnable); } @Override public MDLongArray getMDArrayAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public MDLongArray call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); return getLongMDArrayAttribute(objectId, attributeName, registry); } }; return baseReader.runner.call(getAttributeRunnable); } @Override public long[][] getMatrixAttr(final String objectPath, final String attributeName) throws HDF5JavaException { final MDLongArray array = getMDArrayAttr(objectPath, attributeName); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } // ///////////////////// // Data Sets // ///////////////////// @Override public long read(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public Long call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final long[] data = new long[1]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_UINT64, data); return data[0]; } }; return baseReader.runner.call(readCallable); } @Override public long[] readArray(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public long[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); return readLongArray(dataSetId, registry); } }; return baseReader.runner.call(readCallable); } private long[] readLongArray(int dataSetId, ICleanUpRegistry registry) { try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); final long[] data = new long[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_UINT64, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return data; } catch (HDF5LibraryException ex) { if (ex.getMajorErrorNumber() == HDF5Constants.H5E_DATATYPE && ex.getMinorErrorNumber() == HDF5Constants.H5E_CANTINIT) { // Check whether it is an array data type. final int dataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); if (baseReader.h5.getClassType(dataTypeId) == HDF5Constants.H5T_ARRAY) { return readLongArrayFromArrayType(dataSetId, dataTypeId, registry); } } throw ex; } } private long[] readLongArrayFromArrayType(int dataSetId, final int dataTypeId, ICleanUpRegistry registry) { final int spaceId = baseReader.h5.createScalarDataSpace(); final int[] dimensions = baseReader.h5.getArrayDimensions(dataTypeId); final long[] data = new long[HDF5Utils.getOneDimensionalArraySize(dimensions)]; final int memoryDataTypeId = baseReader.h5.createArrayType(H5T_NATIVE_UINT64, data.length, registry); baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceId, spaceId, data); return data; } @Override public int[] readToMDArrayWithOffset(final String objectPath, final MDLongArray array, final int[] memoryOffset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getBlockSpaceParameters(dataSetId, memoryOffset, array .dimensions(), registry); final int nativeDataTypeId = baseReader.getNativeDataTypeId(dataSetId, H5T_NATIVE_UINT64, registry); baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, array. getAsFlatArray()); return MDArray.toInt(spaceParams.dimensions); } }; return baseReader.runner.call(readCallable); } @Override public int[] readToMDArrayBlockWithOffset(final String objectPath, final MDLongArray array, final int[] blockDimensions, final long[] offset, final int[] memoryOffset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getBlockSpaceParameters(dataSetId, memoryOffset, array .dimensions(), offset, blockDimensions, registry); final int nativeDataTypeId = baseReader.getNativeDataTypeId(dataSetId, H5T_NATIVE_UINT64, registry); baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, array .getAsFlatArray()); return MDArray.toInt(spaceParams.dimensions); } }; return baseReader.runner.call(readCallable); } @Override public long[] readArrayBlock(final String objectPath, final int blockSize, final long blockNumber) { return readArrayBlockWithOffset(objectPath, blockSize, blockNumber * blockSize); } @Override public long[] readArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public long[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockSize, registry); final long[] data = new long[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_UINT64, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return data; } }; return baseReader.runner.call(readCallable); } @Override public long[][] readMatrix(final String objectPath) throws HDF5JavaException { final MDLongArray array = readMDArray(objectPath); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public long[][] readMatrixBlock(final String objectPath, final int blockSizeX, final int blockSizeY, final long blockNumberX, final long blockNumberY) throws HDF5JavaException { final MDLongArray array = readMDArrayBlock(objectPath, new int[] { blockSizeX, blockSizeY }, new long[] { blockNumberX, blockNumberY }); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public long[][] readMatrixBlockWithOffset(final String objectPath, final int blockSizeX, final int blockSizeY, final long offsetX, final long offsetY) throws HDF5JavaException { final MDLongArray array = readMDArrayBlockWithOffset(objectPath, new int[] { blockSizeX, blockSizeY }, new long[] { offsetX, offsetY }); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public MDLongArray readMDArraySlice(String objectPath, IndexMap boundIndices) { baseReader.checkOpen(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; final int cardBoundIndices = cardinalityBoundIndices(boundIndices); checkBoundIndices(objectPath, fullDimensions, cardBoundIndices); final int[] effectiveBlockDimensions = new int[fullBlockDimensions.length - cardBoundIndices]; Arrays.fill(effectiveBlockDimensions, -1); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, null, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDLongArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); if (fullBlockDimensions.length == cardBoundIndices) // no free indices { return new MDLongArray(result.getAsFlatArray(), new int[] { 1 }); } else { return new MDLongArray(result.getAsFlatArray(), effectiveBlockDimensions); } } @Override public MDLongArray readMDArraySlice(String objectPath, long[] boundIndices) { baseReader.checkOpen(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; final int cardBoundIndices = cardinalityBoundIndices(boundIndices); checkBoundIndices(objectPath, fullDimensions, boundIndices); final int[] effectiveBlockDimensions = new int[fullBlockDimensions.length - cardBoundIndices]; Arrays.fill(effectiveBlockDimensions, -1); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, null, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDLongArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); if (fullBlockDimensions.length == cardBoundIndices) // no free indices { return new MDLongArray(result.getAsFlatArray(), new int[] { 1 }); } else { return new MDLongArray(result.getAsFlatArray(), effectiveBlockDimensions); } } @Override public MDLongArray readMDArray(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public MDLongArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); return readLongMDArray(dataSetId, registry); } }; return baseReader.runner.call(readCallable); } MDLongArray readLongMDArray(int dataSetId, ICleanUpRegistry registry) { try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); final long[] data = new long[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_UINT64, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return new MDLongArray(data, spaceParams.dimensions); } catch (HDF5LibraryException ex) { if (ex.getMajorErrorNumber() == HDF5Constants.H5E_DATATYPE && ex.getMinorErrorNumber() == HDF5Constants.H5E_CANTINIT) { // Check whether it is an array data type. final int dataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); if (baseReader.h5.getClassType(dataTypeId) == HDF5Constants.H5T_ARRAY) { return readLongMDArrayFromArrayType(dataSetId, dataTypeId, registry); } } throw ex; } } private MDLongArray readLongMDArrayFromArrayType(int dataSetId, final int dataTypeId, ICleanUpRegistry registry) { final int[] arrayDimensions = baseReader.h5.getArrayDimensions(dataTypeId); final int memoryDataTypeId = baseReader.h5.createArrayType(H5T_NATIVE_UINT64, arrayDimensions, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); if (spaceParams.blockSize == 0) { final int spaceId = baseReader.h5.createScalarDataSpace(); final long[] data = new long[MDArray.getLength(arrayDimensions)]; baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceId, spaceId, data); return new MDLongArray(data, arrayDimensions); } else { final long[] data = new long[MDArray.getLength(arrayDimensions) * spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return new MDLongArray(data, MatrixUtils.concat(MDArray.toInt(spaceParams.dimensions), arrayDimensions)); } } @Override public MDLongArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, IndexMap boundIndices) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readSlicedMDArrayBlockWithOffset(objectPath, blockDimensions, offset, boundIndices); } @Override public MDLongArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, long[] boundIndices) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readSlicedMDArrayBlockWithOffset(objectPath, blockDimensions, offset, boundIndices); } @Override public MDLongArray readMDArrayBlock(final String objectPath, final int[] blockDimensions, final long[] blockNumber) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readMDArrayBlockWithOffset(objectPath, blockDimensions, offset); } @Override public MDLongArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, IndexMap boundIndices) { baseReader.checkOpen(); final int[] effectiveBlockDimensions = blockDimensions.clone(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; checkBoundIndices(objectPath, fullDimensions, blockDimensions, cardinalityBoundIndices(boundIndices)); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, offset, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDLongArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); return new MDLongArray(result.getAsFlatArray(), effectiveBlockDimensions); } @Override public MDLongArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, long[] boundIndices) { baseReader.checkOpen(); final int[] effectiveBlockDimensions = blockDimensions.clone(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; checkBoundIndices(objectPath, fullDimensions, blockDimensions, cardinalityBoundIndices(boundIndices)); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, offset, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDLongArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); return new MDLongArray(result.getAsFlatArray(), effectiveBlockDimensions); } @Override public MDLongArray readMDArrayBlockWithOffset(final String objectPath, final int[] blockDimensions, final long[] offset) { assert objectPath != null; assert blockDimensions != null; assert offset != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public MDLongArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockDimensions, registry); final long[] dataBlock = new long[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_UINT64, spaceParams.memorySpaceId, spaceParams.dataSpaceId, dataBlock); return new MDLongArray(dataBlock, spaceParams.dimensions); } catch (HDF5SpaceRankMismatch ex) { final HDF5DataSetInformation info = baseReader.getDataSetInformation(objectPath, DataTypeInfoOptions.MINIMAL, false); if (ex.getSpaceRankExpected() - ex.getSpaceRankFound() == info .getTypeInformation().getRank()) { return readMDArrayBlockOfArrays(dataSetId, blockDimensions, offset, info, ex.getSpaceRankFound(), registry); } else { throw ex; } } } }; return baseReader.runner.call(readCallable); } private MDLongArray readMDArrayBlockOfArrays(final int dataSetId, final int[] blockDimensions, final long[] offset, final HDF5DataSetInformation info, final int spaceRank, final ICleanUpRegistry registry) { final int[] arrayDimensions = info.getTypeInformation().getDimensions(); int[] effectiveBlockDimensions = blockDimensions; // We do not support block-wise reading of array types, check // that we do not have to and bail out otherwise. for (int i = 0; i < arrayDimensions.length; ++i) { final int j = spaceRank + i; if (effectiveBlockDimensions[j] < 0) { if (effectiveBlockDimensions == blockDimensions) { effectiveBlockDimensions = blockDimensions.clone(); } effectiveBlockDimensions[j] = arrayDimensions[i]; } if (effectiveBlockDimensions[j] != arrayDimensions[i]) { throw new HDF5JavaException( "Block-wise reading of array type data sets is not supported."); } } final int[] spaceBlockDimensions = Arrays.copyOfRange(effectiveBlockDimensions, 0, spaceRank); final long[] spaceOfs = Arrays.copyOfRange(offset, 0, spaceRank); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, spaceOfs, spaceBlockDimensions, registry); final long[] dataBlock = new long[spaceParams.blockSize * info.getTypeInformation().getNumberOfElements()]; final int memoryDataTypeId = baseReader.h5.createArrayType(H5T_NATIVE_UINT64, info.getTypeInformation() .getDimensions(), registry); baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, dataBlock); return new MDLongArray(dataBlock, effectiveBlockDimensions); } @Override public Iterable> getArrayNaturalBlocks(final String dataSetPath) throws HDF5JavaException { baseReader.checkOpen(); final HDF5NaturalBlock1DParameters params = new HDF5NaturalBlock1DParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlock1DParameters.HDF5NaturalBlock1DIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5DataBlock next() { final long offset = index.computeOffsetAndSizeGetOffset(); final long[] block = readArrayBlockWithOffset(dataSetPath, index .getBlockSize(), offset); return new HDF5DataBlock(block, index.getAndIncIndex(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } @Override public Iterable> getMDArrayNaturalBlocks(final String dataSetPath) { baseReader.checkOpen(); final HDF5NaturalBlockMDParameters params = new HDF5NaturalBlockMDParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlockMDParameters.HDF5NaturalBlockMDIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5MDDataBlock next() { final long[] offset = index.computeOffsetAndSizeGetOffsetClone(); final MDLongArray data = readMDArrayBlockWithOffset(dataSetPath, index .getBlockSize(), offset); return new HDF5MDDataBlock(data, index .getIndexClone(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } long[] getLongArrayAttribute(final int objectId, final String attributeName, ICleanUpRegistry registry) { final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, registry); final int memoryTypeId; final int len; if (baseReader.h5.getClassType(attributeTypeId) == H5T_ARRAY) { final int[] arrayDimensions = baseReader.h5.getArrayDimensions(attributeTypeId); if (arrayDimensions.length != 1) { throw new HDF5JavaException( "Array needs to be of rank 1, but is of rank " + arrayDimensions.length); } len = arrayDimensions[0]; memoryTypeId = baseReader.h5.createArrayType(H5T_NATIVE_UINT64, len, registry); } else { final long[] arrayDimensions = baseReader.h5.getDataDimensionsForAttribute(attributeId, registry); memoryTypeId = H5T_NATIVE_UINT64; len = HDF5Utils.getOneDimensionalArraySize(arrayDimensions); } final long[] data = baseReader.h5.readAttributeAsLongArray(attributeId, memoryTypeId, len); return data; } MDLongArray getLongMDArrayAttribute(final int objectId, final String attributeName, ICleanUpRegistry registry) { try { final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, registry); final int memoryTypeId; final int[] arrayDimensions; if (baseReader.h5.getClassType(attributeTypeId) == H5T_ARRAY) { arrayDimensions = baseReader.h5.getArrayDimensions(attributeTypeId); memoryTypeId = baseReader.h5.createArrayType(H5T_NATIVE_UINT64, arrayDimensions, registry); } else { arrayDimensions = MDArray.toInt(baseReader.h5.getDataDimensionsForAttribute( attributeId, registry)); memoryTypeId = H5T_NATIVE_UINT64; } final int len = MDArray.getLength(arrayDimensions); final long[] data = baseReader.h5.readAttributeAsLongArray(attributeId, memoryTypeId, len); return new MDLongArray(data, arrayDimensions); } catch (IllegalArgumentException ex) { throw new HDF5JavaException(ex.getMessage()); } } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5UnsignedLongWriter.java000066400000000000000000000660731256564762100304410ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.HDF5IntStorageFeatures.INT_NO_COMPRESSION; import static ch.systemsx.cisd.hdf5.hdf5lib.H5D.H5Dwrite; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_ALL; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_UINT64; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_U64LE; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDLongArray; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; /** * The implementation of {@link IHDF5LongWriter}. * * @author Bernd Rinn */ class HDF5UnsignedLongWriter extends HDF5UnsignedLongReader implements IHDF5LongWriter { private final HDF5BaseWriter baseWriter; HDF5UnsignedLongWriter(HDF5BaseWriter baseWriter) { super(baseWriter); assert baseWriter != null; this.baseWriter = baseWriter; } // ///////////////////// // Attributes // ///////////////////// @Override public void setAttr(final String objectPath, final String name, final long value) { assert objectPath != null; assert name != null; baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { 1 }, registry); baseWriter.setAttribute(objectPath, name, H5T_STD_U64LE, H5T_NATIVE_UINT64, dataSpaceId, new long[] { value }, registry); } else { baseWriter.setAttribute(objectPath, name, H5T_STD_U64LE, H5T_NATIVE_UINT64, -1, new long[] { value }, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void setArrayAttr(final String objectPath, final String name, final long[] value) { assert objectPath != null; assert name != null; assert value != null; baseWriter.checkOpen(); final ICallableWithCleanUp setAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { value.length }, registry); baseWriter.setAttribute(objectPath, name, H5T_STD_U64LE, H5T_NATIVE_UINT64, dataSpaceId, value, registry); } else { final int memoryTypeId = baseWriter.h5.createArrayType(H5T_NATIVE_UINT64, value.length, registry); final int storageTypeId = baseWriter.h5.createArrayType(H5T_STD_U64LE, value.length, registry); baseWriter.setAttribute(objectPath, name, storageTypeId, memoryTypeId, -1, value, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(setAttributeRunnable); } @Override public void setMDArrayAttr(final String objectPath, final String name, final MDLongArray value) { assert objectPath != null; assert name != null; assert value != null; baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(value.longDimensions(), registry); baseWriter.setAttribute(objectPath, name, H5T_STD_U64LE, H5T_NATIVE_UINT64, dataSpaceId, value.getAsFlatArray(), registry); } else { final int memoryTypeId = baseWriter.h5.createArrayType(H5T_NATIVE_UINT64, value.dimensions(), registry); final int storageTypeId = baseWriter.h5.createArrayType(H5T_STD_U64LE, value.dimensions(), registry); baseWriter.setAttribute(objectPath, name, storageTypeId, memoryTypeId, -1, value.getAsFlatArray(), registry); } return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void setMatrixAttr(final String objectPath, final String name, final long[][] value) { setMDArrayAttr(objectPath, name, new MDLongArray(value)); } // ///////////////////// // Data Sets // ///////////////////// @Override public void write(final String objectPath, final long value) { assert objectPath != null; baseWriter.checkOpen(); baseWriter.writeScalar(objectPath, H5T_STD_U64LE, H5T_NATIVE_UINT64, value); } @Override public void writeArray(final String objectPath, final long[] data) { writeArray(objectPath, data, INT_NO_COMPRESSION); } @Override public void writeArray(final String objectPath, final long[] data, final HDF5IntStorageFeatures features) { assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, H5T_STD_U64LE, new long[] { data.length }, 8, features, registry); H5Dwrite(dataSetId, H5T_NATIVE_UINT64, H5S_ALL, H5S_ALL, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createArray(final String objectPath, final int size) { createArray(objectPath, size, INT_NO_COMPRESSION); } @Override public void createArray(final String objectPath, final long size, final int blockSize) { createArray(objectPath, size, blockSize, INT_NO_COMPRESSION); } @Override public void createArray(final String objectPath, final int size, final HDF5IntStorageFeatures features) { assert objectPath != null; assert size >= 0; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (features.requiresChunking()) { baseWriter.createDataSet(objectPath, H5T_STD_U64LE, features, new long[] { 0 }, new long[] { size }, 8, registry); } else { baseWriter.createDataSet(objectPath, H5T_STD_U64LE, features, new long[] { size }, null, 8, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void createArray(final String objectPath, final long size, final int blockSize, final HDF5IntStorageFeatures features) { assert objectPath != null; assert size >= 0; assert blockSize >= 0 && (blockSize <= size || size == 0); baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { baseWriter.createDataSet(objectPath, H5T_STD_U64LE, features, new long[] { size }, new long[] { blockSize }, 8, registry); return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void writeArrayBlock(final String objectPath, final long[] data, final long blockNumber) { writeArrayBlockWithOffset(objectPath, data, data.length, data.length * blockNumber); } @Override public void writeArrayBlockWithOffset(final String objectPath, final long[] data, final int dataSize, final long offset) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] blockDimensions = new long[] { dataSize }; final long[] slabStartOrNull = new long[] { offset }; final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, new long[] { offset + dataSize }, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, slabStartOrNull, blockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(blockDimensions, registry); H5Dwrite(dataSetId, H5T_NATIVE_UINT64, memorySpaceId, dataSpaceId, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } /** * Writes out a long matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ @Override public void writeMatrix(final String objectPath, final long[][] data) { writeMatrix(objectPath, data, INT_NO_COMPRESSION); } @Override public void writeMatrix(final String objectPath, final long[][] data, final HDF5IntStorageFeatures features) { assert objectPath != null; assert data != null; assert HDF5Utils.areMatrixDimensionsConsistent(data); writeMDArray(objectPath, new MDLongArray(data), features); } @Override public void createMatrix(final String objectPath, final int sizeX, final int sizeY) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; createMDArray(objectPath, new int[] { sizeX, sizeY }); } @Override public void createMatrix(final String objectPath, final int sizeX, final int sizeY, final HDF5IntStorageFeatures features) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; createMDArray(objectPath, new int[] { sizeX, sizeY }, features); } @Override public void createMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; assert blockSizeX >= 0 && (blockSizeX <= sizeX || sizeX == 0); assert blockSizeY >= 0 && (blockSizeY <= sizeY || sizeY == 0); createMDArray(objectPath, new long[] { sizeX, sizeY }, new int[] { blockSizeX, blockSizeY }); } @Override public void createMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY, final HDF5IntStorageFeatures features) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; assert blockSizeX >= 0 && (blockSizeX <= sizeX || sizeX == 0); assert blockSizeY >= 0 && (blockSizeY <= sizeY || sizeY == 0); createMDArray(objectPath, new long[] { sizeX, sizeY }, new int[] { blockSizeX, blockSizeY }, features); } @Override public void writeMatrixBlock(final String objectPath, final long[][] data, final long blockNumberX, final long blockNumberY) { assert objectPath != null; assert data != null; writeMDArrayBlock(objectPath, new MDLongArray(data), new long[] { blockNumberX, blockNumberY }); } @Override public void writeMatrixBlockWithOffset(final String objectPath, final long[][] data, final long offsetX, final long offsetY) { assert objectPath != null; assert data != null; writeMDArrayBlockWithOffset(objectPath, new MDLongArray(data, new int[] { data.length, data[0].length }), new long[] { offsetX, offsetY }); } @Override public void writeMatrixBlockWithOffset(final String objectPath, final long[][] data, final int dataSizeX, final int dataSizeY, final long offsetX, final long offsetY) { assert objectPath != null; assert data != null; writeMDArrayBlockWithOffset(objectPath, new MDLongArray(data, new int[] { dataSizeX, dataSizeY }), new long[] { offsetX, offsetY }); } @Override public void writeMDArray(final String objectPath, final MDLongArray data) { writeMDArray(objectPath, data, INT_NO_COMPRESSION); } @Override public void writeMDArraySlice(String objectPath, MDLongArray data, IndexMap boundIndices) { baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), null, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDLongArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArraySlice(String objectPath, MDLongArray data, long[] boundIndices) { baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), null, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDLongArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArray(final String objectPath, final MDLongArray data, final HDF5IntStorageFeatures features) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, H5T_STD_U64LE, data.longDimensions(), 8, features, registry); H5Dwrite(dataSetId, H5T_NATIVE_UINT64, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createMDArray(final String objectPath, final int[] dimensions) { createMDArray(objectPath, dimensions, INT_NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions) { createMDArray(objectPath, dimensions, blockDimensions, INT_NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final int[] dimensions, final HDF5IntStorageFeatures features) { assert objectPath != null; assert dimensions != null; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (features.requiresChunking()) { final long[] nullDimensions = new long[dimensions.length]; baseWriter.createDataSet(objectPath, H5T_STD_U64LE, features, nullDimensions, MDArray.toLong(dimensions), 8, registry); } else { baseWriter.createDataSet(objectPath, H5T_STD_U64LE, features, MDArray.toLong(dimensions), null, 8, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void createMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions, final HDF5IntStorageFeatures features) { assert objectPath != null; assert dimensions != null; assert blockDimensions != null; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { baseWriter.createDataSet(objectPath, H5T_STD_U64LE, features, dimensions, MDArray.toLong(blockDimensions), 8, registry); return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void writeMDArrayBlock(final String objectPath, final MDLongArray data, final long[] blockNumber) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeMDArrayBlockWithOffset(objectPath, data, offset); } @Override public void writeSlicedMDArrayBlock(final String objectPath, final MDLongArray data, final long[] blockNumber, IndexMap boundIndices) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeSlicedMDArrayBlockWithOffset(objectPath, data, offset, boundIndices); } @Override public void writeSlicedMDArrayBlock(String objectPath, MDLongArray data, long[] blockNumber, long[] boundIndices) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeSlicedMDArrayBlockWithOffset(objectPath, data, offset, boundIndices); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final MDLongArray data, final long[] offset) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] dimensions = data.longDimensions(); assert dimensions.length == offset.length; final long[] dataSetDimensions = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + dimensions[i]; } final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, dimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(dimensions, registry); H5Dwrite(dataSetId, H5T_NATIVE_UINT64, memorySpaceId, dataSpaceId, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeSlicedMDArrayBlockWithOffset(String objectPath, MDLongArray data, long[] offset, IndexMap boundIndices) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), offset, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDLongArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeSlicedMDArrayBlockWithOffset(String objectPath, MDLongArray data, long[] offset, long[] boundIndices) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), offset, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDLongArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final MDLongArray data, final int[] blockDimensions, final long[] offset, final int[] memoryOffset) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] memoryDimensions = data.longDimensions(); assert memoryDimensions.length == offset.length; final long[] longBlockDimensions = MDArray.toLong(blockDimensions); assert longBlockDimensions.length == offset.length; final long[] dataSetDimensions = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + blockDimensions[i]; } final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, longBlockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(memoryDimensions, registry); baseWriter.h5.setHyperslabBlock(memorySpaceId, MDArray.toLong(memoryOffset), longBlockDimensions); H5Dwrite(dataSetId, H5T_NATIVE_UINT64, memorySpaceId, dataSpaceId, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5UnsignedShortReader.java000066400000000000000000001023111256564762100305510ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.MatrixUtils.cardinalityBoundIndices; import static ch.systemsx.cisd.hdf5.MatrixUtils.checkBoundIndices; import static ch.systemsx.cisd.hdf5.MatrixUtils.createFullBlockDimensionsAndOffset; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_ARRAY; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_UINT16; import java.util.Arrays; import java.util.Iterator; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import ncsa.hdf.hdf5lib.exceptions.HDF5SpaceRankMismatch; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDShortArray; import ch.systemsx.cisd.hdf5.HDF5BaseReader.DataSpaceParameters; import ch.systemsx.cisd.hdf5.HDF5DataTypeInformation.DataTypeInfoOptions; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; import ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants; /** * The implementation of {@link IHDF5ShortReader}. * * @author Bernd Rinn */ class HDF5UnsignedShortReader implements IHDF5ShortReader { private final HDF5BaseReader baseReader; HDF5UnsignedShortReader(HDF5BaseReader baseReader) { assert baseReader != null; this.baseReader = baseReader; } // For Unit tests only. HDF5BaseReader getBaseReader() { return baseReader; } // ///////////////////// // Attributes // ///////////////////// @Override public short getAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public Short call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final short[] data = baseReader.h5.readAttributeAsShortArray(attributeId, H5T_NATIVE_UINT16, 1); return data[0]; } }; return baseReader.runner.call(getAttributeRunnable); } @Override public short[] getArrayAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public short[] call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); return getShortArrayAttribute(objectId, attributeName, registry); } }; return baseReader.runner.call(getAttributeRunnable); } @Override public MDShortArray getMDArrayAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public MDShortArray call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); return getShortMDArrayAttribute(objectId, attributeName, registry); } }; return baseReader.runner.call(getAttributeRunnable); } @Override public short[][] getMatrixAttr(final String objectPath, final String attributeName) throws HDF5JavaException { final MDShortArray array = getMDArrayAttr(objectPath, attributeName); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } // ///////////////////// // Data Sets // ///////////////////// @Override public short read(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public Short call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final short[] data = new short[1]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_UINT16, data); return data[0]; } }; return baseReader.runner.call(readCallable); } @Override public short[] readArray(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public short[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); return readShortArray(dataSetId, registry); } }; return baseReader.runner.call(readCallable); } private short[] readShortArray(int dataSetId, ICleanUpRegistry registry) { try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); final short[] data = new short[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_UINT16, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return data; } catch (HDF5LibraryException ex) { if (ex.getMajorErrorNumber() == HDF5Constants.H5E_DATATYPE && ex.getMinorErrorNumber() == HDF5Constants.H5E_CANTINIT) { // Check whether it is an array data type. final int dataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); if (baseReader.h5.getClassType(dataTypeId) == HDF5Constants.H5T_ARRAY) { return readShortArrayFromArrayType(dataSetId, dataTypeId, registry); } } throw ex; } } private short[] readShortArrayFromArrayType(int dataSetId, final int dataTypeId, ICleanUpRegistry registry) { final int spaceId = baseReader.h5.createScalarDataSpace(); final int[] dimensions = baseReader.h5.getArrayDimensions(dataTypeId); final short[] data = new short[HDF5Utils.getOneDimensionalArraySize(dimensions)]; final int memoryDataTypeId = baseReader.h5.createArrayType(H5T_NATIVE_UINT16, data.length, registry); baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceId, spaceId, data); return data; } @Override public int[] readToMDArrayWithOffset(final String objectPath, final MDShortArray array, final int[] memoryOffset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getBlockSpaceParameters(dataSetId, memoryOffset, array .dimensions(), registry); final int nativeDataTypeId = baseReader.getNativeDataTypeId(dataSetId, H5T_NATIVE_UINT16, registry); baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, array. getAsFlatArray()); return MDArray.toInt(spaceParams.dimensions); } }; return baseReader.runner.call(readCallable); } @Override public int[] readToMDArrayBlockWithOffset(final String objectPath, final MDShortArray array, final int[] blockDimensions, final long[] offset, final int[] memoryOffset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getBlockSpaceParameters(dataSetId, memoryOffset, array .dimensions(), offset, blockDimensions, registry); final int nativeDataTypeId = baseReader.getNativeDataTypeId(dataSetId, H5T_NATIVE_UINT16, registry); baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, array .getAsFlatArray()); return MDArray.toInt(spaceParams.dimensions); } }; return baseReader.runner.call(readCallable); } @Override public short[] readArrayBlock(final String objectPath, final int blockSize, final long blockNumber) { return readArrayBlockWithOffset(objectPath, blockSize, blockNumber * blockSize); } @Override public short[] readArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public short[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockSize, registry); final short[] data = new short[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_UINT16, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return data; } }; return baseReader.runner.call(readCallable); } @Override public short[][] readMatrix(final String objectPath) throws HDF5JavaException { final MDShortArray array = readMDArray(objectPath); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public short[][] readMatrixBlock(final String objectPath, final int blockSizeX, final int blockSizeY, final long blockNumberX, final long blockNumberY) throws HDF5JavaException { final MDShortArray array = readMDArrayBlock(objectPath, new int[] { blockSizeX, blockSizeY }, new long[] { blockNumberX, blockNumberY }); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public short[][] readMatrixBlockWithOffset(final String objectPath, final int blockSizeX, final int blockSizeY, final long offsetX, final long offsetY) throws HDF5JavaException { final MDShortArray array = readMDArrayBlockWithOffset(objectPath, new int[] { blockSizeX, blockSizeY }, new long[] { offsetX, offsetY }); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public MDShortArray readMDArraySlice(String objectPath, IndexMap boundIndices) { baseReader.checkOpen(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; final int cardBoundIndices = cardinalityBoundIndices(boundIndices); checkBoundIndices(objectPath, fullDimensions, cardBoundIndices); final int[] effectiveBlockDimensions = new int[fullBlockDimensions.length - cardBoundIndices]; Arrays.fill(effectiveBlockDimensions, -1); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, null, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDShortArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); if (fullBlockDimensions.length == cardBoundIndices) // no free indices { return new MDShortArray(result.getAsFlatArray(), new int[] { 1 }); } else { return new MDShortArray(result.getAsFlatArray(), effectiveBlockDimensions); } } @Override public MDShortArray readMDArraySlice(String objectPath, long[] boundIndices) { baseReader.checkOpen(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; final int cardBoundIndices = cardinalityBoundIndices(boundIndices); checkBoundIndices(objectPath, fullDimensions, boundIndices); final int[] effectiveBlockDimensions = new int[fullBlockDimensions.length - cardBoundIndices]; Arrays.fill(effectiveBlockDimensions, -1); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, null, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDShortArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); if (fullBlockDimensions.length == cardBoundIndices) // no free indices { return new MDShortArray(result.getAsFlatArray(), new int[] { 1 }); } else { return new MDShortArray(result.getAsFlatArray(), effectiveBlockDimensions); } } @Override public MDShortArray readMDArray(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public MDShortArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); return readShortMDArray(dataSetId, registry); } }; return baseReader.runner.call(readCallable); } MDShortArray readShortMDArray(int dataSetId, ICleanUpRegistry registry) { try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); final short[] data = new short[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_UINT16, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return new MDShortArray(data, spaceParams.dimensions); } catch (HDF5LibraryException ex) { if (ex.getMajorErrorNumber() == HDF5Constants.H5E_DATATYPE && ex.getMinorErrorNumber() == HDF5Constants.H5E_CANTINIT) { // Check whether it is an array data type. final int dataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); if (baseReader.h5.getClassType(dataTypeId) == HDF5Constants.H5T_ARRAY) { return readShortMDArrayFromArrayType(dataSetId, dataTypeId, registry); } } throw ex; } } private MDShortArray readShortMDArrayFromArrayType(int dataSetId, final int dataTypeId, ICleanUpRegistry registry) { final int[] arrayDimensions = baseReader.h5.getArrayDimensions(dataTypeId); final int memoryDataTypeId = baseReader.h5.createArrayType(H5T_NATIVE_UINT16, arrayDimensions, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); if (spaceParams.blockSize == 0) { final int spaceId = baseReader.h5.createScalarDataSpace(); final short[] data = new short[MDArray.getLength(arrayDimensions)]; baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceId, spaceId, data); return new MDShortArray(data, arrayDimensions); } else { final short[] data = new short[MDArray.getLength(arrayDimensions) * spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return new MDShortArray(data, MatrixUtils.concat(MDArray.toInt(spaceParams.dimensions), arrayDimensions)); } } @Override public MDShortArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, IndexMap boundIndices) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readSlicedMDArrayBlockWithOffset(objectPath, blockDimensions, offset, boundIndices); } @Override public MDShortArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, long[] boundIndices) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readSlicedMDArrayBlockWithOffset(objectPath, blockDimensions, offset, boundIndices); } @Override public MDShortArray readMDArrayBlock(final String objectPath, final int[] blockDimensions, final long[] blockNumber) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readMDArrayBlockWithOffset(objectPath, blockDimensions, offset); } @Override public MDShortArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, IndexMap boundIndices) { baseReader.checkOpen(); final int[] effectiveBlockDimensions = blockDimensions.clone(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; checkBoundIndices(objectPath, fullDimensions, blockDimensions, cardinalityBoundIndices(boundIndices)); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, offset, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDShortArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); return new MDShortArray(result.getAsFlatArray(), effectiveBlockDimensions); } @Override public MDShortArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, long[] boundIndices) { baseReader.checkOpen(); final int[] effectiveBlockDimensions = blockDimensions.clone(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; checkBoundIndices(objectPath, fullDimensions, blockDimensions, cardinalityBoundIndices(boundIndices)); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, offset, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MDShortArray result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); return new MDShortArray(result.getAsFlatArray(), effectiveBlockDimensions); } @Override public MDShortArray readMDArrayBlockWithOffset(final String objectPath, final int[] blockDimensions, final long[] offset) { assert objectPath != null; assert blockDimensions != null; assert offset != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public MDShortArray call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockDimensions, registry); final short[] dataBlock = new short[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_UINT16, spaceParams.memorySpaceId, spaceParams.dataSpaceId, dataBlock); return new MDShortArray(dataBlock, spaceParams.dimensions); } catch (HDF5SpaceRankMismatch ex) { final HDF5DataSetInformation info = baseReader.getDataSetInformation(objectPath, DataTypeInfoOptions.MINIMAL, false); if (ex.getSpaceRankExpected() - ex.getSpaceRankFound() == info .getTypeInformation().getRank()) { return readMDArrayBlockOfArrays(dataSetId, blockDimensions, offset, info, ex.getSpaceRankFound(), registry); } else { throw ex; } } } }; return baseReader.runner.call(readCallable); } private MDShortArray readMDArrayBlockOfArrays(final int dataSetId, final int[] blockDimensions, final long[] offset, final HDF5DataSetInformation info, final int spaceRank, final ICleanUpRegistry registry) { final int[] arrayDimensions = info.getTypeInformation().getDimensions(); int[] effectiveBlockDimensions = blockDimensions; // We do not support block-wise reading of array types, check // that we do not have to and bail out otherwise. for (int i = 0; i < arrayDimensions.length; ++i) { final int j = spaceRank + i; if (effectiveBlockDimensions[j] < 0) { if (effectiveBlockDimensions == blockDimensions) { effectiveBlockDimensions = blockDimensions.clone(); } effectiveBlockDimensions[j] = arrayDimensions[i]; } if (effectiveBlockDimensions[j] != arrayDimensions[i]) { throw new HDF5JavaException( "Block-wise reading of array type data sets is not supported."); } } final int[] spaceBlockDimensions = Arrays.copyOfRange(effectiveBlockDimensions, 0, spaceRank); final long[] spaceOfs = Arrays.copyOfRange(offset, 0, spaceRank); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, spaceOfs, spaceBlockDimensions, registry); final short[] dataBlock = new short[spaceParams.blockSize * info.getTypeInformation().getNumberOfElements()]; final int memoryDataTypeId = baseReader.h5.createArrayType(H5T_NATIVE_UINT16, info.getTypeInformation() .getDimensions(), registry); baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, dataBlock); return new MDShortArray(dataBlock, effectiveBlockDimensions); } @Override public Iterable> getArrayNaturalBlocks(final String dataSetPath) throws HDF5JavaException { baseReader.checkOpen(); final HDF5NaturalBlock1DParameters params = new HDF5NaturalBlock1DParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlock1DParameters.HDF5NaturalBlock1DIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5DataBlock next() { final long offset = index.computeOffsetAndSizeGetOffset(); final short[] block = readArrayBlockWithOffset(dataSetPath, index .getBlockSize(), offset); return new HDF5DataBlock(block, index.getAndIncIndex(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } @Override public Iterable> getMDArrayNaturalBlocks(final String dataSetPath) { baseReader.checkOpen(); final HDF5NaturalBlockMDParameters params = new HDF5NaturalBlockMDParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlockMDParameters.HDF5NaturalBlockMDIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5MDDataBlock next() { final long[] offset = index.computeOffsetAndSizeGetOffsetClone(); final MDShortArray data = readMDArrayBlockWithOffset(dataSetPath, index .getBlockSize(), offset); return new HDF5MDDataBlock(data, index .getIndexClone(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } short[] getShortArrayAttribute(final int objectId, final String attributeName, ICleanUpRegistry registry) { final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, registry); final int memoryTypeId; final int len; if (baseReader.h5.getClassType(attributeTypeId) == H5T_ARRAY) { final int[] arrayDimensions = baseReader.h5.getArrayDimensions(attributeTypeId); if (arrayDimensions.length != 1) { throw new HDF5JavaException( "Array needs to be of rank 1, but is of rank " + arrayDimensions.length); } len = arrayDimensions[0]; memoryTypeId = baseReader.h5.createArrayType(H5T_NATIVE_UINT16, len, registry); } else { final long[] arrayDimensions = baseReader.h5.getDataDimensionsForAttribute(attributeId, registry); memoryTypeId = H5T_NATIVE_UINT16; len = HDF5Utils.getOneDimensionalArraySize(arrayDimensions); } final short[] data = baseReader.h5.readAttributeAsShortArray(attributeId, memoryTypeId, len); return data; } MDShortArray getShortMDArrayAttribute(final int objectId, final String attributeName, ICleanUpRegistry registry) { try { final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, registry); final int memoryTypeId; final int[] arrayDimensions; if (baseReader.h5.getClassType(attributeTypeId) == H5T_ARRAY) { arrayDimensions = baseReader.h5.getArrayDimensions(attributeTypeId); memoryTypeId = baseReader.h5.createArrayType(H5T_NATIVE_UINT16, arrayDimensions, registry); } else { arrayDimensions = MDArray.toInt(baseReader.h5.getDataDimensionsForAttribute( attributeId, registry)); memoryTypeId = H5T_NATIVE_UINT16; } final int len = MDArray.getLength(arrayDimensions); final short[] data = baseReader.h5.readAttributeAsShortArray(attributeId, memoryTypeId, len); return new MDShortArray(data, arrayDimensions); } catch (IllegalArgumentException ex) { throw new HDF5JavaException(ex.getMessage()); } } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5UnsignedShortWriter.java000066400000000000000000000661461256564762100306420ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.HDF5IntStorageFeatures.INT_NO_COMPRESSION; import static ch.systemsx.cisd.hdf5.hdf5lib.H5D.H5Dwrite; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_ALL; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_UINT16; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_U16LE; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDShortArray; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; /** * The implementation of {@link IHDF5ShortWriter}. * * @author Bernd Rinn */ class HDF5UnsignedShortWriter extends HDF5UnsignedShortReader implements IHDF5ShortWriter { private final HDF5BaseWriter baseWriter; HDF5UnsignedShortWriter(HDF5BaseWriter baseWriter) { super(baseWriter); assert baseWriter != null; this.baseWriter = baseWriter; } // ///////////////////// // Attributes // ///////////////////// @Override public void setAttr(final String objectPath, final String name, final short value) { assert objectPath != null; assert name != null; baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { 1 }, registry); baseWriter.setAttribute(objectPath, name, H5T_STD_U16LE, H5T_NATIVE_UINT16, dataSpaceId, new short[] { value }, registry); } else { baseWriter.setAttribute(objectPath, name, H5T_STD_U16LE, H5T_NATIVE_UINT16, -1, new short[] { value }, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void setArrayAttr(final String objectPath, final String name, final short[] value) { assert objectPath != null; assert name != null; assert value != null; baseWriter.checkOpen(); final ICallableWithCleanUp setAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { value.length }, registry); baseWriter.setAttribute(objectPath, name, H5T_STD_U16LE, H5T_NATIVE_UINT16, dataSpaceId, value, registry); } else { final int memoryTypeId = baseWriter.h5.createArrayType(H5T_NATIVE_UINT16, value.length, registry); final int storageTypeId = baseWriter.h5.createArrayType(H5T_STD_U16LE, value.length, registry); baseWriter.setAttribute(objectPath, name, storageTypeId, memoryTypeId, -1, value, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(setAttributeRunnable); } @Override public void setMDArrayAttr(final String objectPath, final String name, final MDShortArray value) { assert objectPath != null; assert name != null; assert value != null; baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(value.longDimensions(), registry); baseWriter.setAttribute(objectPath, name, H5T_STD_U16LE, H5T_NATIVE_UINT16, dataSpaceId, value.getAsFlatArray(), registry); } else { final int memoryTypeId = baseWriter.h5.createArrayType(H5T_NATIVE_UINT16, value.dimensions(), registry); final int storageTypeId = baseWriter.h5.createArrayType(H5T_STD_U16LE, value.dimensions(), registry); baseWriter.setAttribute(objectPath, name, storageTypeId, memoryTypeId, -1, value.getAsFlatArray(), registry); } return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void setMatrixAttr(final String objectPath, final String name, final short[][] value) { setMDArrayAttr(objectPath, name, new MDShortArray(value)); } // ///////////////////// // Data Sets // ///////////////////// @Override public void write(final String objectPath, final short value) { assert objectPath != null; baseWriter.checkOpen(); baseWriter.writeScalar(objectPath, H5T_STD_U16LE, H5T_NATIVE_UINT16, value); } @Override public void writeArray(final String objectPath, final short[] data) { writeArray(objectPath, data, INT_NO_COMPRESSION); } @Override public void writeArray(final String objectPath, final short[] data, final HDF5IntStorageFeatures features) { assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, H5T_STD_U16LE, new long[] { data.length }, 2, features, registry); H5Dwrite(dataSetId, H5T_NATIVE_UINT16, H5S_ALL, H5S_ALL, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createArray(final String objectPath, final int size) { createArray(objectPath, size, INT_NO_COMPRESSION); } @Override public void createArray(final String objectPath, final long size, final int blockSize) { createArray(objectPath, size, blockSize, INT_NO_COMPRESSION); } @Override public void createArray(final String objectPath, final int size, final HDF5IntStorageFeatures features) { assert objectPath != null; assert size >= 0; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (features.requiresChunking()) { baseWriter.createDataSet(objectPath, H5T_STD_U16LE, features, new long[] { 0 }, new long[] { size }, 2, registry); } else { baseWriter.createDataSet(objectPath, H5T_STD_U16LE, features, new long[] { size }, null, 2, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void createArray(final String objectPath, final long size, final int blockSize, final HDF5IntStorageFeatures features) { assert objectPath != null; assert size >= 0; assert blockSize >= 0 && (blockSize <= size || size == 0); baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { baseWriter.createDataSet(objectPath, H5T_STD_U16LE, features, new long[] { size }, new long[] { blockSize }, 2, registry); return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void writeArrayBlock(final String objectPath, final short[] data, final long blockNumber) { writeArrayBlockWithOffset(objectPath, data, data.length, data.length * blockNumber); } @Override public void writeArrayBlockWithOffset(final String objectPath, final short[] data, final int dataSize, final long offset) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] blockDimensions = new long[] { dataSize }; final long[] slabStartOrNull = new long[] { offset }; final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, new long[] { offset + dataSize }, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, slabStartOrNull, blockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(blockDimensions, registry); H5Dwrite(dataSetId, H5T_NATIVE_UINT16, memorySpaceId, dataSpaceId, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } /** * Writes out a short matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ @Override public void writeMatrix(final String objectPath, final short[][] data) { writeMatrix(objectPath, data, INT_NO_COMPRESSION); } @Override public void writeMatrix(final String objectPath, final short[][] data, final HDF5IntStorageFeatures features) { assert objectPath != null; assert data != null; assert HDF5Utils.areMatrixDimensionsConsistent(data); writeMDArray(objectPath, new MDShortArray(data), features); } @Override public void createMatrix(final String objectPath, final int sizeX, final int sizeY) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; createMDArray(objectPath, new int[] { sizeX, sizeY }); } @Override public void createMatrix(final String objectPath, final int sizeX, final int sizeY, final HDF5IntStorageFeatures features) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; createMDArray(objectPath, new int[] { sizeX, sizeY }, features); } @Override public void createMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; assert blockSizeX >= 0 && (blockSizeX <= sizeX || sizeX == 0); assert blockSizeY >= 0 && (blockSizeY <= sizeY || sizeY == 0); createMDArray(objectPath, new long[] { sizeX, sizeY }, new int[] { blockSizeX, blockSizeY }); } @Override public void createMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY, final HDF5IntStorageFeatures features) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; assert blockSizeX >= 0 && (blockSizeX <= sizeX || sizeX == 0); assert blockSizeY >= 0 && (blockSizeY <= sizeY || sizeY == 0); createMDArray(objectPath, new long[] { sizeX, sizeY }, new int[] { blockSizeX, blockSizeY }, features); } @Override public void writeMatrixBlock(final String objectPath, final short[][] data, final long blockNumberX, final long blockNumberY) { assert objectPath != null; assert data != null; writeMDArrayBlock(objectPath, new MDShortArray(data), new long[] { blockNumberX, blockNumberY }); } @Override public void writeMatrixBlockWithOffset(final String objectPath, final short[][] data, final long offsetX, final long offsetY) { assert objectPath != null; assert data != null; writeMDArrayBlockWithOffset(objectPath, new MDShortArray(data, new int[] { data.length, data[0].length }), new long[] { offsetX, offsetY }); } @Override public void writeMatrixBlockWithOffset(final String objectPath, final short[][] data, final int dataSizeX, final int dataSizeY, final long offsetX, final long offsetY) { assert objectPath != null; assert data != null; writeMDArrayBlockWithOffset(objectPath, new MDShortArray(data, new int[] { dataSizeX, dataSizeY }), new long[] { offsetX, offsetY }); } @Override public void writeMDArray(final String objectPath, final MDShortArray data) { writeMDArray(objectPath, data, INT_NO_COMPRESSION); } @Override public void writeMDArraySlice(String objectPath, MDShortArray data, IndexMap boundIndices) { baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), null, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDShortArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArraySlice(String objectPath, MDShortArray data, long[] boundIndices) { baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), null, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDShortArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArray(final String objectPath, final MDShortArray data, final HDF5IntStorageFeatures features) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, H5T_STD_U16LE, data.longDimensions(), 2, features, registry); H5Dwrite(dataSetId, H5T_NATIVE_UINT16, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createMDArray(final String objectPath, final int[] dimensions) { createMDArray(objectPath, dimensions, INT_NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions) { createMDArray(objectPath, dimensions, blockDimensions, INT_NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final int[] dimensions, final HDF5IntStorageFeatures features) { assert objectPath != null; assert dimensions != null; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (features.requiresChunking()) { final long[] nullDimensions = new long[dimensions.length]; baseWriter.createDataSet(objectPath, H5T_STD_U16LE, features, nullDimensions, MDArray.toLong(dimensions), 2, registry); } else { baseWriter.createDataSet(objectPath, H5T_STD_U16LE, features, MDArray.toLong(dimensions), null, 2, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void createMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions, final HDF5IntStorageFeatures features) { assert objectPath != null; assert dimensions != null; assert blockDimensions != null; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { baseWriter.createDataSet(objectPath, H5T_STD_U16LE, features, dimensions, MDArray.toLong(blockDimensions), 2, registry); return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void writeMDArrayBlock(final String objectPath, final MDShortArray data, final long[] blockNumber) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeMDArrayBlockWithOffset(objectPath, data, offset); } @Override public void writeSlicedMDArrayBlock(final String objectPath, final MDShortArray data, final long[] blockNumber, IndexMap boundIndices) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeSlicedMDArrayBlockWithOffset(objectPath, data, offset, boundIndices); } @Override public void writeSlicedMDArrayBlock(String objectPath, MDShortArray data, long[] blockNumber, long[] boundIndices) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeSlicedMDArrayBlockWithOffset(objectPath, data, offset, boundIndices); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final MDShortArray data, final long[] offset) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] dimensions = data.longDimensions(); assert dimensions.length == offset.length; final long[] dataSetDimensions = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + dimensions[i]; } final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, dimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(dimensions, registry); H5Dwrite(dataSetId, H5T_NATIVE_UINT16, memorySpaceId, dataSpaceId, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeSlicedMDArrayBlockWithOffset(String objectPath, MDShortArray data, long[] offset, IndexMap boundIndices) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), offset, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDShortArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeSlicedMDArrayBlockWithOffset(String objectPath, MDShortArray data, long[] offset, long[] boundIndices) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), offset, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MDShortArray(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final MDShortArray data, final int[] blockDimensions, final long[] offset, final int[] memoryOffset) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] memoryDimensions = data.longDimensions(); assert memoryDimensions.length == offset.length; final long[] longBlockDimensions = MDArray.toLong(blockDimensions); assert longBlockDimensions.length == offset.length; final long[] dataSetDimensions = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + blockDimensions[i]; } final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, longBlockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(memoryDimensions, registry); baseWriter.h5.setHyperslabBlock(memorySpaceId, MDArray.toLong(memoryOffset), longBlockDimensions); H5Dwrite(dataSetId, H5T_NATIVE_UINT16, memorySpaceId, dataSpaceId, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5Utils.java000066400000000000000000000437401256564762100257440ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.lang.reflect.Array; import java.util.Iterator; import java.util.List; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.rinn.restrictions.Private; /** * Some utility methods used by {@link HDF5Reader} and {@link HDF5Writer}. * * @author Bernd Rinn */ final class HDF5Utils { /** * The name for an explicitly saved string length attribute. */ static final String STRING_LENGTH_ATTRIBUTE_NAME = "STRING_LENGTH"; /** * The name for a type variant attribute. */ static final String TYPE_VARIANT_ATTRIBUTE_NAME = "TYPE_VARIANT"; /** The minimal size of a chunk. */ @Private static final int MIN_CHUNK_SIZE = 1; /** The minimal size of a data set in order to allow for chunking. */ private static final long MIN_TOTAL_SIZE_FOR_CHUNKING = 128L; /** The dimensions vector for a scalar data type. */ static final long[] SCALAR_DIMENSIONS = new long[] { 1 }; /** The prefix for opqaue data types. */ static final String OPAQUE_PREFIX = "Opaque_"; /** The prefix for enum data types. */ static final String ENUM_PREFIX = "Enum_"; /** The prefix for compound data types. */ static final String COMPOUND_PREFIX = "Compound_"; /** * The suffix for housekeeping files and groups. Setting this attribute overrides the default, * which is: __NAME__. */ static final String HOUSEKEEPING_NAME_SUFFIX_ATTRIBUTE_NAME = "__HOUSEKEEPING_SUFFIX__"; /** * The length of the suffix for housekeeping files and groups. */ static final String HOUSEKEEPING_NAME_SUFFIX_STRINGLENGTH_ATTRIBUTE_NAME = "__" + STRING_LENGTH_ATTRIBUTE_NAME + "__" + HOUSEKEEPING_NAME_SUFFIX_ATTRIBUTE_NAME + "__"; /** * The legacy attribute to signal that a data set is empty (for backward compatibility with * 8.10). */ static final String DATASET_IS_EMPTY_LEGACY_ATTRIBUTE = "__EMPTY__"; /** Returns the boolean data type. */ static String getBooleanDataTypePath(String houseKeepingNameSuffix) { return getDataTypeGroup(houseKeepingNameSuffix) + "/" + ENUM_PREFIX + "Boolean"; } /** Returns the data type specifying a type variant. */ static String getTypeVariantDataTypePath(String houseKeepingNameSuffix) { return getDataTypeGroup(houseKeepingNameSuffix) + "/" + ENUM_PREFIX + "TypeVariant"; } /** Returns the variable-length string data type. */ static String getVariableLengthStringDataTypePath(String houseKeepingNameSuffix) { return getDataTypeGroup(houseKeepingNameSuffix) + "/String_VariableLength"; } /** * Returns the attribute name to signal that this compound type has members with variant of the * member data type. */ static String getTypeVariantMembersAttributeName(String houseKeepingNameSuffix) { return "".equals(houseKeepingNameSuffix) ? "__TYPE_VARIANT_MEMBERS__" : "TYPE_VARIANT_MEMBERS" + houseKeepingNameSuffix; } /** Returns the attribute to store the name of the enum data type. */ static String getEnumTypeNameAttributeName(String houseKeepingNameSuffix) { return "".equals(houseKeepingNameSuffix) ? "__ENUM_TYPE_NAME__" : "ENUM_TYPE_NAME" + houseKeepingNameSuffix; } /** Returns the group to store all named derived data types in. */ static String getDataTypeGroup(String houseKeepingNameSuffix) { return "".equals(houseKeepingNameSuffix) ? "/__DATA_TYPES__" : "/DATA_TYPES" + houseKeepingNameSuffix; } /** * All integer types in Java. */ static Class[] allIntegerTypes = new Class[] { byte.class, Byte.class, short.class, Short.class, int.class, Integer.class, long.class, Long.class }; /** * All float types in Java. */ static Class[] allFloatTypes = new Class[] { float.class, Float.class, double.class, Double.class }; /** * All types in Java that can store time durations. */ static Class[] allTimeDurationTypes = new Class[] { byte.class, Byte.class, short.class, Short.class, int.class, Integer.class, long.class, Long.class, float.class, Float.class, double.class, Double.class, HDF5TimeDuration.class }; /** * Returns the primitive type for wrapper classes of primitive types, and the clazz * itself, otherwise. */ static Class unwrapClass(Class clazz) { if (clazz == Byte.class) { return byte.class; } else if (clazz == Short.class) { return short.class; } else if (clazz == Integer.class) { return int.class; } else if (clazz == Long.class) { return long.class; } else if (clazz == Float.class) { return float.class; } else if (clazz == Double.class) { return double.class; } else if (clazz == Boolean.class) { return boolean.class; } else { return clazz; } } static String getSuperGroup(String path) { assert path != null; final int lastIndexSlash = path.lastIndexOf('/'); if (lastIndexSlash <= 0) { return "/"; } else { return path.substring(0, lastIndexSlash); } } static boolean isEmpty(long[] dimensions) { for (long d : dimensions) { if (d == 0) { return true; } } return false; } static boolean isNonPositive(long[] dimensions) { for (long d : dimensions) { if (d <= 0) { return true; } } return false; } /** * Returns the dimensions for a scalar, or null, if this data set is too small for * chunking. */ static long[] tryGetChunkSizeForString(int len, boolean tryChunkedDS) { if (tryChunkedDS) { return (len < MIN_TOTAL_SIZE_FOR_CHUNKING) ? null : SCALAR_DIMENSIONS; } else { return null; } } /** * Returns a chunk size suitable for a data set with dimension, or null, * if this data set can't be reasonably chunk-ed. */ static long[] tryGetChunkSize(final long[] dimensions, int elementLength, boolean tryChunkedDS, boolean enforceChunkedDS) { assert dimensions != null; if (enforceChunkedDS == false && tryChunkedDS == false) { return null; } final long[] chunkSize = new long[dimensions.length]; long totalSize = elementLength; for (int i = 0; i < dimensions.length; ++i) { totalSize *= dimensions[i]; chunkSize[i] = Math.max(MIN_CHUNK_SIZE, dimensions[i]); } if (enforceChunkedDS == false && totalSize < MIN_TOTAL_SIZE_FOR_CHUNKING) { return null; } return chunkSize; } /** * Returns a path for a data type with name and (optional) appendices. *

* Special case: If the appendices array contains exactly one element and if * this element starts with '/', this element itself will be considered the (complete) data type * path. */ static String createDataTypePath(String name, String houseKeepingSuffix, String... appendices) { if (appendices.length == 1 && appendices[0].startsWith("/")) { return appendices[0]; } final StringBuilder builder = new StringBuilder(); builder.append(getDataTypeGroup(houseKeepingSuffix)); builder.append('/'); builder.append(name); for (String app : appendices) { builder.append(app); } return builder.toString(); } /** * Returns the name for a committed data type with pathOrNull. If * pathOrNull == null, the method will return UNKNOWN. */ static String getDataTypeNameFromPath(String pathOrNull, String houseKeepingNameSuffix, HDF5DataClass dataClass) { return (pathOrNull == null) ? "UNKNOWN" : tryGetDataTypeNameFromPath(pathOrNull, houseKeepingNameSuffix, dataClass); } /** * Returns the name for a committed data type with pathOrNull. If * pathOrNull == null, the method will return null. */ static String tryGetDataTypeNameFromPath(String pathOrNull, String houseKeepingNameSuffix, HDF5DataClass dataClass) { if (pathOrNull == null) { return null; } else { final String prefix = getPrefixForDataClass(dataClass); final String pathPrefix = createDataTypePath(prefix, houseKeepingNameSuffix); if (pathOrNull.startsWith(pathPrefix)) { return pathOrNull.substring(pathPrefix.length()); } else { final int lastPathSepIdx = pathOrNull.lastIndexOf('/'); if (lastPathSepIdx >= 0) { return pathOrNull.substring(lastPathSepIdx + 1); } else { return pathOrNull; } } } } /** * Returns a prefix for a given data class, or "", if this data class does not have * a prefix. */ static String getPrefixForDataClass(HDF5DataClass dataClass) { switch (dataClass) { case COMPOUND: return COMPOUND_PREFIX; case ENUM: return ENUM_PREFIX; case OPAQUE: return OPAQUE_PREFIX; default: return ""; } } /** * Returns the length of a one-dimension array defined by dimensions. * * @throws HDF5JavaException If dimensions do not define a one-dimensional array. */ static int getOneDimensionalArraySize(final int[] dimensions) { assert dimensions != null; if (dimensions.length == 0) // Scalar data space needs to be treated differently { return 1; } if (dimensions.length != 1) { throw new HDF5JavaException("Data Set is expected to be of rank 1 (rank=" + dimensions.length + ")"); } return dimensions[0]; } /** * Returns the length of a one-dimension array defined by dimensions. * * @throws HDF5JavaException If dimensions do not define a one-dimensional array or * if dimensions[0] overflows the int type. */ static int getOneDimensionalArraySize(final long[] dimensions) { assert dimensions != null; if (dimensions.length == 0) // Scalar data space needs to be treated differently { return 1; } if (dimensions.length != 1) { throw new HDF5JavaException("Data Set is expected to be of rank 1 (rank=" + dimensions.length + ")"); } final int length = (int) dimensions[0]; if (length != dimensions[0]) { throw new HDF5JavaException("Length is too large (" + dimensions[0] + ")"); } return length; } /** Returns the attribute to signal that this is a variant of the data type. */ static String createObjectTypeVariantAttributeName(String houseKeepingNameSuffix) { return "".equals(houseKeepingNameSuffix) ? "__" + TYPE_VARIANT_ATTRIBUTE_NAME + "__" : TYPE_VARIANT_ATTRIBUTE_NAME + houseKeepingNameSuffix; } /** * Returns the type variant attribute for the given attributeName. */ static String createAttributeTypeVariantAttributeName(String attributeName, String suffix) { final boolean noSuffix = "".equals(suffix); return (noSuffix ? "__" : "") + TYPE_VARIANT_ATTRIBUTE_NAME + "__" + attributeName + (noSuffix ? "__" : suffix); } /** * Returns true, if name denotes an internal name used by the library * for house-keeping. */ private static boolean isInternalName(final String name) { return name.startsWith("__") && name.endsWith("__"); } /** * Returns true, if name denotes an internal name used by the library * for house-keeping, given the houseKeepingNameSuffix. */ static boolean isInternalName(String name, String houseKeepingNameSuffix) { return "".equals(houseKeepingNameSuffix) ? isInternalName(name) : name .endsWith(houseKeepingNameSuffix); } /** * Returns true if the given name is an internal name. */ static boolean isInternalName(final String name, final String houseKeepingNameSuffix, final boolean filterRootAttributes) { if (filterRootAttributes) { return isInternalName(name, houseKeepingNameSuffix) || HOUSEKEEPING_NAME_SUFFIX_ATTRIBUTE_NAME.equals(name) || HOUSEKEEPING_NAME_SUFFIX_STRINGLENGTH_ATTRIBUTE_NAME.equals(name); } else { return isInternalName(name, houseKeepingNameSuffix); } } /** * Creates an internal name from the given name, using the * houseKeepingNameSuffix. */ static String toHouseKeepingName(String name, String houseKeepingNameSuffix) { return "".equals(houseKeepingNameSuffix) ? "__" + name + "__" : name + houseKeepingNameSuffix; } /** * Creates an internal name from the given objectPath, using the * houseKeepingNameSuffix. */ static String toHouseKeepingPath(String objectPath, String houseKeepingNameSuffix) { final int lastPathSeparator = objectPath.lastIndexOf('/') + 1; return lastPathSeparator > 0 ? objectPath.substring(0, lastPathSeparator) + toHouseKeepingName(objectPath.substring(lastPathSeparator), houseKeepingNameSuffix) : toHouseKeepingName(objectPath, houseKeepingNameSuffix); } /** * Removes all internal names from the list names. * * @return The list names. */ static List removeInternalNames(final List names, final String houseKeepingNameSuffix, final boolean filterRootAttributes) { for (Iterator iterator = names.iterator(); iterator.hasNext(); /**/) { final String memberName = iterator.next(); if (isInternalName(memberName, houseKeepingNameSuffix, filterRootAttributes)) { iterator.remove(); } } return names; } @SuppressWarnings("unchecked") static T[] createArray(final Class componentClass, final int vectorLength) { final T[] value = (T[]) java.lang.reflect.Array.newInstance(componentClass, vectorLength); return value; } /** * If all elements of dimensions are 1, the data set might be empty, then check * {@link #DATASET_IS_EMPTY_LEGACY_ATTRIBUTE} (for backward compatibility with 8.10) */ static boolean mightBeEmptyInStorage(final long[] dimensions) { for (long d : dimensions) { if (d != 1L) { return false; } } return true; } /** * Checks the consistency of the dimension of a given array. *

* As Java doesn't have a matrix data type, but only arrays of arrays, there is no way to ensure * in the language itself whether all rows have the same length. * * @return true if the given matrix is consisten and false otherwise. */ static boolean areMatrixDimensionsConsistent(Object a) { if (a.getClass().isArray() == false) { return false; } final int length = Array.getLength(a); if (length == 0) { return true; } final Object element = Array.get(a, 0); if (element.getClass().isArray()) { final int elementLength = Array.getLength(element); for (int i = 0; i < length; ++i) { final Object o = Array.get(a, i); if (areMatrixDimensionsConsistent(o) == false) { return false; } if (elementLength != Array.getLength(o)) { return false; } } } return true; } /** * Checks if subDimensions are in bounds of dimensions. */ static boolean isInBounds(long[] dimensions, long[] subDimensions) { assert dimensions.length == subDimensions.length; for (int i = 0; i < dimensions.length; ++i) { if (subDimensions[i] > dimensions[i]) { return false; } } return true; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5ValueObjectByteifyer.java000066400000000000000000000270571256564762100307350ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.lang.reflect.Constructor; import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; import java.util.List; import java.util.Map; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; /** * A class that byteifies Java value objects. The fields have to be specified by name. This class * can handle all primitive types and Strings. * * @author Bernd Rinn */ class HDF5ValueObjectByteifyer { private final HDF5MemberByteifyer[] byteifyers; private final int recordSizeInMemory; private final int recordSizeOnDisk; private final int[] vlMemberIndices; private Class cachedRecordClass; private Constructor cachedDefaultConstructor; @SuppressWarnings("unchecked") private static T newMap(int size) { return (T) new HDF5CompoundDataMap(size); } @SuppressWarnings("unchecked") private static T newList(int size) { return (T) new HDF5CompoundDataList(Collections.nCopies(size, null)); } @SuppressWarnings("unchecked") private static T newArray(int size) { return (T) new Object[size]; } /** A role that provides direct access to the HDF5 file to this byteifyer. */ interface IFileAccessProvider { public int getBooleanDataTypeId(); public int getStringDataTypeId(int maxLength); public int getVariableLengthStringDataTypeId(); public int getArrayTypeId(int baseTypeId, int length); public int getArrayTypeId(int baseTypeId, int[] dimensions); public HDF5EnumerationType getEnumType(String[] options); public CharacterEncoding getCharacterEncoding(int dataTypeId); public byte[] createObjectReference(String referencedObjectPath); } HDF5ValueObjectByteifyer(Class clazz, IFileAccessProvider fileInfoProvider, CompoundTypeInformation compoundTypeInfoOrNull, HDF5CompoundMemberMapping... members) { byteifyers = HDF5CompoundByteifyerFactory.createMemberByteifyers(clazz, fileInfoProvider, compoundTypeInfoOrNull, members); int numberOfVLMembers = 0; if (compoundTypeInfoOrNull != null) { recordSizeOnDisk = compoundTypeInfoOrNull.recordSizeOnDisk; recordSizeInMemory = compoundTypeInfoOrNull.recordSizeInMemory; numberOfVLMembers = compoundTypeInfoOrNull.getNumberOfVLMembers(); } else if (byteifyers.length > 0) { recordSizeOnDisk = byteifyers[byteifyers.length - 1].getTotalSizeOnDisk(); recordSizeInMemory = PaddingUtils.padOffset( byteifyers[byteifyers.length - 1].getTotalSizeInMemory(), PaddingUtils.findMaxElementSize(byteifyers)); for (HDF5MemberByteifyer byteifyer : byteifyers) { if (byteifyer.isVariableLengthType()) { ++numberOfVLMembers; } } } else { recordSizeOnDisk = 0; recordSizeInMemory = 0; } vlMemberIndices = new int[numberOfVLMembers]; int idx = 0; for (HDF5MemberByteifyer byteifyer : byteifyers) { if (byteifyer.isVariableLengthType()) { vlMemberIndices[idx++] = byteifyer.getOffsetInMemory(); } } } public int insertMemberTypes(int dataTypeId) { for (HDF5MemberByteifyer byteifyer : byteifyers) { byteifyer.insertType(dataTypeId); } return dataTypeId; } public int insertNativeMemberTypes(int dataTypeId, HDF5 h5, ICleanUpRegistry registry) { for (HDF5MemberByteifyer byteifyer : byteifyers) { byteifyer.insertNativeType(dataTypeId, h5, registry); } return dataTypeId; } /** * @throw {@link HDF5JavaException} if one of the elements in arr exceeding its * pre-defined size. */ public byte[] byteify(int compoundDataTypeId, T[] arr) throws HDF5JavaException { final byte[] barray = new byte[arr.length * recordSizeInMemory]; int offset = 0; int counter = 0; for (Object obj : arr) { for (HDF5MemberByteifyer byteifyer : byteifyers) { try { final byte[] b = byteifyer.byteify(compoundDataTypeId, obj); if (b.length > byteifyer.getSize() && byteifyer.mayBeCut() == false) { throw new HDF5JavaException("Compound " + byteifyer.describe() + " of array element " + counter + " must not exceed " + byteifyer.getSize() + " bytes, but is of size " + b.length + " bytes."); } System.arraycopy(b, 0, barray, offset + byteifyer.getOffsetInMemory(), Math.min(b.length, byteifyer.getSize())); } catch (IllegalAccessException ex) { throw new HDF5JavaException("Error accessing " + byteifyer.describe()); } } offset += recordSizeInMemory; ++counter; } return barray; } /** * @throw {@link HDF5JavaException} if obj exceeding its pre-defined size. */ public byte[] byteify(int compoundDataTypeId, T obj) throws HDF5JavaException { final byte[] barray = new byte[recordSizeInMemory]; for (HDF5MemberByteifyer byteifyer : byteifyers) { try { final byte[] b = byteifyer.byteify(compoundDataTypeId, obj); if (b.length > byteifyer.getSize() && byteifyer.mayBeCut() == false) { throw new HDF5JavaException("Compound " + byteifyer.describe() + " must not exceed " + byteifyer.getSize() + " bytes, but is of size " + b.length + " bytes."); } System.arraycopy(b, 0, barray, byteifyer.getOffsetInMemory(), Math.min(b.length, byteifyer.getSize())); } catch (IllegalAccessException ex) { throw new HDF5JavaException("Error accessing " + byteifyer.describe()); } } return barray; } public T[] arrayify(int compoundDataTypeId, byte[] byteArr, Class recordClass) { final int length = byteArr.length / recordSizeInMemory; if (length * recordSizeInMemory != byteArr.length) { throw new HDF5JavaException("Illegal byte array for compound type (length " + byteArr.length + " is not a multiple of record size " + recordSizeInMemory + ")"); } final T[] result = HDF5Utils.createArray(recordClass, length); int offset = 0; for (int i = 0; i < length; ++i) { result[i] = primArrayifyScalar(compoundDataTypeId, byteArr, recordClass, offset); offset += recordSizeInMemory; } return result; } public T arrayifyScalar(int compoundDataTypeId, byte[] byteArr, Class recordClass) { if (byteArr.length < recordSizeInMemory) { throw new HDF5JavaException("Illegal byte array for scalar compound type (length " + byteArr.length + " is smaller than record size " + recordSizeInMemory + ")"); } return primArrayifyScalar(compoundDataTypeId, byteArr, recordClass, 0); } private T primArrayifyScalar(int compoundDataTypeId, byte[] byteArr, Class recordClass, int offset) { T result = newInstance(recordClass); for (HDF5MemberByteifyer byteifyer : byteifyers) { try { byteifyer.setFromByteArray(compoundDataTypeId, result, byteArr, offset); } catch (IllegalAccessException ex) { throw new HDF5JavaException("Error accessing " + byteifyer.describe()); } } return result; } @SuppressWarnings("unchecked") private T newInstance(Class recordClass) throws HDF5JavaException { if (Map.class.isAssignableFrom(recordClass)) { return newMap(byteifyers.length); } if (List.class.isAssignableFrom(recordClass)) { return newList(byteifyers.length); } if (recordClass == Object[].class) { return newArray(byteifyers.length); } try { if (recordClass != cachedRecordClass) { cachedRecordClass = recordClass; cachedDefaultConstructor = ReflectionUtils.getDefaultConstructor(recordClass); } return (T) cachedDefaultConstructor.newInstance(); } catch (Exception ex) { throw new HDF5JavaException("Creation of new object of class " + recordClass.getCanonicalName() + " by default constructor failed: " + ex.toString()); } } public int getRecordSizeOnDisk() { return recordSizeOnDisk; } public int getRecordSizeInMemory() { return recordSizeInMemory; } public HDF5MemberByteifyer[] getByteifyers() { return byteifyers; } /** * Returns true if the value object byteifyer has any members that cannot be mapped * to the in-memory representation. */ public boolean hasUnmappedMembers() { for (HDF5MemberByteifyer memberByteifyer : byteifyers) { if (memberByteifyer.isDummy()) { return true; } } return false; } /** * Returns a list with the names of all members that cannot be mapped to the in-memory * representation. */ public String[] getUnmappedMembers() { if (hasUnmappedMembers()) { final List unmappedMembers = new ArrayList(); for (HDF5MemberByteifyer memberByteifyer : byteifyers) { if (memberByteifyer.isDummy()) { unmappedMembers.add(memberByteifyer.getMemberName()); } } return unmappedMembers.toArray(new String[unmappedMembers.size()]); } else { return new String[0]; } } boolean hasVLMembers() { return vlMemberIndices.length > 0; } int[] getVLMemberIndices() { return vlMemberIndices; } // // Object // @Override public String toString() { return "HDF5ValueObjectByteifyer [byteifyers=" + Arrays.toString(byteifyers) + "]"; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5Writer.java000066400000000000000000002665171256564762100261310ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.io.Flushable; import java.util.BitSet; import java.util.Date; import java.util.List; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ncsa.hdf.hdf5lib.exceptions.HDF5SymbolTableException; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDByteArray; import ch.systemsx.cisd.base.mdarray.MDDoubleArray; import ch.systemsx.cisd.base.mdarray.MDFloatArray; import ch.systemsx.cisd.base.mdarray.MDIntArray; import ch.systemsx.cisd.base.mdarray.MDLongArray; import ch.systemsx.cisd.base.mdarray.MDShortArray; import ch.systemsx.cisd.hdf5.HDF5DataTypeInformation.DataTypeInfoOptions; import ch.systemsx.cisd.hdf5.IHDF5CompoundInformationRetriever.IByteArrayInspector; import ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator.FileFormat; /** * A class for writing HDF5 files (HDF5 1.6.x or HDF5 1.8.x). *

* The class focuses on ease of use instead of completeness. As a consequence not all valid HDF5 * files can be generated using this class, but only a subset. *

* Usage: * * 

 * float[] f = new float[100];
 * ...
 * HDF5Writer writer = new HDF5WriterConfig("test.h5").writer();
 * writer.writeFloatArray("/some/path/dataset", f);
 * writer.addAttribute("some key", "some value");
 * writer.close();
 *
* * @author Bernd Rinn */ final class HDF5Writer extends HDF5Reader implements IHDF5Writer { private final HDF5BaseWriter baseWriter; private final IHDF5FileLevelReadWriteHandler fileHandler; private final IHDF5ObjectReadWriteInfoProviderHandler objectHandler; private final IHDF5ByteWriter byteWriter; private final IHDF5ByteWriter ubyteWriter; private final IHDF5ShortWriter shortWriter; private final IHDF5ShortWriter ushortWriter; private final IHDF5IntWriter intWriter; private final IHDF5IntWriter uintWriter; private final IHDF5LongWriter longWriter; private final IHDF5LongWriter ulongWriter; private final IHDF5FloatWriter floatWriter; private final IHDF5DoubleWriter doubleWriter; private final IHDF5BooleanWriter booleanWriter; private final IHDF5StringWriter stringWriter; private final IHDF5EnumWriter enumWriter; private final IHDF5CompoundWriter compoundWriter; private final IHDF5DateTimeWriter dateTimeWriter; private final HDF5TimeDurationWriter timeDurationWriter; private final IHDF5ReferenceWriter referenceWriter; private final IHDF5OpaqueWriter opaqueWriter; HDF5Writer(HDF5BaseWriter baseWriter) { super(baseWriter); this.baseWriter = baseWriter; this.fileHandler = new HDF5FileLevelReadWriteHandler(baseWriter); this.objectHandler = new HDF5ObjectReadWriteInfoProviderHandler(baseWriter); this.byteWriter = new HDF5ByteWriter(baseWriter); this.ubyteWriter = new HDF5UnsignedByteWriter(baseWriter); this.shortWriter = new HDF5ShortWriter(baseWriter); this.ushortWriter = new HDF5UnsignedShortWriter(baseWriter); this.intWriter = new HDF5IntWriter(baseWriter); this.uintWriter = new HDF5UnsignedIntWriter(baseWriter); this.longWriter = new HDF5LongWriter(baseWriter); this.ulongWriter = new HDF5UnsignedLongWriter(baseWriter); this.floatWriter = new HDF5FloatWriter(baseWriter); this.doubleWriter = new HDF5DoubleWriter(baseWriter); this.booleanWriter = new HDF5BooleanWriter(baseWriter); this.stringWriter = new HDF5StringWriter(baseWriter); this.enumWriter = new HDF5EnumWriter(baseWriter); this.compoundWriter = new HDF5CompoundWriter(baseWriter, enumWriter); this.dateTimeWriter = new HDF5DateTimeWriter(baseWriter, (HDF5LongReader) longReader); this.timeDurationWriter = new HDF5TimeDurationWriter(baseWriter, (HDF5LongReader) longReader); this.referenceWriter = new HDF5ReferenceWriter(baseWriter); this.opaqueWriter = new HDF5OpaqueWriter(baseWriter); } HDF5BaseWriter getBaseWriter() { return baseWriter; } // ///////////////////// // File // ///////////////////// @Override public IHDF5FileLevelReadWriteHandler file() { return fileHandler; } @Override public boolean isUseExtendableDataTypes() { return baseWriter.useExtentableDataTypes; } @Override public FileFormat getFileFormat() { return baseWriter.fileFormat; } @Override public void flush() { baseWriter.checkOpen(); baseWriter.flush(); } @Override public void flushSyncBlocking() { baseWriter.checkOpen(); baseWriter.flushSyncBlocking(); } @Override public boolean addFlushable(Flushable flushable) { return baseWriter.addFlushable(flushable); } @Override public boolean removeFlushable(Flushable flushable) { return baseWriter.removeFlushable(flushable); } // ///////////////////////////////// // Objects, links, groups and types // ///////////////////////////////// @Override public IHDF5ObjectReadWriteInfoProviderHandler object() { return objectHandler; } @Override public HDF5LinkInformation getLinkInformation(String objectPath) { return objectHandler.getLinkInformation(objectPath); } @Override public void createHardLink(String currentPath, String newPath) { objectHandler.createHardLink(currentPath, newPath); } @Override public HDF5ObjectInformation getObjectInformation(String objectPath) { return objectHandler.getObjectInformation(objectPath); } @Override public void createSoftLink(String targetPath, String linkPath) { objectHandler.createSoftLink(targetPath, linkPath); } @Override public void createOrUpdateSoftLink(String targetPath, String linkPath) { objectHandler.createOrUpdateSoftLink(targetPath, linkPath); } @Override public HDF5ObjectType getObjectType(String objectPath, boolean followLink) { return objectHandler.getObjectType(objectPath, followLink); } @Override public void createExternalLink(String targetFileName, String targetPath, String linkPath) throws IllegalStateException { objectHandler.createExternalLink(targetFileName, targetPath, linkPath); } @Override public HDF5ObjectType getObjectType(String objectPath) { return objectHandler.getObjectType(objectPath); } @Override public boolean exists(String objectPath, boolean followLink) { return objectHandler.exists(objectPath, followLink); } @Override public boolean exists(String objectPath) { return objectHandler.exists(objectPath); } @Override public void createOrUpdateExternalLink(String targetFileName, String targetPath, String linkPath) throws IllegalStateException { objectHandler.createOrUpdateExternalLink(targetFileName, targetPath, linkPath); } @Override public String toHouseKeepingPath(String objectPath) { return objectHandler.toHouseKeepingPath(objectPath); } @Override public boolean isHouseKeepingObject(String objectPath) { return objectHandler.isHouseKeepingObject(objectPath); } @Override public boolean isGroup(String objectPath, boolean followLink) { return objectHandler.isGroup(objectPath, followLink); } @Override public boolean isGroup(String objectPath) { return objectHandler.isGroup(objectPath); } @Override public void delete(String objectPath) { objectHandler.delete(objectPath); } @Override public void move(String oldLinkPath, String newLinkPath) throws HDF5SymbolTableException { objectHandler.move(oldLinkPath, newLinkPath); } @Override public boolean isDataSet(String objectPath, boolean followLink) { return objectHandler.isDataSet(objectPath, followLink); } @Override public void createGroup(String groupPath) { objectHandler.createGroup(groupPath); } @Override public boolean isDataSet(String objectPath) { return objectHandler.isDataSet(objectPath); } @Override public void createGroup(String groupPath, int sizeHint) { objectHandler.createGroup(groupPath, sizeHint); } @Override public boolean isDataType(String objectPath, boolean followLink) { return objectHandler.isDataType(objectPath, followLink); } @Override public boolean isDataType(String objectPath) { return objectHandler.isDataType(objectPath); } @Override public void createGroup(String groupPath, int maxCompact, int minDense) { objectHandler.createGroup(groupPath, maxCompact, minDense); } @Override public boolean isSoftLink(String objectPath) { return objectHandler.isSoftLink(objectPath); } @Override public boolean isExternalLink(String objectPath) { return objectHandler.isExternalLink(objectPath); } @Override public boolean isSymbolicLink(String objectPath) { return objectHandler.isSymbolicLink(objectPath); } @Override public String tryGetSymbolicLinkTarget(String objectPath) { return objectHandler.tryGetSymbolicLinkTarget(objectPath); } @Override public void setDataSetSize(String objectPath, long newSize) { objectHandler.setDataSetSize(objectPath, newSize); } @Override public boolean hasAttribute(String objectPath, String attributeName) { return objectHandler.hasAttribute(objectPath, attributeName); } @Override public void setDataSetDimensions(String objectPath, long[] newDimensions) { objectHandler.setDataSetDimensions(objectPath, newDimensions); } @Override public List getAttributeNames(String objectPath) { return objectHandler.getAttributeNames(objectPath); } @Override public void setTypeVariant(String objectPath, HDF5DataTypeVariant typeVariant) { objectHandler.setTypeVariant(objectPath, typeVariant); } @Override public List getAllAttributeNames(String objectPath) { return objectHandler.getAllAttributeNames(objectPath); } @Override public void setTypeVariant(String objectPath, String attributeName, HDF5DataTypeVariant typeVariant) { objectHandler.setTypeVariant(objectPath, attributeName, typeVariant); } @Override public HDF5DataTypeInformation getAttributeInformation(String objectPath, String attributeName) { return objectHandler.getAttributeInformation(objectPath, attributeName); } @Override public void deleteTypeVariant(String objectPath) { objectHandler.deleteTypeVariant(objectPath); } @Override public void deleteTypeVariant(String objectPath, String attributeName) { objectHandler.deleteTypeVariant(objectPath, attributeName); } @Override public HDF5DataTypeInformation getAttributeInformation(String objectPath, String attributeName, DataTypeInfoOptions dataTypeInfoOptions) { return objectHandler .getAttributeInformation(objectPath, attributeName, dataTypeInfoOptions); } @Override public void deleteAttribute(String objectPath, String name) { objectHandler.deleteAttribute(objectPath, name); } @Override public HDF5DataSetInformation getDataSetInformation(String dataSetPath) { return objectHandler.getDataSetInformation(dataSetPath); } @Override public HDF5DataSetInformation getDataSetInformation(String dataSetPath, DataTypeInfoOptions dataTypeInfoOptions) { return objectHandler.getDataSetInformation(dataSetPath, dataTypeInfoOptions); } @Override public long getSize(String objectPath) { return objectHandler.getSize(objectPath); } @Override public long getNumberOfElements(String objectPath) { return objectHandler.getNumberOfElements(objectPath); } @Override public void copy(String sourceObject, IHDF5Writer destinationWriter, String destinationObject) { objectHandler.copy(sourceObject, destinationWriter, destinationObject); } @Override public void copy(String sourceObject, IHDF5Writer destinationWriter) { objectHandler.copy(sourceObject, destinationWriter); } @Override public void copyAll(IHDF5Writer destinationWriter) { objectHandler.copyAll(destinationWriter); } @Override public List getGroupMembers(String groupPath) { return objectHandler.getGroupMembers(groupPath); } @Override public List getAllGroupMembers(String groupPath) { return objectHandler.getAllGroupMembers(groupPath); } @Override public List getGroupMemberPaths(String groupPath) { return objectHandler.getGroupMemberPaths(groupPath); } @Override public List getGroupMemberInformation(String groupPath, boolean readLinkTargets) { return objectHandler.getGroupMemberInformation(groupPath, readLinkTargets); } @Override public List getAllGroupMemberInformation(String groupPath, boolean readLinkTargets) { return objectHandler.getAllGroupMemberInformation(groupPath, readLinkTargets); } @Override public HDF5DataTypeVariant tryGetTypeVariant(String objectPath) { return objectHandler.tryGetTypeVariant(objectPath); } @Override public HDF5DataTypeVariant tryGetTypeVariant(String objectPath, String attributeName) { return objectHandler.tryGetTypeVariant(objectPath, attributeName); } @Override public String tryGetDataTypePath(String objectPath) { return objectHandler.tryGetDataTypePath(objectPath); } @Override public String tryGetDataTypePath(HDF5DataType type) { return objectHandler.tryGetDataTypePath(type); } @Override public void setBooleanAttribute(String objectPath, String name, boolean value) { booleanWriter.setAttr(objectPath, name, value); } // ///////////////////////////// // Data Set Reading and Writing // ///////////////////////////// // // Boolean // @Override public IHDF5BooleanWriter bool() { return booleanWriter; } @Override public void writeBitField(String objectPath, BitSet data, HDF5GenericStorageFeatures features) { booleanWriter.writeBitField(objectPath, data, features); } @Override public void writeBitField(String objectPath, BitSet data) { booleanWriter.writeBitField(objectPath, data); } @Override public void writeBoolean(String objectPath, boolean value) { booleanWriter.write(objectPath, value); } @Override public void createBitField(String objectPath, int size) { booleanWriter.createBitField(objectPath, size); } @Override public void createBitField(String objectPath, long size, int blockSize) { booleanWriter.createBitField(objectPath, size, blockSize); } @Override public void createBitField(String objectPath, int size, HDF5IntStorageFeatures features) { booleanWriter.createBitField(objectPath, size, HDF5GenericStorageFeatures.build(features) .features()); } @Override public void createBitField(String objectPath, long size, int blockSize, HDF5IntStorageFeatures features) { booleanWriter.createBitField(objectPath, size, blockSize, HDF5GenericStorageFeatures.build(features).features()); } @Override public void writeBitFieldBlock(String objectPath, BitSet data, int dataSize, long blockNumber) { booleanWriter.writeBitFieldBlock(objectPath, data, dataSize, blockNumber); } @Override public void writeBitFieldBlockWithOffset(String objectPath, BitSet data, int dataSize, long offset) { booleanWriter.writeBitFieldBlockWithOffset(objectPath, data, dataSize, offset); } // // Opaque // @Override public IHDF5OpaqueWriter opaque() { return opaqueWriter; } @Override public HDF5OpaqueType createOpaqueByteArray(String objectPath, String tag, int size, HDF5GenericStorageFeatures features) { return opaqueWriter.createArray(objectPath, tag, size, features); } @Override public HDF5OpaqueType createOpaqueByteArray(String objectPath, String tag, int size) { return opaqueWriter.createArray(objectPath, tag, size); } @Override public HDF5OpaqueType createOpaqueByteArray(String objectPath, String tag, long size, int blockSize, HDF5GenericStorageFeatures features) { return opaqueWriter.createArray(objectPath, tag, size, blockSize, features); } @Override public HDF5OpaqueType createOpaqueByteArray(String objectPath, String tag, long size, int blockSize) { return opaqueWriter.createArray(objectPath, tag, size, blockSize); } @Override public void writeOpaqueByteArray(String objectPath, String tag, byte[] data, HDF5GenericStorageFeatures features) { opaqueWriter.writeArray(objectPath, tag, data, features); } @Override public void writeOpaqueByteArray(String objectPath, String tag, byte[] data) { opaqueWriter.writeArray(objectPath, tag, data); } @Override public void writeOpaqueByteArrayBlock(String objectPath, HDF5OpaqueType dataType, byte[] data, long blockNumber) { opaqueWriter.writeArrayBlock(objectPath, dataType, data, blockNumber); } @Override public void writeOpaqueByteArrayBlockWithOffset(String objectPath, HDF5OpaqueType dataType, byte[] data, int dataSize, long offset) { opaqueWriter.writeArrayBlockWithOffset(objectPath, dataType, data, dataSize, offset); } // // Date // @Override public IHDF5DateTimeWriter time() { return dateTimeWriter; } @Override public IHDF5TimeDurationWriter duration() { return timeDurationWriter; } @Override public void createTimeStampArray(String objectPath, int size, HDF5GenericStorageFeatures features) { dateTimeWriter.createArray(objectPath, size, features); } @Override public void setTimeStampAttribute(String objectPath, String name, long value) { dateTimeWriter.setAttr(objectPath, name, value); } @Override public void setDateAttribute(String objectPath, String name, Date date) { dateTimeWriter.setAttr(objectPath, name, date); } @Override public void setTimeDurationAttribute(String objectPath, String name, HDF5TimeDuration timeDuration) { timeDurationWriter.setAttr(objectPath, name, timeDuration); } @Override public void setTimeDurationAttribute(String objectPath, String name, long timeDuration, HDF5TimeUnit timeUnit) { timeDurationWriter.setAttr(objectPath, name, timeDuration, timeUnit); } @Override public void setDateArrayAttribute(String objectPath, String name, Date[] dates) { dateTimeWriter.setArrayAttr(objectPath, name, dates); } @Override public void setTimeStampArrayAttribute(String objectPath, String name, long[] timeStamps) { dateTimeWriter.setArrayAttr(objectPath, name, timeStamps); } @Override public void setTimeDurationArrayAttribute(String objectPath, String name, HDF5TimeDurationArray timeDurations) { timeDurationWriter.setArrayAttr(objectPath, name, timeDurations); } @Override public void createTimeStampArray(String objectPath, int size) { dateTimeWriter.createArray(objectPath, size); } @Override public void createTimeStampArray(String objectPath, long size, int blockSize, HDF5GenericStorageFeatures features) { dateTimeWriter.createArray(objectPath, size, blockSize, features); } @Override public void createTimeStampArray(String objectPath, long size, int blockSize) { dateTimeWriter.createArray(objectPath, size, blockSize); } @Override public void writeDate(String objectPath, Date date) { dateTimeWriter.write(objectPath, date); } @Override public void writeDateArray(String objectPath, Date[] dates, HDF5GenericStorageFeatures features) { dateTimeWriter.writeArray(objectPath, dates, features); } @Override public void writeDateArray(String objectPath, Date[] dates) { dateTimeWriter.writeArray(objectPath, dates); } @Override public void writeTimeStamp(String objectPath, long timeStamp) { dateTimeWriter.write(objectPath, timeStamp); } @Override public void writeTimeStampArray(String objectPath, long[] timeStamps, HDF5GenericStorageFeatures features) { dateTimeWriter.writeArray(objectPath, timeStamps, features); } @Override public void writeTimeStampArray(String objectPath, long[] timeStamps) { dateTimeWriter.writeArray(objectPath, timeStamps); } @Override public void writeTimeStampArrayBlock(String objectPath, long[] data, long blockNumber) { dateTimeWriter.writeArrayBlock(objectPath, data, blockNumber); } @Override public void writeTimeStampArrayBlockWithOffset(String objectPath, long[] data, int dataSize, long offset) { dateTimeWriter.writeArrayBlockWithOffset(objectPath, data, dataSize, offset); } // // Duration // @Override public void createTimeDurationArray(String objectPath, int size, HDF5TimeUnit timeUnit, HDF5GenericStorageFeatures features) { timeDurationWriter.createArray(objectPath, size, timeUnit, features); } @Override public void createTimeDurationArray(String objectPath, int size, HDF5TimeUnit timeUnit) { timeDurationWriter.createArray(objectPath, size, timeUnit); } @Override public void createTimeDurationArray(String objectPath, long size, int blockSize, HDF5TimeUnit timeUnit, HDF5GenericStorageFeatures features) { timeDurationWriter.createArray(objectPath, size, blockSize, timeUnit, features); } @Override public void createTimeDurationArray(String objectPath, long size, int blockSize, HDF5TimeUnit timeUnit) { timeDurationWriter.createArray(objectPath, size, blockSize, timeUnit); } @Override public void writeTimeDuration(String objectPath, long timeDuration, HDF5TimeUnit timeUnit) { timeDurationWriter.write(objectPath, timeDuration, timeUnit); } @Override public void writeTimeDuration(String objectPath, HDF5TimeDuration timeDuration) { timeDurationWriter.write(objectPath, timeDuration); } @Override @Deprecated public void writeTimeDuration(String objectPath, long timeDuration) { timeDurationWriter.writeTimeDuration(objectPath, timeDuration); } @Override @Deprecated public void writeTimeDurationArray(String objectPath, long[] timeDurations, HDF5TimeUnit timeUnit, HDF5IntStorageFeatures features) { timeDurationWriter.writeTimeDurationArray(objectPath, timeDurations, timeUnit, features); } @Override public void writeTimeDurationArray(String objectPath, HDF5TimeDurationArray timeDurations) { timeDurationWriter.writeArray(objectPath, timeDurations); } @Override public void writeTimeDurationArray(String objectPath, HDF5TimeDurationArray timeDurations, HDF5IntStorageFeatures features) { timeDurationWriter.writeArray(objectPath, timeDurations, features); } @Override @Deprecated public void writeTimeDurationArray(String objectPath, long[] timeDurations, HDF5TimeUnit timeUnit) { timeDurationWriter.writeTimeDurationArray(objectPath, timeDurations, timeUnit); } @Override @Deprecated public void writeTimeDurationArray(String objectPath, long[] timeDurations) { timeDurationWriter.writeTimeDurationArray(objectPath, timeDurations); } @Override @Deprecated public void writeTimeDurationArray(String objectPath, HDF5TimeDuration[] timeDurations) { timeDurationWriter.writeTimeDurationArray(objectPath, timeDurations); } @Override @Deprecated public void writeTimeDurationArray(String objectPath, HDF5TimeDuration[] timeDurations, HDF5IntStorageFeatures features) { timeDurationWriter.writeTimeDurationArray(objectPath, timeDurations, features); } @Override public void writeTimeDurationArrayBlock(String objectPath, HDF5TimeDurationArray data, long blockNumber) { timeDurationWriter.writeArrayBlock(objectPath, data, blockNumber); } @Override public void writeTimeDurationArrayBlockWithOffset(String objectPath, HDF5TimeDurationArray data, int dataSize, long offset) { timeDurationWriter.writeArrayBlockWithOffset(objectPath, data, dataSize, offset); } @Override @Deprecated public void writeTimeDurationArrayBlock(String objectPath, long[] data, long blockNumber, HDF5TimeUnit timeUnit) { timeDurationWriter.writeTimeDurationArrayBlock(objectPath, data, blockNumber, timeUnit); } @Override @Deprecated public void writeTimeDurationArrayBlockWithOffset(String objectPath, long[] data, int dataSize, long offset, HDF5TimeUnit timeUnit) { timeDurationWriter.writeTimeDurationArrayBlockWithOffset(objectPath, data, dataSize, offset, timeUnit); } @Override @Deprecated public void writeTimeDurationArrayBlock(String objectPath, HDF5TimeDuration[] data, long blockNumber) { timeDurationWriter.writeTimeDurationArrayBlock(objectPath, data, blockNumber); } @Override @Deprecated public void writeTimeDurationArrayBlockWithOffset(String objectPath, HDF5TimeDuration[] data, int dataSize, long offset) { timeDurationWriter .writeTimeDurationArrayBlockWithOffset(objectPath, data, dataSize, offset); } // // References // @Override public IHDF5ReferenceWriter reference() { return referenceWriter; } @Override public void writeObjectReference(String objectPath, String referencedObjectPath) { referenceWriter.write(objectPath, referencedObjectPath); } @Override public void writeObjectReferenceArray(String objectPath, String[] referencedObjectPath) { referenceWriter.writeArray(objectPath, referencedObjectPath); } @Override public void writeObjectReferenceArray(String objectPath, String[] referencedObjectPath, HDF5IntStorageFeatures features) { referenceWriter.writeArray(objectPath, referencedObjectPath, features); } @Override public void writeObjectReferenceMDArray(String objectPath, MDArray referencedObjectPaths) { referenceWriter.writeMDArray(objectPath, referencedObjectPaths); } @Override public void writeObjectReferenceMDArray(String objectPath, MDArray referencedObjectPaths, HDF5IntStorageFeatures features) { referenceWriter.writeMDArray(objectPath, referencedObjectPaths, features); } @Override public void setObjectReferenceAttribute(String objectPath, String name, String referencedObjectPath) { referenceWriter.setAttr(objectPath, name, referencedObjectPath); } @Override public void setObjectReferenceArrayAttribute(String objectPath, String name, String[] value) { referenceWriter.setArrayAttr(objectPath, name, value); } // // String // @Override public IHDF5StringWriter string() { return stringWriter; } @Override public void setObjectReferenceMDArrayAttribute(String objectPath, String name, MDArray referencedObjectPaths) { referenceWriter.setMDArrayAttr(objectPath, name, referencedObjectPaths); } @Override public void createObjectReferenceArray(String objectPath, int size) { referenceWriter.createArray(objectPath, size); } @Override public void createObjectReferenceArray(String objectPath, long size, int blockSize) { referenceWriter.createArray(objectPath, size, blockSize); } @Override public void createObjectReferenceArray(String objectPath, int size, HDF5IntStorageFeatures features) { referenceWriter.createArray(objectPath, size, features); } @Override public void createObjectReferenceArray(String objectPath, long size, int blockSize, HDF5IntStorageFeatures features) { referenceWriter.createArray(objectPath, size, blockSize, features); } @Override public void writeObjectReferenceArrayBlock(String objectPath, String[] referencedObjectPaths, long blockNumber) { referenceWriter.writeArrayBlock(objectPath, referencedObjectPaths, blockNumber); } @Override public void writeObjectReferenceArrayBlockWithOffset(String objectPath, String[] referencedObjectPaths, int dataSize, long offset) { referenceWriter.writeArrayBlockWithOffset(objectPath, referencedObjectPaths, dataSize, offset); } @Override public void createObjectReferenceMDArray(String objectPath, int[] dimensions) { referenceWriter.createMDArray(objectPath, dimensions); } @Override public void createObjectReferenceMDArray(String objectPath, long[] dimensions, int[] blockDimensions) { referenceWriter.createMDArray(objectPath, dimensions, blockDimensions); } @Override public void createObjectReferenceMDArray(String objectPath, int[] dimensions, HDF5IntStorageFeatures features) { referenceWriter.createMDArray(objectPath, dimensions, features); } @Override public void createObjectReferenceMDArray(String objectPath, long[] dimensions, int[] blockDimensions, HDF5IntStorageFeatures features) { referenceWriter.createMDArray(objectPath, dimensions, blockDimensions, features); } @Override public void writeObjectReferenceMDArrayBlock(String objectPath, MDArray referencedObjectPaths, long[] blockNumber) { referenceWriter.writeMDArrayBlock(objectPath, referencedObjectPaths, blockNumber); } @Override public void writeObjectReferenceMDArrayBlockWithOffset(String objectPath, MDArray referencedObjectPaths, long[] offset) { referenceWriter.writeMDArrayBlockWithOffset(objectPath, referencedObjectPaths, offset); } @Override public void writeObjectReferenceMDArrayBlockWithOffset(String objectPath, MDLongArray data, int[] blockDimensions, long[] offset, int[] memoryOffset) { referenceWriter.writeMDArrayBlockWithOffset(objectPath, data, blockDimensions, offset, memoryOffset); } @Override public void createStringArray(String objectPath, int maxLength, int size) { stringWriter.createArray(objectPath, maxLength, size); } @Override public void createStringArray(String objectPath, int maxLength, long size, int blockSize) { stringWriter.createArray(objectPath, maxLength, size, blockSize); } @Override public void createStringArray(String objectPath, int maxLength, int size, HDF5GenericStorageFeatures features) { stringWriter.createArray(objectPath, maxLength, size, features); } @Override public void createStringArray(String objectPath, int maxLength, long size, int blockSize, HDF5GenericStorageFeatures features) { stringWriter.createArray(objectPath, maxLength, size, blockSize, features); } @Override public void createStringVariableLengthArray(String objectPath, int size) { stringWriter.createArrayVL(objectPath, size); } @Override public void createStringVariableLengthArray(String objectPath, long size, int blockSize) { stringWriter.createArrayVL(objectPath, size, blockSize); } @Override public void createStringVariableLengthArray(String objectPath, long size, int blockSize, HDF5GenericStorageFeatures features) { stringWriter.createArrayVL(objectPath, size, blockSize, features); } @Override public void createStringVariableLengthArray(String objectPath, int size, HDF5GenericStorageFeatures features) { stringWriter.createArrayVL(objectPath, size, features); } @Override public void setStringAttribute(String objectPath, String name, String value) { stringWriter.setAttr(objectPath, name, value); } @Override public void setStringAttribute(String objectPath, String name, String value, int maxLength) { stringWriter.setAttr(objectPath, name, value, maxLength); } @Override public void setStringArrayAttribute(String objectPath, String name, String[] value, int maxLength) { stringWriter.setArrayAttr(objectPath, name, value, maxLength); } @Override public void setStringArrayAttribute(String objectPath, String name, String[] value) { stringWriter.setArrayAttr(objectPath, name, value); } @Override public void setStringMDArrayAttribute(String objectPath, String name, MDArray value) { stringWriter.setMDArrayAttr(objectPath, name, value); } @Override public void setStringMDArrayAttribute(String objectPath, String name, MDArray value, int maxLength) { stringWriter.setMDArrayAttr(objectPath, name, value, maxLength); } @Override public void setStringAttributeVariableLength(String objectPath, String name, String value) { stringWriter.setAttrVL(objectPath, name, value); } @Override public void writeString(String objectPath, String data, int maxLength) { stringWriter.write(objectPath, data, maxLength); } @Override public void writeString(String objectPath, String data) { stringWriter.write(objectPath, data); } @Override public void writeString(String objectPath, String data, HDF5GenericStorageFeatures features) { stringWriter.write(objectPath, data, features); } @Override public void writeString(String objectPath, String data, int maxLength, HDF5GenericStorageFeatures features) { stringWriter.write(objectPath, data, maxLength, features); } @Override public void writeStringArray(String objectPath, String[] data, HDF5GenericStorageFeatures features) { stringWriter.writeArray(objectPath, data, features); } @Override public void writeStringArray(String objectPath, String[] data) { stringWriter.writeArray(objectPath, data); } @Override public void writeStringArray(String objectPath, String[] data, int maxLength) { stringWriter.writeArray(objectPath, data, maxLength); } @Override public void writeStringArray(String objectPath, String[] data, int maxLength, HDF5GenericStorageFeatures features) { stringWriter.writeArray(objectPath, data, maxLength, features); } @Override public void createStringMDArray(String objectPath, int maxLength, int[] dimensions, HDF5GenericStorageFeatures features) { stringWriter.createMDArray(objectPath, maxLength, dimensions, features); } @Override public void createStringMDArray(String objectPath, int maxLength, int[] dimensions) { stringWriter.createMDArray(objectPath, maxLength, dimensions); } @Override public void createStringMDArray(String objectPath, int maxLength, long[] dimensions, int[] blockSize, HDF5GenericStorageFeatures features) { stringWriter.createMDArray(objectPath, maxLength, dimensions, blockSize, features); } @Override public void createStringMDArray(String objectPath, int maxLength, long[] dimensions, int[] blockSize) { stringWriter.createMDArray(objectPath, maxLength, dimensions, blockSize); } @Override public void writeStringMDArray(String objectPath, MDArray data, int maxLength) { stringWriter.writeMDArray(objectPath, data, maxLength); } @Override public void writeStringMDArray(String objectPath, MDArray data) { stringWriter.writeMDArray(objectPath, data); } @Override public void writeStringMDArray(String objectPath, MDArray data, HDF5GenericStorageFeatures features) { stringWriter.writeMDArray(objectPath, data, features); } @Override public void writeStringMDArray(String objectPath, MDArray data, int maxLength, HDF5GenericStorageFeatures features) { stringWriter.writeMDArray(objectPath, data, maxLength, features); } @Override public void writeStringArrayBlock(String objectPath, String[] data, long blockNumber) { stringWriter.writeArrayBlock(objectPath, data, blockNumber); } @Override public void writeStringArrayBlockWithOffset(String objectPath, String[] data, int dataSize, long offset) { stringWriter.writeArrayBlockWithOffset(objectPath, data, dataSize, offset); } @Override public void writeStringMDArrayBlock(String objectPath, MDArray data, long[] blockNumber) { stringWriter.writeMDArrayBlock(objectPath, data, blockNumber); } @Override public void writeStringMDArrayBlockWithOffset(String objectPath, MDArray data, long[] offset) { stringWriter.writeMDArrayBlockWithOffset(objectPath, data, offset); } @Override public void writeStringVariableLength(String objectPath, String data) { stringWriter.writeVL(objectPath, data); } @Override public void writeStringVariableLengthArray(String objectPath, String[] data) { stringWriter.writeArrayVL(objectPath, data); } @Override public void writeStringVariableLengthArray(String objectPath, String[] data, HDF5GenericStorageFeatures features) { stringWriter.writeArrayVL(objectPath, data, features); } @Override public void writeStringVariableLengthMDArray(String objectPath, MDArray data, HDF5GenericStorageFeatures features) { stringWriter.writeMDArrayVL(objectPath, data, features); } @Override public void writeStringVariableLengthMDArray(String objectPath, MDArray data) { stringWriter.writeMDArrayVL(objectPath, data); } @Override public void createStringVariableLengthMDArray(String objectPath, int[] dimensions, HDF5GenericStorageFeatures features) { stringWriter.createMDArrayVL(objectPath, dimensions, features); } @Override public void createStringVariableLengthMDArray(String objectPath, int[] dimensions) { stringWriter.createMDArrayVL(objectPath, dimensions); } @Override public void createStringVariableLengthMDArray(String objectPath, long[] dimensions, int[] blockSize, HDF5GenericStorageFeatures features) { stringWriter.createMDArrayVL(objectPath, dimensions, blockSize, features); } @Override public void createStringVariableLengthMDArray(String objectPath, long[] dimensions, int[] blockSize) { stringWriter.createMDArrayVL(objectPath, dimensions, blockSize); } // // Enum // @Override public IHDF5EnumWriter enums() { return enumWriter; } @Override public IHDF5EnumWriter enumeration() { return enumWriter; } @Override public HDF5EnumerationType getEnumType(final String name, final String[] values) throws HDF5JavaException { return enumWriter.getType(name, values); } @Override public HDF5EnumerationType getEnumType(final String name, final String[] values, final boolean check) throws HDF5JavaException { return enumWriter.getType(name, values, check); } @Override public HDF5EnumerationType createEnumArray(String objectPath, HDF5EnumerationType enumType, int size) { return enumWriter.createArray(objectPath, enumType, size); } @Override public HDF5EnumerationType createEnumArray(String objectPath, HDF5EnumerationType enumType, long size, HDF5IntStorageFeatures features) { return enumWriter.createArray(objectPath, enumType, size, features); } @Override public HDF5EnumerationType createEnumArray(String objectPath, HDF5EnumerationType enumType, long size, int blockSize, HDF5IntStorageFeatures features) { return enumWriter.createArray(objectPath, enumType, size, blockSize, features); } @Override public HDF5EnumerationType createEnumArray(String objectPath, HDF5EnumerationType enumType, long size, int blockSize) { return enumWriter.createArray(objectPath, enumType, size, blockSize); } @Override public void setEnumAttribute(String objectPath, String name, HDF5EnumerationValue value) { enumWriter.setAttr(objectPath, name, value); } @Override public void setEnumAttribute(String objectPath, String name, Enum value) throws HDF5JavaException { enumWriter.setAttr(objectPath, name, value); } @Override public > void writeEnum(String objectPath, Enum value) throws HDF5JavaException { enumWriter.write(objectPath, value); } @Override public void writeEnum(String objectPath, String[] options, String value) { enumWriter.write(objectPath, enumWriter.newAnonVal(options, value)); } @Override public > void writeEnumArray(String objectPath, Enum[] data) { enumWriter.writeArray(objectPath, enumWriter.newAnonArray(data)); } @Override public void writeEnumArray(String objectPath, String[] options, String[] data) { enumWriter.writeArray(objectPath, enumWriter.newAnonArray(options, data)); } @Override public void setEnumArrayAttribute(String objectPath, String name, HDF5EnumerationValueArray value) { enumWriter.setArrayAttr(objectPath, name, value); } @Override public void writeEnum(String objectPath, HDF5EnumerationValue value) throws HDF5JavaException { enumWriter.write(objectPath, value); } @Override public void writeEnumArray(String objectPath, HDF5EnumerationValueArray data, HDF5IntStorageFeatures features) throws HDF5JavaException { enumWriter.writeArray(objectPath, data, features); } @Override public void writeEnumArray(String objectPath, HDF5EnumerationValueArray data) throws HDF5JavaException { enumWriter.writeArray(objectPath, data); } @Override public void writeEnumArrayBlock(String objectPath, HDF5EnumerationValueArray data, long blockNumber) { enumWriter.writeArrayBlock(objectPath, data, blockNumber); } @Override public void writeEnumArrayBlockWithOffset(String objectPath, HDF5EnumerationValueArray data, int dataSize, long offset) { enumWriter.writeArrayBlockWithOffset(objectPath, data, dataSize, offset); } // // Compound // @Override public IHDF5CompoundWriter compounds() { return compoundWriter; } @Override public IHDF5CompoundWriter compound() { return compoundWriter; } @Override public HDF5CompoundType getCompoundType(final String name, Class pojoClass, HDF5CompoundMemberMapping... members) { return compoundWriter.getType(name, pojoClass, members); } @Override public HDF5CompoundType getCompoundType(Class pojoClass, HDF5CompoundMemberMapping... members) { return compoundWriter.getType(pojoClass, members); } @Override public HDF5CompoundType getInferredCompoundType(final String name, Class pojoClass) { return compoundWriter.getInferredType(name, pojoClass); } @Override public HDF5CompoundType getInferredCompoundType(Class pojoClass) { return compoundWriter.getInferredType(pojoClass); } @Override public HDF5CompoundType getInferredCompoundType(final String name, T template) { return compoundWriter.getInferredType(name, template); } @Override public HDF5CompoundType getInferredCompoundType(T template) { return compoundWriter.getInferredType(template); } @Override public void createCompoundArray(String objectPath, HDF5CompoundType type, int size) { compoundWriter.createArray(objectPath, type, size); } @Override public void createCompoundArray(String objectPath, HDF5CompoundType type, long size, HDF5GenericStorageFeatures features) { compoundWriter.createArray(objectPath, type, size, features); } @Override public void createCompoundArray(String objectPath, HDF5CompoundType type, long size, int blockSize, HDF5GenericStorageFeatures features) { compoundWriter.createArray(objectPath, type, size, blockSize, features); } @Override public void createCompoundArray(String objectPath, HDF5CompoundType type, long size, int blockSize) { compoundWriter.createArray(objectPath, type, size, blockSize); } @Override public void createCompoundMDArray(String objectPath, HDF5CompoundType type, int[] dimensions, HDF5GenericStorageFeatures features) { compoundWriter.createMDArray(objectPath, type, dimensions, features); } @Override public void createCompoundMDArray(String objectPath, HDF5CompoundType type, int[] dimensions) { compoundWriter.createMDArray(objectPath, type, dimensions); } @Override public void createCompoundMDArray(String objectPath, HDF5CompoundType type, long[] dimensions, int[] blockDimensions, HDF5GenericStorageFeatures features) { compoundWriter.createMDArray(objectPath, type, dimensions, blockDimensions, features); } @Override public void createCompoundMDArray(String objectPath, HDF5CompoundType type, long[] dimensions, int[] blockDimensions) { compoundWriter.createMDArray(objectPath, type, dimensions, blockDimensions); } @Override public void writeCompound(String objectPath, HDF5CompoundType type, T data, IByteArrayInspector inspectorOrNull) { compoundWriter.write(objectPath, type, data, inspectorOrNull); } @Override public void writeCompound(String objectPath, HDF5CompoundType type, T data) { compoundWriter.write(objectPath, type, data); } @Override public void writeCompound(String objectPath, T data) { compoundWriter.write(objectPath, data); } @Override public void writeCompoundArray(String objectPath, HDF5CompoundType type, T[] data, HDF5GenericStorageFeatures features, IByteArrayInspector inspectorOrNull) { compoundWriter.writeArray(objectPath, type, data, features, inspectorOrNull); } @Override public void writeCompoundArray(String objectPath, HDF5CompoundType type, T[] data, HDF5GenericStorageFeatures features) { compoundWriter.writeArray(objectPath, type, data, features); } @Override public void writeCompoundArray(String objectPath, HDF5CompoundType type, T[] data) { compoundWriter.writeArray(objectPath, type, data); } @Override public void writeCompoundArrayBlock(String objectPath, HDF5CompoundType type, T[] data, long blockNumber, IByteArrayInspector inspectorOrNull) { compoundWriter.writeArrayBlock(objectPath, type, data, blockNumber, inspectorOrNull); } @Override public void writeCompoundArrayBlock(String objectPath, HDF5CompoundType type, T[] data, long blockNumber) { compoundWriter.writeArrayBlock(objectPath, type, data, blockNumber); } @Override public void writeCompoundArrayBlockWithOffset(String objectPath, HDF5CompoundType type, T[] data, long offset, IByteArrayInspector inspectorOrNull) { compoundWriter.writeArrayBlockWithOffset(objectPath, type, data, offset, inspectorOrNull); } @Override public void writeCompoundArrayBlockWithOffset(String objectPath, HDF5CompoundType type, T[] data, long offset) { compoundWriter.writeArrayBlockWithOffset(objectPath, type, data, offset); } @Override public void writeCompoundMDArray(String objectPath, HDF5CompoundType type, MDArray data, HDF5GenericStorageFeatures features, IByteArrayInspector inspectorOrNull) { compoundWriter.writeMDArray(objectPath, type, data, features, inspectorOrNull); } @Override public void writeCompoundMDArray(String objectPath, HDF5CompoundType type, MDArray data, HDF5GenericStorageFeatures features) { compoundWriter.writeMDArray(objectPath, type, data, features); } @Override public void writeCompoundMDArray(String objectPath, HDF5CompoundType type, MDArray data) { compoundWriter.writeMDArray(objectPath, type, data); } @Override public void writeCompoundArray(String objectPath, T[] data) { compoundWriter.writeArray(objectPath, data); } @Override public void writeCompoundArray(String objectPath, T[] data, HDF5GenericStorageFeatures features) { compoundWriter.writeArray(objectPath, data, features); } @Override public void writeCompoundMDArray(String objectPath, MDArray data) { compoundWriter.writeMDArray(objectPath, data); } @Override public void writeCompoundMDArray(String objectPath, MDArray data, HDF5GenericStorageFeatures features) { compoundWriter.writeMDArray(objectPath, data, features); } @Override public void writeCompoundMDArrayBlock(String objectPath, HDF5CompoundType type, MDArray data, long[] blockDimensions, IByteArrayInspector inspectorOrNull) { compoundWriter.writeMDArrayBlock(objectPath, type, data, blockDimensions, inspectorOrNull); } @Override public void writeCompoundMDArrayBlock(String objectPath, HDF5CompoundType type, MDArray data, long[] blockDimensions) { compoundWriter.writeMDArrayBlock(objectPath, type, data, blockDimensions); } @Override public void writeCompoundMDArrayBlockWithOffset(String objectPath, HDF5CompoundType type, MDArray data, int[] blockDimensions, long[] offset, int[] memoryOffset, IByteArrayInspector inspectorOrNull) { compoundWriter.writeMDArrayBlockWithOffset(objectPath, type, data, blockDimensions, offset, memoryOffset, inspectorOrNull); } @Override public void writeCompoundMDArrayBlockWithOffset(String objectPath, HDF5CompoundType type, MDArray data, int[] blockDimensions, long[] offset, int[] memoryOffset) { compoundWriter.writeMDArrayBlockWithOffset(objectPath, type, data, blockDimensions, offset, memoryOffset); } @Override public void writeCompoundMDArrayBlockWithOffset(String objectPath, HDF5CompoundType type, MDArray data, long[] offset, IByteArrayInspector inspectorOrNull) { compoundWriter.writeMDArrayBlockWithOffset(objectPath, type, data, offset, inspectorOrNull); } @Override public void writeCompoundMDArrayBlockWithOffset(String objectPath, HDF5CompoundType type, MDArray data, long[] offset) { compoundWriter.writeMDArrayBlockWithOffset(objectPath, type, data, offset); } @Override public HDF5CompoundMemberInformation[] getCompoundMemberInformation(Class compoundClass) { return compoundWriter.getMemberInfo(compoundClass); } @Override public HDF5CompoundMemberInformation[] getCompoundMemberInformation(String dataTypeName) { return compoundWriter.getMemberInfo(dataTypeName); } @Override public HDF5CompoundMemberInformation[] getCompoundDataSetInformation(String dataSetPath) throws HDF5JavaException { return compoundWriter.getDataSetInfo(dataSetPath); } @Override public HDF5CompoundType> getInferredCompoundType(String name, List memberNames, List template) { return compoundWriter.getInferredType(name, memberNames, template); } @Override public HDF5CompoundType> getInferredCompoundType(List memberNames, List template) { return compoundWriter.getInferredType(memberNames, template); } @Override public HDF5CompoundType getInferredCompoundType(String name, String[] memberNames, Object[] template) { return compoundWriter.getInferredType(name, memberNames, template); } @Override public HDF5CompoundType getInferredCompoundType(String[] memberNames, Object[] template) { return compoundWriter.getInferredType(memberNames, template); } @Override public HDF5CompoundType getDataSetCompoundType(String objectPath, Class pojoClass) { return compoundWriter.getDataSetType(objectPath, pojoClass); } @Override public HDF5CompoundType getNamedCompoundType(String dataTypeName, Class pojoClass) { return compoundWriter.getNamedType(dataTypeName, pojoClass); } @Override public HDF5CompoundType getNamedCompoundType(Class pojoClass) { return compoundWriter.getNamedType(pojoClass); } // ------------------------------------------------------------------------------ // Primitive types - START // ------------------------------------------------------------------------------ @Override public void createByteArray(String objectPath, int blockSize) { byteWriter.createArray(objectPath, blockSize); } @Override public void createByteArray(String objectPath, long size, int blockSize) { byteWriter.createArray(objectPath, size, blockSize); } @Override public void createByteArray(String objectPath, int size, HDF5IntStorageFeatures features) { byteWriter.createArray(objectPath, size, features); } @Override public void createByteArray(String objectPath, long size, int blockSize, HDF5IntStorageFeatures features) { byteWriter.createArray(objectPath, size, blockSize, features); } @Override public void createByteMDArray(String objectPath, int[] blockDimensions) { byteWriter.createMDArray(objectPath, blockDimensions); } @Override public void createByteMDArray(String objectPath, long[] dimensions, int[] blockDimensions) { byteWriter.createMDArray(objectPath, dimensions, blockDimensions); } @Override public void createByteMDArray(String objectPath, int[] dimensions, HDF5IntStorageFeatures features) { byteWriter.createMDArray(objectPath, dimensions, features); } @Override public void createByteMDArray(String objectPath, long[] dimensions, int[] blockDimensions, HDF5IntStorageFeatures features) { byteWriter.createMDArray(objectPath, dimensions, blockDimensions, features); } @Override public void createByteMatrix(String objectPath, int blockSizeX, int blockSizeY) { byteWriter.createMatrix(objectPath, blockSizeX, blockSizeY); } @Override public void createByteMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY) { byteWriter.createMatrix(objectPath, sizeX, sizeY, blockSizeX, blockSizeY); } @Override public void createByteMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY, HDF5IntStorageFeatures features) { byteWriter.createMatrix(objectPath, sizeX, sizeY, blockSizeX, blockSizeY, features); } @Override public void setByteArrayAttribute(String objectPath, String name, byte[] value) { byteWriter.setArrayAttr(objectPath, name, value); } @Override public void setByteAttribute(String objectPath, String name, byte value) { byteWriter.setAttr(objectPath, name, value); } @Override public void setByteMDArrayAttribute(String objectPath, String name, MDByteArray value) { byteWriter.setMDArrayAttr(objectPath, name, value); } @Override public void setByteMatrixAttribute(String objectPath, String name, byte[][] value) { byteWriter.setMatrixAttr(objectPath, name, value); } @Override public void writeByte(String objectPath, byte value) { byteWriter.write(objectPath, value); } @Override public void writeByteArray(String objectPath, byte[] data) { byteWriter.writeArray(objectPath, data); } @Override public void writeByteArray(String objectPath, byte[] data, HDF5IntStorageFeatures features) { byteWriter.writeArray(objectPath, data, features); } @Override public void writeByteArrayBlock(String objectPath, byte[] data, long blockNumber) { byteWriter.writeArrayBlock(objectPath, data, blockNumber); } @Override public void writeByteArrayBlockWithOffset(String objectPath, byte[] data, int dataSize, long offset) { byteWriter.writeArrayBlockWithOffset(objectPath, data, dataSize, offset); } @Override public void writeByteMDArray(String objectPath, MDByteArray data) { byteWriter.writeMDArray(objectPath, data); } @Override public void writeByteMDArray(String objectPath, MDByteArray data, HDF5IntStorageFeatures features) { byteWriter.writeMDArray(objectPath, data, features); } @Override public void writeByteMDArrayBlock(String objectPath, MDByteArray data, long[] blockNumber) { byteWriter.writeMDArrayBlock(objectPath, data, blockNumber); } @Override public void writeByteMDArrayBlockWithOffset(String objectPath, MDByteArray data, long[] offset) { byteWriter.writeMDArrayBlockWithOffset(objectPath, data, offset); } @Override public void writeByteMDArrayBlockWithOffset(String objectPath, MDByteArray data, int[] blockDimensions, long[] offset, int[] memoryOffset) { byteWriter.writeMDArrayBlockWithOffset(objectPath, data, blockDimensions, offset, memoryOffset); } @Override public void writeByteMatrix(String objectPath, byte[][] data) { byteWriter.writeMatrix(objectPath, data); } @Override public void writeByteMatrix(String objectPath, byte[][] data, HDF5IntStorageFeatures features) { byteWriter.writeMatrix(objectPath, data, features); } @Override public void writeByteMatrixBlock(String objectPath, byte[][] data, long blockNumberX, long blockNumberY) { byteWriter.writeMatrixBlock(objectPath, data, blockNumberX, blockNumberY); } @Override public void writeByteMatrixBlockWithOffset(String objectPath, byte[][] data, long offsetX, long offsetY) { byteWriter.writeMatrixBlockWithOffset(objectPath, data, offsetX, offsetY); } @Override public void writeByteMatrixBlockWithOffset(String objectPath, byte[][] data, int dataSizeX, int dataSizeY, long offsetX, long offsetY) { byteWriter.writeMatrixBlockWithOffset(objectPath, data, dataSizeX, dataSizeY, offsetX, offsetY); } @Override public void createDoubleArray(String objectPath, int blockSize) { doubleWriter.createArray(objectPath, blockSize); } @Override public void createDoubleArray(String objectPath, long size, int blockSize) { doubleWriter.createArray(objectPath, size, blockSize); } @Override public void createDoubleArray(String objectPath, int size, HDF5FloatStorageFeatures features) { doubleWriter.createArray(objectPath, size, features); } @Override public void createDoubleArray(String objectPath, long size, int blockSize, HDF5FloatStorageFeatures features) { doubleWriter.createArray(objectPath, size, blockSize, features); } @Override public void createDoubleMDArray(String objectPath, int[] blockDimensions) { doubleWriter.createMDArray(objectPath, blockDimensions); } @Override public void createDoubleMDArray(String objectPath, long[] dimensions, int[] blockDimensions) { doubleWriter.createMDArray(objectPath, dimensions, blockDimensions); } @Override public void createDoubleMDArray(String objectPath, int[] dimensions, HDF5FloatStorageFeatures features) { doubleWriter.createMDArray(objectPath, dimensions, features); } @Override public void createDoubleMDArray(String objectPath, long[] dimensions, int[] blockDimensions, HDF5FloatStorageFeatures features) { doubleWriter.createMDArray(objectPath, dimensions, blockDimensions, features); } @Override public void createDoubleMatrix(String objectPath, int blockSizeX, int blockSizeY) { doubleWriter.createMatrix(objectPath, blockSizeX, blockSizeY); } @Override public void createDoubleMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY) { doubleWriter.createMatrix(objectPath, sizeX, sizeY, blockSizeX, blockSizeY); } @Override public void createDoubleMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY, HDF5FloatStorageFeatures features) { doubleWriter.createMatrix(objectPath, sizeX, sizeY, blockSizeX, blockSizeY, features); } @Override public void setDoubleArrayAttribute(String objectPath, String name, double[] value) { doubleWriter.setArrayAttr(objectPath, name, value); } @Override public void setDoubleAttribute(String objectPath, String name, double value) { doubleWriter.setAttr(objectPath, name, value); } @Override public void setDoubleMDArrayAttribute(String objectPath, String name, MDDoubleArray value) { doubleWriter.setMDArrayAttr(objectPath, name, value); } @Override public void setDoubleMatrixAttribute(String objectPath, String name, double[][] value) { doubleWriter.setMatrixAttr(objectPath, name, value); } @Override public void writeDouble(String objectPath, double value) { doubleWriter.write(objectPath, value); } @Override public void writeDoubleArray(String objectPath, double[] data) { doubleWriter.writeArray(objectPath, data); } @Override public void writeDoubleArray(String objectPath, double[] data, HDF5FloatStorageFeatures features) { doubleWriter.writeArray(objectPath, data, features); } @Override public void writeDoubleArrayBlock(String objectPath, double[] data, long blockNumber) { doubleWriter.writeArrayBlock(objectPath, data, blockNumber); } @Override public void writeDoubleArrayBlockWithOffset(String objectPath, double[] data, int dataSize, long offset) { doubleWriter.writeArrayBlockWithOffset(objectPath, data, dataSize, offset); } @Override public void writeDoubleMDArray(String objectPath, MDDoubleArray data) { doubleWriter.writeMDArray(objectPath, data); } @Override public void writeDoubleMDArray(String objectPath, MDDoubleArray data, HDF5FloatStorageFeatures features) { doubleWriter.writeMDArray(objectPath, data, features); } @Override public void writeDoubleMDArrayBlock(String objectPath, MDDoubleArray data, long[] blockNumber) { doubleWriter.writeMDArrayBlock(objectPath, data, blockNumber); } @Override public void writeDoubleMDArrayBlockWithOffset(String objectPath, MDDoubleArray data, long[] offset) { doubleWriter.writeMDArrayBlockWithOffset(objectPath, data, offset); } @Override public void writeDoubleMDArrayBlockWithOffset(String objectPath, MDDoubleArray data, int[] blockDimensions, long[] offset, int[] memoryOffset) { doubleWriter.writeMDArrayBlockWithOffset(objectPath, data, blockDimensions, offset, memoryOffset); } @Override public void writeDoubleMatrix(String objectPath, double[][] data) { doubleWriter.writeMatrix(objectPath, data); } @Override public void writeDoubleMatrix(String objectPath, double[][] data, HDF5FloatStorageFeatures features) { doubleWriter.writeMatrix(objectPath, data, features); } @Override public void writeDoubleMatrixBlock(String objectPath, double[][] data, long blockNumberX, long blockNumberY) { doubleWriter.writeMatrixBlock(objectPath, data, blockNumberX, blockNumberY); } @Override public void writeDoubleMatrixBlockWithOffset(String objectPath, double[][] data, long offsetX, long offsetY) { doubleWriter.writeMatrixBlockWithOffset(objectPath, data, offsetX, offsetY); } @Override public void writeDoubleMatrixBlockWithOffset(String objectPath, double[][] data, int dataSizeX, int dataSizeY, long offsetX, long offsetY) { doubleWriter.writeMatrixBlockWithOffset(objectPath, data, dataSizeX, dataSizeY, offsetX, offsetY); } @Override public void createFloatArray(String objectPath, int blockSize) { floatWriter.createArray(objectPath, blockSize); } @Override public void createFloatArray(String objectPath, long size, int blockSize) { floatWriter.createArray(objectPath, size, blockSize); } @Override public void createFloatArray(String objectPath, int size, HDF5FloatStorageFeatures features) { floatWriter.createArray(objectPath, size, features); } @Override public void createFloatArray(String objectPath, long size, int blockSize, HDF5FloatStorageFeatures features) { floatWriter.createArray(objectPath, size, blockSize, features); } @Override public void createFloatMDArray(String objectPath, int[] blockDimensions) { floatWriter.createMDArray(objectPath, blockDimensions); } @Override public void createFloatMDArray(String objectPath, long[] dimensions, int[] blockDimensions) { floatWriter.createMDArray(objectPath, dimensions, blockDimensions); } @Override public void createFloatMDArray(String objectPath, int[] dimensions, HDF5FloatStorageFeatures features) { floatWriter.createMDArray(objectPath, dimensions, features); } @Override public void createFloatMDArray(String objectPath, long[] dimensions, int[] blockDimensions, HDF5FloatStorageFeatures features) { floatWriter.createMDArray(objectPath, dimensions, blockDimensions, features); } @Override public void createFloatMatrix(String objectPath, int blockSizeX, int blockSizeY) { floatWriter.createMatrix(objectPath, blockSizeX, blockSizeY); } @Override public void createFloatMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY) { floatWriter.createMatrix(objectPath, sizeX, sizeY, blockSizeX, blockSizeY); } @Override public void createFloatMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY, HDF5FloatStorageFeatures features) { floatWriter.createMatrix(objectPath, sizeX, sizeY, blockSizeX, blockSizeY, features); } @Override public void setFloatArrayAttribute(String objectPath, String name, float[] value) { floatWriter.setArrayAttr(objectPath, name, value); } @Override public void setFloatAttribute(String objectPath, String name, float value) { floatWriter.setAttr(objectPath, name, value); } @Override public void setFloatMDArrayAttribute(String objectPath, String name, MDFloatArray value) { floatWriter.setMDArrayAttr(objectPath, name, value); } @Override public void setFloatMatrixAttribute(String objectPath, String name, float[][] value) { floatWriter.setMatrixAttr(objectPath, name, value); } @Override public void writeFloat(String objectPath, float value) { floatWriter.write(objectPath, value); } @Override public void writeFloatArray(String objectPath, float[] data) { floatWriter.writeArray(objectPath, data); } @Override public void writeFloatArray(String objectPath, float[] data, HDF5FloatStorageFeatures features) { floatWriter.writeArray(objectPath, data, features); } @Override public void writeFloatArrayBlock(String objectPath, float[] data, long blockNumber) { floatWriter.writeArrayBlock(objectPath, data, blockNumber); } @Override public void writeFloatArrayBlockWithOffset(String objectPath, float[] data, int dataSize, long offset) { floatWriter.writeArrayBlockWithOffset(objectPath, data, dataSize, offset); } @Override public void writeFloatMDArray(String objectPath, MDFloatArray data) { floatWriter.writeMDArray(objectPath, data); } @Override public void writeFloatMDArray(String objectPath, MDFloatArray data, HDF5FloatStorageFeatures features) { floatWriter.writeMDArray(objectPath, data, features); } @Override public void writeFloatMDArrayBlock(String objectPath, MDFloatArray data, long[] blockNumber) { floatWriter.writeMDArrayBlock(objectPath, data, blockNumber); } @Override public void writeFloatMDArrayBlockWithOffset(String objectPath, MDFloatArray data, long[] offset) { floatWriter.writeMDArrayBlockWithOffset(objectPath, data, offset); } @Override public void writeFloatMDArrayBlockWithOffset(String objectPath, MDFloatArray data, int[] blockDimensions, long[] offset, int[] memoryOffset) { floatWriter.writeMDArrayBlockWithOffset(objectPath, data, blockDimensions, offset, memoryOffset); } @Override public void writeFloatMatrix(String objectPath, float[][] data) { floatWriter.writeMatrix(objectPath, data); } @Override public void writeFloatMatrix(String objectPath, float[][] data, HDF5FloatStorageFeatures features) { floatWriter.writeMatrix(objectPath, data, features); } @Override public void writeFloatMatrixBlock(String objectPath, float[][] data, long blockNumberX, long blockNumberY) { floatWriter.writeMatrixBlock(objectPath, data, blockNumberX, blockNumberY); } @Override public void writeFloatMatrixBlockWithOffset(String objectPath, float[][] data, long offsetX, long offsetY) { floatWriter.writeMatrixBlockWithOffset(objectPath, data, offsetX, offsetY); } @Override public void writeFloatMatrixBlockWithOffset(String objectPath, float[][] data, int dataSizeX, int dataSizeY, long offsetX, long offsetY) { floatWriter.writeMatrixBlockWithOffset(objectPath, data, dataSizeX, dataSizeY, offsetX, offsetY); } @Override public void createIntArray(String objectPath, int blockSize) { intWriter.createArray(objectPath, blockSize); } @Override public void createIntArray(String objectPath, long size, int blockSize) { intWriter.createArray(objectPath, size, blockSize); } @Override public void createIntArray(String objectPath, int size, HDF5IntStorageFeatures features) { intWriter.createArray(objectPath, size, features); } @Override public void createIntArray(String objectPath, long size, int blockSize, HDF5IntStorageFeatures features) { intWriter.createArray(objectPath, size, blockSize, features); } @Override public void createIntMDArray(String objectPath, int[] blockDimensions) { intWriter.createMDArray(objectPath, blockDimensions); } @Override public void createIntMDArray(String objectPath, long[] dimensions, int[] blockDimensions) { intWriter.createMDArray(objectPath, dimensions, blockDimensions); } @Override public void createIntMDArray(String objectPath, int[] dimensions, HDF5IntStorageFeatures features) { intWriter.createMDArray(objectPath, dimensions, features); } @Override public void createIntMDArray(String objectPath, long[] dimensions, int[] blockDimensions, HDF5IntStorageFeatures features) { intWriter.createMDArray(objectPath, dimensions, blockDimensions, features); } @Override public void createIntMatrix(String objectPath, int blockSizeX, int blockSizeY) { intWriter.createMatrix(objectPath, blockSizeX, blockSizeY); } @Override public void createIntMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY) { intWriter.createMatrix(objectPath, sizeX, sizeY, blockSizeX, blockSizeY); } @Override public void createIntMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY, HDF5IntStorageFeatures features) { intWriter.createMatrix(objectPath, sizeX, sizeY, blockSizeX, blockSizeY, features); } @Override public void setIntArrayAttribute(String objectPath, String name, int[] value) { intWriter.setArrayAttr(objectPath, name, value); } @Override public void setIntAttribute(String objectPath, String name, int value) { intWriter.setAttr(objectPath, name, value); } @Override public void setIntMDArrayAttribute(String objectPath, String name, MDIntArray value) { intWriter.setMDArrayAttr(objectPath, name, value); } @Override public void setIntMatrixAttribute(String objectPath, String name, int[][] value) { intWriter.setMatrixAttr(objectPath, name, value); } @Override public void writeInt(String objectPath, int value) { intWriter.write(objectPath, value); } @Override public void writeIntArray(String objectPath, int[] data) { intWriter.writeArray(objectPath, data); } @Override public void writeIntArray(String objectPath, int[] data, HDF5IntStorageFeatures features) { intWriter.writeArray(objectPath, data, features); } @Override public void writeIntArrayBlock(String objectPath, int[] data, long blockNumber) { intWriter.writeArrayBlock(objectPath, data, blockNumber); } @Override public void writeIntArrayBlockWithOffset(String objectPath, int[] data, int dataSize, long offset) { intWriter.writeArrayBlockWithOffset(objectPath, data, dataSize, offset); } @Override public void writeIntMDArray(String objectPath, MDIntArray data) { intWriter.writeMDArray(objectPath, data); } @Override public void writeIntMDArray(String objectPath, MDIntArray data, HDF5IntStorageFeatures features) { intWriter.writeMDArray(objectPath, data, features); } @Override public void writeIntMDArrayBlock(String objectPath, MDIntArray data, long[] blockNumber) { intWriter.writeMDArrayBlock(objectPath, data, blockNumber); } @Override public void writeIntMDArrayBlockWithOffset(String objectPath, MDIntArray data, long[] offset) { intWriter.writeMDArrayBlockWithOffset(objectPath, data, offset); } @Override public void writeIntMDArrayBlockWithOffset(String objectPath, MDIntArray data, int[] blockDimensions, long[] offset, int[] memoryOffset) { intWriter.writeMDArrayBlockWithOffset(objectPath, data, blockDimensions, offset, memoryOffset); } @Override public void writeIntMatrix(String objectPath, int[][] data) { intWriter.writeMatrix(objectPath, data); } @Override public void writeIntMatrix(String objectPath, int[][] data, HDF5IntStorageFeatures features) { intWriter.writeMatrix(objectPath, data, features); } @Override public void writeIntMatrixBlock(String objectPath, int[][] data, long blockNumberX, long blockNumberY) { intWriter.writeMatrixBlock(objectPath, data, blockNumberX, blockNumberY); } @Override public void writeIntMatrixBlockWithOffset(String objectPath, int[][] data, long offsetX, long offsetY) { intWriter.writeMatrixBlockWithOffset(objectPath, data, offsetX, offsetY); } @Override public void writeIntMatrixBlockWithOffset(String objectPath, int[][] data, int dataSizeX, int dataSizeY, long offsetX, long offsetY) { intWriter.writeMatrixBlockWithOffset(objectPath, data, dataSizeX, dataSizeY, offsetX, offsetY); } @Override public void createLongArray(String objectPath, int blockSize) { longWriter.createArray(objectPath, blockSize); } @Override public void createLongArray(String objectPath, long size, int blockSize) { longWriter.createArray(objectPath, size, blockSize); } @Override public void createLongArray(String objectPath, int size, HDF5IntStorageFeatures features) { longWriter.createArray(objectPath, size, features); } @Override public void createLongArray(String objectPath, long size, int blockSize, HDF5IntStorageFeatures features) { longWriter.createArray(objectPath, size, blockSize, features); } @Override public void createLongMDArray(String objectPath, int[] blockDimensions) { longWriter.createMDArray(objectPath, blockDimensions); } @Override public void createLongMDArray(String objectPath, long[] dimensions, int[] blockDimensions) { longWriter.createMDArray(objectPath, dimensions, blockDimensions); } @Override public void createLongMDArray(String objectPath, int[] dimensions, HDF5IntStorageFeatures features) { longWriter.createMDArray(objectPath, dimensions, features); } @Override public void createLongMDArray(String objectPath, long[] dimensions, int[] blockDimensions, HDF5IntStorageFeatures features) { longWriter.createMDArray(objectPath, dimensions, blockDimensions, features); } @Override public void createLongMatrix(String objectPath, int blockSizeX, int blockSizeY) { longWriter.createMatrix(objectPath, blockSizeX, blockSizeY); } @Override public void createLongMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY) { longWriter.createMatrix(objectPath, sizeX, sizeY, blockSizeX, blockSizeY); } @Override public void createLongMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY, HDF5IntStorageFeatures features) { longWriter.createMatrix(objectPath, sizeX, sizeY, blockSizeX, blockSizeY, features); } @Override public void setLongArrayAttribute(String objectPath, String name, long[] value) { longWriter.setArrayAttr(objectPath, name, value); } @Override public void setLongAttribute(String objectPath, String name, long value) { longWriter.setAttr(objectPath, name, value); } @Override public void setLongMDArrayAttribute(String objectPath, String name, MDLongArray value) { longWriter.setMDArrayAttr(objectPath, name, value); } @Override public void setLongMatrixAttribute(String objectPath, String name, long[][] value) { longWriter.setMatrixAttr(objectPath, name, value); } @Override public void writeLong(String objectPath, long value) { longWriter.write(objectPath, value); } @Override public void writeLongArray(String objectPath, long[] data) { longWriter.writeArray(objectPath, data); } @Override public void writeLongArray(String objectPath, long[] data, HDF5IntStorageFeatures features) { longWriter.writeArray(objectPath, data, features); } @Override public void writeLongArrayBlock(String objectPath, long[] data, long blockNumber) { longWriter.writeArrayBlock(objectPath, data, blockNumber); } @Override public void writeLongArrayBlockWithOffset(String objectPath, long[] data, int dataSize, long offset) { longWriter.writeArrayBlockWithOffset(objectPath, data, dataSize, offset); } @Override public void writeLongMDArray(String objectPath, MDLongArray data) { longWriter.writeMDArray(objectPath, data); } @Override public void writeLongMDArray(String objectPath, MDLongArray data, HDF5IntStorageFeatures features) { longWriter.writeMDArray(objectPath, data, features); } @Override public void writeLongMDArrayBlock(String objectPath, MDLongArray data, long[] blockNumber) { longWriter.writeMDArrayBlock(objectPath, data, blockNumber); } @Override public void writeLongMDArrayBlockWithOffset(String objectPath, MDLongArray data, long[] offset) { longWriter.writeMDArrayBlockWithOffset(objectPath, data, offset); } @Override public void writeLongMDArrayBlockWithOffset(String objectPath, MDLongArray data, int[] blockDimensions, long[] offset, int[] memoryOffset) { longWriter.writeMDArrayBlockWithOffset(objectPath, data, blockDimensions, offset, memoryOffset); } @Override public void writeLongMatrix(String objectPath, long[][] data) { longWriter.writeMatrix(objectPath, data); } @Override public void writeLongMatrix(String objectPath, long[][] data, HDF5IntStorageFeatures features) { longWriter.writeMatrix(objectPath, data, features); } @Override public void writeLongMatrixBlock(String objectPath, long[][] data, long blockNumberX, long blockNumberY) { longWriter.writeMatrixBlock(objectPath, data, blockNumberX, blockNumberY); } @Override public void writeLongMatrixBlockWithOffset(String objectPath, long[][] data, long offsetX, long offsetY) { longWriter.writeMatrixBlockWithOffset(objectPath, data, offsetX, offsetY); } @Override public void writeLongMatrixBlockWithOffset(String objectPath, long[][] data, int dataSizeX, int dataSizeY, long offsetX, long offsetY) { longWriter.writeMatrixBlockWithOffset(objectPath, data, dataSizeX, dataSizeY, offsetX, offsetY); } @Override public void createShortArray(String objectPath, int blockSize) { shortWriter.createArray(objectPath, blockSize); } @Override public void createShortArray(String objectPath, long size, int blockSize) { shortWriter.createArray(objectPath, size, blockSize); } @Override public void createShortArray(String objectPath, int size, HDF5IntStorageFeatures features) { shortWriter.createArray(objectPath, size, features); } @Override public void createShortArray(String objectPath, long size, int blockSize, HDF5IntStorageFeatures features) { shortWriter.createArray(objectPath, size, blockSize, features); } @Override public void createShortMDArray(String objectPath, int[] blockDimensions) { shortWriter.createMDArray(objectPath, blockDimensions); } @Override public void createShortMDArray(String objectPath, long[] dimensions, int[] blockDimensions) { shortWriter.createMDArray(objectPath, dimensions, blockDimensions); } @Override public void createShortMDArray(String objectPath, int[] dimensions, HDF5IntStorageFeatures features) { shortWriter.createMDArray(objectPath, dimensions, features); } @Override public void createShortMDArray(String objectPath, long[] dimensions, int[] blockDimensions, HDF5IntStorageFeatures features) { shortWriter.createMDArray(objectPath, dimensions, blockDimensions, features); } @Override public void createShortMatrix(String objectPath, int blockSizeX, int blockSizeY) { shortWriter.createMatrix(objectPath, blockSizeX, blockSizeY); } @Override public void createShortMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY) { shortWriter.createMatrix(objectPath, sizeX, sizeY, blockSizeX, blockSizeY); } @Override public void createShortMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY, HDF5IntStorageFeatures features) { shortWriter.createMatrix(objectPath, sizeX, sizeY, blockSizeX, blockSizeY, features); } @Override public void setShortArrayAttribute(String objectPath, String name, short[] value) { shortWriter.setArrayAttr(objectPath, name, value); } @Override public void setShortAttribute(String objectPath, String name, short value) { shortWriter.setAttr(objectPath, name, value); } @Override public void setShortMDArrayAttribute(String objectPath, String name, MDShortArray value) { shortWriter.setMDArrayAttr(objectPath, name, value); } @Override public void setShortMatrixAttribute(String objectPath, String name, short[][] value) { shortWriter.setMatrixAttr(objectPath, name, value); } @Override public void writeShort(String objectPath, short value) { shortWriter.write(objectPath, value); } @Override public void writeShortArray(String objectPath, short[] data) { shortWriter.writeArray(objectPath, data); } @Override public void writeShortArray(String objectPath, short[] data, HDF5IntStorageFeatures features) { shortWriter.writeArray(objectPath, data, features); } @Override public void writeShortArrayBlock(String objectPath, short[] data, long blockNumber) { shortWriter.writeArrayBlock(objectPath, data, blockNumber); } @Override public void writeShortArrayBlockWithOffset(String objectPath, short[] data, int dataSize, long offset) { shortWriter.writeArrayBlockWithOffset(objectPath, data, dataSize, offset); } @Override public void writeShortMDArray(String objectPath, MDShortArray data) { shortWriter.writeMDArray(objectPath, data); } @Override public void writeShortMDArray(String objectPath, MDShortArray data, HDF5IntStorageFeatures features) { shortWriter.writeMDArray(objectPath, data, features); } @Override public void writeShortMDArrayBlock(String objectPath, MDShortArray data, long[] blockNumber) { shortWriter.writeMDArrayBlock(objectPath, data, blockNumber); } @Override public void writeShortMDArrayBlockWithOffset(String objectPath, MDShortArray data, long[] offset) { shortWriter.writeMDArrayBlockWithOffset(objectPath, data, offset); } @Override public void writeShortMDArrayBlockWithOffset(String objectPath, MDShortArray data, int[] blockDimensions, long[] offset, int[] memoryOffset) { shortWriter.writeMDArrayBlockWithOffset(objectPath, data, blockDimensions, offset, memoryOffset); } @Override public void writeShortMatrix(String objectPath, short[][] data) { shortWriter.writeMatrix(objectPath, data); } @Override public void writeShortMatrix(String objectPath, short[][] data, HDF5IntStorageFeatures features) { shortWriter.writeMatrix(objectPath, data, features); } @Override public void writeShortMatrixBlock(String objectPath, short[][] data, long blockNumberX, long blockNumberY) { shortWriter.writeMatrixBlock(objectPath, data, blockNumberX, blockNumberY); } @Override public void writeShortMatrixBlockWithOffset(String objectPath, short[][] data, long offsetX, long offsetY) { shortWriter.writeMatrixBlockWithOffset(objectPath, data, offsetX, offsetY); } @Override public void writeShortMatrixBlockWithOffset(String objectPath, short[][] data, int dataSizeX, int dataSizeY, long offsetX, long offsetY) { shortWriter.writeMatrixBlockWithOffset(objectPath, data, dataSizeX, dataSizeY, offsetX, offsetY); } @Override public IHDF5ByteWriter int8() { return byteWriter; } @Override public IHDF5ByteWriter uint8() { return ubyteWriter; } @Override public IHDF5ShortWriter int16() { return shortWriter; } @Override public IHDF5ShortWriter uint16() { return ushortWriter; } @Override public IHDF5IntWriter int32() { return intWriter; } @Override public IHDF5IntWriter uint32() { return uintWriter; } @Override public IHDF5LongWriter int64() { return longWriter; } @Override public IHDF5LongWriter uint64() { return ulongWriter; } @Override public IHDF5FloatWriter float32() { return floatWriter; } @Override public IHDF5DoubleWriter float64() { return doubleWriter; } // ------------------------------------------------------------------------------ // Primitive Types - END // ------------------------------------------------------------------------------ } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5WriterConfigurator.java000066400000000000000000000074151256564762100305020ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.io.File; import ch.systemsx.cisd.base.utilities.OSUtilities; /** * The configuration of the writer is done by chaining calls to configuration methods before calling * {@link #writer()}. * * @author Bernd Rinn */ final class HDF5WriterConfigurator extends HDF5ReaderConfigurator implements IHDF5WriterConfigurator { private boolean useExtentableDataTypes = true; private boolean overwriteFile = false; private boolean keepDataSetIfExists = false; private boolean useSimpleDataSpaceForAttributes = false; private FileFormat fileFormat = FileFormat.ALLOW_1_8; private String houseKeepingNameSuffix = ""; // For Windows, use a blocking sync mode by default as otherwise the mandatory locks are up for // some surprises after the file has been closed. private SyncMode syncMode = OSUtilities.isWindows() ? SyncMode.SYNC_ON_FLUSH_BLOCK : SyncMode.SYNC_ON_FLUSH; public HDF5WriterConfigurator(File hdf5File) { super(hdf5File); } @Override public HDF5WriterConfigurator overwrite() { this.overwriteFile = true; return this; } @Override public HDF5WriterConfigurator keepDataSetsIfTheyExist() { this.keepDataSetIfExists = true; return this; } @Override public HDF5WriterConfigurator dontUseExtendableDataTypes() { this.useExtentableDataTypes = false; return this; } @Override public HDF5WriterConfigurator useSimpleDataSpaceForAttributes() { this.useSimpleDataSpaceForAttributes = true; return this; } @Override public HDF5WriterConfigurator fileFormat(FileFormat newFileFormat) { this.fileFormat = newFileFormat; return this; } @Override public HDF5WriterConfigurator syncMode(SyncMode newSyncMode) { this.syncMode = newSyncMode; return this; } @Override public IHDF5WriterConfigurator houseKeepingNameSuffix(@SuppressWarnings("hiding") String houseKeepingNameSuffix) { this.houseKeepingNameSuffix = houseKeepingNameSuffix; return this; } @Override public HDF5WriterConfigurator performNumericConversions() { return (HDF5WriterConfigurator) super.performNumericConversions(); } @Override public HDF5WriterConfigurator useUTF8CharacterEncoding() { return (HDF5WriterConfigurator) super.useUTF8CharacterEncoding(); } @Override public HDF5WriterConfigurator noAutoDereference() { return (HDF5WriterConfigurator) super.noAutoDereference(); } @Override public IHDF5Writer writer() { if (readerWriterOrNull == null) { readerWriterOrNull = new HDF5Writer(new HDF5BaseWriter(hdf5File, performNumericConversions, useUTF8CharEncoding, autoDereference, fileFormat, useExtentableDataTypes, overwriteFile, keepDataSetIfExists, useSimpleDataSpaceForAttributes, houseKeepingNameSuffix, syncMode)); } return (HDF5Writer) readerWriterOrNull; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5BooleanReader.java000066400000000000000000000201671256564762100274550ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.util.BitSet; import ncsa.hdf.hdf5lib.exceptions.HDF5DatatypeInterfaceException; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; /** * An interface that provides methods for reading boolean and bit field values from HDF5 files. * * @author Bernd Rinn */ public interface IHDF5BooleanReader { /** * Reads a boolean attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. * @throws HDF5JavaException If the attribute is not a boolean type. */ public boolean getAttr(String objectPath, String attributeName) throws HDF5JavaException; /** * Reads a Boolean value from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a boolean type. */ public boolean read(String objectPath) throws HDF5JavaException; /** * Reads a bit field (which can be considered the equivalent to a boolean array of rank 1) from * the data set objectPath and returns it as a Java {@link BitSet}. *

* Note that the storage form of the bit array is a long[]. However, it is marked * in HDF5 to be interpreted bit-wise. Thus a data set written by * {@link IHDF5LongWriter#writeArray(String, long[])} cannot be read back by this method but * will throw a {@link HDF5DatatypeInterfaceException}. * * @param objectPath The name (including path information) of the data set object in the file. * @return The {@link BitSet} read from the data set. * @throws HDF5DatatypeInterfaceException If the objectPath is not of bit field type. */ public BitSet readBitField(String objectPath) throws HDF5DatatypeInterfaceException; /** * Reads a block of a bit field (which can be considered the equivalent to a boolean array of * rank 1) from the data set objectPath and returns it as a Java {@link BitSet}. *

* Note that the storage form of the bit array is a long[]. However, it is marked * in HDF5 to be interpreted bit-wise. Thus a data set written by * {@link IHDF5LongWriter#writeArray(String, long[])} cannot be read back by this method but * will throw a {@link HDF5DatatypeInterfaceException}. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The size of the block (in 64 bit words) to read. * @param blockNumber The number of the block to read. * @return The {@link BitSet} read from the data set. * @throws HDF5DatatypeInterfaceException If the objectPath is not of bit field type. */ public BitSet readBitFieldBlock(String objectPath, int blockSize, long blockNumber); /** * Reads a block of a bit field (which can be considered the equivalent to a boolean array of * rank 1) from the data set objectPath and returns it as a Java {@link BitSet}. *

* Note that the storage form of the bit array is a long[]. However, it is marked * in HDF5 to be interpreted bit-wise. Thus a data set written by * {@link IHDF5LongWriter#writeArray(String, long[])} cannot be read back by this method but * will throw a {@link HDF5DatatypeInterfaceException}. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The size of the block (in 64 bit words) to read. * @param offset The offset of the block (in 64 bit words) to start reading from. * @return The {@link BitSet} read from the data set. * @throws HDF5DatatypeInterfaceException If the objectPath is not of bit field type. */ public BitSet readBitFieldBlockWithOffset(String objectPath, int blockSize, long offset); /** * Returns true if the bitIndex of the bit field dataset * objectPath is set, false otherwise. *

* Will also return false, if bitIndex is outside of the bitfield * dataset. */ public boolean isBitSet(String objectPath, int bitIndex); /** * Reads a bit field array (which can be considered the equivalent to a boolean array of rank 2) * from the data set objectPath and returns it as a Java {@link BitSet}. *

* Note that the storage form of the bit array is a long[]. However, it is marked * in HDF5 to be interpreted bit-wise. Thus a data set written by * {@link IHDF5LongWriter#writeMatrix(String, long[][])} cannot be read back by this method but * will throw a {@link HDF5DatatypeInterfaceException}. * * @param objectPath The name (including path information) of the data set object in the file. * @return The {@link BitSet} array read from the data set. * @throws HDF5DatatypeInterfaceException If the objectPath is not of bit field type. */ public BitSet[] readBitFieldArray(String objectPath); /** * Reads a block of a bit field array (which can be considered the equivalent to a boolean array * of rank 2) from the data set objectPath and returns it as a Java {@link BitSet}. *

* Note that the storage form of the bit array is a long[]. However, it is marked * in HDF5 to be interpreted bit-wise. Thus a data set written by * {@link IHDF5LongWriter#writeMatrix(String, long[][])} cannot be read back by this method but * will throw a {@link HDF5DatatypeInterfaceException}. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The size of the array block. * @param offset The offset in the array where to start reading the block. * @return The {@link BitSet} array read from the data set. * @throws HDF5DatatypeInterfaceException If the objectPath is not of bit field type. */ public BitSet[] readBitFieldArrayBlockWithOffset(String objectPath, int blockSize, long offset); /** * Reads a block of a bit field array (which can be considered the equivalent to a boolean array * of rank 2) from the data set objectPath and returns it as a Java {@link BitSet}. *

* Note that the storage form of the bit array is a long[]. However, it is marked * in HDF5 to be interpreted bit-wise. Thus a data set written by * {@link IHDF5LongWriter#writeMatrix(String, long[][])} cannot be read back by this method but * will throw a {@link HDF5DatatypeInterfaceException}. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The size of the array block. * @param blockNumber The number of the array block (offset is blockNumber * blockSize.). * @return The {@link BitSet} array read from the data set. * @throws HDF5DatatypeInterfaceException If the objectPath is not of bit field type. */ public BitSet[] readBitFieldArrayBlock(String objectPath, int blockSize, long blockNumber); }libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5BooleanWriter.java000066400000000000000000000445271256564762100275350ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.util.BitSet; /** * An interface that provides methods for writing boolean values to HDF5 files. * * @author Bernd Rinn */ public interface IHDF5BooleanWriter extends IHDF5BooleanReader { /** * Sets a boolean attribute to the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setAttr(String objectPath, String name, boolean value); /** * Writes out a boolean value. * * @param objectPath The name (including path information) of the data set object in the file. * @param value The value of the data set. */ public void write(String objectPath, boolean value); /** * Writes out a bit field ((which can be considered the equivalent to a boolean array of rank * 1), provided as a Java {@link BitSet}. *

* Note that the storage form of the bit array is a long[]. However, it is marked * in HDF5 to be interpreted bit-wise. Thus a data set written by this method cannot be read * back by {@link IHDF5LongReader#readArray(String)} but will throw a * {@link ncsa.hdf.hdf5lib.exceptions.HDF5DatatypeInterfaceException}. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ public void writeBitField(String objectPath, BitSet data); /** * Writes out a bit field ((which can be considered the equivalent to a boolean array of rank * 1), provided as a Java {@link BitSet}. *

* Note that the storage form of the bit array is a long[]. However, it is marked * in HDF5 to be interpreted bit-wise. Thus a data set written by this method cannot be read * back by {@link IHDF5LongReader#readArray(String)} but will throw a * {@link ncsa.hdf.hdf5lib.exceptions.HDF5DatatypeInterfaceException}. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param features The storage features of the data set. */ public void writeBitField(String objectPath, BitSet data, HDF5GenericStorageFeatures features); /** * Creates a bit field (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size (in 64 bit words) of the bit field to create. This will be the total * size for non-extendable data sets and the size of one chunk for extendable * (chunked) data sets. For extendable data sets the initial size of the array will * be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. */ public void createBitField(String objectPath, int size); /** * Creates a bit field (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size (in 64 bit words) of the bit field to create. When using extendable data * sets ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no * data set smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). */ public void createBitField(String objectPath, long size, int blockSize); /** * Creates a bit field array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size (in 64 bit words) of the bit field to create. This will be the total * size for non-extendable data sets and the size of one chunk for extendable * (chunked) data sets. For extendable data sets the initial size of the array will * be 0, see {@link HDF5IntStorageFeatures}. * @param features The storage features of the data set. */ public void createBitField(String objectPath, int size, HDF5GenericStorageFeatures features); /** * Creates a bit field (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size (in 64 bit words) of the bit field to create. When using extendable data * sets ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no * data set smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) * and features is HDF5IntStorageFeature.INT_NO_COMPRESSION * . * @param features The storage features of the data set. */ public void createBitField(String objectPath, long size, int blockSize, HDF5GenericStorageFeatures features); /** * Writes out a block of a bit field (of rank 1). The data set needs to have been created by * {@link #createBitField(String, long, int, HDF5GenericStorageFeatures)} beforehand. *

* Note: For best performance, the block size in this method should be chosen to be equal * to the blockSize argument of the * {@link #createBitField(String, long, int, HDF5GenericStorageFeatures)} call that was used to * create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param dataSize The (real) size of data * @param blockNumber The number of the block to write. */ public void writeBitFieldBlock(String objectPath, BitSet data, int dataSize, long blockNumber); /** * Writes out a block of a long array (of rank 1). The data set needs to have been * created by {@link #createBitFieldArray(String, int, long, long, HDF5IntStorageFeatures)} * beforehand. *

* Use this method instead of {@link #writeBitFieldBlock(String, BitSet, int, long)} if the * total size of the data set is not a multiple of the block size. *

* Note: For best performance, the typical dataSize in this method should be * chosen to be equal to the blockSize argument of the * {@link #createBitField(String, long, int, HDF5GenericStorageFeatures)} call that was used to * create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param dataSize The (real) size of data * @param offset The offset in the data set to start writing to. */ public void writeBitFieldBlockWithOffset(String objectPath, BitSet data, int dataSize, long offset); /** * Writes out an array of bit fields (which can be considered the equivalent to a boolean array * of rank 2), provided as a Java array of {@link BitSet}s. *

* Note that the storage form of the bit array is a long[]. However, it is marked * in HDF5 to be interpreted bit-wise. Thus a data set written by this method cannot be read * back by {@link IHDF5LongReader#readArray(String)} but will throw a * {@link ncsa.hdf.hdf5lib.exceptions.HDF5DatatypeInterfaceException}. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param features The storage features of the data set. */ public void writeBitFieldArray(String objectPath, BitSet[] data, HDF5IntStorageFeatures features); /** * Writes out an array of bit fields (which can be considered the equivalent to a boolean array * of rank 2), provided as a Java array of {@link BitSet}s. *

* Note that the storage form of the bit array is a long[]. However, it is marked * in HDF5 to be interpreted bit-wise. Thus a data set written by this method cannot be read * back by {@link IHDF5LongReader#readArray(String)} but will throw a * {@link ncsa.hdf.hdf5lib.exceptions.HDF5DatatypeInterfaceException}. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ public void writeBitFieldArray(String objectPath, BitSet[] data); /** * Creates an array of bit fields (of rank 1) (which can be considered the equivalent to a * boolean array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param bitFieldSize The size of the bit fields in the array (in 64 bit words). * @param arraySize The size of the array of bit fields to create. When using extendable data * sets ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no * data set smaller than this size can be created, however data sets may be larger. * @param arrayBlockSize The size of one block (for block-wise IO). Ignored if no extendable * data sets are used (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) and * features is HDF5IntStorageFeature.INT_NO_COMPRESSION. * @param features The storage features of the data set. */ public void createBitFieldArray(String objectPath, int bitFieldSize, long arraySize, long arrayBlockSize, HDF5IntStorageFeatures features); /** * Creates an array of bit fields (of rank 1) (which can be considered the equivalent to a * boolean array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param bitFieldSize The size of the bit fields in the array (in 64 bit words). * @param arraySize The size of the array of bit fields to create. When using extendable data * sets ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no * data set smaller than this size can be created, however data sets may be larger. * @param arrayBlockSize The size of one block (for block-wise IO). Ignored if no extendable * data sets are used (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) and * features is HDF5IntStorageFeature.INT_NO_COMPRESSION. */ public void createBitFieldArray(String objectPath, int bitFieldSize, long arraySize, long arrayBlockSize); /** * Creates an empty array of bit fields (of rank 1) (which can be considered the equivalent to a * boolean array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param bitFieldSize The size of the bit fields in the array (in 64 bit words). * @param arraySize The size of the long array to create. When requesting a chunked data * set (e.g. {@link HDF5IntStorageFeatures#INT_CHUNKED}), the initial size of the * array will be 0 and the chunk size will be arraySize. When * allowing a chunked data set (e.g. * {@link HDF5IntStorageFeatures#INT_NO_COMPRESSION} when the writer is not * configured to avoid extendable data types, see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be arraySize. When * enforcing a on-extendable data set (e.g. * {@link HDF5IntStorageFeatures#INT_CONTIGUOUS}), the initial size equals the total size * and will be arraySize. * @param features The storage features of the data set. */ public void createBitFieldArray(String objectPath, int bitFieldSize, long arraySize, HDF5IntStorageFeatures features); /** * Creates an empty array of bit fields (of rank 1) (which can be considered the equivalent to a * boolean array of rank 2). This method always creates an extendable data sets. * * @param objectPath The name (including path information) of the data set object in the file. * @param bitFieldSize The size of the bit fields in the array (in 64 bit words). * @param arraySize When the writer is configured to use extendable data types (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be arraySize. When the writer is * configured to enforce a on-extendable data set, the initial size equals the * total size and will be arraySize. */ public void createBitFieldArray(String objectPath, int bitFieldSize, long arraySize); /** * Writes out an array of bit fields (which can be considered the equivalent to a boolean array * of rank 2), provided as a Java array of {@link BitSet}s. *

* Note that the storage form of the bit array is a long[]. However, it is marked * in HDF5 to be interpreted bit-wise. Thus a data set written by this method cannot be read * back by {@link IHDF5LongReader#readArray(String)} but will throw a * {@link ncsa.hdf.hdf5lib.exceptions.HDF5DatatypeInterfaceException}. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param dataSize The number of entries from data to write to the bitfield array * (must be smaller or equals to data.length. * @param blockNumber The block number in the array (offset: multiply with * dataSize>). */ public void writeBitFieldArrayBlock(String objectPath, BitSet[] data, int dataSize, long blockNumber); /** * Writes out an array of bit fields (which can be considered the equivalent to a boolean array * of rank 2), provided as a Java array of {@link BitSet}s. *

* Note that the storage form of the bit array is a long[]. However, it is marked * in HDF5 to be interpreted bit-wise. Thus a data set written by this method cannot be read * back by {@link IHDF5LongReader#readArray(String)} but will throw a * {@link ncsa.hdf.hdf5lib.exceptions.HDF5DatatypeInterfaceException}. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param blockNumber The block number in the array (offset: multiply with * data.length). */ public void writeBitFieldArrayBlock(String objectPath, BitSet[] data, long blockNumber); /** * Writes out an array of bit fields (which can be considered the equivalent to a boolean array * of rank 2), provided as a Java array of {@link BitSet}s. *

* Note that the storage form of the bit array is a long[]. However, it is marked * in HDF5 to be interpreted bit-wise. Thus a data set written by this method cannot be read * back by {@link IHDF5LongReader#readArray(String)} but will throw a * {@link ncsa.hdf.hdf5lib.exceptions.HDF5DatatypeInterfaceException}. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param dataSize The number of entries from data to write to the bitfield array * (must be smaller or equals to data.length. * @param offset The offset in the bitfield array where to start writing the data. */ public void writeBitFieldArrayBlockWithOffset(String objectPath, BitSet[] data, int dataSize, long offset); /** * Writes out an array of bit fields (which can be considered the equivalent to a boolean array * of rank 2), provided as a Java array of {@link BitSet}s. *

* Note that the storage form of the bit array is a long[]. However, it is marked * in HDF5 to be interpreted bit-wise. Thus a data set written by this method cannot be read * back by {@link IHDF5LongReader#readArray(String)} but will throw a * {@link ncsa.hdf.hdf5lib.exceptions.HDF5DatatypeInterfaceException}. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param offset The offset in the bitfield array where to start writing the data. */ public void writeBitFieldArrayBlockWithOffset(String objectPath, BitSet[] data, long offset); }libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5ByteReader.java000066400000000000000000000424501256564762100270000ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.base.mdarray.MDByteArray; /** * An interface that provides methods for reading byte values from HDF5 files. *

* Note: This interface supports block access and sliced access (which is a special cases of * block access) to arrays. The performance of this block access can vary greatly depending on how * the data are layed out in the HDF5 file. For best performance, the block (or slice) dimension should * be chosen to be equal to the chunk dimensions of the array, as in this case the block written / read * are stored as consecutive value in the HDF5 file and one write / read access will suffice. *

* Note: If the values read are unsigned, use the methods in {@link UnsignedIntUtils} to convert * to a larger Java integer type that can hold all values as unsigned. * * @author Bernd Rinn */ public interface IHDF5ByteReader { // ///////////////////// // Attributes // ///////////////////// /** * Reads a byte attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. */ public byte getAttr(String objectPath, String attributeName); /** * Reads a byte[] attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. */ public byte[] getArrayAttr(String objectPath, String attributeName); /** * Reads a multi-dimensional array byte attribute named attributeName * from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute array value read from the data set. */ public MDByteArray getMDArrayAttr(String objectPath, String attributeName); /** * Reads a byte matrix attribute named attributeName * from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute matrix value read from the data set. */ public byte[][] getMatrixAttr(String objectPath, String attributeName) throws HDF5JavaException; // ///////////////////// // Data Sets // ///////////////////// /** * Reads a byte value from the data set objectPath. This method * doesn't check the data space but simply reads the first value. * * @param objectPath The name (including path information) of the data set object in the file. * @return The value read from the data set. */ public byte read(String objectPath); /** * Reads a byte array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. */ public byte[] readArray(String objectPath); /** * Reads a multi-dimensional byte array data set objectPath * into a given array in memory. * * @param objectPath The name (including path information) of the data set object in the file. * @param array The array to read the data into. * @param memoryOffset The offset in the array to write the data to. * @return The effective dimensions of the block in array that was filled. */ public int[] readToMDArrayWithOffset(String objectPath, MDByteArray array, int[] memoryOffset); /** * Reads a block of the multi-dimensional byte array data set * objectPath into a given array in memory. * * @param objectPath The name (including path information) of the data set object in the file. * @param array The array to read the data into. * @param blockDimensions The size of the block to read along each axis. * @param offset The offset of the block in the data set. * @param memoryOffset The offset of the block in the array to write the data to. * @return The effective dimensions of the block in array that was filled. */ public int[] readToMDArrayBlockWithOffset(String objectPath, MDByteArray array, int[] blockDimensions, long[] offset, int[] memoryOffset); /** * Reads a block from a byte array (of rank 1) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the byte[] returned * if the data set is long enough). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @return The data read from the data set. The length will be min(size - blockSize*blockNumber, * blockSize). */ public byte[] readArrayBlock(String objectPath, int blockSize, long blockNumber); /** * Reads a block from byte array (of rank 1) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the byte[] * returned). * @param offset The offset of the block in the data set to start reading from (starting with 0). * @return The data block read from the data set. */ public byte[] readArrayBlockWithOffset(String objectPath, int blockSize, long offset); /** * Reads a byte matrix (array of arrays) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * * @throws HDF5JavaException If the data set objectPath is not of rank 2. */ public byte[][] readMatrix(String objectPath) throws HDF5JavaException; /** * Reads a byte matrix (array of arrays) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSizeX The size of the block in the x dimension. * @param blockSizeY The size of the block in the y dimension. * @param blockNumberX The block number in the x dimension (offset: multiply with * blockSizeX). * @param blockNumberY The block number in the y dimension (offset: multiply with * blockSizeY). * @return The data block read from the data set. * * @throws HDF5JavaException If the data set objectPath is not of rank 2. */ public byte[][] readMatrixBlock(String objectPath, int blockSizeX, int blockSizeY, long blockNumberX, long blockNumberY) throws HDF5JavaException; /** * Reads a byte matrix (array of arrays) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSizeX The size of the block in the x dimension. * @param blockSizeY The size of the block in the y dimension. * @param offsetX The offset in x dimension in the data set to start reading from. * @param offsetY The offset in y dimension in the data set to start reading from. * @return The data block read from the data set. * * @throws HDF5JavaException If the data set objectPath is not of rank 2. */ public byte[][] readMatrixBlockWithOffset(String objectPath, int blockSizeX, int blockSizeY, long offsetX, long offsetY) throws HDF5JavaException; /** * Reads a multi-dimensional byte array from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. */ public MDByteArray readMDArray(String objectPath); /** * Reads a slice of a multi-dimensional byte array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDByteArray readMDArraySlice(String objectPath, IndexMap boundIndices); /** * Reads a slice of a multi-dimensional byte array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDByteArray readMDArraySlice(String objectPath, long[] boundIndices); /** * Reads a block from a multi-dimensional byte array from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @return The data block read from the data set. */ public MDByteArray readMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber); /** * Reads a sliced block from a multi-dimensional byte array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDByteArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, IndexMap boundIndices); /** * Reads a sliced block from a multi-dimensional byte array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDByteArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, long[] boundIndices); /** * Reads a block from a multi-dimensional byte array from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @return The data block read from the data set. */ public MDByteArray readMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset); /** * Reads a sliced block of a multi-dimensional byte array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDByteArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, IndexMap boundIndices); /** * Reads a sliced block of a multi-dimensional byte array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDByteArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, long[] boundIndices); /** * Provides all natural blocks of this one-dimensional data set to iterate over. * * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1. */ public Iterable> getArrayNaturalBlocks( String dataSetPath) throws HDF5JavaException; /** * Provides all natural blocks of this multi-dimensional data set to iterate over. * * @see HDF5MDDataBlock */ public Iterable> getMDArrayNaturalBlocks( String dataSetPath); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5ByteWriter.java000066400000000000000000000712741256564762100270600ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ch.systemsx.cisd.base.mdarray.MDByteArray; /** * An interface that provides methods for writing byte values to HDF5 files. *

* Note: This interface supports block access and sliced access (which is a special cases of * block access) to arrays. The performance of this block access can vary greatly depending on how * the data are layed out in the HDF5 file. For best performance, the block (or slice) dimension should * be chosen to be equal to the chunk dimensions of the array, as in this case the block written / read * are stored as consecutive value in the HDF5 file and one write / read access will suffice. *

* Note: If you need to convert from and to unsigned values, use the methods of * {@link UnsignedIntUtils}. * * @author Bernd Rinn */ // Note: It is a trick for keeping backward compatibility to let this interface extend // IHDF5UnsignedByteWriter instead of IHDF5ByteReader as it logically should. // Once we remove IHDF5UnsignedByteWriter, uncomment the following line and remove // all @Override annotations and we are fine again. //public interface IHDF5ByteWriter extends IHDF5ByteReader @SuppressWarnings("deprecation") public interface IHDF5ByteWriter extends IHDF5UnsignedByteWriter { // ///////////////////// // Attributes // ///////////////////// /** * Set a byte attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ @Override public void setAttr(String objectPath, String name, byte value); /** * Set a byte[] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ @Override public void setArrayAttr(String objectPath, String name, byte[] value); /** * Set a multi-dimensional code>byte attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ @Override public void setMDArrayAttr(String objectPath, String name, MDByteArray value); /** * Set a byte[][] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ @Override public void setMatrixAttr(String objectPath, String name, byte[][] value); // ///////////////////// // Data Sets // ///////////////////// /** * Writes out a byte value. * * @param objectPath The name (including path information) of the data set object in the file. * @param value The value to write. */ @Override public void write(String objectPath, byte value); /** * Writes out a byte array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ @Override public void writeArray(String objectPath, byte[] data); /** * Writes out a byte array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param features The storage features of the data set. */ @Override public void writeArray(String objectPath, byte[] data, HDF5IntStorageFeatures features); /** * Creates a byte array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size When the writer is configured to use extendable data types (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be size. When the writer is * configured to enforce a non-extendable data set, the initial size equals the * total size and will be size. */ @Override public void createArray(String objectPath, int size); /** * Creates a byte array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the byte array to create. When using extendable data sets * ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data * set smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). */ @Override public void createArray(String objectPath, long size, int blockSize); /** * Creates a byte array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the byte array to create. When requesting a * chunked data set (e.g. {@link HDF5IntStorageFeatures#INT_CHUNKED}), * the initial size of the array will be 0 and the chunk size will be arraySize. * When allowing a chunked data set (e.g. * {@link HDF5IntStorageFeatures#INT_NO_COMPRESSION} when the writer is * not configured to avoid extendable data types, see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be arraySize. When enforcing a * on-extendable data set (e.g. * {@link HDF5IntStorageFeatures#INT_CONTIGUOUS}), the initial size equals * the total size and will be arraySize. * @param features The storage features of the data set. */ @Override public void createArray(String objectPath, int size, HDF5IntStorageFeatures features); /** * Creates a byte array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the byte array to create. When using extendable data sets * ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data * set smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) and * features is HDF5IntStorageFeature.INT_NO_COMPRESSION. * @param features The storage features of the data set. */ @Override public void createArray(String objectPath, long size, int blockSize, HDF5IntStorageFeatures features); /** * Writes out a block of a byte array (of rank 1). The data set needs to have * been created by {@link #createArray(String, long, int, HDF5IntStorageFeatures)} * beforehand. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumber The number of the block to write. */ @Override public void writeArrayBlock(String objectPath, byte[] data, long blockNumber); /** * Writes out a block of a byte array (of rank 1). The data set needs to have * been created by {@link #createArray(String, long, int, HDF5IntStorageFeatures)} * beforehand. *

* Use this method instead of {@link #writeArrayBlock(String, byte[], long)} if the * total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param dataSize The (real) size of data (needs to be <= data.length * ) * @param offset The offset in the data set to start writing to. */ @Override public void writeArrayBlockWithOffset(String objectPath, byte[] data, int dataSize, long offset); /** * Writes out a byte matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ @Override public void writeMatrix(String objectPath, byte[][] data); /** * Writes out a byte matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. */ @Override public void writeMatrix(String objectPath, byte[][] data, HDF5IntStorageFeatures features); /** * Creates a byte matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of one block in the x dimension. See * {@link #createMDArray(String, int[])} on the different * meanings of this parameter. * @param sizeY The size of one block in the y dimension. See * {@link #createMDArray(String, int[])} on the different * meanings of this parameter. */ @Override public void createMatrix(String objectPath, int sizeX, int sizeY); /** * Creates a byte matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of one block in the x dimension. See * {@link #createMDArray(String, int[], HDF5IntStorageFeatures)} on the different * meanings of this parameter. * @param sizeY The size of one block in the y dimension. See * {@link #createMDArray(String, int[], HDF5IntStorageFeatures)} on the different * meanings of this parameter. * @param features The storage features of the data set. */ @Override public void createMatrix(String objectPath, int sizeX, int sizeY, HDF5IntStorageFeatures features); /** * Creates a byte matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the byte matrix to create. * @param sizeY The size of the y dimension of the byte matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. */ @Override public void createMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY); /** * Creates a byte matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the byte matrix to create. * @param sizeY The size of the y dimension of the byte matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. * @param features The storage features of the data set. */ @Override public void createMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY, HDF5IntStorageFeatures features); /** * Writes out a block of a byte matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of * {@link #createMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} if the total * size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumberX The block number in the x dimension (offset: multiply with * data.length). * @param blockNumberY The block number in the y dimension (offset: multiply with * data[0.length). */ @Override public void writeMatrixBlock(String objectPath, byte[][] data, long blockNumberX, long blockNumberY); /** * Writes out a block of a byte matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeMatrixBlock(String, byte[][], long, long)} if * the total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. */ @Override public void writeMatrixBlockWithOffset(String objectPath, byte[][] data, long offsetX, long offsetY); /** * Writes out a block of a byte matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeMatrixBlock(String, byte[][], long, long)} if * the total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param dataSizeX The (real) size of data along the x axis (needs to be * <= data.length ) * @param dataSizeY The (real) size of data along the y axis (needs to be * <= data[0].length ) * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. */ @Override public void writeMatrixBlockWithOffset(String objectPath, byte[][] data, int dataSizeX, int dataSizeY, long offsetX, long offsetY); /** * Writes out a multi-dimensional byte array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ @Override public void writeMDArray(String objectPath, MDByteArray data); /** * Writes out a multi-dimensional byte array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. */ @Override public void writeMDArray(String objectPath, MDByteArray data, HDF5IntStorageFeatures features); /** * Writes out a slice of a multi-dimensional byte array. The slice is defined by * "bound indices", each of which is fixed to a given value. The data object only * contains the free (i.e. non-fixed) indices. *

* Note:The object identified by objectPath needs to exist when this method is * called. This method will not create the array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. */ public void writeMDArraySlice(String objectPath, MDByteArray data, IndexMap boundIndices); /** * Writes out a slice of a multi-dimensional byte array. The slice is defined by * "bound indices", each of which is fixed to a given value. The data object only * contains the free (i.e. non-fixed) indices. *

* Note:The object identified by objectPath needs to exist when this method is * called. This method will not create the array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. */ public void writeMDArraySlice(String objectPath, MDByteArray data, long[] boundIndices); /** * Creates a multi-dimensional byte array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions When the writer is configured to use extendable data types (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial dimensions * and the dimensions of a chunk of the array will be dimensions. When the * writer is configured to enforce a non-extendable data set, the initial dimensions * equal the dimensions and will be dimensions. */ @Override public void createMDArray(String objectPath, int[] dimensions); /** * Creates a multi-dimensional byte array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. */ @Override public void createMDArray(String objectPath, long[] dimensions, int[] blockDimensions); /** * Creates a multi-dimensional byte array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the byte array to create. When requesting * a chunked data set (e.g. {@link HDF5IntStorageFeatures#INT_CHUNKED}), * the initial size of the array will be 0 and the chunk size will be dimensions. * When allowing a chunked data set (e.g. * {@link HDF5IntStorageFeatures#INT_NO_COMPRESSION} when the writer is * not configured to avoid extendable data types, see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be dimensions. When enforcing a * on-extendable data set (e.g. * {@link HDF5IntStorageFeatures#INT_CONTIGUOUS}), the initial size equals * the total size and will be dimensions. * @param features The storage features of the data set. */ @Override public void createMDArray(String objectPath, int[] dimensions, HDF5IntStorageFeatures features); /** * Creates a multi-dimensional byte array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. * @param features The storage features of the data set. */ @Override public void createMDArray(String objectPath, long[] dimensions, int[] blockDimensions, HDF5IntStorageFeatures features); /** * Writes out a block of a multi-dimensional byte array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). */ @Override public void writeMDArrayBlock(String objectPath, MDByteArray data, long[] blockNumber); /** * Writes out a sliced block of a multi-dimensional byte array. The slice is * defined by "bound indices", each of which is fixed to a given value. The data * object only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. */ public void writeSlicedMDArrayBlock(String objectPath, MDByteArray data, long[] blockNumber, IndexMap boundIndices); /** * Writes out a sliced block of a multi-dimensional byte array. The slice is * defined by "bound indices", each of which is fixed to a given value. The data * object only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. */ public void writeSlicedMDArrayBlock(String objectPath, MDByteArray data, long[] blockNumber, long[] boundIndices); /** * Writes out a block of a multi-dimensional byte array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. */ @Override public void writeMDArrayBlockWithOffset(String objectPath, MDByteArray data, long[] offset); /** * Writes out a sliced block of a multi-dimensional byte array. The slice is * defined by "bound indices", each of which is fixed to a given value. The data * object only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. */ public void writeSlicedMDArrayBlockWithOffset(String objectPath, MDByteArray data, long[] offset, IndexMap boundIndices); /** * Writes out a sliced block of a multi-dimensional byte array. The slice is * defined by "bound indices", each of which is fixed to a given value. The data * object only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. */ public void writeSlicedMDArrayBlockWithOffset(String objectPath, MDByteArray data, long[] offset, long[] boundIndices); /** * Writes out a block of a multi-dimensional byte array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param blockDimensions The dimensions of the block to write to the data set. * @param offset The offset of the block in the data set to start writing to in each dimension. * @param memoryOffset The offset of the block in the data array. */ @Override public void writeMDArrayBlockWithOffset(String objectPath, MDByteArray data, int[] blockDimensions, long[] offset, int[] memoryOffset); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5CompoundBasicReader.java000066400000000000000000001024411256564762100306200ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.util.List; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.hdf5.IHDF5CompoundInformationRetriever.IByteArrayInspector; /** * An interface with legacy methods for reading compound values from HDF5 files. Do not use in any * new code as it will be removed in a future version of JHDF5. * * @author Bernd Rinn */ @Deprecated public interface IHDF5CompoundBasicReader { // ///////////////////// // Information // ///////////////////// /** * Returns the member information for the committed compound data type compoundClass * (using its "simple name") in the order that the members appear in the compound type. It is a * failure condition if this compound data type does not exist. * * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public HDF5CompoundMemberInformation[] getCompoundMemberInformation( final Class compoundClass); /** * Returns the member information for the committed compound data type dataTypeName * in the order that the members appear in the compound type. It is a failure condition if this * compound data type does not exist. If the dataTypeName starts with '/', it will be * considered a data type path instead of a data type name. * * @param dataTypeName The name of the compound data type to get the member information for. * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public HDF5CompoundMemberInformation[] getCompoundMemberInformation(final String dataTypeName); /** * Returns the compound member information for the data set dataSetPath in the order * that the members appear in the compound type. It is a failure condition if this data set does * not exist or is not of compound type. *

* Call Arrays.sort(compoundInformation) to sort the array in alphabetical order of * names. * * @throws HDF5JavaException If the data set is not of compound type. * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public HDF5CompoundMemberInformation[] getCompoundDataSetInformation(final String dataSetPath) throws HDF5JavaException; /** * Returns the compound member information for the data set dataSetPath in the order * that the members appear in the compound type. The returned array will contain the members in * alphabetical order, if sortAlphabetically is true or else in the * order of definition of the compound type. It is a failure condition if this data set does not * exist or is not of compound type. *

* * @throws HDF5JavaException If the data set is not of type compound. * @deprecated Use {@link #getCompoundDataSetInformation(String)} and * Arrays.sort(compoundInformation), if needed. */ @Deprecated public HDF5CompoundMemberInformation[] getCompoundDataSetInformation(final String dataSetPath, final boolean sortAlphabetically) throws HDF5JavaException; // ///////////////////// // Types // ///////////////////// /** * Returns the compound type name> for this HDF5 file. * * @param name The name of the compound in the HDF5 file. * @param pojoClass The plain old Java type that corresponds to this HDF5 type. * @param members The mapping from the Java compound type to the HDF5 type. * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public HDF5CompoundType getCompoundType(final String name, Class pojoClass, HDF5CompoundMemberMapping... members); /** * Returns the compound type for this HDF5 file, using the default name chosen by JHDF5 which is * based on the simple name of pojoClass. * * @param pojoClass The plain old Java type that corresponds to this HDF5 type. * @param members The mapping from the Java compound type to the HDF5 type. * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public HDF5CompoundType getCompoundType(Class pojoClass, HDF5CompoundMemberMapping... members); /** * Returns the compound type name> for this HDF5 file, inferring the mapping from the * Java compound type to the HDF5 type by reflection. * * @param name The name of the compound in the HDF5 file. * @param pojoClass The plain old Java type that corresponds to this HDF5 type. * @see HDF5CompoundMemberMapping#inferMapping * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public HDF5CompoundType getInferredCompoundType(final String name, final Class pojoClass); /** * Returns the compound type for this HDF5 file, inferring the mapping from the Java compound * type to the HDF5 type by reflection and using the default name chosen by JHDF5 which is based * on the simple name of pojoClass. * * @param pojoClass The plain old Java type that corresponds to this HDF5 type. * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public HDF5CompoundType getInferredCompoundType(final Class pojoClass); /** * Returns the compound type name> for this HDF5 file, inferring the mapping from the * Java compound type to the HDF5 type by reflection. * * @param name The name of the compound type in the HDF5 file. * @param template The compound to infer the HDF5 compound type from. * @param hints The hints to provide to the mapping procedure. * @see HDF5CompoundMemberMapping#inferMapping * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public HDF5CompoundType getInferredCompoundType(final String name, final T template, HDF5CompoundMappingHints hints); /** * Returns the compound type name> for this HDF5 file, inferring the mapping from the * Java compound type to the HDF5 type by reflection. * * @param name The name of the compound type in the HDF5 file. * @param template The compound to infer the HDF5 compound type from. * @see HDF5CompoundMemberMapping#inferMapping * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public HDF5CompoundType getInferredCompoundType(final String name, final T template); /** * Returns the compound type for this HDF5 file, inferring the mapping from the Java compound * type to the HDF5 type by reflection and using the default name chosen by JHDF5 which is based * on the simple name of T. * * @param template The compound to infer the HDF5 compound type from. * @see HDF5CompoundMemberMapping#inferMapping * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public HDF5CompoundType getInferredCompoundType(final T template); /** * Returns the compound type for this HDF5 file, inferring the mapping from the Java types of * the members. * * @param name The name of the compound type in the HDF5 file. * @param memberNames The names of the members. * @param template The compound to infer the HDF5 compound type from. Needs to have the same * length as memberNames. * @see HDF5CompoundMemberMapping#inferMapping * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public HDF5CompoundType> getInferredCompoundType(final String name, List memberNames, List template); /** * Returns the compound type for this HDF5 file, inferring the mapping from the Java types of * the members. * * @param memberNames The names of the members. * @param template The compound to infer the HDF5 compound type from. Needs to have the same * length as memberNames. * @see HDF5CompoundMemberMapping#inferMapping * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public HDF5CompoundType> getInferredCompoundType(List memberNames, List template); /** * Returns the compound type for this HDF5 file, inferring the mapping from the Java types of * the members. * * @param name The name of the compound type in the HDF5 file. * @param memberNames The names of the members. * @param template The compound to infer the HDF5 compound type from. Needs to have the same * length than memberNames. * @see HDF5CompoundMemberMapping#inferMapping * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public HDF5CompoundType getInferredCompoundType(final String name, String[] memberNames, Object[] template); /** * Returns the compound type for this HDF5 file, inferring the mapping from the Java types of * the members. * * @param memberNames The names of the members. * @param template The compound to infer the HDF5 compound type from. Needs to have the same * length than memberNames. * @see HDF5CompoundMemberMapping#inferMapping * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public HDF5CompoundType getInferredCompoundType(String[] memberNames, Object[] template); /** * Returns the compound type for the given compound data set in objectPath, mapping * it to pojoClass. * * @param objectPath The path of the compound dataset to get the type from. * @param pojoClass The class to use for the mapping. * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public HDF5CompoundType getDataSetCompoundType(String objectPath, Class pojoClass); /** * Returns the compound type for the given compound attribute in attributeName of * objectPath, mapping it to pojoClass. * * @param objectPath The path of the compound dataset to get the type from. * @param pojoClass The class to use for the mapping. * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public HDF5CompoundType getAttributeCompoundType(String objectPath, String attributeName, Class pojoClass); /** * Returns the named compound type with name dataTypeName from file, mapping it to * pojoClass. If the dataTypeName starts with '/', it will be considered a * data type path instead of a data type name. *

* Note: This method only works for compound data types 'committed' to the HDF5 file. * For files written with JHDF5 this will always be true, however, files created with other * libraries may not choose to commit compound data types. * * @param dataTypeName The path to a committed data type, if starting with '/', or a name of a * committed data type otherwise. * @param pojoClass The class to use for the mapping. * @return The compound data type. * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public HDF5CompoundType getNamedCompoundType(String dataTypeName, Class pojoClass); /** * Returns the named compound type with name dataTypeName from file, mapping it to * pojoClass. This method will use the default name for the compound data type as * chosen by JHDF5 and thus will likely only work on files written with JHDF5. The default name * is based on the simple name of compoundType. * * @param pojoClass The class to use for the mapping and to get the name of named data type * from. * @return The compound data type. * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public HDF5CompoundType getNamedCompoundType(Class pojoClass); // ///////////////////// // Data Sets // ///////////////////// /** * Reads a compound from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public T readCompound(String objectPath, HDF5CompoundType type) throws HDF5JavaException; /** * Reads a compound from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param pojoClass The class to return the result in. Use {@link HDF5CompoundDataMap} to get it * in a map, {@link HDF5CompoundDataList} to get it in a list, and * Object[] to get it in an array, or use a pojo (Data Transfer Object), * in which case the compound members will be mapped to Java fields. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set or if the * mapping between the compound type and the POJO is not complete. * @see CompoundType * @see CompoundElement */ public T readCompound(String objectPath, Class pojoClass) throws HDF5JavaException; /** * Reads a compound from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param inspectorOrNull The inspector to be called before the byte array read from the HDF5 * file is translated back into a Java object. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public T readCompound(String objectPath, HDF5CompoundType type, IByteArrayInspector inspectorOrNull) throws HDF5JavaException; /** * Reads a compound array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public T[] readCompoundArray(String objectPath, HDF5CompoundType type) throws HDF5JavaException; /** * Reads a compound array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param inspectorOrNull The inspector to be called before the byte array read from the HDF5 * file is translated back into Java objects. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public T[] readCompoundArray(String objectPath, HDF5CompoundType type, IByteArrayInspector inspectorOrNull) throws HDF5JavaException; /** * Reads a compound array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param pojoClass The class to return the result in. Use {@link HDF5CompoundDataMap} to get it * in a map, {@link HDF5CompoundDataList} to get it in a list, and * Object[] to get it in an array, or use a pojo (Data Transfer Object), * in which case the compound members will be mapped to Java fields. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set or if the * mapping between the compound type and the POJO is not complete. * @see CompoundType * @see CompoundElement */ public T[] readCompoundArray(String objectPath, Class pojoClass) throws HDF5JavaException; /** * Reads a compound array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param blockSize The block size (this will be the length of the float[] returned * if the data set is long enough). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public T[] readCompoundArrayBlock(String objectPath, HDF5CompoundType type, int blockSize, long blockNumber) throws HDF5JavaException; /** * Reads a compound array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param blockSize The block size (this will be the length of the float[] returned * if the data set is long enough). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @param inspectorOrNull The inspector to be called before the byte array read from the HDF5 * file is translated back into Java objects. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public T[] readCompoundArrayBlock(String objectPath, HDF5CompoundType type, int blockSize, long blockNumber, IByteArrayInspector inspectorOrNull) throws HDF5JavaException; /** * Reads a compound array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param blockSize The block size (this will be the length of the float[] returned * if the data set is long enough). * @param offset The offset of the block to read (starting with 0). * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public T[] readCompoundArrayBlockWithOffset(String objectPath, HDF5CompoundType type, int blockSize, long offset) throws HDF5JavaException; /** * Reads a compound array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param blockSize The block size (this will be the length of the float[] returned * if the data set is long enough). * @param offset The offset of the block to read (starting with 0). * @param inspectorOrNull The inspector to be called before the byte array read from the HDF5 * file is translated back into Java objects. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public T[] readCompoundArrayBlockWithOffset(String objectPath, HDF5CompoundType type, int blockSize, long offset, IByteArrayInspector inspectorOrNull) throws HDF5JavaException; /** * Provides all natural blocks of this one-dimensional data set of compounds to iterate over. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1 or not a compound data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public Iterable> getCompoundArrayNaturalBlocks(String objectPath, HDF5CompoundType type) throws HDF5JavaException; /** * Provides all natural blocks of this one-dimensional data set of compounds to iterate over. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param inspectorOrNull The inspector to be called before the byte array read from the HDF5 * file is translated back into Java objects. * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1 or not a compound data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public Iterable> getCompoundArrayNaturalBlocks(String objectPath, HDF5CompoundType type, IByteArrayInspector inspectorOrNull) throws HDF5JavaException; /** * Provides all natural blocks of this one-dimensional data set of compounds to iterate over. * * @param objectPath The name (including path information) of the data set object in the file. * @param pojoClass The class to return the result in. Use {@link HDF5CompoundDataMap} to get it * in a map, {@link HDF5CompoundDataList} to get it in a list, and * Object[] to get it in an array, or use a pojo (Data Transfer Object), * in which case the compound members will be mapped to Java fields. * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1 or not a compound data set. * @throws HDF5JavaException If the data set is not of rank 1, not a compound data set or if the * mapping between the compound type and the POJO is not complete. * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public Iterable> getCompoundArrayNaturalBlocks(String objectPath, Class pojoClass) throws HDF5JavaException; /** * Reads a compound array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public MDArray readCompoundMDArray(String objectPath, HDF5CompoundType type) throws HDF5JavaException; /** * Reads a compound array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param pojoClass The class to return the result in. Use {@link HDF5CompoundDataMap} to get it * in a map, {@link HDF5CompoundDataList} to get it in a list, and * Object[] to get it in an array, or use a pojo (Data Transfer Object), * in which case the compound members will be mapped to Java fields. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set or if the * mapping between the compound type and the POJO is not complete. * @see CompoundType * @see CompoundElement * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public MDArray readCompoundMDArray(String objectPath, Class pojoClass) throws HDF5JavaException; /** * Reads a compound array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param inspectorOrNull The inspector to be called before the byte array read from the HDF5 * file is translated back into Java objects. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public MDArray readCompoundMDArray(String objectPath, HDF5CompoundType type, IByteArrayInspector inspectorOrNull) throws HDF5JavaException; /** * Reads a block from a compound array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param blockDimensions The extent of the block to write along each axis. * @param blockNumber The number of the block to write along each axis. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public MDArray readCompoundMDArrayBlock(String objectPath, HDF5CompoundType type, int[] blockDimensions, long[] blockNumber) throws HDF5JavaException; /** * Reads a block from a compound array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param blockDimensions The extent of the block to write along each axis. * @param blockNumber The number of the block to write along each axis. * @param inspectorOrNull The inspector to be called before the byte array read from the HDF5 * file is translated back into Java objects. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound type. * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public MDArray readCompoundMDArrayBlock(String objectPath, HDF5CompoundType type, int[] blockDimensions, long[] blockNumber, IByteArrayInspector inspectorOrNull) throws HDF5JavaException; /** * Reads a block from a compound array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param blockDimensions The extent of the block to write along each axis. * @param offset The offset of the block to write in the data set along each axis. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public MDArray readCompoundMDArrayBlockWithOffset(String objectPath, HDF5CompoundType type, int[] blockDimensions, long[] offset) throws HDF5JavaException; /** * Reads a block from a compound array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param blockDimensions The extent of the block to write along each axis. * @param offset The offset of the block to write in the data set along each axis. * @param inspectorOrNull The inspector to be called before the byte array read from the HDF5 * file is translated back into Java objects. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public MDArray readCompoundMDArrayBlockWithOffset(String objectPath, HDF5CompoundType type, int[] blockDimensions, long[] offset, IByteArrayInspector inspectorOrNull) throws HDF5JavaException; /** * Provides all natural blocks of this multi-dimensional data set to iterate over. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @see HDF5MDDataBlock * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public Iterable>> getCompoundMDArrayNaturalBlocks( String objectPath, HDF5CompoundType type) throws HDF5JavaException; /** * Provides all natural blocks of this multi-dimensional data set to iterate over. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param inspectorOrNull The inspector to be called before the byte array read from the HDF5 * file is translated back into Java objects. * @see HDF5MDDataBlock * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public Iterable>> getCompoundMDArrayNaturalBlocks( String objectPath, HDF5CompoundType type, IByteArrayInspector inspectorOrNull) throws HDF5JavaException; /** * Provides all natural blocks of this multi-dimensional data set of compounds to iterate over. * * @param objectPath The name (including path information) of the data set object in the file. * @param pojoClass The class to return the result in. Use {@link HDF5CompoundDataMap} to get it * in a map, {@link HDF5CompoundDataList} to get it in a list, and * Object[] to get it in an array. * @see HDF5DataBlock * @see CompoundType * @see CompoundElement * @throws HDF5JavaException If the data set is not a compound data set or if the mapping * between the compound type and the POJO is not complete. * @deprecated Use the corresponding method in {@link IHDF5Reader#compound()} instead. */ @Deprecated public Iterable>> getCompoundMDArrayNaturalBlocks( String objectPath, Class pojoClass) throws HDF5JavaException; } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5CompoundBasicWriter.java000066400000000000000000000601601256564762100306730ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.hdf5.IHDF5CompoundInformationRetriever.IByteArrayInspector; /** * An interface with legacy methods for writing compound values to HDF5 files. Do not use in any new * code as it will be removed in a future version of JHDF5. * * @author Bernd Rinn */ @Deprecated public interface IHDF5CompoundBasicWriter extends IHDF5CompoundBasicReader { // ///////////////////// // Data Sets // ///////////////////// /** * Writes out a compound value of type given in data. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The value of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#compounds()} instead. */ @Deprecated public void writeCompound(String objectPath, HDF5CompoundType type, T data); /** * Writes out a compound value. The type is inferred based on the values. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The value of the data set. May be a pojo (Data Transfer Object), a * {@link HDF5CompoundDataMap}, {@link HDF5CompoundDataList} or Object[] * . * @see CompoundType * @see CompoundElement */ public void writeCompound(String objectPath, T data); /** * Writes out an array (of rank 1) of compound values. Uses a compact storage layout. Must only * be used for small data sets. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The value of the data set. * @param inspectorOrNull The inspector to be called after translating the Java objects to a * byte array and before writing the byte array to the HDF5 file. * @deprecated Use the corresponding method in {@link IHDF5Writer#compounds()} instead. */ @Deprecated public void writeCompound(String objectPath, HDF5CompoundType type, T data, IByteArrayInspector inspectorOrNull); /** * Writes out an array (of rank 1) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The value of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#compounds()} instead. */ @Deprecated public void writeCompoundArray(String objectPath, HDF5CompoundType type, T[] data); /** * Writes out an array (of rank 1) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The value of the data set. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#compounds()} instead. */ @Deprecated public void writeCompoundArray(String objectPath, HDF5CompoundType type, T[] data, HDF5GenericStorageFeatures features); /** * Writes out an array (of rank 1) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The value of the data set. * @param features The storage features of the data set. * @param inspectorOrNull The inspector to be called after translating the Java objects to a * byte array and before writing the byte array to the HDF5 file. * @deprecated Use the corresponding method in {@link IHDF5Writer#compounds()} instead. */ @Deprecated public void writeCompoundArray(String objectPath, HDF5CompoundType type, T[] data, HDF5GenericStorageFeatures features, IByteArrayInspector inspectorOrNull); /** * Writes out an array (of rank 1) of compound values. The type is inferred based on the values. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The value of the data set. May be a pojo (Data Transfer Object), a * {@link HDF5CompoundDataMap}, {@link HDF5CompoundDataList} or Object[] * . * @see CompoundType * @see CompoundElement */ @Deprecated public void writeCompoundArray(String objectPath, T[] data); /** * Writes out an array (of rank 1) of compound values. The type is inferred based on the values. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The value of the data set. May be a {@link HDF5CompoundDataMap}, * {@link HDF5CompoundDataList} or Object[]. * @param features The storage features of the data set. * @see CompoundType * @see CompoundElement * @deprecated Use the corresponding method in {@link IHDF5Writer#compounds()} instead. */ @Deprecated public void writeCompoundArray(String objectPath, T[] data, HDF5GenericStorageFeatures features); /** * Writes out a block blockNumber of an array (of rank 1) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The value of the data set. * @param blockNumber The number of the block to write. * @deprecated Use the corresponding method in {@link IHDF5Writer#compounds()} instead. */ @Deprecated public void writeCompoundArrayBlock(String objectPath, HDF5CompoundType type, T[] data, long blockNumber); /** * Writes out a block blockNumber of an array (of rank 1) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The value of the data set. * @param blockNumber The number of the block to write. * @param inspectorOrNull The inspector to be called after translating the Java objects to a * byte array and before writing the byte array to the HDF5 file. * @deprecated Use the corresponding method in {@link IHDF5Writer#compounds()} instead. */ @Deprecated public void writeCompoundArrayBlock(String objectPath, HDF5CompoundType type, T[] data, long blockNumber, IByteArrayInspector inspectorOrNull); /** * Writes out a block of an array (of rank 1) of compound values with given offset. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The value of the data set. * @param offset The offset of the block in the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#compounds()} instead. */ @Deprecated public void writeCompoundArrayBlockWithOffset(String objectPath, HDF5CompoundType type, T[] data, long offset); /** * Writes out a block of an array (of rank 1) of compound values with given offset. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The value of the data set. * @param offset The offset of the block in the data set. * @param inspectorOrNull The inspector to be called after translating the Java objects to a * byte array and before writing the byte array to the HDF5 file. * @deprecated Use the corresponding method in {@link IHDF5Writer#compounds()} instead. */ @Deprecated public void writeCompoundArrayBlockWithOffset(String objectPath, HDF5CompoundType type, T[] data, long offset, IByteArrayInspector inspectorOrNull); /** * Creates an array (of rank 1) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param size The size of the array to create. This will be the total size for non-extendable * data sets and the size of one chunk for extendable (chunked) data sets. For * extendable data sets the initial size of the array will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. * @deprecated Use the corresponding method in {@link IHDF5Writer#compounds()} instead. */ @Deprecated public void createCompoundArray(String objectPath, HDF5CompoundType type, int size); /** * Creates an array (of rank 1) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param size The size of the compound array to create. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) * and deflate == false. * @deprecated Use the corresponding method in {@link IHDF5Writer#compounds()} instead. */ @Deprecated public void createCompoundArray(String objectPath, HDF5CompoundType type, long size, int blockSize); /** * Creates an array (of rank 1) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param size The size of the compound array to create. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) * and deflate == false. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#compounds()} instead. */ @Deprecated public void createCompoundArray(String objectPath, HDF5CompoundType type, long size, int blockSize, HDF5GenericStorageFeatures features); /** * Creates an array (of rank 1) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param size The size of the byte array to create. This will be the total size for * non-extendable data sets and the size of one chunk for extendable (chunked) data * sets. For extendable data sets the initial size of the array will be 0, see * {@link HDF5GenericStorageFeatures}. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#compounds()} instead. */ @Deprecated public void createCompoundArray(String objectPath, HDF5CompoundType type, long size, HDF5GenericStorageFeatures features); /** * Writes out an array (of rank N) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The data to write. * @deprecated Use the corresponding method in {@link IHDF5Writer#compounds()} instead. */ @Deprecated public void writeCompoundMDArray(String objectPath, HDF5CompoundType type, MDArray data); /** * Writes out an array (of rank N) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The data to write. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#compounds()} instead. */ @Deprecated public void writeCompoundMDArray(String objectPath, HDF5CompoundType type, MDArray data, HDF5GenericStorageFeatures features); /** * Writes out an array (of rank N) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The data to write. * @param features The storage features of the data set. * @param inspectorOrNull The inspector to be called after translating the Java objects to a * byte array and before writing the byte array to the HDF5. * @deprecated Use the corresponding method in {@link IHDF5Writer#compounds()} instead. */ @Deprecated public void writeCompoundMDArray(String objectPath, HDF5CompoundType type, MDArray data, HDF5GenericStorageFeatures features, IByteArrayInspector inspectorOrNull); /** * Writes out an array (of rank N) of compound values. The type is inferred based on the values. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The value of the data set. May be a pojo (Data Transfer Object), a * {@link HDF5CompoundDataMap}, {@link HDF5CompoundDataList} or Object[] * . * @see CompoundType * @see CompoundElement * @deprecated Use the corresponding method in {@link IHDF5Writer#compounds()} instead. */ @Deprecated public void writeCompoundMDArray(String objectPath, MDArray data); /** * Writes out an array (of rank N) of compound values. The type is inferred based on the values. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The value of the data set. May be a pojo (Data Transfer Object), a * {@link HDF5CompoundDataMap}, {@link HDF5CompoundDataList} or Object[] * . * @param features The storage features of the data set. * @see CompoundType * @see CompoundElement * @deprecated Use the corresponding method in {@link IHDF5Writer#compounds()} instead. */ @Deprecated public void writeCompoundMDArray(String objectPath, MDArray data, HDF5GenericStorageFeatures features); /** * Writes out a block of an array (of rank N) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The data to write. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). * @deprecated Use the corresponding method in {@link IHDF5Writer#compounds()} instead. */ @Deprecated public void writeCompoundMDArrayBlock(String objectPath, HDF5CompoundType type, MDArray data, long[] blockNumber); /** * Writes out a block of an array (of rank N) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The data to write. * @param blockNumber The extent of the block to write on each axis. * @param inspectorOrNull The inspector to be called after translating the Java objects to a * byte array and before writing the byte array to the HDF5. * @deprecated Use the corresponding method in {@link IHDF5Writer#compounds()} instead. */ @Deprecated public void writeCompoundMDArrayBlock(String objectPath, HDF5CompoundType type, MDArray data, long[] blockNumber, IByteArrayInspector inspectorOrNull); /** * Writes out a block of an array (of rank N) of compound values give a given offset. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The data to write. * @param offset The offset of the block to write on each axis. * @deprecated Use the corresponding method in {@link IHDF5Writer#compounds()} instead. */ @Deprecated public void writeCompoundMDArrayBlockWithOffset(String objectPath, HDF5CompoundType type, MDArray data, long[] offset); /** * Writes out a block of an array (of rank N) of compound values give a given offset. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The data to write. * @param offset The offset of the block to write on each axis. * @param inspectorOrNull The inspector to be called after translating the Java objects to a * byte array and before writing the byte array to the HDF5. * @deprecated Use the corresponding method in {@link IHDF5Writer#compounds()} instead. */ @Deprecated public void writeCompoundMDArrayBlockWithOffset(String objectPath, HDF5CompoundType type, MDArray data, long[] offset, IByteArrayInspector inspectorOrNull); /** * Writes out a block of an array (of rank N) of compound values give a given offset. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The data to write. * @param blockDimensions The dimensions of the block to write to the data set. * @param offset The offset of the block in the data set to start writing to in each dimension. * @param memoryOffset The offset of the block in the data array. * @deprecated Use the corresponding method in {@link IHDF5Writer#compounds()} instead. */ @Deprecated public void writeCompoundMDArrayBlockWithOffset(String objectPath, HDF5CompoundType type, MDArray data, int[] blockDimensions, long[] offset, int[] memoryOffset); /** * Writes out a block of an array (of rank N) of compound values give a given offset. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The data to write. * @param blockDimensions The dimensions of the block to write to the data set. * @param offset The offset of the block in the data set to start writing to in each dimension. * @param memoryOffset The offset of the block in the data array. * @param inspectorOrNull The inspector to be called after translating the Java objects to a * byte array and before writing the byte array to the HDF5. * @deprecated Use the corresponding method in {@link IHDF5Writer#compounds()} instead. */ @Deprecated public void writeCompoundMDArrayBlockWithOffset(String objectPath, HDF5CompoundType type, MDArray data, int[] blockDimensions, long[] offset, int[] memoryOffset, IByteArrayInspector inspectorOrNull); /** * Creates an array (of rank N) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param dimensions The dimensions of the compound array to create. This will be the total * dimensions for non-extendable data sets and the dimensions of one chunk (along * each axis) for extendable (chunked) data sets. For extendable data sets the * initial size of the array (along each axis) will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. * @deprecated Use the corresponding method in {@link IHDF5Writer#compounds()} instead. */ @Deprecated public void createCompoundMDArray(String objectPath, HDF5CompoundType type, int[] dimensions); /** * Creates an array (of rank N) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param dimensions The extent of the compound array along each of the axis. * @param blockDimensions The extent of one block along each of the axis. (for block-wise IO). * Ignored if no extendable data sets are used (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) and * deflate == false. * @deprecated Use the corresponding method in {@link IHDF5Writer#compounds()} instead. */ @Deprecated public void createCompoundMDArray(String objectPath, HDF5CompoundType type, long[] dimensions, int[] blockDimensions); /** * Creates an array (of rank N) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param dimensions The extent of the compound array along each of the axis. * @param blockDimensions The extent of one block along each of the axis. (for block-wise IO). * Ignored if no extendable data sets are used (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) and * deflate == false. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#compounds()} instead. */ @Deprecated public void createCompoundMDArray(String objectPath, HDF5CompoundType type, long[] dimensions, int[] blockDimensions, HDF5GenericStorageFeatures features); /** * Creates an array (of rank N) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param dimensions The dimensions of the byte array to create. This will be the total * dimensions for non-extendable data sets and the dimensions of one chunk (along * each axis) for extendable (chunked) data sets. For extendable data sets the * initial size of the array (along each axis) will be 0, see * {@link HDF5GenericStorageFeatures}. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#compounds()} instead. */ @Deprecated public void createCompoundMDArray(String objectPath, HDF5CompoundType type, int[] dimensions, HDF5GenericStorageFeatures features); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5CompoundInformationRetriever.java000066400000000000000000001172611256564762100326370ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.util.List; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.base.mdarray.MDAbstractArray; import ch.systemsx.cisd.hdf5.HDF5DataTypeInformation.DataTypeInfoOptions; /** * An interface to get information on HDF5 compound data sets and compound data types, and to create * compound types from mappings to Java classes. *

*

What is an {@link HDF5CompoundType}?

*

* A {@link HDF5CompoundType} is a Java object representing both an HDF5 compound type in a * particular HDF5 file and the mapping of this HDF5 compound type to a representation in Java. A * Java representation can be either a plain-old Java object (POJO) where Java fields correspond to * HDF5 compound members, a map (see {@link HDF5CompoundDataMap}) where each HDF5 compound member is * represented by one key-value pair, a list (see {@link HDF5CompoundDataList}) or * Object[], where the members of the HDF5 compound type are stored by their position * (or order) in the HDF5 compound type. *

* It is important to understand that creating the HDF5 compound type in memory (what members of what types * it contains in what order) and mapping the members to Java (including the Java type and, for POJOs, the * field) are two distinct steps. Different methods of this interface use two different approaches on how * to create the HDF5 compound type: getType() and getInferredType() create them * anew, based on the POJO class and the HDF5CompoundMemberMappings provided, while * getNamedType(), getDataSetType() and getAttributeType() read them * from the HDF5 file. Whenever you are reading a compound from an HDF5 file, the second approach should be * preferred as the HDF5 file is the authorative source of information on HDF5 types. *

* The following Java types can be mapped to compound members: *

    *
  • Primitive values
    • *
  • Primitive arrays
    • *
  • Primitive matrices (except char[][])
    • *
  • {@link String} (fixed-length and variable-lengt)
    • *
  • {@link java.util.BitSet}
    • *
  • {@link java.util.Date}
    • *
  • {@link HDF5EnumerationValue}
    • *
  • {@link HDF5EnumerationValueArray}
    • *
  • Sub-classes of {@link MDAbstractArray}
    • *
  • References to data sets
    • *
* * @author Bernd Rinn */ public interface IHDF5CompoundInformationRetriever { /** * An interface for inspecting the byte array of compounds and compound arrays just after they * are read from or before they are written to the HDF5 file. */ public interface IByteArrayInspector { /** * Called with the byte array. The method can change the byteArray but does so on * its own risk! */ void inspect(byte[] byteArray); } // ///////////////////// // Information // ///////////////////// /** * Returns the member information for the committed compound data type compoundClass * (using its "simple name") in the order that the members appear in the compound type. It is a * failure condition if this compound data type does not exist. */ public HDF5CompoundMemberInformation[] getMemberInfo(Class compoundClass); /** * Returns the member information for the committed compound data type dataTypeName * in the order that the members appear in the compound type. It is a failure condition if this * compound data type does not exist. If the dataTypeName starts with '/', it will be * considered a data type path instead of a data type name. * * @param dataTypeName The name of the compound data type to get the member information for. */ public HDF5CompoundMemberInformation[] getMemberInfo(String dataTypeName); /** * Returns the member information for the committed compound data type dataTypeName * in the order that the members appear in the compound type. It is a failure condition if this * compound data type does not exist. If the dataTypeName starts with '/', it will be * considered a data type path instead of a data type name. * * @param dataTypeName The name of the compound data type to get the member information for. * @param dataTypeInfoOptions The options on which information to get about the member data * types. */ public HDF5CompoundMemberInformation[] getMemberInfo(String dataTypeName, DataTypeInfoOptions dataTypeInfoOptions); /** * Returns the compound member information for the data set dataSetPath in the order * that the members appear in the compound type. It is a failure condition if this data set does * not exist or is not of compound type. *

* Call Arrays.sort(compoundInformation) to sort the array in alphabetical order of * names. * * @throws HDF5JavaException If the data set is not of type compound. */ public HDF5CompoundMemberInformation[] getDataSetInfo(String dataSetPath) throws HDF5JavaException; /** * Returns the compound member information for the data set dataSetPath in the order * that the members appear in the compound type. It is a failure condition if this data set does * not exist or is not of compound type. *

* Call Arrays.sort(compoundInformation) to sort the array in alphabetical order of * names. * * @param dataSetPath The name of the data set to get the member information for. * @param dataTypeInfoOptions The options on which information to get about the member data * types. * @throws HDF5JavaException If the data set is not of type compound. */ public HDF5CompoundMemberInformation[] getDataSetInfo(String dataSetPath, DataTypeInfoOptions dataTypeInfoOptions) throws HDF5JavaException; // ///////////////////// // Types // ///////////////////// /** * Returns a compound type name> for this HDF5 file, compatible with * pojoClass. The mapping is defined by members. * * @param name The name of the compound in the HDF5 file. * @param pojoClass The plain old Java type that corresponds to this HDF5 type. * @param requireTypesToBeEqual If true, this type is required to be equal to the * type it tries to read, or else an {@link HDF5JavaException} will be thrown. * @param members The mapping from the Java compound type to the HDF5 type. */ public HDF5CompoundType getType(String name, Class pojoClass, boolean requireTypesToBeEqual, HDF5CompoundMemberMapping... members); /** * Returns the compound type name> for this HDF5 file. * * @param name The name of the compound in the HDF5 file. * @param pojoClass The plain old Java type that corresponds to this HDF5 type. * @param members The mapping from the Java compound type to the HDF5 type. */ public HDF5CompoundType getType(String name, Class pojoClass, HDF5CompoundMemberMapping... members); /** * Returns a compound type name> for this HDF5 file, compatible with * pojoClass. The name of the compound data type is chosen to be the simple name of * pojoClass. The mapping is defined by members. * * @param pojoClass The plain old Java type that corresponds to this HDF5 type. * @param members The mapping from the Java compound type to the HDF5 type. */ public HDF5CompoundType getType(Class pojoClass, HDF5CompoundMemberMapping... members); /** * Returns a compound type name> for this HDF5 file, compatible with * pojoClass. The mapping of the Java compound type to the HDF5 type is inferred by * reflection from pojoClass following basic rules on how Java data types are mapped * to HDF5 data types. * * @param name The name of the compound in the HDF5 file. * @param pojoClass The plain old Java type that corresponds to this HDF5 type. * @param hints The hints to provide to the mapping procedure. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType getInferredType(String name, Class pojoClass, HDF5CompoundMappingHints hints); /** * Returns a compound type name> for this HDF5 file, compatible with * pojoClass. The mapping of the Java compound type to the HDF5 type is inferred by * reflection from pojoClass following basic rules on how Java data types are mapped * to HDF5 data types. * * @param name The name of the compound in the HDF5 file. * @param pojoClass The plain old Java type that corresponds to this HDF5 type. * @param hints The hints to provide to the mapping procedure. * @param requireTypesToBeEqual If true, this type is required to be equal to the * type it tries to read, or else an {@link HDF5JavaException} will be thrown. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType getInferredType(String name, Class pojoClass, HDF5CompoundMappingHints hints, boolean requireTypesToBeEqual); /** * Returns a compound type name> for this HDF5 file, compatible with * pojoClass. The mapping of the Java compound type to the HDF5 type is inferred by * reflection from pojoClass following basic rules on how Java data types are mapped * to HDF5 data types. * * @param name The name of the compound in the HDF5 file. * @param pojoClass The plain old Java type that corresponds to this HDF5 type. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType getInferredType(String name, Class pojoClass); /** * Returns a compound type for this HDF5 file, compatible with pojoClass. The mapping * of the Java compound type to the HDF5 type is inferred by reflection from * pojoClass following basic rules on how Java data types are mapped to HDF5 data * types. As name of the HDF5 compound type, the simple name of pojoClass is chosen. * * @param pojoClass The plain old Java type that corresponds to this HDF5 type. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType getInferredType(Class pojoClass); /** * Returns a compound type for this HDF5 file, compatible with pojoClass. The mapping * of the Java compound type to the HDF5 type is inferred by reflection from * pojoClass following basic rules on how Java data types are mapped to HDF5 data * types. As name of the HDF5 compound type, the simple name of pojoClass is chosen. * * @param pojoClass The plain old Java type that corresponds to this HDF5 type. * @param hints The hints to provide to the mapping procedure. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType getInferredType(Class pojoClass, HDF5CompoundMappingHints hints); /** * Returns a compound type name> for this HDF5 file, compatible with * template. The mapping of the Java compound type to the HDF5 type is inferred by * reflection from template following basic rules on how Java data types are mapped * to HDF5 data types. * * @param name The name of the compound type in the HDF5 file. * @param template The compound to infer the HDF5 compound type from. * @param hints The hints to provide to the mapping procedure. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType getInferredType(String name, T template, HDF5CompoundMappingHints hints); /** * Returns a compound type name> for this HDF5 file, compatible with * template. The mapping of the Java compound type to the HDF5 type is inferred by * reflection from template following basic rules on how Java data types are mapped * to HDF5 data types. * * @param name The name of the compound type in the HDF5 file. * @param template The compound to infer the HDF5 compound type from. * @param hints The hints to provide to the mapping procedure. * @param requireTypesToBeEqual If true, this type is required to be equal to the * type it tries to read, or else an {@link HDF5JavaException} will be thrown. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType getInferredType(String name, T template, HDF5CompoundMappingHints hints, boolean requireTypesToBeEqual); /** * Returns a compound type name> for this HDF5 file, compatible with * template. The mapping of the Java compound type to the HDF5 type is inferred by * reflection from template following basic rules on how Java data types are mapped * to HDF5 data types. * * @param name The name of the compound type in the HDF5 file. * @param template The compound to infer the HDF5 compound type from. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType getInferredType(String name, T template); /** * Returns a compound type for this HDF5 file, compatible with template. The mapping * of the Java compound type to the HDF5 type is inferred by reflection from template * following basic rules on how Java data types are mapped to HDF5 data types. As name of the * HDF5 compound type, the simple name of the class of template is chosen. * * @param template The compound to infer the HDF5 compound type from. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType getInferredType(T template); /** * Returns a compound type name> for this HDF5 file, compatible with * template. The mapping of the Java compound type to the HDF5 type is inferred by * reflection from template following basic rules on how Java data types are mapped * to HDF5 data types. * * @param name The name of the compound type in the HDF5 file. * @param template The compound array to infer the HDF5 compound type from. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType getInferredType(final String name, final T[] template); /** * Returns a compound type for this HDF5 file, compatible with template. The mapping * of the Java compound type to the HDF5 type is inferred by reflection from template * following basic rules on how Java data types are mapped to HDF5 data types. As name of the * HDF5 compound type, the simple name of the class of template is chosen. * * @param template The compound array to infer the HDF5 compound type from. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType getInferredType(final T[] template); /** * Returns a compound type name> for this HDF5 file, compatible with * template. The mapping of the Java compound type to the HDF5 type is inferred by * reflection from template following basic rules on how Java data types are mapped * to HDF5 data types. * * @param name The name of the compound type in the HDF5 file. * @param template The compound array to infer the HDF5 compound type from. * @param hints The hints to provide to the mapping procedure. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType getInferredType(String name, T[] template, HDF5CompoundMappingHints hints); /** * Returns a compound type name> for this HDF5 file, compatible with * template. The mapping of the Java compound type to the HDF5 type is inferred by * reflection from template following basic rules on how Java data types are mapped * to HDF5 data types. * * @param name The name of the compound type in the HDF5 file. * @param template The compound array to infer the HDF5 compound type from. * @param hints The hints to provide to the mapping procedure. * @param requireTypesToBeEqual If true, this type is required to be equal to the * type it tries to read, or else an {@link HDF5JavaException} will be thrown. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType getInferredType(String name, T[] template, HDF5CompoundMappingHints hints, boolean requireTypesToBeEqual); /** * Returns a compound type name> for this HDF5 file, compatible with * template and memberNames. The mapping of the Java compound type to the * HDF5 type is inferred by reflection of the elements of template following basic * rules on how Java data types are mapped to HDF5 data types. Each element of * template is considered a member of the compound. The names are taken from * memberNames in the same order as in template. * * @param name The name of the compound type in the HDF5 file. * @param memberNames The names of the members. * @param template The compound to infer the HDF5 compound type from. Needs to have the same * length as memberNames. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType> getInferredType(String name, List memberNames, List template); /** * Returns a compound type name> for this HDF5 file, compatible with * template and memberNames. The mapping of the Java compound type to the * HDF5 type is inferred by reflection of the elements of template following basic * rules on how Java data types are mapped to HDF5 data types. Each element of * template is considered a member of the compound. The names are taken from * memberNames in the same order as in template. * * @param name The name of the compound type in the HDF5 file. * @param memberNames The names of the members. * @param template The compound to infer the HDF5 compound type from. Needs to have the same * length as memberNames. * @param hints The hints to provide to the mapping procedure. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType> getInferredType(String name, List memberNames, List template, HDF5CompoundMappingHints hints); /** * Returns a compound type name> for this HDF5 file, compatible with * template and memberNames. The mapping of the Java compound type to the * HDF5 type is inferred by reflection of the elements of template following basic * rules on how Java data types are mapped to HDF5 data types. Each element of * template is considered a member of the compound. The names are taken from * memberNames in the same order as in template. * * @param name The name of the compound type in the HDF5 file. * @param memberNames The names of the members. * @param template The compound to infer the HDF5 compound type from. Needs to have the same * length as memberNames. * @param hints The hints to provide to the mapping procedure. * @param requireTypesToBeEqual If true, this type is required to be equal to the * type it tries to read, or else an {@link HDF5JavaException} will be thrown. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType> getInferredType(String name, List memberNames, List template, HDF5CompoundMappingHints hints, boolean requireTypesToBeEqual); /** * Returns a compound type name> for this HDF5 file, compatible with * template and memberNames. The mapping of the Java compound type to the * HDF5 type is inferred by reflection of the elements of template following basic * rules on how Java data types are mapped to HDF5 data types. Each element of * template is considered a member of the compound. The names are taken from * memberNames in the same order as in template. * * @param memberNames The names of the members. * @param template The compound to infer the HDF5 compound type from. Needs to have the same * length as memberNames. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType> getInferredType(List memberNames, List template); /** * Returns a compound type name> for this HDF5 file, compatible with * template and memberNames. The mapping of the Java compound type to the * HDF5 type is inferred by reflection of the elements of template following basic * rules on how Java data types are mapped to HDF5 data types. Each element of * template is considered a member of the compound. The names are taken from * memberNames in the same order as in template. * * @param memberNames The names of the members. * @param template The compound to infer the HDF5 compound type from. Needs to have the same * length as memberNames. * @param hints The hints to provide to the mapping procedure. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType> getInferredType(List memberNames, List template, HDF5CompoundMappingHints hints); /** * Returns a compound type name> for this HDF5 file, compatible with * template and memberNames. The mapping of the Java compound type to the * HDF5 type is inferred by reflection of the elements of template following basic * rules on how Java data types are mapped to HDF5 data types. Each element of * template is considered a member of the compound. The names are taken from * memberNames in the same order as in template. * * @param name The name of the compound type in the HDF5 file. * @param memberNames The names of the members. * @param template The compound to infer the HDF5 compound type from. Needs to have the same * length than memberNames. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType getInferredType(String name, String[] memberNames, Object[] template); /** * Returns a compound type name> for this HDF5 file, compatible with * template and memberNames. The mapping of the Java compound type to the * HDF5 type is inferred by reflection of the elements of template following basic * rules on how Java data types are mapped to HDF5 data types. Each element of * template is considered a member of the compound. The names are taken from * memberNames in the same order as in template. * * @param name The name of the compound type in the HDF5 file. * @param memberNames The names of the members. * @param template The compound to infer the HDF5 compound type from. Needs to have the same * length than memberNames. * @param hints The hints to provide to the mapping procedure. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType getInferredType(String name, String[] memberNames, Object[] template, HDF5CompoundMappingHints hints); /** * Returns a compound type name> for this HDF5 file, compatible with * template and memberNames. The mapping of the Java compound type to the * HDF5 type is inferred by reflection of the elements of template following basic * rules on how Java data types are mapped to HDF5 data types. Each element of * template is considered a member of the compound. The names are taken from * memberNames in the same order as in template. * * @param name The name of the compound type in the HDF5 file. * @param memberNames The names of the members. * @param template The compound to infer the HDF5 compound type from. Needs to have the same * length than memberNames. * @param hints The hints to provide to the mapping procedure. * @param requireTypesToBeEqual If true, this type is required to be equal to the * type it tries to read, or else an {@link HDF5JavaException} will be thrown. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType getInferredType(String name, String[] memberNames, Object[] template, HDF5CompoundMappingHints hints, boolean requireTypesToBeEqual); /** * Returns a compound type name> for this HDF5 file, compatible with * template and memberNames. The mapping of the Java compound type to the * HDF5 type is inferred by reflection of the elements of template following basic * rules on how Java data types are mapped to HDF5 data types. Each element of * template is considered a member of the compound. The names are taken from * memberNames in the same order as in template. * * @param memberNames The names of the members. * @param template The compound to infer the HDF5 compound type from. Needs to have the same * length than memberNames. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType getInferredType(String[] memberNames, Object[] template); /** * Returns a compound type name> for this HDF5 file, compatible with * template and memberNames. The mapping of the Java compound type to the * HDF5 type is inferred by reflection of the elements of template following basic * rules on how Java data types are mapped to HDF5 data types. Each element of * template is considered a member of the compound. The names are taken from * memberNames in the same order as in template. * * @param memberNames The names of the members. * @param template The compound to infer the HDF5 compound type from. Needs to have the same * length than memberNames. * @param hints The hints to provide to the mapping procedure. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType getInferredType(String[] memberNames, Object[] template, HDF5CompoundMappingHints hints); /** * Returns the compound type for the given compound data set in objectPath, mapping * it to pojoClass. * * @param objectPath The path of the compound dataset to get the type from. * @param pojoClass The class to use for the mapping. * @param requireTypesToBeEqual If true, this type is required to be equal to the * type it tries to read, or else an {@link HDF5JavaException} will be thrown. * @param members The mapping from the Java compound type to the HDF5 type. * @return The compound data type. */ public HDF5CompoundType getDataSetType(String objectPath, Class pojoClass, boolean requireTypesToBeEqual, HDF5CompoundMemberMapping... members); /** * Returns the compound type for the given compound data set in objectPath, mapping * it to pojoClass. * * @param objectPath The path of the compound dataset to get the type from. * @param pojoClass The class to use for the mapping. * @param members The mapping from the Java compound type to the HDF5 type. * @return The compound data type. */ public HDF5CompoundType getDataSetType(String objectPath, Class pojoClass, HDF5CompoundMemberMapping... members); /** * Returns the compound type for the given compound data set in objectPath, mapping * it to pojoClass. * * @param objectPath The path of the compound dataset to get the type from. * @param pojoClass The class to use for the mapping. * @param hints The hints to provide to the mapping procedure. * @return The compound data type. */ public HDF5CompoundType getDataSetType(String objectPath, Class pojoClass, HDF5CompoundMappingHints hints); /** * Returns the compound type for the given compound data set in objectPath, mapping * it to pojoClass. * * @param objectPath The path of the compound dataset to get the type from. * @param pojoClass The class to use for the mapping. * @param hints The hints to provide to the mapping procedure. * @param requireTypesToBeEqual If true, this type is required to be equal to the * type it tries to read, or else an {@link HDF5JavaException} will be thrown. * @return The compound data type. */ public HDF5CompoundType getDataSetType(String objectPath, Class pojoClass, HDF5CompoundMappingHints hints, boolean requireTypesToBeEqual); /** * Returns the compound type for the given compound data set in objectPath, mapping * it to pojoClass. * * @param objectPath The path of the compound dataset to get the type from. * @param pojoClass The class to use for the mapping. */ public HDF5CompoundType getDataSetType(String objectPath, Class pojoClass); /** * Returns the compound type for the given compound attribute in attributeName of * objectPath, mapping it to pojoClass. * * @param objectPath The path of the compound dataset. * @param attributeName The name of the attribute to get the type for. * @param pojoClass The class to use for the mapping. */ public HDF5CompoundType getAttributeType(String objectPath, String attributeName, Class pojoClass); /** * Returns the compound type for the given compound attribute in attributeName of * objectPath, mapping it to pojoClass. * * @param objectPath The path of the compound dataset. * @param attributeName The name of the attribute to get the type for. * @param pojoClass The class to use for the mapping. * @param hints The hints to provide to the mapping procedure. */ public HDF5CompoundType getAttributeType(String objectPath, String attributeName, Class pojoClass, HDF5CompoundMappingHints hints); /** * Returns the compound type for the given compound attribute in attributeName of * objectPath, mapping it to pojoClass. * * @param objectPath The path of the compound dataset. * @param attributeName The name of the attribute to get the type for. * @param pojoClass The class to use for the mapping. * @param hints The hints to provide to the mapping procedure. * @param dataTypeInfoOptions The options on which information to get about the member data * types. */ public HDF5CompoundType getAttributeType(String objectPath, String attributeName, Class pojoClass, HDF5CompoundMappingHints hints, DataTypeInfoOptions dataTypeInfoOptions); /** * Returns the compound type for the given compound attribute in attributeName of * objectPath, mapping it to pojoClass. * * @param objectPath The path of the compound dataset. * @param attributeName The name of the attribute to get the type for. * @param pojoClass The class to use for the mapping. * @param hints The hints to provide to the mapping procedure. * @param dataTypeInfoOptions The options on which information to get about the member data * types. * @param requireTypesToBeEqual If true, this type is required to be equal to the * type it tries to read, or else an {@link HDF5JavaException} will be thrown. */ public HDF5CompoundType getAttributeType(String objectPath, String attributeName, Class pojoClass, HDF5CompoundMappingHints hints, DataTypeInfoOptions dataTypeInfoOptions, boolean requireTypesToBeEqual); /** * Returns the named compound type with name dataTypeName from file, mapping it to * pojoClass. If the dataTypeName starts with '/', it will be considered a * data type path instead of a data type name. *

* Note: This method only works for compound data types 'committed' to the HDF5 file. * For files written with JHDF5 this will always be true, however, files created with other * libraries may not choose to commit compound data types. * * @param dataTypeName The path to a committed data type, if starting with '/', or a name of a * committed data type otherwise. * @param pojoClass The class to use for the mapping. * @return The compound data type. */ public HDF5CompoundType getNamedType(String dataTypeName, Class pojoClass); /** * Returns the named compound type with name dataTypeName from file, mapping it to * pojoClass. This method will use the default name for the compound data type as * chosen by JHDF5 and thus will likely only work on files written with JHDF5. The default name * is based on the simple name of compoundType. * * @param pojoClass The class to use for the mapping and to get the name of named data type * from. * @return The compound data type. */ public HDF5CompoundType getNamedType(Class pojoClass); /** * Returns the named compound type with name dataTypeName from file, mapping it to * pojoClass. If the dataTypeName starts with '/', it will be considered a * data type path instead of a data type name. *

* Note: This method only works for compound data types 'committed' to the HDF5 file. * For files written with JHDF5 this will always be true, however, files created with other * libraries may not choose to commit compound data types. * * @param dataTypeName The path to a committed data type, if starting with '/', or a name of a * committed data type otherwise. * @param pojoClass The class to use for the mapping. * @param hints The hints to provide to the mapping procedure. * @return The compound data type. */ public HDF5CompoundType getNamedType(String dataTypeName, Class pojoClass, HDF5CompoundMappingHints hints); /** * Returns the named compound type with name dataTypeName from file, mapping it to * pojoClass. If the dataTypeName starts with '/', it will be considered a * data type path instead of a data type name. *

* Note: This method only works for compound data types 'committed' to the HDF5 file. * For files written with JHDF5 this will always be true, however, files created with other * libraries may not choose to commit compound data types. * * @param dataTypeName The path to a committed data type, if starting with '/', or a name of a * committed data type otherwise. * @param pojoClass The class to use for the mapping. * @param dataTypeInfoOptions The options on which information to get about the member data * types. * @return The compound data type. */ public HDF5CompoundType getNamedType(String dataTypeName, Class pojoClass, DataTypeInfoOptions dataTypeInfoOptions); /** * Returns the named compound type with name dataTypeName from file, mapping it to * pojoClass. If the dataTypeName starts with '/', it will be considered a * data type path instead of a data type name. *

* Note: This method only works for compound data types 'committed' to the HDF5 file. * For files written with JHDF5 this will always be true, however, files created with other * libraries may not choose to commit compound data types. * * @param dataTypeName The path to a committed data type, if starting with '/', or a name of a * committed data type otherwise. * @param pojoClass The class to use for the mapping. * @param hints The hints to provide to the mapping procedure. * @param dataTypeInfoOptions The options on which information to get about the member data * types. * @return The compound data type. */ public HDF5CompoundType getNamedType(String dataTypeName, Class pojoClass, HDF5CompoundMappingHints hints, DataTypeInfoOptions dataTypeInfoOptions); /** * Returns the named compound type with name dataTypeName from file, mapping it to * pojoClass. If the dataTypeName starts with '/', it will be considered a * data type path instead of a data type name. *

* Note: This method only works for compound data types 'committed' to the HDF5 file. * For files written with JHDF5 this will always be true, however, files created with other * libraries may not choose to commit compound data types. * * @param dataTypeName The path to a committed data type, if starting with '/', or a name of a * committed data type otherwise. * @param pojoClass The class to use for the mapping. * @param hints The hints to provide to the mapping procedure. * @param dataTypeInfoOptions The options on which information to get about the member data * types. * @param requireTypesToBeEqual If true, this type is required to be equal to the * type it tries to read, or else an {@link HDF5JavaException} will be thrown. * @return The compound data type. */ public HDF5CompoundType getNamedType(String dataTypeName, Class pojoClass, HDF5CompoundMappingHints hints, DataTypeInfoOptions dataTypeInfoOptions, boolean requireTypesToBeEqual); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5CompoundReader.java000066400000000000000000000553711256564762100276670ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.base.mdarray.MDArray; /** * An interface that provides methods for reading compound values from HDF5 files. * * @author Bernd Rinn */ public interface IHDF5CompoundReader extends IHDF5CompoundInformationRetriever { // ///////////////////// // Attributes // ///////////////////// /** * Reads a compound attribute named attributeName from the object * objectPath. * * @param objectPath The name (including path information) of the object in the file. * @param type The type definition of this compound type. * @return The data read from the attribute. * @throws HDF5JavaException If the attributeName is not a compound attribute. */ public T getAttr(String objectPath, String attributeName, HDF5CompoundType type) throws HDF5JavaException; /** * Reads a compound attribute named attributeName from the object * objectPath. * * @param objectPath The name (including path information) of the object in the file. * @param pojoClass The class to return the result in. Use {@link HDF5CompoundDataMap} to get it * in a map, {@link HDF5CompoundDataList} to get it in a list, and * Object[] to get it in an array, or use a pojo (Data Transfer Object), * in which case the compound members will be mapped to Java fields. * @return The data read from the attribute. * @throws HDF5JavaException If the attributeName is not a compound attribute. */ public T getAttr(String objectPath, String attributeName, Class pojoClass) throws HDF5JavaException; /** * Reads a compound array (of rank 1) attribute named attributeName from the object * objectPath. * * @param objectPath The name (including path information) of the object in the file. * @param type The type definition of this compound type. * @return The data read from the attribute. * @throws HDF5JavaException If the attributeName is not a compound attribute. */ public T[] getArrayAttr(String objectPath, String attributeName, HDF5CompoundType type) throws HDF5JavaException; /** * Reads a compound array (of rank 1) attribute named attributeName from the object * objectPath. * * @param objectPath The name (including path information) of the object in the file. * @param pojoClass The class to return the result in. Use {@link HDF5CompoundDataMap} to get it * in a map, {@link HDF5CompoundDataList} to get it in a list, and * Object[] to get it in an array, or use a pojo (Data Transfer Object), * in which case the compound members will be mapped to Java fields. * @return The data read from the attribute. * @throws HDF5JavaException If the attributeName is not a compound attribute. */ public T[] getArrayAttr(String objectPath, String attributeName, Class pojoClass) throws HDF5JavaException; /** * Reads a compound array (of rank N) attribute named attributeName from the object * objectPath. * * @param objectPath The name (including path information) of the object in the file. * @param type The type definition of this compound type. * @return The data read from the attribute. * @throws HDF5JavaException If the attributeName is not a compound attribute. */ public MDArray getMDArrayAttr(String objectPath, String attributeName, HDF5CompoundType type) throws HDF5JavaException; /** * Reads a compound array (of rank N) attribute named attributeName from the object * objectPath. * * @param objectPath The name (including path information) of the object in the file. * @param pojoClass The class to return the result in. Use {@link HDF5CompoundDataMap} to get it * in a map, {@link HDF5CompoundDataList} to get it in a list, and * Object[] to get it in an array, or use a pojo (Data Transfer Object), * in which case the compound members will be mapped to Java fields. * @return The data read from the attribute. * @throws HDF5JavaException If the attributeName is not a compound attribute. */ public MDArray getMDArrayAttr(String objectPath, String attributeName, Class pojoClass) throws HDF5JavaException; // ///////////////////// // Data Sets // ///////////////////// /** * Reads a compound from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set. */ public T read(String objectPath, HDF5CompoundType type) throws HDF5JavaException; /** * Reads a compound from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param pojoClass The class to return the result in. Use {@link HDF5CompoundDataMap} to get it * in a map, {@link HDF5CompoundDataList} to get it in a list, and * Object[] to get it in an array, or use a pojo (Data Transfer Object), * in which case the compound members will be mapped to Java fields. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set or if the * mapping between the compound type and the POJO is not complete. * @see CompoundType * @see CompoundElement */ public T read(String objectPath, Class pojoClass) throws HDF5JavaException; /** * Reads a compound from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param inspectorOrNull The inspector to be called before the byte array read from the HDF5 * file is translated back into a Java object. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set. */ public T read(String objectPath, HDF5CompoundType type, IByteArrayInspector inspectorOrNull) throws HDF5JavaException; /** * Reads a compound array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set. */ public T[] readArray(String objectPath, HDF5CompoundType type) throws HDF5JavaException; /** * Reads a compound array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param inspectorOrNull The inspector to be called before the byte array read from the HDF5 * file is translated back into Java objects. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set. */ public T[] readArray(String objectPath, HDF5CompoundType type, IByteArrayInspector inspectorOrNull) throws HDF5JavaException; /** * Reads a compound array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param pojoClass The class to return the result in. Use {@link HDF5CompoundDataMap} to get it * in a map, {@link HDF5CompoundDataList} to get it in a list, and * Object[] to get it in an array, or use a pojo (Data Transfer Object), * in which case the compound members will be mapped to Java fields. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set or if the * mapping between the compound type and the POJO is not complete. * @see CompoundType * @see CompoundElement */ public T[] readArray(String objectPath, Class pojoClass) throws HDF5JavaException; /** * Reads a compound array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param blockSize The block size (this will be the length of the float[] returned * if the data set is long enough). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set. */ public T[] readArrayBlock(String objectPath, HDF5CompoundType type, int blockSize, long blockNumber) throws HDF5JavaException; /** * Reads a compound array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param blockSize The block size (this will be the length of the float[] returned * if the data set is long enough). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @param inspectorOrNull The inspector to be called before the byte array read from the HDF5 * file is translated back into Java objects. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set. */ public T[] readArrayBlock(String objectPath, HDF5CompoundType type, int blockSize, long blockNumber, IByteArrayInspector inspectorOrNull) throws HDF5JavaException; /** * Reads a compound array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param blockSize The block size (this will be the length of the float[] returned * if the data set is long enough). * @param offset The offset of the block to read (starting with 0). * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set. */ public T[] readArrayBlockWithOffset(String objectPath, HDF5CompoundType type, int blockSize, long offset) throws HDF5JavaException; /** * Reads a compound array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param blockSize The block size (this will be the length of the float[] returned * if the data set is long enough). * @param offset The offset of the block to read (starting with 0). * @param inspectorOrNull The inspector to be called before the byte array read from the HDF5 * file is translated back into Java objects. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set. */ public T[] readArrayBlockWithOffset(String objectPath, HDF5CompoundType type, int blockSize, long offset, IByteArrayInspector inspectorOrNull) throws HDF5JavaException; /** * Provides all natural blocks of this one-dimensional data set of compounds to iterate over. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1 or not a compound data set. */ public Iterable> getArrayBlocks(String objectPath, HDF5CompoundType type) throws HDF5JavaException; /** * Provides all natural blocks of this one-dimensional data set of compounds to iterate over. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param inspectorOrNull The inspector to be called before the byte array read from the HDF5 * file is translated back into Java objects. * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1 or not a compound data set. */ public Iterable> getArrayBlocks(String objectPath, HDF5CompoundType type, IByteArrayInspector inspectorOrNull) throws HDF5JavaException; /** * Provides all natural blocks of this one-dimensional data set of compounds to iterate over. * * @param objectPath The name (including path information) of the data set object in the file. * @param pojoClass The class to return the result in. Use {@link HDF5CompoundDataMap} to get it * in a map, {@link HDF5CompoundDataList} to get it in a list, and * Object[] to get it in an array, or use a pojo (Data Transfer Object), * in which case the compound members will be mapped to Java fields. * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1 or not a compound data set. * @throws HDF5JavaException If the data set is not of rank 1, not a compound data set or if the * mapping between the compound type and the POJO is not complete. */ public Iterable> getArrayBlocks(String objectPath, Class pojoClass) throws HDF5JavaException; /** * Reads a compound array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set. */ public MDArray readMDArray(String objectPath, HDF5CompoundType type) throws HDF5JavaException; /** * Reads a compound array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param pojoClass The class to return the result in. Use {@link HDF5CompoundDataMap} to get it * in a map, {@link HDF5CompoundDataList} to get it in a list, and * Object[] to get it in an array, or use a pojo (Data Transfer Object), * in which case the compound members will be mapped to Java fields. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set or if the * mapping between the compound type and the POJO is not complete. * @see CompoundType * @see CompoundElement */ public MDArray readMDArray(String objectPath, Class pojoClass) throws HDF5JavaException; /** * Reads a compound array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param inspectorOrNull The inspector to be called before the byte array read from the HDF5 * file is translated back into Java objects. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set. */ public MDArray readMDArray(String objectPath, HDF5CompoundType type, IByteArrayInspector inspectorOrNull) throws HDF5JavaException; /** * Reads a block from a compound array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param blockDimensions The extent of the block to write along each axis. * @param blockNumber The number of the block to write along each axis. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set. */ public MDArray readMDArrayBlock(String objectPath, HDF5CompoundType type, int[] blockDimensions, long[] blockNumber) throws HDF5JavaException; /** * Reads a block from a compound array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param blockDimensions The extent of the block to write along each axis. * @param blockNumber The number of the block to write along each axis. * @param inspectorOrNull The inspector to be called before the byte array read from the HDF5 * file is translated back into Java objects. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound type. */ public MDArray readMDArrayBlock(String objectPath, HDF5CompoundType type, int[] blockDimensions, long[] blockNumber, IByteArrayInspector inspectorOrNull) throws HDF5JavaException; /** * Reads a block from a compound array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param blockDimensions The extent of the block to write along each axis. * @param offset The offset of the block to write in the data set along each axis. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set. */ public MDArray readMDArrayBlockWithOffset(String objectPath, HDF5CompoundType type, int[] blockDimensions, long[] offset) throws HDF5JavaException; /** * Reads a block from a compound array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param blockDimensions The extent of the block to write along each axis. * @param offset The offset of the block to write in the data set along each axis. * @param inspectorOrNull The inspector to be called before the byte array read from the HDF5 * file is translated back into Java objects. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set. */ public MDArray readMDArrayBlockWithOffset(String objectPath, HDF5CompoundType type, int[] blockDimensions, long[] offset, IByteArrayInspector inspectorOrNull) throws HDF5JavaException; /** * Provides all natural blocks of this multi-dimensional data set to iterate over. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @see HDF5MDDataBlock */ public Iterable>> getMDArrayBlocks(String objectPath, HDF5CompoundType type) throws HDF5JavaException; /** * Provides all natural blocks of this multi-dimensional data set to iterate over. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param inspectorOrNull The inspector to be called before the byte array read from the HDF5 * file is translated back into Java objects. * @see HDF5MDDataBlock */ public Iterable>> getMDArrayBlocks(String objectPath, HDF5CompoundType type, IByteArrayInspector inspectorOrNull) throws HDF5JavaException; /** * Provides all natural blocks of this multi-dimensional data set of compounds to iterate over. * * @param objectPath The name (including path information) of the data set object in the file. * @param pojoClass The class to return the result in. Use {@link HDF5CompoundDataMap} to get it * in a map, {@link HDF5CompoundDataList} to get it in a list, and * Object[] to get it in an array. * @see HDF5DataBlock * @see CompoundType * @see CompoundElement * @throws HDF5JavaException If the data set is not a compound data set or if the mapping * between the compound type and the POJO is not complete. */ public Iterable>> getMDArrayBlocks(String objectPath, Class pojoClass) throws HDF5JavaException; } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5CompoundWriter.java000066400000000000000000000753461256564762100277450ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.util.List; import ch.systemsx.cisd.base.mdarray.MDArray; /** * An interface that provides methods for writing compound values to HDF5 files. * * @author Bernd Rinn */ public interface IHDF5CompoundWriter extends IHDF5CompoundReader { // ///////////////////// // Types // ///////////////////// /** * Returns the compound type cloned from the given templateType. This method can be * used to get a compound type from a different file. * * @param templateType The compound type to clone. Will typically be a compound type from * another reader or writer. The type needs to be open (which means that the * reader / writer from which it has been obtained has to be still open). */ public HDF5CompoundType getClonedType(final HDF5CompoundType templateType); /** * Returns the anonymous compound type for this HDF5 file, using the default name chosen by * JHDF5 which is based on the simple name of pojoClass. * * @param pojoClass The plain old Java type that corresponds to this HDF5 type. * @param members The mapping from the Java compound type to the HDF5 type. */ public HDF5CompoundType getAnonType(Class pojoClass, HDF5CompoundMemberMapping... members); /** * Returns the anonymous compound type name> for this HDF5 file, inferring the * mapping from the Java compound type to the HDF5 type by reflection. * * @param pojoClass The plain old Java type that corresponds to this HDF5 type. * @param hints The hints to provide to the mapping procedure. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType getInferredAnonType(Class pojoClass, HDF5CompoundMappingHints hints); /** * Returns the anonymous compound type name> for this HDF5 file, inferring the * mapping from the Java compound type to the HDF5 type by reflection. * * @param pojoClass The plain old Java type that corresponds to this HDF5 type. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType getInferredAnonType(Class pojoClass); /** * Returns anonyous the compound type name> for this HDF5 file, inferring the mapping * from the Java compound type to the HDF5 type by reflection. * * @param template The compound to infer the HDF5 compound type from. * @param hints The hints to provide to the mapping procedure. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType getInferredAnonType(T template, HDF5CompoundMappingHints hints); /** * Returns the anonymous compound type for this HDF5 file, inferring the mapping from the Java * compound type to the HDF5 type by reflection and using the default name chosen by JHDF5 which * is based on the simple name of T. * * @param template The compound to infer the HDF5 compound type from. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType getInferredAnonType(T template); /** * Returns the anonymous compound type name> for this HDF5 file, inferring the * mapping from the Java compound type to the HDF5 type by reflection. * * @param template The compound array to infer the HDF5 compound type from. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType getInferredAnonType(final T[] template); /** * Returns the anonymous compound type name> for this HDF5 file, inferring the * mapping from the Java compound type to the HDF5 type by reflection. * * @param template The compound array to infer the HDF5 compound type from. * @param hints The hints to provide to the mapping procedure. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType getInferredAnonType(T[] template, HDF5CompoundMappingHints hints); /** * Returns the anonymous compound type for this HDF5 file, inferring the mapping from the Java * types of the members. * * @param memberNames The names of the members. * @param template The compound to infer the HDF5 compound type from. Needs to have the same * length as memberNames. * @param hints The hints to provide to the mapping procedure. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType> getInferredAnonType(List memberNames, List template, HDF5CompoundMappingHints hints); /** * Returns the anonymous compound type for this HDF5 file, inferring the mapping from the Java * types of the members. * * @param memberNames The names of the members. * @param template The compound to infer the HDF5 compound type from. Needs to have the same * length as memberNames. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType> getInferredAnonType(List memberNames, List template); /** * Returns the anonymous compound type for this HDF5 file, inferring the mapping from the Java * types of the members. * * @param memberNames The names of the members. * @param template The compound to infer the HDF5 compound type from. Needs to have the same * length than memberNames. * @param hints The hints to provide to the mapping procedure. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType getInferredAnonType(String[] memberNames, Object[] template, HDF5CompoundMappingHints hints); /** * Returns the anonymous compound type for this HDF5 file, inferring the mapping from the Java * types of the members. * * @param memberNames The names of the members. * @param template The compound to infer the HDF5 compound type from. Needs to have the same * length than memberNames. * @see HDF5CompoundMemberMapping#inferMapping */ public HDF5CompoundType getInferredAnonType(String[] memberNames, Object[] template); // ///////////////////// // Attributes // ///////////////////// /** * Sets a compound attribute to the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param attributeName The name of the attribute. * @param type The type definition of this compound type. * @param value The value of the attribute. May be a Data Transfer Object, a * {@link HDF5CompoundDataMap}, {@link HDF5CompoundDataList} or Object[] * . */ public void setAttr(String objectPath, String attributeName, HDF5CompoundType type, T value); /** * Sets a compound attribute to the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param attributeName The name of the attribute. * @param value The value of the attribute. May be a Data Transfer Object, a * {@link HDF5CompoundDataMap}, {@link HDF5CompoundDataList} or Object[] * . */ public void setAttr(String objectPath, String attributeName, T value); /** * Sets a compound attribute array (of rank 1) to the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param attributeName The name of the attribute. * @param type The type definition of this compound type. * @param value The value of the attribute. Data Transfer Object, a {@link HDF5CompoundDataMap}, * {@link HDF5CompoundDataList} or Object[] . */ public void setArrayAttr(String objectPath, String attributeName, HDF5CompoundType type, T[] value); /** * Sets a compound attribute array (of rank 1) to the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param attributeName The name of the attribute. * @param value The value of the attribute. May be a Data Transfer Object, a * {@link HDF5CompoundDataMap}, {@link HDF5CompoundDataList} or Object[] * . */ public void setArrayAttr(String objectPath, String attributeName, T[] value); /** * Sets a compound attribute array (of rank N) to the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param attributeName The name of the attribute. * @param type The type definition of this compound type. * @param value The value of the attribute. Data Transfer Object, a {@link HDF5CompoundDataMap}, * {@link HDF5CompoundDataList} or Object[] . */ public void setMDArrayAttr(String objectPath, String attributeName, HDF5CompoundType type, MDArray value); /** * Sets a compound attribute array (of rank N) to the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param attributeName The name of the attribute. * @param value The value of the attribute. May be a Data Transfer Object, a * {@link HDF5CompoundDataMap}, {@link HDF5CompoundDataList} or Object[] * . */ public void setMDArrayAttr(String objectPath, String attributeName, MDArray value); // ///////////////////// // Data Sets // ///////////////////// /** * Writes out a compound value of type given in data. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The value of the data set. */ public void write(String objectPath, HDF5CompoundType type, T data); /** * Writes out a compound value. The type is inferred based on the values. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The value of the data set. May be a pojo (Data Transfer Object), a * {@link HDF5CompoundDataMap}, {@link HDF5CompoundDataList} or Object[] * . * @see CompoundType * @see CompoundElement */ public void write(String objectPath, T data); /** * Writes out an array (of rank 1) of compound values. Uses a compact storage layout. Must only * be used for small data sets. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The value of the data set. * @param inspectorOrNull The inspector to be called after translating the Java objects to a * byte array and before writing the byte array to the HDF5 file. */ public void write(String objectPath, HDF5CompoundType type, T data, IByteArrayInspector inspectorOrNull); /** * Writes out an array (of rank 1) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The value of the data set. */ public void writeArray(String objectPath, HDF5CompoundType type, T[] data); /** * Writes out an array (of rank 1) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The value of the data set. * @param features The storage features of the data set. */ public void writeArray(String objectPath, HDF5CompoundType type, T[] data, HDF5GenericStorageFeatures features); /** * Writes out an array (of rank 1) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The value of the data set. * @param features The storage features of the data set. * @param inspectorOrNull The inspector to be called after translating the Java objects to a * byte array and before writing the byte array to the HDF5 file. */ public void writeArray(String objectPath, HDF5CompoundType type, T[] data, HDF5GenericStorageFeatures features, IByteArrayInspector inspectorOrNull); /** * Writes out an array (of rank 1) of compound values. The type is inferred based on the values. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The value of the data set. May be a pojo (Data Transfer Object), a * {@link HDF5CompoundDataMap}, {@link HDF5CompoundDataList} or Object[] * . * @see CompoundType * @see CompoundElement */ public void writeArray(String objectPath, T[] data); /** * Writes out an array (of rank 1) of compound values. The type is inferred based on the values. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The value of the data set. May be a {@link HDF5CompoundDataMap}, * {@link HDF5CompoundDataList} or Object[]. * @param features The storage features of the data set. * @see CompoundType * @see CompoundElement */ public void writeArray(String objectPath, T[] data, HDF5GenericStorageFeatures features); /** * Writes out a block blockNumber of an array (of rank 1) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The value of the data set. * @param blockNumber The number of the block to write. */ public void writeArrayBlock(String objectPath, HDF5CompoundType type, T[] data, long blockNumber); /** * Writes out a block blockNumber of an array (of rank 1) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The value of the data set. * @param blockNumber The number of the block to write. * @param inspectorOrNull The inspector to be called after translating the Java objects to a * byte array and before writing the byte array to the HDF5 file. */ public void writeArrayBlock(String objectPath, HDF5CompoundType type, T[] data, long blockNumber, IByteArrayInspector inspectorOrNull); /** * Writes out a block of an array (of rank 1) of compound values with given offset. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The value of the data set. * @param offset The offset of the block in the data set. */ public void writeArrayBlockWithOffset(String objectPath, HDF5CompoundType type, T[] data, long offset); /** * Writes out a block of an array (of rank 1) of compound values with given offset. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The value of the data set. * @param offset The offset of the block in the data set. * @param inspectorOrNull The inspector to be called after translating the Java objects to a * byte array and before writing the byte array to the HDF5 file. */ public void writeArrayBlockWithOffset(String objectPath, HDF5CompoundType type, T[] data, long offset, IByteArrayInspector inspectorOrNull); /** * Creates an array (of rank 1) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param size The size of the array to create. This will be the total size for non-extendable * data sets and the size of one chunk for extendable (chunked) data sets. For * extendable data sets the initial size of the array will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. */ public void createArray(String objectPath, HDF5CompoundType type, int size); /** * Creates an array (of rank 1) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param size The size of the compound array to create. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) * and deflate == false. */ public void createArray(String objectPath, HDF5CompoundType type, long size, int blockSize); /** * Creates an array (of rank 1) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param size The size of the compound array to create. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) * and deflate == false. * @param features The storage features of the data set. */ public void createArray(String objectPath, HDF5CompoundType type, long size, int blockSize, HDF5GenericStorageFeatures features); /** * Creates an array (of rank 1) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param size The size of the byte array to create. This will be the total size for * non-extendable data sets and the size of one chunk for extendable (chunked) data * sets. For extendable data sets the initial size of the array will be 0, see * {@link HDF5GenericStorageFeatures}. * @param features The storage features of the data set. */ public void createArray(String objectPath, HDF5CompoundType type, long size, HDF5GenericStorageFeatures features); /** * Writes out an array (of rank N) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The data to write. */ public void writeMDArray(String objectPath, HDF5CompoundType type, MDArray data); /** * Writes out an array (of rank N) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The data to write. * @param features The storage features of the data set. */ public void writeMDArray(String objectPath, HDF5CompoundType type, MDArray data, HDF5GenericStorageFeatures features); /** * Writes out an array (of rank N) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The data to write. * @param features The storage features of the data set. * @param inspectorOrNull The inspector to be called after translating the Java objects to a * byte array and before writing the byte array to the HDF5. */ public void writeMDArray(String objectPath, HDF5CompoundType type, MDArray data, HDF5GenericStorageFeatures features, IByteArrayInspector inspectorOrNull); /** * Writes out an array (of rank N) of compound values. The type is inferred based on the values. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The value of the data set. May be a pojo (Data Transfer Object), a * {@link HDF5CompoundDataMap}, {@link HDF5CompoundDataList} or Object[] * . * @see CompoundType * @see CompoundElement */ public void writeMDArray(String objectPath, MDArray data); /** * Writes out an array (of rank N) of compound values. The type is inferred based on the values. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The value of the data set. May be a pojo (Data Transfer Object), a * {@link HDF5CompoundDataMap}, {@link HDF5CompoundDataList} or Object[] * . * @param features The storage features of the data set. * @see CompoundType * @see CompoundElement */ public void writeMDArray(String objectPath, MDArray data, HDF5GenericStorageFeatures features); /** * Writes out a block of an array (of rank N) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The data to write. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). */ public void writeMDArrayBlock(String objectPath, HDF5CompoundType type, MDArray data, long[] blockNumber); /** * Writes out a block of an array (of rank N) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The data to write. * @param blockNumber The extent of the block to write on each axis. * @param inspectorOrNull The inspector to be called after translating the Java objects to a * byte array and before writing the byte array to the HDF5. */ public void writeMDArrayBlock(String objectPath, HDF5CompoundType type, MDArray data, long[] blockNumber, IByteArrayInspector inspectorOrNull); /** * Writes out a block of an array (of rank N) of compound values give a given offset. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The data to write. * @param offset The offset of the block to write on each axis. */ public void writeMDArrayBlockWithOffset(String objectPath, HDF5CompoundType type, MDArray data, long[] offset); /** * Writes out a block of an array (of rank N) of compound values give a given offset. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The data to write. * @param offset The offset of the block to write on each axis. * @param inspectorOrNull The inspector to be called after translating the Java objects to a * byte array and before writing the byte array to the HDF5. */ public void writeMDArrayBlockWithOffset(String objectPath, HDF5CompoundType type, MDArray data, long[] offset, IByteArrayInspector inspectorOrNull); /** * Writes out a block of an array (of rank N) of compound values give a given offset. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The data to write. * @param blockDimensions The dimensions of the block to write to the data set. * @param offset The offset of the block in the data set to start writing to in each dimension. * @param memoryOffset The offset of the block in the data array. */ public void writeMDArrayBlockWithOffset(String objectPath, HDF5CompoundType type, MDArray data, int[] blockDimensions, long[] offset, int[] memoryOffset); /** * Writes out a block of an array (of rank N) of compound values give a given offset. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param data The data to write. * @param blockDimensions The dimensions of the block to write to the data set. * @param offset The offset of the block in the data set to start writing to in each dimension. * @param memoryOffset The offset of the block in the data array. * @param inspectorOrNull The inspector to be called after translating the Java objects to a * byte array and before writing the byte array to the HDF5. */ public void writeMDArrayBlockWithOffset(String objectPath, HDF5CompoundType type, MDArray data, int[] blockDimensions, long[] offset, int[] memoryOffset, IByteArrayInspector inspectorOrNull); /** * Creates an array (of rank N) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param dimensions The dimensions of the compound array to create. This will be the total * dimensions for non-extendable data sets and the dimensions of one chunk (along * each axis) for extendable (chunked) data sets. For extendable data sets the * initial size of the array (along each axis) will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. */ public void createMDArray(String objectPath, HDF5CompoundType type, int[] dimensions); /** * Creates an array (of rank N) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param dimensions The extent of the compound array along each of the axis. * @param blockDimensions The extent of one block along each of the axis. (for block-wise IO). * Ignored if no extendable data sets are used (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) and * deflate == false. */ public void createMDArray(String objectPath, HDF5CompoundType type, long[] dimensions, int[] blockDimensions); /** * Creates an array (of rank N) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param dimensions The extent of the compound array along each of the axis. * @param blockDimensions The extent of one block along each of the axis. (for block-wise IO). * Ignored if no extendable data sets are used (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) and * deflate == false. * @param features The storage features of the data set. */ public void createMDArray(String objectPath, HDF5CompoundType type, long[] dimensions, int[] blockDimensions, HDF5GenericStorageFeatures features); /** * Creates an array (of rank N) of compound values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this compound type. * @param dimensions The dimensions of the byte array to create. This will be the total * dimensions for non-extendable data sets and the dimensions of one chunk (along * each axis) for extendable (chunked) data sets. For extendable data sets the * initial size of the array (along each axis) will be 0, see * {@link HDF5GenericStorageFeatures}. * @param features The storage features of the data set. */ public void createMDArray(String objectPath, HDF5CompoundType type, int[] dimensions, HDF5GenericStorageFeatures features); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5DateTimeReader.java000066400000000000000000000524571256564762100276010ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.util.Date; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDLongArray; /** * An interface that provides methods for reading time and date values from HDF5 files. * * @author Bernd Rinn */ public interface IHDF5DateTimeReader { // ///////////////////// // Attributes // ///////////////////// /** * Returns true, if the attribute attributeName of data set * objectPath is a time stamp and false otherwise. */ public boolean isTimeStamp(String objectPath, String attributeName) throws HDF5JavaException; /** * Reads a time stamp attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The time stamp as number of milliseconds since January 1, 1970, 00:00:00 GMT. * @throws HDF5JavaException If the attribute attributeName of objct * objectPath is not defined as type variant * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. */ public long getAttrAsLong(String objectPath, String attributeName); /** * Reads a time stamp array attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The time stamp array; each element is a number of milliseconds since January 1, 1970, * 00:00:00 GMT. * @throws HDF5JavaException If the attribute attributeName of objct * objectPath is not defined as type variant * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. */ public long[] getArrayAttrAsLong(String objectPath, String attributeName); /** * Reads a multi-dimension time stamp array attribute named attributeName from the * data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The time stamp array; each element is a number of milliseconds since January 1, 1970, * 00:00:00 GMT. * @throws HDF5JavaException If the attribute attributeName of objct * objectPath is not defined as type variant * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. */ public MDLongArray getMDArrayAttrAsLong(String objectPath, String attributeName); /** * Reads a time stamp attribute named attributeName from the data set * objectPath and returns it as a Date. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The time stamp as {@link java.util.Date}. * @throws HDF5JavaException If the attribute attributeName of objct * objectPath is not defined as type variant * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. */ public Date getAttr(String objectPath, String attributeName); /** * Reads a time stamp array attribute named attributeName from the data set * objectPath and returns it as a Date[]. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The time stamp as {@link java.util.Date}. * @throws HDF5JavaException If the attribute attributeName of objct * objectPath is not defined as type variant * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. */ public Date[] getArrayAttr(String objectPath, String attributeName); /** * Reads a multi-dimension time stamp array attribute named attributeName from the * data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The time stamp as {@link java.util.Date}. * @throws HDF5JavaException If the attribute attributeName of objct * objectPath is not defined as type variant * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. */ public MDArray getMDArrayAttr(String objectPath, String attributeName); // ///////////////////// // Data Sets // ///////////////////// /** * Returns true, if the data set given by objectPath is a time stamp and * false otherwise. */ public boolean isTimeStamp(String objectPath) throws HDF5JavaException; /** * Reads a time stamp value from the data set objectPath. The time stamp is stored as * a long value in the HDF5 file. It needs to be tagged as type variant * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. *

* This tagging is done by the writer when using * {@link IHDF5Writer#writeTimeDuration(String, HDF5TimeDuration)} or can be done by calling * {@link IHDF5ObjectReadWriteInfoProviderHandler#setTypeVariant(String, HDF5DataTypeVariant)}, * most conveniently by code like * * 

     * writer.addTypeVariant("/dataSetPath", HDF5TimeUnit.SECONDS.getTypeVariant());
     *
* * @param objectPath The name (including path information) of the data set object in the file. * @return The time stamp as number of milliseconds since January 1, 1970, 00:00:00 GMT. * @throws HDF5JavaException If the objectPath is not defined as type variant * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. */ public long readTimeStamp(String objectPath) throws HDF5JavaException; /** * Reads a time stamp array from the data set objectPath. The time stamp is stored as * a long value in the HDF5 file. It needs to be tagged as type variant * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. *

* This tagging is done by the writer when using * {@link IHDF5Writer#writeTimeDuration(String, HDF5TimeDuration)} or can be done by calling * {@link IHDF5ObjectReadWriteInfoProviderHandler#setTypeVariant(String, HDF5DataTypeVariant)}, * most conveniently by code like * * 

     * writer.addTypeVariant("/dataSetPath", HDF5TimeUnit.SECONDS.getTypeVariant());
     *
* * @param objectPath The name (including path information) of the data set object in the file. * @return The time stamp as number of milliseconds since January 1, 1970, 00:00:00 GMT. * @throws HDF5JavaException If the objectPath is not defined as type variant * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. */ public long[] readTimeStampArray(String objectPath) throws HDF5JavaException; /** * Reads a block of a time stamp array (of rank 1) from the data set objectPath. The * time stamp is stored as a long value in the HDF5 file. It needs to be tagged as * type variant {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. *

* This tagging is done by the writer when using * {@link IHDF5Writer#writeTimeDuration(String, HDF5TimeDuration)} or can be done by calling * {@link IHDF5ObjectReadWriteInfoProviderHandler#setTypeVariant(String, HDF5DataTypeVariant)}, * most conveniently by code like * * 

     * writer.addTypeVariant("/dataSetPath", HDF5TimeUnit.SECONDS.getTypeVariant());
     *
* * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the long[] returned * if the data set is long enough). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @return The data read from the data set. The length will be min(size - blockSize*blockNumber, * blockSize). */ public long[] readTimeStampArrayBlock(String objectPath, int blockSize, long blockNumber); /** * Reads a block of a time stamp array (of rank 1) from the data set objectPath. The * time stamp is stored as a long value in the HDF5 file. It needs to be tagged as * type variant {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. *

* This tagging is done by the writer when using * {@link IHDF5Writer#writeTimeDuration(String, HDF5TimeDuration)} or can be done by calling * {@link IHDF5ObjectReadWriteInfoProviderHandler#setTypeVariant(String, HDF5DataTypeVariant)}, * most conveniently by code like * * 

     * writer.addTypeVariant("/dataSetPath", HDF5TimeUnit.SECONDS.getTypeVariant());
     *
* * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the long[] * returned). * @param offset The offset of the block in the data set to start reading from (starting with * 0). * @return The data block read from the data set. */ public long[] readTimeStampArrayBlockWithOffset(String objectPath, int blockSize, long offset); /** * Provides all natural blocks of this one-dimensional data set of time stamps to iterate over. * * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1. */ public Iterable> getTimeStampArrayNaturalBlocks(String dataSetPath) throws HDF5JavaException; /** * Reads a time stamp value from the data set objectPath and returns it as a * {@link Date}. The time stamp is stored as a long value in the HDF5 file. It * needs to be tagged as type variant * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. *

* This tagging is done by the writer when using * {@link IHDF5Writer#writeTimeDuration(String, HDF5TimeDuration)} or can be done by calling * {@link IHDF5ObjectReadWriteInfoProviderHandler#setTypeVariant(String, HDF5DataTypeVariant)}, * most conveniently by code like * * 

     * writer.addTypeVariant("/dataSetPath", HDF5TimeUnit.SECONDS.getTypeVariant());
     *
* * @param objectPath The name (including path information) of the data set object in the file. * @return The time stamp as {@link Date}. * @throws HDF5JavaException If the objectPath does not denote a time stamp. */ public Date readDate(String objectPath) throws HDF5JavaException; /** * Reads a time stamp array (of rank 1) from the data set objectPath and returns it * as an array of {@link Date}s. The time stamp array is stored as a an array of * long values in the HDF5 file. It needs to be tagged as type variant * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. *

* This tagging is done by the writer when using * {@link IHDF5Writer#writeTimeDuration(String, HDF5TimeDuration)} or can be done by calling * {@link IHDF5ObjectReadWriteInfoProviderHandler#setTypeVariant(String, HDF5DataTypeVariant)}, * most conveniently by code like * * 

     * writer.addTypeVariant("/dataSetPath", HDF5TimeUnit.SECONDS.getTypeVariant());
     *
* * @param objectPath The name (including path information) of the data set object in the file. * @return The time stamp as {@link Date}. * @throws HDF5JavaException If the objectPath does not denote a time stamp. */ public Date[] readDateArray(String objectPath) throws HDF5JavaException; /** * Reads a block of a {@link Date} array (of rank 1) from the data set objectPath. * The time stamp is stored as a long value in the HDF5 file. It needs to be tagged * as type variant {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. *

* This tagging is done by the writer when using * {@link IHDF5Writer#writeTimeDuration(String, HDF5TimeDuration)} or can be done by calling * {@link IHDF5ObjectReadWriteInfoProviderHandler#setTypeVariant(String, HDF5DataTypeVariant)}, * most conveniently by code like * * 

     * writer.addTypeVariant("/dataSetPath", HDF5TimeUnit.SECONDS.getTypeVariant());
     *
* * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the long[] returned * if the data set is long enough). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @return The data read from the data set. The length will be min(size - blockSize*blockNumber, * blockSize). */ public Date[] readDateArrayBlock(String objectPath, int blockSize, long blockNumber); /** * Reads a block of a {@link Date} array (of rank 1) from the data set objectPath. * The time stamp is stored as a long value in the HDF5 file. It needs to be tagged * as type variant {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. *

* This tagging is done by the writer when using * {@link IHDF5Writer#writeTimeDuration(String, HDF5TimeDuration)} or can be done by calling * {@link IHDF5ObjectReadWriteInfoProviderHandler#setTypeVariant(String, HDF5DataTypeVariant)}, * most conveniently by code like * * 

     * writer.addTypeVariant("/dataSetPath", HDF5TimeUnit.SECONDS.getTypeVariant());
     *
* * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the long[] * returned). * @param offset The offset of the block in the data set to start reading from (starting with * 0). * @return The data block read from the data set. */ public Date[] readDateArrayBlockWithOffset(String objectPath, int blockSize, long offset); /** * Provides all natural blocks of this one-dimensional data set of {@link Date}s to iterate * over. * * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1. */ public Iterable> getDateArrayNaturalBlocks(String dataSetPath) throws HDF5JavaException; /** * Reads a multi-dimensional array of time stamps from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not tagged as a type variant that * corresponds to a time duration. */ public MDLongArray readTimeStampMDArray(String objectPath); /** * Reads a multi-dimensional array of time stamps from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @return The data block read from the data set. */ public MDLongArray readTimeStampMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber); /** * Reads a multi-dimensional array of time stamps from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @return The data block read from the data set. */ public MDLongArray readTimeStampMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset); /** * Reads a multi-dimensional array data set objectPath of type time stamp into a * given array in memory. * * @param objectPath The name (including path information) of the data set object in the file. * @param array The array to read the data into. * @param memoryOffset The offset in the array to write the data to. * @return The effective dimensions of the block in array that was filled. */ public int[] readToMDArrayWithOffset(String objectPath, MDLongArray array, int[] memoryOffset); /** * Reads a block of the multi-dimensional array data set objectPath of type time * stamp into a given array in memory. * * @param objectPath The name (including path information) of the data set object in the file. * @param array The array to read the data into. * @param blockDimensions The size of the block to read along each axis. * @param offset The offset of the block in the data set. * @param memoryOffset The offset of the block in the array to write the data to. * @return The effective dimensions of the block in array that was filled. */ public int[] readToMDArrayBlockWithOffset(String objectPath, MDLongArray array, int[] blockDimensions, long[] offset, int[] memoryOffset); /** * Provides all natural blocks of this multi-dimensional data set to iterate over. * * @see HDF5MDDataBlock */ public Iterable> getTimeStampMDArrayNaturalBlocks( String dataSetPath); /** * Reads a multi-dimensional array of {@link Date}s from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not tagged as a type variant that * corresponds to a time duration. */ public MDArray readDateMDArray(String objectPath); /** * Reads a multi-dimensional array of {@link Date}s from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @return The data block read from the data set. */ public MDArray readDateMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber); /** * Reads a multi-dimensional array of {@link Date}s from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @return The data block read from the data set. */ public MDArray readDateMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset); /** * Provides all natural blocks of this multi-dimensional data set to iterate over. * * @see HDF5MDDataBlock */ public Iterable>> getDateMDArrayNaturalBlocks(String dataSetPath); }libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5DateTimeWriter.java000066400000000000000000000472561256564762100276540ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.util.Date; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDLongArray; /** * An interface that provides methods for writing time and date values from HDF5 files. * * @author Bernd Rinn */ public interface IHDF5DateTimeWriter extends IHDF5DateTimeReader { // ///////////////////// // Attributes // ///////////////////// /** * Set a date value as attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param attributeName The name of the attribute. * @param date The value of the attribute. */ public void setAttr(String objectPath, String attributeName, Date date); /** * Set a date array value as attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param attributeName The name of the attribute. * @param dates The value of the attribute. */ public void setArrayAttr(String objectPath, String attributeName, Date[] dates); /** * Set a time stamp value as attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param attributeName The name of the attribute. * @param timeStamp The value of the attribute. */ public void setAttr(String objectPath, String attributeName, long timeStamp); /** * Set a time stamp array value as attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param attributeName The name of the attribute. * @param timeStamps The value of the attribute. */ public void setArrayAttr(String objectPath, String attributeName, long[] timeStamps); /** * Sets a multi-dimensional timestamp array attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setMDArrayAttr(String objectPath, String name, MDLongArray value); /** * Sets a multi-dimensional timestamp array attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setMDArrayAttr(String objectPath, String name, MDArray value); // ///////////////////// // Data Sets // ///////////////////// /** * Writes out a time stamp value. The data set will be tagged as type variant * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. *

* Note: Time stamps are stored as long values. * * @param objectPath The name (including path information) of the data set object in the file. * @param timeStamp The timestamp to write as number of milliseconds since January 1, 1970, * 00:00:00 GMT. */ public void write(String objectPath, long timeStamp); /** * Creates a time stamp array (of rank 1). *

* Note: Time stamps are stored as long values. * * @param objectPath The name (including path information) of the data set object in the file. * @param size The length of the data set to create. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) * and deflate == false. */ public void createArray(String objectPath, long size, int blockSize); /** * Creates a time stamp array (of rank 1). *

* Note: Time stamps are stored as long values. * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the byte array to create. This will be the total size for * non-extendable data sets and the size of one chunk for extendable (chunked) data * sets. For extendable data sets the initial size of the array will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. */ public void createArray(String objectPath, int size); /** * Creates a time stamp array (of rank 1). *

* Note: Time stamps are stored as long values. * * @param objectPath The name (including path information) of the data set object in the file. * @param size The length of the data set to create. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) * and deflate == false. * @param features The storage features of the data set. */ public void createArray(String objectPath, long size, int blockSize, HDF5GenericStorageFeatures features); /** * Creates a time stamp array (of rank 1). *

* Note: Time stamps are stored as long values. * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the array to create. This will be the total size for non-extendable * data sets and the size of one chunk for extendable (chunked) data sets. For * extendable data sets the initial size of the array will be 0, see * {@link HDF5GenericStorageFeatures}. * @param features The storage features of the data set. */ public void createArray(String objectPath, int size, HDF5GenericStorageFeatures features); /** * Writes out a time stamp array (of rank 1). The data set will be tagged as type variant * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. *

* Note: Time stamps are stored as long values. * * @param objectPath The name (including path information) of the data set object in the file. * @param timeStamps The timestamps to write as number of milliseconds since January 1, 1970, * 00:00:00 GMT. */ public void writeArray(String objectPath, long[] timeStamps); /** * Writes out a time stamp array (of rank 1). The data set will be tagged as type variant * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. *

* Note: Time stamps are stored as long values. * * @param objectPath The name (including path information) of the data set object in the file. * @param timeStamps The timestamps to write as number of milliseconds since January 1, 1970, * 00:00:00 GMT. * @param features The storage features of the data set. */ public void writeArray(String objectPath, long[] timeStamps, HDF5GenericStorageFeatures features); /** * Writes out a block of a time stamp array (which is stored as a long array of * rank 1). The data set needs to have been created by * {@link #createArray(String, long, int, HDF5GenericStorageFeatures)} beforehand. *

* Note: For best performance, the block size in this method should be chosen to be equal * to the blockSize argument of the * {@link IHDF5LongWriter#createArray(String, long, int, HDF5IntStorageFeatures)} call that * was used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumber The number of the block to write. */ public void writeArrayBlock(String objectPath, long[] data, long blockNumber); /** * Writes out a block of a time stamp array (which is stored as a long array of * rank 1). The data set needs to have been created by * {@link #createArray(String, long, int, HDF5GenericStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeArrayBlock(String, long[], long)} if the * total size of the data set is not a multiple of the block size. *

* Note: For best performance, the typical dataSize in this method should be * chosen to be equal to the blockSize argument of the * {@link IHDF5LongWriter#createArray(String, long, int, HDF5IntStorageFeatures)} call that * was used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param dataSize The (real) size of data (needs to be <= data.length * ) * @param offset The offset in the data set to start writing to. */ public void writeArrayBlockWithOffset(String objectPath, long[] data, int dataSize, long offset); /** * Writes out a time stamp value provided as a {@link Date}. *

* Note: The time stamp is stored as long array and tagged as the according * type variant. * * @param objectPath The name (including path information) of the data set object in the file. * @param date The date to write. * @see #write(String, long) */ public void write(String objectPath, Date date); /** * Writes out a {@link Date} array (of rank 1). *

* Note: Time stamps are stored as long[] arrays and tagged as the according * type variant. * * @param objectPath The name (including path information) of the data set object in the file. * @param dates The dates to write. * @see #writeArray(String, long[]) */ public void writeArray(String objectPath, Date[] dates); /** * Writes out a {@link Date} array (of rank 1). *

* Note: Time date is stored as long[] arrays and tagged as the according * type variant. * * @param objectPath The name (including path information) of the data set object in the file. * @param dates The dates to write. * @param features The storage features of the data set. * @see #writeArray(String, long[], HDF5GenericStorageFeatures) */ public void writeArray(String objectPath, Date[] dates, HDF5GenericStorageFeatures features); /** * Writes out a multi-dimensional array of time stamps. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. */ public void writeMDArray(String objectPath, MDLongArray data, HDF5IntStorageFeatures features); /** * Creates a multi-dimensional array of time stamps / dates. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions When the writer is configured to use extendable data types (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial dimensions * and the dimensions of a chunk of the array will be dimensions. When the * writer is configured to enforce a on-extendable data set, the initial dimensions * equal the dimensions and will be dimensions. */ public void createMDArray(String objectPath, int[] dimensions); /** * Creates a multi-dimensional array of time stamps / dates. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. */ public void createMDArray(String objectPath, long[] dimensions, int[] blockDimensions); /** * Creates a multi-dimensional array of time stamps / dates. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the long array to create. When requesting * a chunked data set (e.g. {@link HDF5IntStorageFeatures#INT_CHUNKED}), * the initial size of the array will be 0 and the chunk size will be dimensions. * When allowing a chunked data set (e.g. * {@link HDF5IntStorageFeatures#INT_NO_COMPRESSION} when the writer is * not configured to avoid extendable data types, see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be dimensions. When enforcing a * on-extendable data set (e.g. * {@link HDF5IntStorageFeatures#INT_CONTIGUOUS}), the initial size equals * the total size and will be dimensions. * @param features The storage features of the data set. */ public void createMDArray(String objectPath, int[] dimensions, HDF5IntStorageFeatures features); /** * Creates a multi-dimensional array of time stamps / dates. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. * @param features The storage features of the data set. */ public void createMDArray(String objectPath, long[] dimensions, int[] blockDimensions, HDF5IntStorageFeatures features); /** * Writes out a block of a multi-dimensional array of time stamps. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). */ public void writeMDArrayBlock(String objectPath, MDLongArray data, long[] blockNumber); /** * Writes out a block of a multi-dimensional array of time stamps. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. */ public void writeMDArrayBlockWithOffset(String objectPath, MDLongArray data, long[] offset); /** * Writes out a block of a multi-dimensional array of time stamps. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param blockDimensions The dimensions of the block to write to the data set. * @param offset The offset of the block in the data set to start writing to in each dimension. * @param memoryOffset The offset of the block in the data array. */ public void writeMDArrayBlockWithOffset(String objectPath, MDLongArray data, int[] blockDimensions, long[] offset, int[] memoryOffset); /** * Writes out a multi-dimensional array of dates. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. */ public void writeMDArray(String objectPath, MDArray data, HDF5IntStorageFeatures features); /** * Writes out a block of a multi-dimensional array of dates. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). */ public void writeMDArrayBlock(String objectPath, MDArray data, long[] blockNumber); /** * Writes out a block of a multi-dimensional array of daates. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. */ public void writeMDArrayBlockWithOffset(String objectPath, MDArray data, long[] offset); /** * Writes out a block of a multi-dimensional array of dates. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param blockDimensions The dimensions of the block to write to the data set. * @param offset The offset of the block in the data set to start writing to in each dimension. * @param memoryOffset The offset of the block in the data array. */ public void writeMDArrayBlockWithOffset(String objectPath, MDArray data, int[] blockDimensions, long[] offset, int[] memoryOffset); }libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5DoubleReader.java000066400000000000000000000426161256564762100273130ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.base.mdarray.MDDoubleArray; /** * An interface that provides methods for reading double values from HDF5 files. *

* Note: This interface supports block access and sliced access (which is a special cases of * block access) to arrays. The performance of this block access can vary greatly depending on how * the data are layed out in the HDF5 file. For best performance, the block (or slice) dimension should * be chosen to be equal to the chunk dimensions of the array, as in this case the block written / read * are stored as consecutive value in the HDF5 file and one write / read access will suffice. *

* Note: If the values read are unsigned, use the methods in {@link UnsignedIntUtils} to convert * to a larger Java integer type that can hold all values as unsigned. * * @author Bernd Rinn */ public interface IHDF5DoubleReader { // ///////////////////// // Attributes // ///////////////////// /** * Reads a double attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. */ public double getAttr(String objectPath, String attributeName); /** * Reads a double[] attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. */ public double[] getArrayAttr(String objectPath, String attributeName); /** * Reads a multi-dimensional array double attribute named attributeName * from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute array value read from the data set. */ public MDDoubleArray getMDArrayAttr(String objectPath, String attributeName); /** * Reads a double matrix attribute named attributeName * from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute matrix value read from the data set. */ public double[][] getMatrixAttr(String objectPath, String attributeName) throws HDF5JavaException; // ///////////////////// // Data Sets // ///////////////////// /** * Reads a double value from the data set objectPath. This method * doesn't check the data space but simply reads the first value. * * @param objectPath The name (including path information) of the data set object in the file. * @return The value read from the data set. */ public double read(String objectPath); /** * Reads a double array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. */ public double[] readArray(String objectPath); /** * Reads a multi-dimensional double array data set objectPath * into a given array in memory. * * @param objectPath The name (including path information) of the data set object in the file. * @param array The array to read the data into. * @param memoryOffset The offset in the array to write the data to. * @return The effective dimensions of the block in array that was filled. */ public int[] readToMDArrayWithOffset(String objectPath, MDDoubleArray array, int[] memoryOffset); /** * Reads a block of the multi-dimensional double array data set * objectPath into a given array in memory. * * @param objectPath The name (including path information) of the data set object in the file. * @param array The array to read the data into. * @param blockDimensions The size of the block to read along each axis. * @param offset The offset of the block in the data set. * @param memoryOffset The offset of the block in the array to write the data to. * @return The effective dimensions of the block in array that was filled. */ public int[] readToMDArrayBlockWithOffset(String objectPath, MDDoubleArray array, int[] blockDimensions, long[] offset, int[] memoryOffset); /** * Reads a block from a double array (of rank 1) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the double[] returned * if the data set is long enough). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @return The data read from the data set. The length will be min(size - blockSize*blockNumber, * blockSize). */ public double[] readArrayBlock(String objectPath, int blockSize, long blockNumber); /** * Reads a block from double array (of rank 1) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the double[] * returned). * @param offset The offset of the block in the data set to start reading from (starting with 0). * @return The data block read from the data set. */ public double[] readArrayBlockWithOffset(String objectPath, int blockSize, long offset); /** * Reads a double matrix (array of arrays) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * * @throws HDF5JavaException If the data set objectPath is not of rank 2. */ public double[][] readMatrix(String objectPath) throws HDF5JavaException; /** * Reads a double matrix (array of arrays) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSizeX The size of the block in the x dimension. * @param blockSizeY The size of the block in the y dimension. * @param blockNumberX The block number in the x dimension (offset: multiply with * blockSizeX). * @param blockNumberY The block number in the y dimension (offset: multiply with * blockSizeY). * @return The data block read from the data set. * * @throws HDF5JavaException If the data set objectPath is not of rank 2. */ public double[][] readMatrixBlock(String objectPath, int blockSizeX, int blockSizeY, long blockNumberX, long blockNumberY) throws HDF5JavaException; /** * Reads a double matrix (array of arrays) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSizeX The size of the block in the x dimension. * @param blockSizeY The size of the block in the y dimension. * @param offsetX The offset in x dimension in the data set to start reading from. * @param offsetY The offset in y dimension in the data set to start reading from. * @return The data block read from the data set. * * @throws HDF5JavaException If the data set objectPath is not of rank 2. */ public double[][] readMatrixBlockWithOffset(String objectPath, int blockSizeX, int blockSizeY, long offsetX, long offsetY) throws HDF5JavaException; /** * Reads a multi-dimensional double array from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. */ public MDDoubleArray readMDArray(String objectPath); /** * Reads a slice of a multi-dimensional double array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDDoubleArray readMDArraySlice(String objectPath, IndexMap boundIndices); /** * Reads a slice of a multi-dimensional double array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDDoubleArray readMDArraySlice(String objectPath, long[] boundIndices); /** * Reads a block from a multi-dimensional double array from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @return The data block read from the data set. */ public MDDoubleArray readMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber); /** * Reads a sliced block from a multi-dimensional double array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDDoubleArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, IndexMap boundIndices); /** * Reads a sliced block from a multi-dimensional double array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDDoubleArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, long[] boundIndices); /** * Reads a block from a multi-dimensional double array from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @return The data block read from the data set. */ public MDDoubleArray readMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset); /** * Reads a sliced block of a multi-dimensional double array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDDoubleArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, IndexMap boundIndices); /** * Reads a sliced block of a multi-dimensional double array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDDoubleArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, long[] boundIndices); /** * Provides all natural blocks of this one-dimensional data set to iterate over. * * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1. */ public Iterable> getArrayNaturalBlocks( String dataSetPath) throws HDF5JavaException; /** * Provides all natural blocks of this multi-dimensional data set to iterate over. * * @see HDF5MDDataBlock */ public Iterable> getMDArrayNaturalBlocks( String dataSetPath); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5DoubleWriter.java000066400000000000000000000677161256564762100273750ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ch.systemsx.cisd.base.mdarray.MDDoubleArray; /** * An interface that provides methods for writing double values to HDF5 files. *

* Note: This interface supports block access and sliced access (which is a special cases of * block access) to arrays. The performance of this block access can vary greatly depending on how * the data are layed out in the HDF5 file. For best performance, the block (or slice) dimension should * be chosen to be equal to the chunk dimensions of the array, as in this case the block written / read * are stored as consecutive value in the HDF5 file and one write / read access will suffice. * * @author Bernd Rinn */ public interface IHDF5DoubleWriter extends IHDF5DoubleReader { // ///////////////////// // Attributes // ///////////////////// /** * Set a double attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setAttr(String objectPath, String name, double value); /** * Set a double[] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setArrayAttr(String objectPath, String name, double[] value); /** * Set a multi-dimensional code>double attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setMDArrayAttr(String objectPath, String name, MDDoubleArray value); /** * Set a double[][] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setMatrixAttr(String objectPath, String name, double[][] value); // ///////////////////// // Data Sets // ///////////////////// /** * Writes out a double value. * * @param objectPath The name (including path information) of the data set object in the file. * @param value The value to write. */ public void write(String objectPath, double value); /** * Writes out a double array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ public void writeArray(String objectPath, double[] data); /** * Writes out a double array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param features The storage features of the data set. */ public void writeArray(String objectPath, double[] data, HDF5FloatStorageFeatures features); /** * Creates a double array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size When the writer is configured to use extendable data types (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be size. When the writer is * configured to enforce a non-extendable data set, the initial size equals the * total size and will be size. */ public void createArray(String objectPath, int size); /** * Creates a double array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the double array to create. When using extendable data sets * ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data * set smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). */ public void createArray(String objectPath, long size, int blockSize); /** * Creates a double array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the double array to create. When requesting a * chunked data set (e.g. {@link HDF5FloatStorageFeatures#FLOAT_CHUNKED}), * the initial size of the array will be 0 and the chunk size will be arraySize. * When allowing a chunked data set (e.g. * {@link HDF5FloatStorageFeatures#FLOAT_NO_COMPRESSION} when the writer is * not configured to avoid extendable data types, see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be arraySize. When enforcing a * on-extendable data set (e.g. * {@link HDF5FloatStorageFeatures#FLOAT_CONTIGUOUS}), the initial size equals * the total size and will be arraySize. * @param features The storage features of the data set. */ public void createArray(String objectPath, int size, HDF5FloatStorageFeatures features); /** * Creates a double array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the double array to create. When using extendable data sets * ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data * set smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) and * features is HDF5FloatStorageFeature.FLOAT_NO_COMPRESSION. * @param features The storage features of the data set. */ public void createArray(String objectPath, long size, int blockSize, HDF5FloatStorageFeatures features); /** * Writes out a block of a double array (of rank 1). The data set needs to have * been created by {@link #createArray(String, long, int, HDF5FloatStorageFeatures)} * beforehand. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumber The number of the block to write. */ public void writeArrayBlock(String objectPath, double[] data, long blockNumber); /** * Writes out a block of a double array (of rank 1). The data set needs to have * been created by {@link #createArray(String, long, int, HDF5FloatStorageFeatures)} * beforehand. *

* Use this method instead of {@link #writeArrayBlock(String, double[], long)} if the * total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param dataSize The (real) size of data (needs to be <= data.length * ) * @param offset The offset in the data set to start writing to. */ public void writeArrayBlockWithOffset(String objectPath, double[] data, int dataSize, long offset); /** * Writes out a double matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ public void writeMatrix(String objectPath, double[][] data); /** * Writes out a double matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. */ public void writeMatrix(String objectPath, double[][] data, HDF5FloatStorageFeatures features); /** * Creates a double matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of one block in the x dimension. See * {@link #createMDArray(String, int[])} on the different * meanings of this parameter. * @param sizeY The size of one block in the y dimension. See * {@link #createMDArray(String, int[])} on the different * meanings of this parameter. */ public void createMatrix(String objectPath, int sizeX, int sizeY); /** * Creates a double matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of one block in the x dimension. See * {@link #createMDArray(String, int[], HDF5FloatStorageFeatures)} on the different * meanings of this parameter. * @param sizeY The size of one block in the y dimension. See * {@link #createMDArray(String, int[], HDF5FloatStorageFeatures)} on the different * meanings of this parameter. * @param features The storage features of the data set. */ public void createMatrix(String objectPath, int sizeX, int sizeY, HDF5FloatStorageFeatures features); /** * Creates a double matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the double matrix to create. * @param sizeY The size of the y dimension of the double matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. */ public void createMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY); /** * Creates a double matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the double matrix to create. * @param sizeY The size of the y dimension of the double matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. * @param features The storage features of the data set. */ public void createMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY, HDF5FloatStorageFeatures features); /** * Writes out a block of a double matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5FloatStorageFeatures)} beforehand. *

* Use this method instead of * {@link #createMatrix(String, long, long, int, int, HDF5FloatStorageFeatures)} if the total * size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumberX The block number in the x dimension (offset: multiply with * data.length). * @param blockNumberY The block number in the y dimension (offset: multiply with * data[0.length). */ public void writeMatrixBlock(String objectPath, double[][] data, long blockNumberX, long blockNumberY); /** * Writes out a block of a double matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5FloatStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeMatrixBlock(String, double[][], long, long)} if * the total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. */ public void writeMatrixBlockWithOffset(String objectPath, double[][] data, long offsetX, long offsetY); /** * Writes out a block of a double matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5FloatStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeMatrixBlock(String, double[][], long, long)} if * the total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param dataSizeX The (real) size of data along the x axis (needs to be * <= data.length ) * @param dataSizeY The (real) size of data along the y axis (needs to be * <= data[0].length ) * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. */ public void writeMatrixBlockWithOffset(String objectPath, double[][] data, int dataSizeX, int dataSizeY, long offsetX, long offsetY); /** * Writes out a multi-dimensional double array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ public void writeMDArray(String objectPath, MDDoubleArray data); /** * Writes out a multi-dimensional double array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. */ public void writeMDArray(String objectPath, MDDoubleArray data, HDF5FloatStorageFeatures features); /** * Writes out a slice of a multi-dimensional double array. The slice is defined by * "bound indices", each of which is fixed to a given value. The data object only * contains the free (i.e. non-fixed) indices. *

* Note:The object identified by objectPath needs to exist when this method is * called. This method will not create the array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. */ public void writeMDArraySlice(String objectPath, MDDoubleArray data, IndexMap boundIndices); /** * Writes out a slice of a multi-dimensional double array. The slice is defined by * "bound indices", each of which is fixed to a given value. The data object only * contains the free (i.e. non-fixed) indices. *

* Note:The object identified by objectPath needs to exist when this method is * called. This method will not create the array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. */ public void writeMDArraySlice(String objectPath, MDDoubleArray data, long[] boundIndices); /** * Creates a multi-dimensional double array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions When the writer is configured to use extendable data types (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial dimensions * and the dimensions of a chunk of the array will be dimensions. When the * writer is configured to enforce a non-extendable data set, the initial dimensions * equal the dimensions and will be dimensions. */ public void createMDArray(String objectPath, int[] dimensions); /** * Creates a multi-dimensional double array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. */ public void createMDArray(String objectPath, long[] dimensions, int[] blockDimensions); /** * Creates a multi-dimensional double array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the double array to create. When requesting * a chunked data set (e.g. {@link HDF5FloatStorageFeatures#FLOAT_CHUNKED}), * the initial size of the array will be 0 and the chunk size will be dimensions. * When allowing a chunked data set (e.g. * {@link HDF5FloatStorageFeatures#FLOAT_NO_COMPRESSION} when the writer is * not configured to avoid extendable data types, see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be dimensions. When enforcing a * on-extendable data set (e.g. * {@link HDF5FloatStorageFeatures#FLOAT_CONTIGUOUS}), the initial size equals * the total size and will be dimensions. * @param features The storage features of the data set. */ public void createMDArray(String objectPath, int[] dimensions, HDF5FloatStorageFeatures features); /** * Creates a multi-dimensional double array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. * @param features The storage features of the data set. */ public void createMDArray(String objectPath, long[] dimensions, int[] blockDimensions, HDF5FloatStorageFeatures features); /** * Writes out a block of a multi-dimensional double array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). */ public void writeMDArrayBlock(String objectPath, MDDoubleArray data, long[] blockNumber); /** * Writes out a sliced block of a multi-dimensional double array. The slice is * defined by "bound indices", each of which is fixed to a given value. The data * object only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. */ public void writeSlicedMDArrayBlock(String objectPath, MDDoubleArray data, long[] blockNumber, IndexMap boundIndices); /** * Writes out a sliced block of a multi-dimensional double array. The slice is * defined by "bound indices", each of which is fixed to a given value. The data * object only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. */ public void writeSlicedMDArrayBlock(String objectPath, MDDoubleArray data, long[] blockNumber, long[] boundIndices); /** * Writes out a block of a multi-dimensional double array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. */ public void writeMDArrayBlockWithOffset(String objectPath, MDDoubleArray data, long[] offset); /** * Writes out a sliced block of a multi-dimensional double array. The slice is * defined by "bound indices", each of which is fixed to a given value. The data * object only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. */ public void writeSlicedMDArrayBlockWithOffset(String objectPath, MDDoubleArray data, long[] offset, IndexMap boundIndices); /** * Writes out a sliced block of a multi-dimensional double array. The slice is * defined by "bound indices", each of which is fixed to a given value. The data * object only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. */ public void writeSlicedMDArrayBlockWithOffset(String objectPath, MDDoubleArray data, long[] offset, long[] boundIndices); /** * Writes out a block of a multi-dimensional double array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param blockDimensions The dimensions of the block to write to the data set. * @param offset The offset of the block in the data set to start writing to in each dimension. * @param memoryOffset The offset of the block in the data array. */ public void writeMDArrayBlockWithOffset(String objectPath, MDDoubleArray data, int[] blockDimensions, long[] offset, int[] memoryOffset); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5EnumBasicReader.java000066400000000000000000000423341256564762100277440ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; /** * An interface with legacy methods for reading enumeration values from HDF5 files. Do not use in * any new code as it will be removed in a future version of JHDF5. * * @author Bernd Rinn */ @Deprecated public interface IHDF5EnumBasicReader { // ///////////////////// // Types // ///////////////////// /** * Returns the enumeration type name for this HDF5 file. Use this method only when * you know that the type exists. If the dataTypeName starts with '/', it will be * considered a data type path instead of a data type name. * * @param dataTypeName The name of the enumeration in the HDF5 file. * @deprecated Use the corresponding method in {@link IHDF5Reader#enumeration()} instead. */ @Deprecated public HDF5EnumerationType getEnumType(final String dataTypeName); /** * Returns the enumeration type name for this HDF5 file. Will check the type in the * file with the values. If the dataTypeName starts with '/', it will be * considered a data type path instead of a data type name. * * @param dataTypeName The name of the enumeration in the HDF5 file. * @param values The values of the enumeration. * @throws HDF5JavaException If the data type exists and is not compatible with the * values provided. * @deprecated Use the corresponding method in {@link IHDF5Reader#enumeration()} instead. */ @Deprecated public HDF5EnumerationType getEnumType(final String dataTypeName, final String[] values) throws HDF5JavaException; /** * Returns the enumeration type name for this HDF5 file. If the * dataTypeName starts with '/', it will be considered a data type path instead of a * data type name. * * @param dataTypeName The name of the enumeration in the HDF5 file. * @param values The values of the enumeration. * @param check If true and if the data type already exists, check whether it is * compatible with the values provided. * @throws HDF5JavaException If check = true, the data type exists and is not * compatible with the values provided. * @deprecated Use the corresponding method in {@link IHDF5Reader#enumeration()} instead. */ @Deprecated public HDF5EnumerationType getEnumType(final String dataTypeName, final String[] values, final boolean check) throws HDF5JavaException; /** * Returns the enumeration type for the data set dataSetPath. * * @param dataSetPath The name of data set to get the enumeration type for. * @deprecated Use {@link #getDataSetEnumType(String)} instead. */ @Deprecated public HDF5EnumerationType getEnumTypeForObject(final String dataSetPath); /** * Returns the enumeration type for the data set dataSetPath. * * @param dataSetPath The name of data set to get the enumeration type for. * @deprecated Use the corresponding method in {@link IHDF5Reader#enumeration()} instead. */ @Deprecated public HDF5EnumerationType getDataSetEnumType(final String dataSetPath); // ///////////////////// // Attributes // ///////////////////// /** * Reads an enum attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set as a String. * @throws HDF5JavaException If the attribute is not an enum type. * @deprecated Use the corresponding method in {@link IHDF5Reader#enumeration()} instead. */ @Deprecated public String getEnumAttributeAsString(final String objectPath, final String attributeName) throws HDF5JavaException; /** * Reads an enum attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. * @throws HDF5JavaException If the attribute is not an enum type. * @deprecated Use the corresponding method in {@link IHDF5Reader#enumeration()} instead. */ @Deprecated public HDF5EnumerationValue getEnumAttribute(final String objectPath, final String attributeName) throws HDF5JavaException; /** * Reads an enum attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @param enumClass the {@link Enum} class to represent the values of. * @return The attribute value read from the data set. * @throws HDF5JavaException If the attribute is not an enum type. * @deprecated Use the corresponding method in {@link IHDF5Reader#enumeration()} instead. */ @Deprecated public > T getEnumAttribute(final String objectPath, final String attributeName, Class enumClass) throws HDF5JavaException; /** * Reads an enum array attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute values as read from the data set as Strinsg. * @throws HDF5JavaException If the attribute is not an enum type. * @deprecated Use {@link #getEnumArrayAttribute(String, String)} instead and call * {@link HDF5EnumerationValueArray#toStringArray()}. */ @Deprecated public String[] getEnumArrayAttributeAsString(final String objectPath, final String attributeName) throws HDF5JavaException; /** * Reads an enum array attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute values as read from the data set. * @throws HDF5JavaException If the attribute is not an enum type. * @deprecated Use the corresponding method in {@link IHDF5Reader#enumeration()} instead. */ @Deprecated public HDF5EnumerationValueArray getEnumArrayAttribute(final String objectPath, final String attributeName) throws HDF5JavaException; // ///////////////////// // Data Sets // ///////////////////// /** * Reads an Enum value from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set as a String. * @throws HDF5JavaException If the objectPath is not an enum type. */ public String readEnumAsString(final String objectPath) throws HDF5JavaException; /** * Reads an Enum value from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not of enumType. * @deprecated Use the corresponding method in {@link IHDF5Reader#enumeration()} instead. */ @Deprecated public HDF5EnumerationValue readEnum(final String objectPath) throws HDF5JavaException; /** * Reads an Enum value from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param enumClass the {@link Enum} class to represent the values of. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not of enumType or if * enumClass is incompatible with the HDF5 enumeration type of * objectPath. */ public > T readEnum(final String objectPath, Class enumClass) throws HDF5JavaException; /** * Reads an Enum value from the data set objectPath. *

* This method is faster than {@link #readEnum(String)} if the {@link HDF5EnumerationType} is * already available. * * @param objectPath The name (including path information) of the data set object in the file. * @param enumType The enum type in the HDF5 file. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not of enumType. * @deprecated Use the corresponding method in {@link IHDF5Reader#enumeration()} instead. */ @Deprecated public HDF5EnumerationValue readEnum(final String objectPath, final HDF5EnumerationType enumType) throws HDF5JavaException; /** * Reads an Enum value from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param enumType The enumeration type of this array. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not of enumType. * @deprecated Use the corresponding method in {@link IHDF5Reader#enumeration()} instead. */ @Deprecated public HDF5EnumerationValueArray readEnumArray(final String objectPath, final HDF5EnumerationType enumType) throws HDF5JavaException; /** * Reads an Enum value array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not of enumType. * @deprecated Use the corresponding method in {@link IHDF5Reader#enumeration()} instead. */ @Deprecated public HDF5EnumerationValueArray readEnumArray(final String objectPath) throws HDF5JavaException; /** * Reads an Enum value array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param enumClass the {@link Enum} class to represent the values of. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not of enumType. */ public > T[] readEnumArray(final String objectPath, Class enumClass) throws HDF5JavaException; /** * Reads an Enum array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set as an array of Strings. * @throws HDF5JavaException If the objectPath is not an enum type. */ public String[] readEnumArrayAsString(final String objectPath) throws HDF5JavaException; /** * Reads an Enum value array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the return value of the * {@link HDF5EnumerationValueArray#getLength()} returned if the data set is long * enough). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @return The data read from the data set. The length will be min(size - blockSize*blockNumber, * blockSize). * @deprecated Use the corresponding method in {@link IHDF5Reader#enumeration()} instead. */ @Deprecated public HDF5EnumerationValueArray readEnumArrayBlock(final String objectPath, final int blockSize, final long blockNumber); /** * Reads an Enum value array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param enumType The enumeration type of this array. * @param blockSize The block size (this will be the return value of the * {@link HDF5EnumerationValueArray#getLength()} returned if the data set is long * enough). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @return The data read from the data set. The length will be min(size - blockSize*blockNumber, * blockSize). * @deprecated Use the corresponding method in {@link IHDF5Reader#enumeration()} instead. */ @Deprecated public HDF5EnumerationValueArray readEnumArrayBlock(final String objectPath, final HDF5EnumerationType enumType, final int blockSize, final long blockNumber); /** * Reads an Enum value array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the return value of the * {@link HDF5EnumerationValueArray#getLength()} returned if the data set is long * enough). * @param offset The offset of the block in the data set to start reading from (starting with * 0). * @return The data read from the data set. The length will be min(size - blockSize*blockNumber, * blockSize). * @deprecated Use the corresponding method in {@link IHDF5Reader#enumeration()} instead. */ @Deprecated public HDF5EnumerationValueArray readEnumArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset); /** * Reads an Enum value array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param enumType The enumeration type of this array. * @param blockSize The block size (this will be the return value of the * {@link HDF5EnumerationValueArray#getLength()} returned if the data set is long * enough). * @param offset The offset of the block in the data set to start reading from (starting with * 0). * @return The data read from the data set. The length will be min(size - blockSize*blockNumber, * blockSize). * @deprecated Use the corresponding method in {@link IHDF5Reader#enumeration()} instead. */ @Deprecated public HDF5EnumerationValueArray readEnumArrayBlockWithOffset(final String objectPath, final HDF5EnumerationType enumType, final int blockSize, final long offset); /** * Provides all natural blocks of this one-dimensional data set to iterate over. * * @param objectPath The name (including path information) of the data set object in the file. * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1. * @deprecated Use the corresponding method in {@link IHDF5Reader#enums()} instead. */ @Deprecated public Iterable> getEnumArrayNaturalBlocks( final String objectPath) throws HDF5JavaException; /** * Provides all natural blocks of this one-dimensional data set to iterate over. * * @param objectPath The name (including path information) of the data set object in the file. * @param enumType The enumeration type of this array. * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1. * @deprecated Use the corresponding method in {@link IHDF5Reader#enumeration()} instead. */ @Deprecated public Iterable> getEnumArrayNaturalBlocks( final String objectPath, final HDF5EnumerationType enumType) throws HDF5JavaException; } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5EnumBasicWriter.java000066400000000000000000000331211256564762100300100ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; /** * An interface with legacy methods for writing enumeration values from HDF5 files. Do not use in any * new code as it will be removed in a future version of JHDF5. * * @author Bernd Rinn */ @Deprecated public interface IHDF5EnumBasicWriter { // ///////////////////// // Types // ///////////////////// /** * Returns the enumeration type name for this HDF5 file. Will check the type in the * file with the values. If the dataTypeName starts with '/', it will be * considered a data type path instead of a data type name. * * @param dataTypeName The name of the enumeration in the HDF5 file. * @param values The values of the enumeration. * @throws HDF5JavaException If the data type exists and is not compatible with the * values provided. * @deprecated Use the corresponding method in {@link IHDF5Writer#enumeration()} instead. */ @Deprecated public HDF5EnumerationType getEnumType(String dataTypeName, String[] values) throws HDF5JavaException; /** * Returns the enumeration type name for this HDF5 file. If the * dataTypeName starts with '/', it will be considered a data type path instead of a * data type name. * * @param dataTypeName The name of the enumeration in the HDF5 file. * @param values The values of the enumeration. * @param check If true and if the data type already exists, check whether it is * compatible with the values provided. * @throws HDF5JavaException If check = true, the data type exists and is not * compatible with the values provided. * @deprecated Use the corresponding method in {@link IHDF5Writer#enumeration()} instead. */ @Deprecated public HDF5EnumerationType getEnumType(String dataTypeName, String[] values, boolean check) throws HDF5JavaException; // ///////////////////// // Attributes // ///////////////////// /** * Sets an enum attribute to the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#enumeration()} instead. */ @Deprecated public void setEnumAttribute(String objectPath, String name, HDF5EnumerationValue value); /** * Sets an enum attribute to the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#enumeration()} instead. */ @Deprecated public void setEnumAttribute(String objectPath, String name, Enum value); /** * Sets an enum array attribute to the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#enumeration()} instead. */ @Deprecated public void setEnumArrayAttribute(String objectPath, String name, HDF5EnumerationValueArray value); // ///////////////////// // Data Sets // ///////////////////// /** * Writes out an enum value. * * @param objectPath The name (including path information) of the data set object in the file. * @param value The value of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#enumeration()} instead. */ @Deprecated public void writeEnum(String objectPath, HDF5EnumerationValue value); /** * Writes out an enum value. * * @param objectPath The name (including path information) of the data set object in the file. * @param value The value of the data set. */ public > void writeEnum(String objectPath, Enum value); /** * Writes out an enum value. * * @param objectPath The name (including path information) of the data set object in the file. * @param options The allowed values of the enumeration type. * @param value The value of the data set. */ public void writeEnum(String objectPath, String[] options, String value); /** * Writes out an array of enum values. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @deprecated Use the corresponding method in {@link IHDF5Writer#enumeration()} instead. */ @Deprecated public void writeEnumArray(String objectPath, HDF5EnumerationValueArray data); /** * Writes out an array of enum values. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. */ public > void writeEnumArray(String objectPath, Enum[] data); /** * Writes out an array of enum values. * * @param objectPath The name (including path information) of the data set object in the file. * @param options The allowed values of the enumeration type. * @param data The data to write. */ public void writeEnumArray(String objectPath, String[] options, String[] data); /** * Writes out an array of enum values. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param features The storage features of the data set. Note that for scaling compression the * compression factor is ignored. Instead, the scaling factor is computed from the * number of entries in the enumeration. * @deprecated Use the corresponding method in {@link IHDF5Writer#enumeration()} instead. */ @Deprecated public void writeEnumArray(String objectPath, HDF5EnumerationValueArray data, HDF5IntStorageFeatures features); /** * Creates am enum array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param enumType The enumeration type of this array. * @param size The size of the byte array to create. This will be the total size for * non-extendable data sets and the size of one chunk for extendable (chunked) data * sets. For extendable data sets the initial size of the array will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. * @deprecated Use the corresponding method in {@link IHDF5Writer#enumeration()} instead. */ @Deprecated public HDF5EnumerationType createEnumArray(String objectPath, HDF5EnumerationType enumType, int size); /** * Creates am enum array (of rank 1). The initial size of the array is 0. * * @param objectPath The name (including path information) of the data set object in the file. * @param enumType The enumeration type of this array. * @param size The size of the enum array to create. When using extendable data sets ((see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data set * smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). * @deprecated Use the corresponding method in {@link IHDF5Writer#enumeration()} instead. */ @Deprecated public HDF5EnumerationType createEnumArray(String objectPath, HDF5EnumerationType enumType, long size, int blockSize); /** * Creates am enum array (of rank 1). The initial size of the array is 0. * * @param objectPath The name (including path information) of the data set object in the file. * @param enumType The enumeration type of this array. * @param size The size of the enum array to create. When using extendable data sets ((see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data set * smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#enumeration()} instead. */ @Deprecated public HDF5EnumerationType createEnumArray(String objectPath, HDF5EnumerationType enumType, long size, int blockSize, HDF5IntStorageFeatures features); /** * Creates am enum array (of rank 1). The initial size of the array is 0. * * @param objectPath The name (including path information) of the data set object in the file. * @param enumType The enumeration type of this array. * @param size The size of the enum array to create. This will be the total size for * non-extendable data sets and the size of one chunk for extendable (chunked) data * sets. For extendable data sets the initial size of the array will be 0, see * {@link HDF5IntStorageFeatures}. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#enumeration()} instead. */ @Deprecated public HDF5EnumerationType createEnumArray(String objectPath, HDF5EnumerationType enumType, long size, HDF5IntStorageFeatures features); /** * Writes out a block of an enum array (of rank 1). The data set needs to have been created by * {@link #createEnumArray(String, HDF5EnumerationType, long, int, HDF5IntStorageFeatures)} * beforehand. Obviously the {@link HDF5EnumerationType} of the create call and this call needs * to match. *

* Note: For best performance, the block size in this method should be chosen to be equal * to the blockSize argument of the * {@link #createEnumArray(String, HDF5EnumerationType, long, int, HDF5IntStorageFeatures)} call * that was used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The value of {@link HDF5EnumerationValueArray#getLength()} * defines the block size. Must not be null or of length 0. * @param blockNumber The number of the block to write. * @deprecated Use the corresponding method in {@link IHDF5Writer#enumeration()} instead. */ @Deprecated public void writeEnumArrayBlock(String objectPath, HDF5EnumerationValueArray data, long blockNumber); /** * Writes out a block of an enum array (of rank 1). The data set needs to have been created by * {@link #createEnumArray(String, HDF5EnumerationType, long, int, HDF5IntStorageFeatures)} * beforehand. Obviously the {@link HDF5EnumerationType} of the create call and this call needs * to match. *

* Note: For best performance, the block size in this method should be chosen to be equal * to the blockSize argument of the * {@link #createEnumArray(String, HDF5EnumerationType, long, int, HDF5IntStorageFeatures)} call * that was used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The value of {@link HDF5EnumerationValueArray#getLength()} * defines the block size. Must not be null or of length 0. * @param dataSize The (real) size of data (needs to be * <= data.getLength() ) * @param offset The offset in the data set to start writing to. * @deprecated Use the corresponding method in {@link IHDF5Writer#enumeration()} instead. */ @Deprecated public void writeEnumArrayBlockWithOffset(String objectPath, HDF5EnumerationValueArray data, int dataSize, long offset); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5EnumReader.java000066400000000000000000000410271256564762100270000ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; /** * An interface that provides methods for reading enumeration values from HDF5 files. * * @author Bernd Rinn */ public interface IHDF5EnumReader extends IHDF5EnumTypeRetriever { // ///////////////////// // Attributes // ///////////////////// /** * Reads an enum attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set as a String. * @throws HDF5JavaException If the attribute is not an enum type. */ public String getAttrAsString(final String objectPath, final String attributeName) throws HDF5JavaException; /** * Reads an enum attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. * @throws HDF5JavaException If the attribute is not an enum type. */ public HDF5EnumerationValue getAttr(final String objectPath, final String attributeName) throws HDF5JavaException; /** * Reads an enum attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @param enumClass the {@link Enum} class to represent the values of. * @return The attribute value read from the data set. * @throws HDF5JavaException If the attribute is not an enum type. */ public > T getAttr(final String objectPath, final String attributeName, Class enumClass) throws HDF5JavaException; /** * Reads an enum array (of rank 1) attribute named attributeName from * the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute values as read from the data set. * @throws HDF5JavaException If the attribute is not an enum type. */ public HDF5EnumerationValueArray getArrayAttr(final String objectPath, final String attributeName) throws HDF5JavaException; /** * Reads an enum array (of rank 1) attribute named attributeName from * the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute values as read from the data set. * @throws HDF5JavaException If the attribute is not an enum type. */ public HDF5EnumerationValueMDArray getMDArrayAttr(final String objectPath, final String attributeName) throws HDF5JavaException; // ///////////////////// // Data Sets // ///////////////////// /** * Reads an Enum value from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set as a String. * @throws HDF5JavaException If the objectPath is not an enum type. */ public String readAsString(final String objectPath) throws HDF5JavaException; /** * Reads an Enum value from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not of enumType. */ public HDF5EnumerationValue read(final String objectPath) throws HDF5JavaException; /** * Reads an Enum value from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param enumClass the {@link Enum} class to represent the values of. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not of enumType or if * enumClass is incompatible with the HDF5 enumeration type of * objectPath. */ public > T read(final String objectPath, Class enumClass) throws HDF5JavaException; /** * Reads an Enum value from the data set objectPath. *

* This method is faster than {@link #read(String)} if the {@link HDF5EnumerationType} is * already available. * * @param objectPath The name (including path information) of the data set object in the file. * @param enumType The enum type in the HDF5 file. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not of enumType. */ public HDF5EnumerationValue read(final String objectPath, final HDF5EnumerationType enumType) throws HDF5JavaException; /** * Reads an Enum value from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param enumType The enumeration type of this array. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not of enumType. */ public HDF5EnumerationValueArray readArray(final String objectPath, final HDF5EnumerationType enumType) throws HDF5JavaException; /** * Reads an Enum value array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not of enumType. */ public HDF5EnumerationValueArray readArray(final String objectPath) throws HDF5JavaException; /** * Reads an Enum value array block from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the return value of the * {@link HDF5EnumerationValueArray#getLength()} returned if the data set is long * enough). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @return The data read from the data set. The length will be min(size - blockSize*blockNumber, * blockSize). */ public HDF5EnumerationValueArray readArrayBlock(final String objectPath, final int blockSize, final long blockNumber); /** * Reads an Enum value array block from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param enumType The enumeration type of this array. * @param blockSize The block size (this will be the return value of the * {@link HDF5EnumerationValueArray#getLength()} returned if the data set is long * enough). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @return The data read from the data set. The length will be min(size - blockSize*blockNumber, * blockSize). */ public HDF5EnumerationValueArray readArrayBlock(final String objectPath, final HDF5EnumerationType enumType, final int blockSize, final long blockNumber); /** * Reads an Enum value array block from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the return value of the * {@link HDF5EnumerationValueArray#getLength()} returned if the data set is long * enough). * @param offset The offset of the block in the data set to start reading from (starting with * 0). * @return The data read from the data set. The length will be min(size - blockSize*blockNumber, * blockSize). */ public HDF5EnumerationValueArray readArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset); /** * Reads an Enum value array block from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param enumType The enumeration type of this array. * @param blockSize The block size (this will be the return value of the * {@link HDF5EnumerationValueArray#getLength()} returned if the data set is long * enough). * @param offset The offset of the block in the data set to start reading from (starting with * 0). * @return The data read from the data set. The length will be min(size - blockSize*blockNumber, * blockSize). */ public HDF5EnumerationValueArray readArrayBlockWithOffset(final String objectPath, final HDF5EnumerationType enumType, final int blockSize, final long offset); /** * Reads an Enum array (of rank N) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not of enumType. */ public HDF5EnumerationValueMDArray readMDArray(final String objectPath) throws HDF5JavaException; /** * Reads an Enum array (of rank N) from the data set objectPath. *

* This method is faster than {@link #read(String)} if the {@link HDF5EnumerationType} is * already available. * * @param objectPath The name (including path information) of the data set object in the file. * @param enumType The enum type in the HDF5 file. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not of enumType. */ public HDF5EnumerationValueMDArray readMDArray(final String objectPath, final HDF5EnumerationType enumType) throws HDF5JavaException; /** * Reads a block from a Enum array block (of rank N) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this enumeration type. * @param blockDimensions The extent of the block to write along each axis. * @param blockNumber The number of the block to write along each axis. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not an enum data set. */ public HDF5EnumerationValueMDArray readMDArrayBlock(final String objectPath, final HDF5EnumerationType type, final int[] blockDimensions, final long[] blockNumber) throws HDF5JavaException; /** * Reads a block from a Enum array block (of rank N) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block to write along each axis. * @param blockNumber The number of the block to write along each axis. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not an enum data set. */ public HDF5EnumerationValueMDArray readMDArrayBlock(final String objectPath, final int[] blockDimensions, final long[] blockNumber) throws HDF5JavaException; /** * Reads a block from a Enum array block (of rank N) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this Enum type. * @param blockDimensions The extent of the block to write along each axis. * @param offset The offset of the block to write in the data set along each axis. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not an enum data set. */ public HDF5EnumerationValueMDArray readMDArrayBlockWithOffset(final String objectPath, final HDF5EnumerationType type, final int[] blockDimensions, final long[] offset) throws HDF5JavaException; /** * Reads a block from a Enum array block (of rank N) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block to write along each axis. * @param offset The offset of the block to write in the data set along each axis. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not an enum data set. */ public HDF5EnumerationValueMDArray readMDArrayBlockWithOffset(final String objectPath, final int[] blockDimensions, final long[] offset) throws HDF5JavaException; /** * Provides all natural blocks of this one-dimensional data set to iterate over. * * @param objectPath The name (including path information) of the data set object in the file. * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1. */ public Iterable> getArrayBlocks( final String objectPath) throws HDF5JavaException; /** * Provides all natural blocks of this one-dimensional data set to iterate over. * * @param objectPath The name (including path information) of the data set object in the file. * @param enumType The enumeration type of this array. * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1. */ public Iterable> getArrayBlocks( final String objectPath, final HDF5EnumerationType enumType) throws HDF5JavaException; /** * Provides all natural blocks of this multi-dimensional data set to iterate over. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this enum type. * @see HDF5MDDataBlock * @throws HDF5JavaException If the data set is not an enum data set. */ public Iterable getMDArrayBlocks(final String objectPath, final HDF5EnumerationType type) throws HDF5JavaException; /** * Provides all natural blocks of this multi-dimensional data set to iterate over. * * @param objectPath The name (including path information) of the data set object in the file. * @see HDF5MDDataBlock * @throws HDF5JavaException If the data set is not an enum data set. */ public Iterable getMDArrayBlocks(final String objectPath) throws HDF5JavaException; } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5EnumTypeRetriever.java000066400000000000000000000173631256564762100304150ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; /** * An interface for retrieving HDF5 enum types. Depending on whether it is reader or a writer that * implements it, non-existing enum types may be created by calling the methods of this interface or * an exception may be thrown. * * @author Bernd Rinn */ public interface IHDF5EnumTypeRetriever { /** * Returns the enumeration type name for this HDF5 file. Use this method only when * you know that the type exists. If the dataTypeName starts with '/', it will be * considered a data type path instead of a data type name. * * @param dataTypeName The name of the enumeration in the HDF5 file. */ public HDF5EnumerationType getType(String dataTypeName); /** * Returns the enumeration type for the data set dataSetPath. * * @param dataSetPath The name of data set to get the enumeration type for. */ public HDF5EnumerationType getDataSetType(String dataSetPath); /** * Returns the enumeration type for the data set dataSetPath. * * @param dataSetPath The name of data set. * @param attributeName The name of the attribute to get the type for. */ public HDF5EnumerationType getAttributeType(String dataSetPath, String attributeName); /** * Returns the enumeration type name for this HDF5 file. If the type is read from the * file, it will check the type in the file with the values. If the * dataTypeName starts with '/', it will be considered a data type path instead of a * data type name. * * @param dataTypeName The name of the enumeration in the HDF5 file. * @param values The values of the enumeration. * @throws HDF5JavaException If the data type exists and is not compatible with the * values provided. */ public HDF5EnumerationType getType(String dataTypeName, String[] values) throws HDF5JavaException; /** * Returns the enumeration type name for this HDF5 file. If the type is read from the * file, it will check the type in the file with the values. If the * dataTypeName starts with '/', it will be considered a data type path instead of a * data type name. * * @param genericType The generic enum type (independent of this file). * @throws HDF5JavaException If the data type exists and is not compatible with the * values provided. */ public HDF5EnumerationType getType(EnumerationType genericType) throws HDF5JavaException; /** * Returns the enumeration type name for this HDF5 file. If the * dataTypeName starts with '/', it will be considered a data type path instead of a * data type name. * * @param dataTypeName The name of the enumeration in the HDF5 file. * @param values The values of the enumeration. * @param check If true and if the data type already exists, check whether it is * compatible with the values provided. * @throws HDF5JavaException If check = true, the data type exists and is not * compatible with the values provided. */ public HDF5EnumerationType getType(String dataTypeName, String[] values, boolean check) throws HDF5JavaException; /** * Returns the enumeration type name for this HDF5 file. If the type is read from the * file, it will check the type in the file with the values. If the * dataTypeName starts with '/', it will be considered a data type path instead of a * data type name. * * @param genericType The generic enum type (independent of this file). * @param check If true and if the data type already exists, check whether it is * compatible with the values provided. * @throws HDF5JavaException If check = true, the data type exists and is not * compatible with the values provided. */ public HDF5EnumerationType getType(EnumerationType genericType, boolean check) throws HDF5JavaException; /** * Returns the enumeration type name for this HDF5 file. Will check the type in the * file with the values. If the dataTypeName starts with '/', it will be * considered a data type path instead of a data type name. * * @param dataTypeName The name of the enumeration in the HDF5 file. * @param enumClass The enumeration class to get the values from. * @throws HDF5JavaException If the data type exists and is not compatible with the * enumClass provided. */ public HDF5EnumerationType getType(String dataTypeName, Class> enumClass) throws HDF5JavaException; /** * Returns the enumeration type name for this HDF5 file. Will check the type in the * file with the values. If the dataTypeName starts with '/', it will be * considered a data type path instead of a data type name. * * @param dataTypeName The name of the enumeration in the HDF5 file. * @param enumClass The enumeration class to get the values from. * @param check If true and if the data type already exists, check whether it is * compatible with the enumClass provided. * @throws HDF5JavaException If the data type exists and is not compatible with the * values provided. */ public > HDF5EnumerationType getType(String dataTypeName, Class enumClass, boolean check) throws HDF5JavaException; /** * Returns the enumeration type name for this HDF5 file. Will check the type in the * file with the values. Will use the simple class name of enumClass as * the data type name. * * @param enumClass The enumeration class to get the values from. * @throws HDF5JavaException If the data type exists and is not compatible with the * values provided. */ public > HDF5EnumerationType getType(Class enumClass) throws HDF5JavaException; /** * Returns the enumeration type name for this HDF5 file. Will check the type in the * file with the values. Will use the simple class name of enumClass as * the data type name. * * @param enumClass The enumeration class to get the values from. * @param check If true and if the data type already exists, check whether it is * compatible with the enumClass provided. * @throws HDF5JavaException If the data type exists and is not compatible with the * values provided. */ public HDF5EnumerationType getType(Class> enumClass, boolean check) throws HDF5JavaException; } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5EnumValueCreator.java000066400000000000000000000457321256564762100302010ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDByteArray; import ch.systemsx.cisd.base.mdarray.MDIntArray; import ch.systemsx.cisd.base.mdarray.MDShortArray; /** * Interface for creation of enumeration values. * * @author Bernd Rinn */ public interface IHDF5EnumValueCreator { /** * Creates a new enumeration value with enumeration type name typeName. *

* Shortcut for * new HDF5EnumerationValue(writer.getEnumType(typeName, options), value). * * @param typeName The name of the enumeration type. * @param options The values of the enumeration type. * @param value The string representation of the created enumeration value. * @return The created enumeration value. */ public HDF5EnumerationValue newVal(String typeName, String[] options, String value); /** * Creates a new enumeration value with an anonymous enumeration type. *

* Shortcut for * new HDF5EnumerationValue(writer.getAnonymousEnumType(options), value). * * @param options The values of the enumeration type. * @param value The string representation of the created enumeration value. * @return The created enumeration value. */ public HDF5EnumerationValue newAnonVal(String[] options, String value); /** * Creates a new enumeration value with enumeration type name typeName. *

* Shortcut for * new HDF5EnumerationValue(writer.getEnumType(typeName, options), value). * * @param typeName The name of the enumeration type. * @param options The values of the enumeration type. * @param value The ordinal value of the created enumeration value. * @return The created enumeration value. */ public HDF5EnumerationValue newVal(String typeName, String[] options, final int value); /** * Creates a new enumeration value with an anonymous enumeration type. *

* Shortcut for * new HDF5EnumerationValue(writer.getAnonymousEnumType(options), value). * * @param options The values of the enumeration type. * @param value The ordinal of the created enumeration value. * @return The created enumeration value. */ public HDF5EnumerationValue newAnonVal(String[] options, int value); /** * Creates a new enumeration value with enumeration type name typeName. *

* Shortcut for * new HDF5EnumerationValue(writer.getEnumType(typeName, options), value). * * @param typeName The name of the enumeration type. * @param options The values of the enumeration type. * @param value The ordinal value of the created enumeration value. * @return The created enumeration value. */ public HDF5EnumerationValue newVal(String typeName, String[] options, final short value); /** * Creates a new enumeration value with an anonymous enumeration type. *

* Shortcut for * new HDF5EnumerationValue(writer.getAnonymousEnumType(options), value). * * @param options The values of the enumeration type. * @param value The ordinal value of the created enumeration value. * @return The created enumeration value. */ public HDF5EnumerationValue newAnonVal(String[] options, short value); /** * Creates a new enumeration value with enumeration type name typeName. *

* Shortcut for * new HDF5EnumerationValue(writer.getEnumType(typeName, options), value). * * @param typeName The name of the enumeration type. * @param options The values of the enumeration type. * @param value The ordinal value of the created enumeration value. * @return The created enumeration value. */ public HDF5EnumerationValue newVal(String typeName, String[] options, final byte value); /** * Creates a new enumeration value with an anonymous enumeration type. *

* Shortcut for * new HDF5EnumerationValue(writer.getAnonymousEnumType(options), value). * * @param options The values of the enumeration type. * @param value The ordinal of the created enumeration value. * @return The created enumeration value. */ public HDF5EnumerationValue newAnonVal(String[] options, byte value); /** * Creates a new enumeration value with an anonymous enumeration type. *

* Shortcut for * new HDF5EnumerationValue(writer.getAnonymousEnumType(value.class), getClass()). * * @param value The value (including the type) of the created enumeration value. * @return The created enumeration value. */ public > HDF5EnumerationValue newAnonVal(Enum value); /** * Creates a new enumeration value with an enumeration type of name * value.getClass().getSimpleName(). *

* Shortcut for * new HDF5EnumerationValue(writer.getEnumType(value.getClass()), value). * * @param value The value (including the type) of the created enumeration value. * @return The created enumeration value. */ public > HDF5EnumerationValue newVal(Enum value); /** * Creates a new enumeration value with an enumeration type of name typeName. *

* Shortcut for * new HDF5EnumerationValue(writer.getEnumType(typeName, value.getClass()), value). * * @param typeName The name of the enumeration type. * @param value The value (including the type) of the created enumeration value. * @return The created enumeration value. */ public > HDF5EnumerationValue newVal(String typeName, Enum value); /** * Creates a new enumeration value array (of rank 1) with an enumeration type of name * typeName. *

* Shortcut for * new HDF5EnumerationValueArray(writer.getEnumType(typeName, options), value). * * @param typeName The name of the enumeration type. * @param options The values of the enumeration type. * @param values The string representations of the elements of the created enumeration value * array. * @return The created enumeration value. */ public HDF5EnumerationValueArray newArray(String typeName, String[] options, String[] values); /** * Creates a new enumeration value array (of rank 1) with an anonymous enumeration type. *

* Shortcut for * new HDF5EnumerationValueArray(writer.getAnonymousEnumType(options), value). * * @param options The values of the enumeration type. * @param values The string representations of the elements of the created enumeration value * array. * @return The created enumeration value. */ public HDF5EnumerationValueArray newAnonArray(String[] options, String[] values); /** * Creates a new enumeration value array (of rank 1) with an enumeration type of name * typeName. *

* Shortcut for * new HDF5EnumerationValueArray(writer.getEnumType(typeName, options), value). * * @param typeName The name of the enumeration type. * @param options The values of the enumeration type. * @param values The ordinal values of the elements of the created enumeration value array. * @return The created enumeration value. */ public HDF5EnumerationValueArray newArray(String typeName, String[] options, int[] values); /** * Creates a new enumeration value array (of rank 1) with an anonymous enumeration type. *

* Shortcut for * new HDF5EnumerationValueArray(writer.getAnonymousEnumType(options), value). * * @param options The values of the enumeration type. * @param values The ordinal values of the elements of the created enumeration value array. * @return The created enumeration value. */ public HDF5EnumerationValueArray newAnonArray(String[] options, int[] values); /** * Creates a new enumeration value array (of rank 1) with an enumeration type of name * typeName. *

* Shortcut for * new HDF5EnumerationValueArray(writer.getEnumType(typeName, options), value). * * @param typeName The name of the enumeration type. * @param options The values of the enumeration type. * @param values The ordinal values of the elements of the created enumeration value array. * @return The created enumeration value. */ public HDF5EnumerationValueArray newArray(String typeName, String[] options, short[] values); /** * Creates a new enumeration value array (of rank 1) with an anonymous enumeration type. *

* Shortcut for * new HDF5EnumerationValueArray(writer.getAnonymousEnumType(options), value). * * @param options The values of the enumeration type. * @param values The ordinal values of the elements of the created enumeration value array. * @return The created enumeration value. */ public HDF5EnumerationValueArray newAnonArray(String[] options, short[] values); /** * Creates a new enumeration value array (of rank 1) with an enumeration type of name * typeName. *

* Shortcut for * new HDF5EnumerationValueArray(writer.getEnumType(typeName, options), value). * * @param typeName The name of the enumeration type. * @param options The values of the enumeration type. * @param values The ordinal values of the elements of the created enumeration value array. * @return The created enumeration value. */ public HDF5EnumerationValueArray newArray(String typeName, String[] options, byte[] values); /** * Creates a new enumeration value array (of rank 1) with an anonymous enumeration type. *

* Shortcut for * new HDF5EnumerationValueArray(writer.getAnonymousEnumType(options), value). * * @param options The values of the enumeration type. * @param values The ordinal values of the elements of the created enumeration value array. * @return The created enumeration value. */ public HDF5EnumerationValueArray newAnonArray(String[] options, byte[] values); /** * Creates a new enumeration value array (of rank 1) with an anonymous enumeration type. *

* Shortcut for * new HDF5EnumerationValueArray(writer.getAnonymousEnumType(value.getClass().getComponentType()), value). * * @param values The value array (which has the type) of the created enumeration value array. * @return The created enumeration value. */ public > HDF5EnumerationValueArray newAnonArray(Enum[] values); /** * Creates a new enumeration value array (of rank 1) with an enumeration type of name * typeName. *

* Shortcut for * new HDF5EnumerationValueArray(writer.getEnumType(typeName, value.getClass().getComponentType()), value). * * @param typeName The name of the enumeration type. * @param values The value array (which has the type) of the created enumeration value array. * @return The created enumeration value. */ public > HDF5EnumerationValueArray newArray(String typeName, Enum[] values); /** * Creates a new enumeration value array (of rank 1) with an enumeration type of name * value.class.getSimpleName(). *

* Shortcut for * new HDF5EnumerationValueArray(writer.getEnumType(value.getClass().getComponentType()), value). * * @param values The value array (which has the type) of the created enumeration value array. * @return The created enumeration value. */ public > HDF5EnumerationValueArray newArray(Enum[] values); /** * Creates a new enumeration value array (of rank N) with an enumeration type of name * typeName. *

* Shortcut for * new HDF5EnumerationValueArray(writer.getEnumType(typeName, options), value). * * @param typeName The name of the enumeration type. * @param options The values of the enumeration type. * @param values The string representations of the elements of the created enumeration value * array. * @return The created enumeration value. */ public HDF5EnumerationValueMDArray newMDArray(String typeName, String[] options, MDArray values); /** * Creates a new enumeration value array (of rank N) with an anonymous enumeration type. *

* Shortcut for * new HDF5EnumerationValueArray(writer.getAnonymousEnumType(options), value). * * @param options The values of the enumeration type. * @param values The string representations of the elements of the created enumeration value * array. * @return The created enumeration value. */ public HDF5EnumerationValueMDArray newAnonMDArray(String[] options, MDArray values); /** * Creates a new enumeration value array (of rank N) with an enumeration type of name * typeName. *

* Shortcut for * new HDF5EnumerationValueArray(writer.getEnumType(typeName, options), value). * * @param typeName The name of the enumeration type. * @param options The values of the enumeration type. * @param values The ordinal values of the elements of the created enumeration value array. * @return The created enumeration value. */ public HDF5EnumerationValueMDArray newMDArray(String typeName, String[] options, MDIntArray values); /** * Creates a new enumeration value array (of rank N) with an anonymous enumeration type. *

* Shortcut for * new HDF5EnumerationValueArray(writer.getAnonymousEnumType(options), value). * * @param options The values of the enumeration type. * @param values The ordinal values of the elements of the created enumeration value array. * @return The created enumeration value. */ public HDF5EnumerationValueMDArray newAnonMDArray(String[] options, MDIntArray values); /** * Creates a new enumeration value array (of rank N) with an enumeration type of name * typeName. *

* Shortcut for * new HDF5EnumerationValueArray(writer.getEnumType(typeName, options), value). * * @param typeName The name of the enumeration type. * @param options The values of the enumeration type. * @param values The ordinal values of the elements of the created enumeration value array. * @return The created enumeration value. */ public HDF5EnumerationValueMDArray newMDArray(String typeName, String[] options, MDShortArray values); /** * Creates a new enumeration value array (of rank N) with an anonymous enumeration type. *

* Shortcut for * new HDF5EnumerationValueArray(writer.getAnonymousEnumType(options), value). * * @param options The values of the enumeration type. * @param values The ordinal values of the elements of the created enumeration value array. * @return The created enumeration value. */ public HDF5EnumerationValueMDArray newAnonMDArray(String[] options, MDShortArray values); /** * Creates a new enumeration value array (of rank N) with an enumeration type of name * typeName. *

* Shortcut for * new HDF5EnumerationValueArray(writer.getEnumType(typeName, options), value). * * @param typeName The name of the enumeration type. * @param options The values of the enumeration type. * @param values The ordinal values of the elements of the created enumeration value array. * @return The created enumeration value. */ public HDF5EnumerationValueMDArray newMDArray(String typeName, String[] options, MDByteArray values); /** * Creates a new enumeration value array (of rank N) with an anonymous enumeration type. *

* Shortcut for * new HDF5EnumerationValueArray(writer.getEnumType(typeName, options), value). * * @param options The values of the enumeration type. * @param values The ordinal values of the elements of the created enumeration value array. * @return The created enumeration value. */ public HDF5EnumerationValueMDArray newAnonMDArray(String[] options, MDByteArray values); /** * Creates a new enumeration value array (of rank N) with an anonymous enumeration type. *

* Shortcut for * new HDF5EnumerationValueArray(writer.getAnonymousEnumType(value.getAsFlatArray().getClass().getComponentType()), value). * * @param values The value array (which has the type) of the created enumeration value array. * @return The created enumeration value. */ public > HDF5EnumerationValueMDArray newAnonMDArray(MDArray> values); /** * Creates a new enumeration value array (of rank N) with an enumeration type of name * typeName. *

* Shortcut for * new HDF5EnumerationValueArray(writer.getEnumType(typeName, value.getAsFlatArray().getClass().getComponentType()), value). * * @param typeName The name of the enumeration type. * @param values The value array (which has the type) of the created enumeration value array. * @return The created enumeration value. */ public > HDF5EnumerationValueMDArray newMDArray(String typeName, MDArray> values); /** * Creates a new enumeration value array (of rank N) with an enumeration type of name * value.class.getSimpleName(). *

* Shortcut for * new HDF5EnumerationValueArray(writer.getEnumType(value.getAsFlatArray().getClass().getComponentType()), value). * * @param values The value array (which has the type) of the created enumeration value array. * @return The created enumeration value. */ public > HDF5EnumerationValueMDArray newMDArray(MDArray> values); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5EnumWriter.java000066400000000000000000000411761256564762100270570ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; /** * An interface that provides methods for writing enumeration values from HDF5 files. * * @author Bernd Rinn */ public interface IHDF5EnumWriter extends IHDF5EnumReader, IHDF5EnumValueCreator { // ///////////////////// // Types // ///////////////////// /** * Returns an anonymous enumeration type for this HDF5 file. * * @param options The values of the enumeration type. * @throws HDF5JavaException If the data type exists and is not compatible with the * values provided. */ public HDF5EnumerationType getAnonType(String[] options) throws HDF5JavaException; /** * Returns an anonymous enumeration type for this HDF5 file. * * @param enumClass The enumeration class to get the values from. * @throws HDF5JavaException If the data type exists and is not compatible with the * enumClass provided. */ public HDF5EnumerationType getAnonType(Class> enumClass) throws HDF5JavaException; // ///////////////////// // Attributes // ///////////////////// /** * Sets an enum attribute to the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setAttr(String objectPath, String name, HDF5EnumerationValue value); /** * Sets an enum attribute to the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @throws HDF5JavaException If the enum type of value is not a type of this file. */ public void setAttr(String objectPath, String name, Enum value) throws HDF5JavaException; /** * Sets an enum array attribute (of rank 1) to the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setArrayAttr(String objectPath, String name, HDF5EnumerationValueArray value); /** * Sets an enum array (of rank N) attribute to the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setMDArrayAttr(String objectPath, String name, HDF5EnumerationValueMDArray value); // ///////////////////// // Data Sets // ///////////////////// /** * Writes out an enum value. * * @param objectPath The name (including path information) of the data set object in the file. * @param value The value of the data set. * @throws HDF5JavaException If the enum type of value is not a type of this file. */ public void write(String objectPath, HDF5EnumerationValue value) throws HDF5JavaException; /** * Writes out an enum value. * * @param objectPath The name (including path information) of the data set object in the file. * @param value The value of the data set. * @throws HDF5JavaException If the enum type of value is not a type of this file. */ public void write(String objectPath, Enum value) throws HDF5JavaException; /** * Writes out an array of enum values. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @throws HDF5JavaException If the enum type of value is not a type of this file. */ public void writeArray(String objectPath, HDF5EnumerationValueArray data) throws HDF5JavaException; /** * Writes out an array of enum values. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param features The storage features of the data set. Note that for scaling compression the * compression factor is ignored. Instead, the scaling factor is computed from the * number of entries in the enumeration. * @throws HDF5JavaException If the enum type of value is not a type of this file. */ public void writeArray(String objectPath, HDF5EnumerationValueArray data, HDF5IntStorageFeatures features) throws HDF5JavaException; /** * Creates am enum array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param enumType The enumeration type of this array. * @param size The size of the byte array to create. This will be the total size for * non-extendable data sets and the size of one chunk for extendable (chunked) data * sets. For extendable data sets the initial size of the array will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. * @return enumType */ public HDF5EnumerationType createArray(String objectPath, HDF5EnumerationType enumType, int size); /** * Creates am enum array (of rank 1). The initial size of the array is 0. * * @param objectPath The name (including path information) of the data set object in the file. * @param enumType The enumeration type of this array. * @param size The size of the enum array to create. When using extendable data sets ((see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data set * smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). * @return enumType */ public HDF5EnumerationType createArray(String objectPath, HDF5EnumerationType enumType, long size, int blockSize); /** * Creates am enum array (of rank 1). The initial size of the array is 0. * * @param objectPath The name (including path information) of the data set object in the file. * @param enumType The enumeration type of this array. * @param size The size of the enum array to create. This will be the total size for * non-extendable data sets and the size of one chunk for extendable (chunked) data * sets. For extendable data sets the initial size of the array will be 0, see * {@link HDF5IntStorageFeatures}. * @param features The storage features of the data set. * @return enumType */ public HDF5EnumerationType createArray(String objectPath, HDF5EnumerationType enumType, long size, HDF5IntStorageFeatures features); /** * Creates am enum array (of rank 1). The initial size of the array is 0. * * @param objectPath The name (including path information) of the data set object in the file. * @param enumType The enumeration type of this array. * @param size The size of the enum array to create. When using extendable data sets ((see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data set * smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). * @param features The storage features of the data set. * @return enumType */ public HDF5EnumerationType createArray(String objectPath, HDF5EnumerationType enumType, long size, int blockSize, HDF5IntStorageFeatures features); /** * Writes out a block of an enum array (of rank 1). The data set needs to have been created by * {@link #createArray(String, HDF5EnumerationType, long, int, HDF5IntStorageFeatures)} * beforehand. Obviously the {@link HDF5EnumerationType} of the create call and this call needs * to match. *

* Note: For best performance, the block size in this method should be chosen to be equal * to the blockSize argument of the * {@link #createArray(String, HDF5EnumerationType, long, int, HDF5IntStorageFeatures)} call * that was used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The value of {@link HDF5EnumerationValueArray#getLength()} * defines the block size. Must not be null or of length 0. * @param blockNumber The number of the block to write. */ public void writeArrayBlock(String objectPath, HDF5EnumerationValueArray data, long blockNumber); /** * Writes out a block of an enum array (of rank 1). The data set needs to have been created by * {@link #createArray(String, HDF5EnumerationType, long, int, HDF5IntStorageFeatures)} * beforehand. Obviously the {@link HDF5EnumerationType} of the create call and this call needs * to match. *

* Note: For best performance, the block size in this method should be chosen to be equal * to the blockSize argument of the * {@link #createArray(String, HDF5EnumerationType, long, int, HDF5IntStorageFeatures)} call * that was used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The value of {@link HDF5EnumerationValueArray#getLength()} * defines the block size. Must not be null or of length 0. * @param dataSize The (real) size of data (needs to be * <= data.getLength() ) * @param offset The offset in the data set to start writing to. */ public void writeArrayBlockWithOffset(String objectPath, HDF5EnumerationValueArray data, int dataSize, long offset); /** * Writes out an array (of rank N) of Enum values. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param features The storage features of the data set. */ public void writeMDArray(String objectPath, HDF5EnumerationValueMDArray data, HDF5IntStorageFeatures features); /** * Writes out an array (of rank N) of Enum values. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. */ public void writeMDArray(String objectPath, HDF5EnumerationValueMDArray data); /** * Creates an array (of rank N) of Enum values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this Enum type. * @param dimensions The dimensions of the byte array to create. This will be the total * dimensions for non-extendable data sets and the dimensions of one chunk (along * each axis) for extendable (chunked) data sets. For extendable data sets the * initial size of the array (along each axis) will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. * @return enumType */ public HDF5EnumerationType createMDArray(String objectPath, HDF5EnumerationType type, int[] dimensions); /** * Creates an array (of rank N) of Enum values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this Enum type. * @param dimensions The extent of the Enum array along each of the axis. * @param blockDimensions The extent of one block along each of the axis. (for block-wise IO). * Ignored if no extendable data sets are used (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) and * deflate == false. * @return enumType */ public HDF5EnumerationType createMDArray(String objectPath, HDF5EnumerationType type, long[] dimensions, int[] blockDimensions); /** * Creates an array (of rank N) of Enum values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this Enum type. * @param dimensions The extent of the Enum array along each of the axis. * @param blockDimensions The extent of one block along each of the axis. (for block-wise IO). * Ignored if no extendable data sets are used (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) and * deflate == false. * @param features The storage features of the data set. * @return enumType */ public HDF5EnumerationType createMDArray(String objectPath, HDF5EnumerationType type, long[] dimensions, int[] blockDimensions, HDF5IntStorageFeatures features); /** * Creates an array (of rank N) of Enum values. * * @param objectPath The name (including path information) of the data set object in the file. * @param type The type definition of this Enum type. * @param dimensions The dimensions of the byte array to create. This will be the total * dimensions for non-extendable data sets and the dimensions of one chunk (along * each axis) for extendable (chunked) data sets. For extendable data sets the * initial size of the array (along each axis) will be 0, see * {@link HDF5GenericStorageFeatures}. * @param features The storage features of the data set. * @return enumType */ public HDF5EnumerationType createMDArray(String objectPath, HDF5EnumerationType type, int[] dimensions, HDF5IntStorageFeatures features); /** * Writes out a block of an array (of rank N) of Enum values give a given offset. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). */ public void writeMDArrayBlock(String objectPath, HDF5EnumerationValueMDArray data, long[] blockNumber); /** * Writes out a block of an array (of rank N) of Enum values give a given offset. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param offset The offset of the block in the data set to start writing to in each dimension. */ public void writeMDArrayBlockWithOffset(String objectPath, HDF5EnumerationValueMDArray data, long[] offset); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5Factory.java000066400000000000000000000041461256564762100263610ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.io.File; /** * A factory for creating writers and readers of HDF5 files. For straight-forward creation, see * methods {@link #open(File)} and {@link #openForReading(File)}. If you need full control over the * creation process, see the methods {@link #configure(File)} and {@link #configureForReading(File)} * . * * @author Bernd Rinn */ public interface IHDF5Factory { /** * Opens an HDF5 file for writing and reading. If the file does not yet exist, it * will be created. */ public IHDF5Writer open(File file); /** * Opens an HDF5 file for reading. It is an error if the file does not exist. */ public IHDF5Reader openForReading(File file); /** * Opens a configurator for an HDF5 file for writing and reading. Configure the * writer as you need and then call {@link IHDF5WriterConfigurator#writer()} in order to start * reading and writing the file. */ public IHDF5WriterConfigurator configure(File file); /** * Opens a configurator for an HDF5 file for reading. Configure the reader as you * need and then call {@link IHDF5ReaderConfigurator#reader()} in order to start reading the * file. */ public IHDF5ReaderConfigurator configureForReading(File file); /** * Returns true, if the file is an HDF5 file and false * otherwise. */ public boolean isHDF5File(File file); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5FileLevelReadOnlyHandler.java000066400000000000000000000036111256564762100315510ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.io.File; /** * An interface for handling file-level information and status of the reader. * * @author Bernd Rinn */ public interface IHDF5FileLevelReadOnlyHandler { // ///////////////////// // Configuration // ///////////////////// /** * Returns true, if numeric conversions should be performed automatically, e.g. * between float and int. */ public boolean isPerformNumericConversions(); /** * Returns the suffix used to mark and recognize internal (house keeping) files and groups. An * empty string ("") encodes for the default, which is two leading and two trailing underscores * ("__NAME__") */ public String getHouseKeepingNameSuffix(); /** * Returns the HDF5 file that this class is reading. */ public File getFile(); // ///////////////////// // Status // ///////////////////// /** * Closes this object and the file referenced by this object. This object must not be used after * being closed. Calling this method for a second time is a no-op. */ public void close(); /** * Returns true if this reader has been already closed. */ public boolean isClosed(); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5FileLevelReadWriteHandler.java000066400000000000000000000067211256564762100317270ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.io.Flushable; import ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator.FileFormat; /** * An interface for handling file-level information and status of the writer. * * @author Bernd Rinn */ public interface IHDF5FileLevelReadWriteHandler extends IHDF5FileLevelReadOnlyHandler { // ///////////////////// // Configuration // ///////////////////// /** * Returns true, if the {@link IHDF5WriterConfigurator} was not configured * with {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}, that is if extendable data * types are used for new data sets. */ public boolean isUseExtendableDataTypes(); /** * Returns the {@link FileFormat} compatibility setting for this writer. */ public FileFormat getFileFormat(); // ///////////////////// // Flushing and Syncing // ///////////////////// /** * Flushes the cache to disk (without discarding it). Note that this may or may not trigger a * fsync(2), depending on the {@link IHDF5WriterConfigurator.SyncMode} used. */ public void flush(); /** * Flushes the cache to disk (without discarding it) and synchronizes the file with the * underlying storage using a method like fsync(2), regardless of what * {@link IHDF5WriterConfigurator.SyncMode} has been set for this file. *

* This method blocks until fsync(2) has returned. */ public void flushSyncBlocking(); /** * Adds a {@link Flushable} to the set of flushables. This set is flushed when {@link #flush()} * or {@link #flushSyncBlocking()} are called and before the writer is closed. *

* This function is supposed to be used for in-memory caching structures that need to make it * into the HDF5 file. *

* If the flushable implements * {@link ch.systemsx.cisd.base.exceptions.IErrorStrategy}, in case of an exception in * {@link Flushable#flush()}, the method * {@link ch.systemsx.cisd.base.exceptions.IErrorStrategy#dealWithError(Throwable)} will be * called to decide how do deal with the exception. * * @param flushable The {@link Flushable} to add. Needs to fulfill the {@link Object#hashCode()} * contract. * @return true if the set of flushables did not already contain the specified * element. */ public boolean addFlushable(Flushable flushable); /** * Removes a {@link Flushable} from the set of flushables. * * @param flushable The {@link Flushable} to remove. Needs to fulfill the * {@link Object#hashCode()} contract. * @return true if the set of flushables contained the specified element. */ public boolean removeFlushable(Flushable flushable); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5FloatReader.java000066400000000000000000000425331256564762100271440ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.base.mdarray.MDFloatArray; /** * An interface that provides methods for reading float values from HDF5 files. *

* Note: This interface supports block access and sliced access (which is a special cases of * block access) to arrays. The performance of this block access can vary greatly depending on how * the data are layed out in the HDF5 file. For best performance, the block (or slice) dimension should * be chosen to be equal to the chunk dimensions of the array, as in this case the block written / read * are stored as consecutive value in the HDF5 file and one write / read access will suffice. *

* Note: If the values read are unsigned, use the methods in {@link UnsignedIntUtils} to convert * to a larger Java integer type that can hold all values as unsigned. * * @author Bernd Rinn */ public interface IHDF5FloatReader { // ///////////////////// // Attributes // ///////////////////// /** * Reads a float attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. */ public float getAttr(String objectPath, String attributeName); /** * Reads a float[] attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. */ public float[] getArrayAttr(String objectPath, String attributeName); /** * Reads a multi-dimensional array float attribute named attributeName * from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute array value read from the data set. */ public MDFloatArray getMDArrayAttr(String objectPath, String attributeName); /** * Reads a float matrix attribute named attributeName * from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute matrix value read from the data set. */ public float[][] getMatrixAttr(String objectPath, String attributeName) throws HDF5JavaException; // ///////////////////// // Data Sets // ///////////////////// /** * Reads a float value from the data set objectPath. This method * doesn't check the data space but simply reads the first value. * * @param objectPath The name (including path information) of the data set object in the file. * @return The value read from the data set. */ public float read(String objectPath); /** * Reads a float array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. */ public float[] readArray(String objectPath); /** * Reads a multi-dimensional float array data set objectPath * into a given array in memory. * * @param objectPath The name (including path information) of the data set object in the file. * @param array The array to read the data into. * @param memoryOffset The offset in the array to write the data to. * @return The effective dimensions of the block in array that was filled. */ public int[] readToMDArrayWithOffset(String objectPath, MDFloatArray array, int[] memoryOffset); /** * Reads a block of the multi-dimensional float array data set * objectPath into a given array in memory. * * @param objectPath The name (including path information) of the data set object in the file. * @param array The array to read the data into. * @param blockDimensions The size of the block to read along each axis. * @param offset The offset of the block in the data set. * @param memoryOffset The offset of the block in the array to write the data to. * @return The effective dimensions of the block in array that was filled. */ public int[] readToMDArrayBlockWithOffset(String objectPath, MDFloatArray array, int[] blockDimensions, long[] offset, int[] memoryOffset); /** * Reads a block from a float array (of rank 1) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the float[] returned * if the data set is long enough). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @return The data read from the data set. The length will be min(size - blockSize*blockNumber, * blockSize). */ public float[] readArrayBlock(String objectPath, int blockSize, long blockNumber); /** * Reads a block from float array (of rank 1) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the float[] * returned). * @param offset The offset of the block in the data set to start reading from (starting with 0). * @return The data block read from the data set. */ public float[] readArrayBlockWithOffset(String objectPath, int blockSize, long offset); /** * Reads a float matrix (array of arrays) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * * @throws HDF5JavaException If the data set objectPath is not of rank 2. */ public float[][] readMatrix(String objectPath) throws HDF5JavaException; /** * Reads a float matrix (array of arrays) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSizeX The size of the block in the x dimension. * @param blockSizeY The size of the block in the y dimension. * @param blockNumberX The block number in the x dimension (offset: multiply with * blockSizeX). * @param blockNumberY The block number in the y dimension (offset: multiply with * blockSizeY). * @return The data block read from the data set. * * @throws HDF5JavaException If the data set objectPath is not of rank 2. */ public float[][] readMatrixBlock(String objectPath, int blockSizeX, int blockSizeY, long blockNumberX, long blockNumberY) throws HDF5JavaException; /** * Reads a float matrix (array of arrays) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSizeX The size of the block in the x dimension. * @param blockSizeY The size of the block in the y dimension. * @param offsetX The offset in x dimension in the data set to start reading from. * @param offsetY The offset in y dimension in the data set to start reading from. * @return The data block read from the data set. * * @throws HDF5JavaException If the data set objectPath is not of rank 2. */ public float[][] readMatrixBlockWithOffset(String objectPath, int blockSizeX, int blockSizeY, long offsetX, long offsetY) throws HDF5JavaException; /** * Reads a multi-dimensional float array from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. */ public MDFloatArray readMDArray(String objectPath); /** * Reads a slice of a multi-dimensional float array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDFloatArray readMDArraySlice(String objectPath, IndexMap boundIndices); /** * Reads a slice of a multi-dimensional float array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDFloatArray readMDArraySlice(String objectPath, long[] boundIndices); /** * Reads a block from a multi-dimensional float array from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @return The data block read from the data set. */ public MDFloatArray readMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber); /** * Reads a sliced block from a multi-dimensional float array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDFloatArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, IndexMap boundIndices); /** * Reads a sliced block from a multi-dimensional float array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDFloatArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, long[] boundIndices); /** * Reads a block from a multi-dimensional float array from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @return The data block read from the data set. */ public MDFloatArray readMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset); /** * Reads a sliced block of a multi-dimensional float array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDFloatArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, IndexMap boundIndices); /** * Reads a sliced block of a multi-dimensional float array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDFloatArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, long[] boundIndices); /** * Provides all natural blocks of this one-dimensional data set to iterate over. * * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1. */ public Iterable> getArrayNaturalBlocks( String dataSetPath) throws HDF5JavaException; /** * Provides all natural blocks of this multi-dimensional data set to iterate over. * * @see HDF5MDDataBlock */ public Iterable> getMDArrayNaturalBlocks( String dataSetPath); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5FloatWriter.java000066400000000000000000000676011256564762100272210ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ch.systemsx.cisd.base.mdarray.MDFloatArray; /** * An interface that provides methods for writing float values to HDF5 files. *

* Note: This interface supports block access and sliced access (which is a special cases of * block access) to arrays. The performance of this block access can vary greatly depending on how * the data are layed out in the HDF5 file. For best performance, the block (or slice) dimension should * be chosen to be equal to the chunk dimensions of the array, as in this case the block written / read * are stored as consecutive value in the HDF5 file and one write / read access will suffice. * * @author Bernd Rinn */ public interface IHDF5FloatWriter extends IHDF5FloatReader { // ///////////////////// // Attributes // ///////////////////// /** * Set a float attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setAttr(String objectPath, String name, float value); /** * Set a float[] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setArrayAttr(String objectPath, String name, float[] value); /** * Set a multi-dimensional code>float attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setMDArrayAttr(String objectPath, String name, MDFloatArray value); /** * Set a float[][] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setMatrixAttr(String objectPath, String name, float[][] value); // ///////////////////// // Data Sets // ///////////////////// /** * Writes out a float value. * * @param objectPath The name (including path information) of the data set object in the file. * @param value The value to write. */ public void write(String objectPath, float value); /** * Writes out a float array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ public void writeArray(String objectPath, float[] data); /** * Writes out a float array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param features The storage features of the data set. */ public void writeArray(String objectPath, float[] data, HDF5FloatStorageFeatures features); /** * Creates a float array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size When the writer is configured to use extendable data types (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be size. When the writer is * configured to enforce a non-extendable data set, the initial size equals the * total size and will be size. */ public void createArray(String objectPath, int size); /** * Creates a float array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the float array to create. When using extendable data sets * ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data * set smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). */ public void createArray(String objectPath, long size, int blockSize); /** * Creates a float array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the float array to create. When requesting a * chunked data set (e.g. {@link HDF5FloatStorageFeatures#FLOAT_CHUNKED}), * the initial size of the array will be 0 and the chunk size will be arraySize. * When allowing a chunked data set (e.g. * {@link HDF5FloatStorageFeatures#FLOAT_NO_COMPRESSION} when the writer is * not configured to avoid extendable data types, see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be arraySize. When enforcing a * on-extendable data set (e.g. * {@link HDF5FloatStorageFeatures#FLOAT_CONTIGUOUS}), the initial size equals * the total size and will be arraySize. * @param features The storage features of the data set. */ public void createArray(String objectPath, int size, HDF5FloatStorageFeatures features); /** * Creates a float array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the float array to create. When using extendable data sets * ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data * set smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) and * features is HDF5FloatStorageFeature.FLOAT_NO_COMPRESSION. * @param features The storage features of the data set. */ public void createArray(String objectPath, long size, int blockSize, HDF5FloatStorageFeatures features); /** * Writes out a block of a float array (of rank 1). The data set needs to have * been created by {@link #createArray(String, long, int, HDF5FloatStorageFeatures)} * beforehand. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumber The number of the block to write. */ public void writeArrayBlock(String objectPath, float[] data, long blockNumber); /** * Writes out a block of a float array (of rank 1). The data set needs to have * been created by {@link #createArray(String, long, int, HDF5FloatStorageFeatures)} * beforehand. *

* Use this method instead of {@link #writeArrayBlock(String, float[], long)} if the * total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param dataSize The (real) size of data (needs to be <= data.length * ) * @param offset The offset in the data set to start writing to. */ public void writeArrayBlockWithOffset(String objectPath, float[] data, int dataSize, long offset); /** * Writes out a float matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ public void writeMatrix(String objectPath, float[][] data); /** * Writes out a float matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. */ public void writeMatrix(String objectPath, float[][] data, HDF5FloatStorageFeatures features); /** * Creates a float matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of one block in the x dimension. See * {@link #createMDArray(String, int[])} on the different * meanings of this parameter. * @param sizeY The size of one block in the y dimension. See * {@link #createMDArray(String, int[])} on the different * meanings of this parameter. */ public void createMatrix(String objectPath, int sizeX, int sizeY); /** * Creates a float matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of one block in the x dimension. See * {@link #createMDArray(String, int[], HDF5FloatStorageFeatures)} on the different * meanings of this parameter. * @param sizeY The size of one block in the y dimension. See * {@link #createMDArray(String, int[], HDF5FloatStorageFeatures)} on the different * meanings of this parameter. * @param features The storage features of the data set. */ public void createMatrix(String objectPath, int sizeX, int sizeY, HDF5FloatStorageFeatures features); /** * Creates a float matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the float matrix to create. * @param sizeY The size of the y dimension of the float matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. */ public void createMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY); /** * Creates a float matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the float matrix to create. * @param sizeY The size of the y dimension of the float matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. * @param features The storage features of the data set. */ public void createMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY, HDF5FloatStorageFeatures features); /** * Writes out a block of a float matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5FloatStorageFeatures)} beforehand. *

* Use this method instead of * {@link #createMatrix(String, long, long, int, int, HDF5FloatStorageFeatures)} if the total * size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumberX The block number in the x dimension (offset: multiply with * data.length). * @param blockNumberY The block number in the y dimension (offset: multiply with * data[0.length). */ public void writeMatrixBlock(String objectPath, float[][] data, long blockNumberX, long blockNumberY); /** * Writes out a block of a float matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5FloatStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeMatrixBlock(String, float[][], long, long)} if * the total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. */ public void writeMatrixBlockWithOffset(String objectPath, float[][] data, long offsetX, long offsetY); /** * Writes out a block of a float matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5FloatStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeMatrixBlock(String, float[][], long, long)} if * the total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param dataSizeX The (real) size of data along the x axis (needs to be * <= data.length ) * @param dataSizeY The (real) size of data along the y axis (needs to be * <= data[0].length ) * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. */ public void writeMatrixBlockWithOffset(String objectPath, float[][] data, int dataSizeX, int dataSizeY, long offsetX, long offsetY); /** * Writes out a multi-dimensional float array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ public void writeMDArray(String objectPath, MDFloatArray data); /** * Writes out a multi-dimensional float array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. */ public void writeMDArray(String objectPath, MDFloatArray data, HDF5FloatStorageFeatures features); /** * Writes out a slice of a multi-dimensional float array. The slice is defined by * "bound indices", each of which is fixed to a given value. The data object only * contains the free (i.e. non-fixed) indices. *

* Note:The object identified by objectPath needs to exist when this method is * called. This method will not create the array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. */ public void writeMDArraySlice(String objectPath, MDFloatArray data, IndexMap boundIndices); /** * Writes out a slice of a multi-dimensional float array. The slice is defined by * "bound indices", each of which is fixed to a given value. The data object only * contains the free (i.e. non-fixed) indices. *

* Note:The object identified by objectPath needs to exist when this method is * called. This method will not create the array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. */ public void writeMDArraySlice(String objectPath, MDFloatArray data, long[] boundIndices); /** * Creates a multi-dimensional float array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions When the writer is configured to use extendable data types (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial dimensions * and the dimensions of a chunk of the array will be dimensions. When the * writer is configured to enforce a non-extendable data set, the initial dimensions * equal the dimensions and will be dimensions. */ public void createMDArray(String objectPath, int[] dimensions); /** * Creates a multi-dimensional float array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. */ public void createMDArray(String objectPath, long[] dimensions, int[] blockDimensions); /** * Creates a multi-dimensional float array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the float array to create. When requesting * a chunked data set (e.g. {@link HDF5FloatStorageFeatures#FLOAT_CHUNKED}), * the initial size of the array will be 0 and the chunk size will be dimensions. * When allowing a chunked data set (e.g. * {@link HDF5FloatStorageFeatures#FLOAT_NO_COMPRESSION} when the writer is * not configured to avoid extendable data types, see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be dimensions. When enforcing a * on-extendable data set (e.g. * {@link HDF5FloatStorageFeatures#FLOAT_CONTIGUOUS}), the initial size equals * the total size and will be dimensions. * @param features The storage features of the data set. */ public void createMDArray(String objectPath, int[] dimensions, HDF5FloatStorageFeatures features); /** * Creates a multi-dimensional float array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. * @param features The storage features of the data set. */ public void createMDArray(String objectPath, long[] dimensions, int[] blockDimensions, HDF5FloatStorageFeatures features); /** * Writes out a block of a multi-dimensional float array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). */ public void writeMDArrayBlock(String objectPath, MDFloatArray data, long[] blockNumber); /** * Writes out a sliced block of a multi-dimensional float array. The slice is * defined by "bound indices", each of which is fixed to a given value. The data * object only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. */ public void writeSlicedMDArrayBlock(String objectPath, MDFloatArray data, long[] blockNumber, IndexMap boundIndices); /** * Writes out a sliced block of a multi-dimensional float array. The slice is * defined by "bound indices", each of which is fixed to a given value. The data * object only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. */ public void writeSlicedMDArrayBlock(String objectPath, MDFloatArray data, long[] blockNumber, long[] boundIndices); /** * Writes out a block of a multi-dimensional float array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. */ public void writeMDArrayBlockWithOffset(String objectPath, MDFloatArray data, long[] offset); /** * Writes out a sliced block of a multi-dimensional float array. The slice is * defined by "bound indices", each of which is fixed to a given value. The data * object only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. */ public void writeSlicedMDArrayBlockWithOffset(String objectPath, MDFloatArray data, long[] offset, IndexMap boundIndices); /** * Writes out a sliced block of a multi-dimensional float array. The slice is * defined by "bound indices", each of which is fixed to a given value. The data * object only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. */ public void writeSlicedMDArrayBlockWithOffset(String objectPath, MDFloatArray data, long[] offset, long[] boundIndices); /** * Writes out a block of a multi-dimensional float array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param blockDimensions The dimensions of the block to write to the data set. * @param offset The offset of the block in the data set to start writing to in each dimension. * @param memoryOffset The offset of the block in the data array. */ public void writeMDArrayBlockWithOffset(String objectPath, MDFloatArray data, int[] blockDimensions, long[] offset, int[] memoryOffset); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5IntReader.java000066400000000000000000000423651256564762100266340ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.base.mdarray.MDIntArray; /** * An interface that provides methods for reading int values from HDF5 files. *

* Note: This interface supports block access and sliced access (which is a special cases of * block access) to arrays. The performance of this block access can vary greatly depending on how * the data are layed out in the HDF5 file. For best performance, the block (or slice) dimension should * be chosen to be equal to the chunk dimensions of the array, as in this case the block written / read * are stored as consecutive value in the HDF5 file and one write / read access will suffice. *

* Note: If the values read are unsigned, use the methods in {@link UnsignedIntUtils} to convert * to a larger Java integer type that can hold all values as unsigned. * * @author Bernd Rinn */ public interface IHDF5IntReader { // ///////////////////// // Attributes // ///////////////////// /** * Reads a int attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. */ public int getAttr(String objectPath, String attributeName); /** * Reads a int[] attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. */ public int[] getArrayAttr(String objectPath, String attributeName); /** * Reads a multi-dimensional array int attribute named attributeName * from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute array value read from the data set. */ public MDIntArray getMDArrayAttr(String objectPath, String attributeName); /** * Reads a int matrix attribute named attributeName * from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute matrix value read from the data set. */ public int[][] getMatrixAttr(String objectPath, String attributeName) throws HDF5JavaException; // ///////////////////// // Data Sets // ///////////////////// /** * Reads a int value from the data set objectPath. This method * doesn't check the data space but simply reads the first value. * * @param objectPath The name (including path information) of the data set object in the file. * @return The value read from the data set. */ public int read(String objectPath); /** * Reads a int array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. */ public int[] readArray(String objectPath); /** * Reads a multi-dimensional int array data set objectPath * into a given array in memory. * * @param objectPath The name (including path information) of the data set object in the file. * @param array The array to read the data into. * @param memoryOffset The offset in the array to write the data to. * @return The effective dimensions of the block in array that was filled. */ public int[] readToMDArrayWithOffset(String objectPath, MDIntArray array, int[] memoryOffset); /** * Reads a block of the multi-dimensional int array data set * objectPath into a given array in memory. * * @param objectPath The name (including path information) of the data set object in the file. * @param array The array to read the data into. * @param blockDimensions The size of the block to read along each axis. * @param offset The offset of the block in the data set. * @param memoryOffset The offset of the block in the array to write the data to. * @return The effective dimensions of the block in array that was filled. */ public int[] readToMDArrayBlockWithOffset(String objectPath, MDIntArray array, int[] blockDimensions, long[] offset, int[] memoryOffset); /** * Reads a block from a int array (of rank 1) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the int[] returned * if the data set is long enough). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @return The data read from the data set. The length will be min(size - blockSize*blockNumber, * blockSize). */ public int[] readArrayBlock(String objectPath, int blockSize, long blockNumber); /** * Reads a block from int array (of rank 1) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the int[] * returned). * @param offset The offset of the block in the data set to start reading from (starting with 0). * @return The data block read from the data set. */ public int[] readArrayBlockWithOffset(String objectPath, int blockSize, long offset); /** * Reads a int matrix (array of arrays) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * * @throws HDF5JavaException If the data set objectPath is not of rank 2. */ public int[][] readMatrix(String objectPath) throws HDF5JavaException; /** * Reads a int matrix (array of arrays) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSizeX The size of the block in the x dimension. * @param blockSizeY The size of the block in the y dimension. * @param blockNumberX The block number in the x dimension (offset: multiply with * blockSizeX). * @param blockNumberY The block number in the y dimension (offset: multiply with * blockSizeY). * @return The data block read from the data set. * * @throws HDF5JavaException If the data set objectPath is not of rank 2. */ public int[][] readMatrixBlock(String objectPath, int blockSizeX, int blockSizeY, long blockNumberX, long blockNumberY) throws HDF5JavaException; /** * Reads a int matrix (array of arrays) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSizeX The size of the block in the x dimension. * @param blockSizeY The size of the block in the y dimension. * @param offsetX The offset in x dimension in the data set to start reading from. * @param offsetY The offset in y dimension in the data set to start reading from. * @return The data block read from the data set. * * @throws HDF5JavaException If the data set objectPath is not of rank 2. */ public int[][] readMatrixBlockWithOffset(String objectPath, int blockSizeX, int blockSizeY, long offsetX, long offsetY) throws HDF5JavaException; /** * Reads a multi-dimensional int array from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. */ public MDIntArray readMDArray(String objectPath); /** * Reads a slice of a multi-dimensional int array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDIntArray readMDArraySlice(String objectPath, IndexMap boundIndices); /** * Reads a slice of a multi-dimensional int array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDIntArray readMDArraySlice(String objectPath, long[] boundIndices); /** * Reads a block from a multi-dimensional int array from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @return The data block read from the data set. */ public MDIntArray readMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber); /** * Reads a sliced block from a multi-dimensional int array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDIntArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, IndexMap boundIndices); /** * Reads a sliced block from a multi-dimensional int array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDIntArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, long[] boundIndices); /** * Reads a block from a multi-dimensional int array from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @return The data block read from the data set. */ public MDIntArray readMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset); /** * Reads a sliced block of a multi-dimensional int array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDIntArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, IndexMap boundIndices); /** * Reads a sliced block of a multi-dimensional int array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDIntArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, long[] boundIndices); /** * Provides all natural blocks of this one-dimensional data set to iterate over. * * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1. */ public Iterable> getArrayNaturalBlocks( String dataSetPath) throws HDF5JavaException; /** * Provides all natural blocks of this multi-dimensional data set to iterate over. * * @see HDF5MDDataBlock */ public Iterable> getMDArrayNaturalBlocks( String dataSetPath); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5IntWriter.java000066400000000000000000000711521256564762100267020ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ch.systemsx.cisd.base.mdarray.MDIntArray; /** * An interface that provides methods for writing int values to HDF5 files. *

* Note: This interface supports block access and sliced access (which is a special cases of * block access) to arrays. The performance of this block access can vary greatly depending on how * the data are layed out in the HDF5 file. For best performance, the block (or slice) dimension should * be chosen to be equal to the chunk dimensions of the array, as in this case the block written / read * are stored as consecutive value in the HDF5 file and one write / read access will suffice. *

* Note: If you need to convert from and to unsigned values, use the methods of * {@link UnsignedIntUtils}. * * @author Bernd Rinn */ // Note: It is a trick for keeping backward compatibility to let this interface extend // IHDF5UnsignedIntWriter instead of IHDF5IntReader as it logically should. // Once we remove IHDF5UnsignedIntWriter, uncomment the following line and remove // all @Override annotations and we are fine again. //public interface IHDF5IntWriter extends IHDF5IntReader @SuppressWarnings("deprecation") public interface IHDF5IntWriter extends IHDF5UnsignedIntWriter { // ///////////////////// // Attributes // ///////////////////// /** * Set a int attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ @Override public void setAttr(String objectPath, String name, int value); /** * Set a int[] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ @Override public void setArrayAttr(String objectPath, String name, int[] value); /** * Set a multi-dimensional code>int attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ @Override public void setMDArrayAttr(String objectPath, String name, MDIntArray value); /** * Set a int[][] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ @Override public void setMatrixAttr(String objectPath, String name, int[][] value); // ///////////////////// // Data Sets // ///////////////////// /** * Writes out a int value. * * @param objectPath The name (including path information) of the data set object in the file. * @param value The value to write. */ @Override public void write(String objectPath, int value); /** * Writes out a int array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ @Override public void writeArray(String objectPath, int[] data); /** * Writes out a int array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param features The storage features of the data set. */ @Override public void writeArray(String objectPath, int[] data, HDF5IntStorageFeatures features); /** * Creates a int array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size When the writer is configured to use extendable data types (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be size. When the writer is * configured to enforce a non-extendable data set, the initial size equals the * total size and will be size. */ @Override public void createArray(String objectPath, int size); /** * Creates a int array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the int array to create. When using extendable data sets * ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data * set smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). */ @Override public void createArray(String objectPath, long size, int blockSize); /** * Creates a int array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the int array to create. When requesting a * chunked data set (e.g. {@link HDF5IntStorageFeatures#INT_CHUNKED}), * the initial size of the array will be 0 and the chunk size will be arraySize. * When allowing a chunked data set (e.g. * {@link HDF5IntStorageFeatures#INT_NO_COMPRESSION} when the writer is * not configured to avoid extendable data types, see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be arraySize. When enforcing a * on-extendable data set (e.g. * {@link HDF5IntStorageFeatures#INT_CONTIGUOUS}), the initial size equals * the total size and will be arraySize. * @param features The storage features of the data set. */ @Override public void createArray(String objectPath, int size, HDF5IntStorageFeatures features); /** * Creates a int array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the int array to create. When using extendable data sets * ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data * set smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) and * features is HDF5IntStorageFeature.INT_NO_COMPRESSION. * @param features The storage features of the data set. */ @Override public void createArray(String objectPath, long size, int blockSize, HDF5IntStorageFeatures features); /** * Writes out a block of a int array (of rank 1). The data set needs to have * been created by {@link #createArray(String, long, int, HDF5IntStorageFeatures)} * beforehand. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumber The number of the block to write. */ @Override public void writeArrayBlock(String objectPath, int[] data, long blockNumber); /** * Writes out a block of a int array (of rank 1). The data set needs to have * been created by {@link #createArray(String, long, int, HDF5IntStorageFeatures)} * beforehand. *

* Use this method instead of {@link #writeArrayBlock(String, int[], long)} if the * total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param dataSize The (real) size of data (needs to be <= data.length * ) * @param offset The offset in the data set to start writing to. */ @Override public void writeArrayBlockWithOffset(String objectPath, int[] data, int dataSize, long offset); /** * Writes out a int matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ @Override public void writeMatrix(String objectPath, int[][] data); /** * Writes out a int matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. */ @Override public void writeMatrix(String objectPath, int[][] data, HDF5IntStorageFeatures features); /** * Creates a int matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of one block in the x dimension. See * {@link #createMDArray(String, int[])} on the different * meanings of this parameter. * @param sizeY The size of one block in the y dimension. See * {@link #createMDArray(String, int[])} on the different * meanings of this parameter. */ @Override public void createMatrix(String objectPath, int sizeX, int sizeY); /** * Creates a int matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of one block in the x dimension. See * {@link #createMDArray(String, int[], HDF5IntStorageFeatures)} on the different * meanings of this parameter. * @param sizeY The size of one block in the y dimension. See * {@link #createMDArray(String, int[], HDF5IntStorageFeatures)} on the different * meanings of this parameter. * @param features The storage features of the data set. */ @Override public void createMatrix(String objectPath, int sizeX, int sizeY, HDF5IntStorageFeatures features); /** * Creates a int matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the int matrix to create. * @param sizeY The size of the y dimension of the int matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. */ @Override public void createMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY); /** * Creates a int matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the int matrix to create. * @param sizeY The size of the y dimension of the int matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. * @param features The storage features of the data set. */ @Override public void createMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY, HDF5IntStorageFeatures features); /** * Writes out a block of a int matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of * {@link #createMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} if the total * size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumberX The block number in the x dimension (offset: multiply with * data.length). * @param blockNumberY The block number in the y dimension (offset: multiply with * data[0.length). */ @Override public void writeMatrixBlock(String objectPath, int[][] data, long blockNumberX, long blockNumberY); /** * Writes out a block of a int matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeMatrixBlock(String, int[][], long, long)} if * the total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. */ @Override public void writeMatrixBlockWithOffset(String objectPath, int[][] data, long offsetX, long offsetY); /** * Writes out a block of a int matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeMatrixBlock(String, int[][], long, long)} if * the total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param dataSizeX The (real) size of data along the x axis (needs to be * <= data.length ) * @param dataSizeY The (real) size of data along the y axis (needs to be * <= data[0].length ) * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. */ @Override public void writeMatrixBlockWithOffset(String objectPath, int[][] data, int dataSizeX, int dataSizeY, long offsetX, long offsetY); /** * Writes out a multi-dimensional int array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ @Override public void writeMDArray(String objectPath, MDIntArray data); /** * Writes out a multi-dimensional int array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. */ @Override public void writeMDArray(String objectPath, MDIntArray data, HDF5IntStorageFeatures features); /** * Writes out a slice of a multi-dimensional int array. The slice is defined by * "bound indices", each of which is fixed to a given value. The data object only * contains the free (i.e. non-fixed) indices. *

* Note:The object identified by objectPath needs to exist when this method is * called. This method will not create the array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. */ public void writeMDArraySlice(String objectPath, MDIntArray data, IndexMap boundIndices); /** * Writes out a slice of a multi-dimensional int array. The slice is defined by * "bound indices", each of which is fixed to a given value. The data object only * contains the free (i.e. non-fixed) indices. *

* Note:The object identified by objectPath needs to exist when this method is * called. This method will not create the array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. */ public void writeMDArraySlice(String objectPath, MDIntArray data, long[] boundIndices); /** * Creates a multi-dimensional int array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions When the writer is configured to use extendable data types (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial dimensions * and the dimensions of a chunk of the array will be dimensions. When the * writer is configured to enforce a non-extendable data set, the initial dimensions * equal the dimensions and will be dimensions. */ @Override public void createMDArray(String objectPath, int[] dimensions); /** * Creates a multi-dimensional int array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. */ @Override public void createMDArray(String objectPath, long[] dimensions, int[] blockDimensions); /** * Creates a multi-dimensional int array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the int array to create. When requesting * a chunked data set (e.g. {@link HDF5IntStorageFeatures#INT_CHUNKED}), * the initial size of the array will be 0 and the chunk size will be dimensions. * When allowing a chunked data set (e.g. * {@link HDF5IntStorageFeatures#INT_NO_COMPRESSION} when the writer is * not configured to avoid extendable data types, see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be dimensions. When enforcing a * on-extendable data set (e.g. * {@link HDF5IntStorageFeatures#INT_CONTIGUOUS}), the initial size equals * the total size and will be dimensions. * @param features The storage features of the data set. */ @Override public void createMDArray(String objectPath, int[] dimensions, HDF5IntStorageFeatures features); /** * Creates a multi-dimensional int array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. * @param features The storage features of the data set. */ @Override public void createMDArray(String objectPath, long[] dimensions, int[] blockDimensions, HDF5IntStorageFeatures features); /** * Writes out a block of a multi-dimensional int array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). */ @Override public void writeMDArrayBlock(String objectPath, MDIntArray data, long[] blockNumber); /** * Writes out a sliced block of a multi-dimensional int array. The slice is * defined by "bound indices", each of which is fixed to a given value. The data * object only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. */ public void writeSlicedMDArrayBlock(String objectPath, MDIntArray data, long[] blockNumber, IndexMap boundIndices); /** * Writes out a sliced block of a multi-dimensional int array. The slice is * defined by "bound indices", each of which is fixed to a given value. The data * object only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. */ public void writeSlicedMDArrayBlock(String objectPath, MDIntArray data, long[] blockNumber, long[] boundIndices); /** * Writes out a block of a multi-dimensional int array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. */ @Override public void writeMDArrayBlockWithOffset(String objectPath, MDIntArray data, long[] offset); /** * Writes out a sliced block of a multi-dimensional int array. The slice is * defined by "bound indices", each of which is fixed to a given value. The data * object only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. */ public void writeSlicedMDArrayBlockWithOffset(String objectPath, MDIntArray data, long[] offset, IndexMap boundIndices); /** * Writes out a sliced block of a multi-dimensional int array. The slice is * defined by "bound indices", each of which is fixed to a given value. The data * object only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. */ public void writeSlicedMDArrayBlockWithOffset(String objectPath, MDIntArray data, long[] offset, long[] boundIndices); /** * Writes out a block of a multi-dimensional int array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param blockDimensions The dimensions of the block to write to the data set. * @param offset The offset of the block in the data set to start writing to in each dimension. * @param memoryOffset The offset of the block in the data array. */ @Override public void writeMDArrayBlockWithOffset(String objectPath, MDIntArray data, int[] blockDimensions, long[] offset, int[] memoryOffset); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5LegacyReader.java000066400000000000000000005033311256564762100273010ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.io.File; import java.util.BitSet; import java.util.Date; import java.util.List; import ncsa.hdf.hdf5lib.exceptions.HDF5DatatypeInterfaceException; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDByteArray; import ch.systemsx.cisd.base.mdarray.MDDoubleArray; import ch.systemsx.cisd.base.mdarray.MDFloatArray; import ch.systemsx.cisd.base.mdarray.MDIntArray; import ch.systemsx.cisd.base.mdarray.MDLongArray; import ch.systemsx.cisd.base.mdarray.MDShortArray; import ch.systemsx.cisd.hdf5.HDF5DataTypeInformation.DataTypeInfoOptions; /** * The legacy interface for reading HDF5 files. Do not use in any new code as it will be removed in * a future version of JHDF5. * * @author Bernd Rinn */ @Deprecated public interface IHDF5LegacyReader extends IHDF5EnumBasicReader, IHDF5CompoundBasicReader { // ********************* // File level // ********************* // ///////////////////// // Configuration // ///////////////////// /** * Returns true, if numeric conversions should be performed automatically, e.g. * between float and int. * @deprecated Use the corresponding method in {@link IHDF5Reader#file()} instead. */ @Deprecated public boolean isPerformNumericConversions(); /** * Returns the suffix used to mark and recognize internal (house keeping) files and groups. An * empty string ("") encodes for the default, which is two leading and two trailing underscores * ("__NAME__") * @deprecated Use the corresponding method in {@link IHDF5Reader#file()} instead. */ @Deprecated public String getHouseKeepingNameSuffix(); /** * Returns the HDF5 file that this class is reading. * @deprecated Use the corresponding method in {@link IHDF5Reader#file()} instead. */ @Deprecated public File getFile(); // ///////////////////// // Status // ///////////////////// /** * Returns true if this reader has been already closed. * @deprecated Use the corresponding method in {@link IHDF5Reader#file()} instead. */ @Deprecated public boolean isClosed(); // *********************** // Objects, Links, Groups // *********************** // ///////////////////// // Objects & Links // ///////////////////// /** * Returns the link information for the given objectPath. If objectPath * does not exist, the link information will have a type {@link HDF5ObjectType#NONEXISTENT}. */ public HDF5LinkInformation getLinkInformation(final String objectPath); /** * Returns the object information for the given objectPath. If objectPath * is a symbolic link, this method will return the type of the object that this link points to * rather than the type of the link. If objectPath does not exist, the object * information will have a type {@link HDF5ObjectType#NONEXISTENT} and the other fields will not * be set. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public HDF5ObjectInformation getObjectInformation(final String objectPath); /** * Returns the type of the given objectPath. If followLink is * false and objectPath is a symbolic link, this method will return the * type of the link rather than the type of the object that the link points to. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public HDF5ObjectType getObjectType(final String objectPath, boolean followLink); /** * Returns the type of the given objectPath. If objectPath is a symbolic * link, this method will return the type of the object that this link points to rather than the * type of the link, that is, it will follow symbolic links. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public HDF5ObjectType getObjectType(final String objectPath); /** * Returns true, if objectPath exists and false otherwise. * if followLink is false and objectPath is a symbolic link, * this method will return true regardless of whether the link target exists or * not. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public boolean exists(final String objectPath, boolean followLink); /** * Creates and returns an internal (house-keeping) version of objectPath. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public String toHouseKeepingPath(final String objectPath); /** * Returns true if objectPath denotes an internal (house-keeping) * object. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public boolean isHouseKeepingObject(final String objectPath); /** * Returns true if the objectPath exists and represents a group and * false otherwise. Note that if followLink is false this * method will return false if objectPath is a symbolic link that points * to a group. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public boolean isGroup(final String objectPath, boolean followLink); /** * Returns true if the objectPath exists and represents a data set and * false otherwise. Note that if followLink is false this * method will return false if objectPath is a symbolic link that points * to a data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public boolean isDataSet(final String objectPath, boolean followLink); /** * Returns true if the objectPath exists and represents a data set and * false otherwise. Note that if objectPath is a symbolic link, this * method will return true if the link target of the symbolic link is a data set, * that is, this method will follow symbolic links. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public boolean isDataSet(final String objectPath); /** * Returns true if the objectPath exists and represents a data type and * false otherwise. Note that if followLink is false this * method will return false if objectPath is a symbolic link that points * to a data type. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public boolean isDataType(final String objectPath, boolean followLink); /** * Returns true if the objectPath exists and represents a data type and * false otherwise. Note that if objectPath is a symbolic link, this * method will return true if the link target of the symbolic link is a data type, * that is, this method will follow symbolic links. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public boolean isDataType(final String objectPath); /** * Returns true if the objectPath exists and represents a soft link and * false otherwise. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public boolean isSoftLink(final String objectPath); /** * Returns true if the objectPath exists and represents an external link * and false otherwise. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public boolean isExternalLink(final String objectPath); /** * Returns true if the objectPath exists and represents either a soft * link or an external link and false otherwise. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public boolean isSymbolicLink(final String objectPath); /** * Returns the target of the symbolic link that objectPath points to, or * null, if objectPath is not a symbolic link. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public String tryGetSymbolicLinkTarget(final String objectPath); // ///////////////////// // Attributes // ///////////////////// /** * Returns true, if the objectPath has an attribute with name * attributeName. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return true, if the attribute exists for the object. */ public boolean hasAttribute(final String objectPath, final String attributeName); /** * Returns the names of the attributes of the given objectPath. * * @param objectPath The name (including path information) of the object (data set or group) to * return the attributes for. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public List getAttributeNames(final String objectPath); /** * Returns the names of all attributes of the given objectPath. *

* This may include attributes that are used internally by the library and are not supposed to * be changed by application programmers. * * @param objectPath The name (including path information) of the object (data set or group) to * return the attributes for. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public List getAllAttributeNames(final String objectPath); /** * Returns the information about a data set as a {@link HDF5DataTypeInformation} object. * * @param objectPath The name (including path information) of the object that has the attribute * to return information about. * @param attributeName The name of the attribute to get information about. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public HDF5DataTypeInformation getAttributeInformation(final String objectPath, final String attributeName); /** * Returns the information about a data set as a {@link HDF5DataTypeInformation} object. * * @param objectPath The name (including path information) of the object that has the attribute * to return information about. * @param attributeName The name of the attribute to get information about. * @param dataTypeInfoOptions The options on which information to get about the member data * types. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public HDF5DataTypeInformation getAttributeInformation(final String objectPath, final String attributeName, final DataTypeInfoOptions dataTypeInfoOptions); /** * Returns the information about a data set as a {@link HDF5DataSetInformation} object. It is a * failure condition if the dataSetPath does not exist or does not identify a data * set. * * @param dataSetPath The name (including path information) of the data set to return * information about. * @param dataTypeInfoOptions The options on which information to get about the member data * types. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public HDF5DataSetInformation getDataSetInformation(final String dataSetPath, final DataTypeInfoOptions dataTypeInfoOptions); /** * Returns the total size (in bytes) of objectPath. It is a failure condition if the * dataSetPath does not exist or does not identify a data set. This method follows * symbolic links. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public long getSize(final String objectPath); /** * Returns the total number of elements of objectPath It is a failure condition if * the dataSetPath does not exist or does not identify a data set. This method * follows symbolic links. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public long getNumberOfElements(final String objectPath); /** * Copies the sourceObject to the destinationObject of the HDF5 file * represented by the destinationWriter. If destiantionObject ends with * "/", it will be considered a group and the name of sourceObject will be appended. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public void copy(String sourceObject, IHDF5Writer destinationWriter, String destinationObject); /** * Copies the sourceObject to the root group of the HDF5 file represented by the * destinationWriter. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public void copy(String sourceObject, IHDF5Writer destinationWriter); /** * Copies all objects of the file represented by this reader to the root group of the HDF5 file * represented by the destinationWriter. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public void copyAll(IHDF5Writer destinationWriter); // ///////////////////// // Group // ///////////////////// /** * Returns all members of groupPath, including internal groups that may be used by * the library to do house-keeping. The order is not well defined. * * @param groupPath The path of the group to get the members for. * @throws IllegalArgumentException If groupPath is not a group. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public List getAllGroupMembers(final String groupPath); /** * Returns the paths of the members of groupPath (including the parent). The order is * not well defined. * * @param groupPath The path of the group to get the member paths for. * @throws IllegalArgumentException If groupPath is not a group. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public List getGroupMemberPaths(final String groupPath); /** * Returns the link information about the members of groupPath. The order is * not well defined. * * @param groupPath The path of the group to get the members for. * @param readLinkTargets If true, for symbolic links the link targets will be * available via {@link HDF5LinkInformation#tryGetSymbolicLinkTarget()}. * @throws IllegalArgumentException If groupPath is not a group. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public List getGroupMemberInformation(final String groupPath, boolean readLinkTargets); /** * Returns the link information about all members of groupPath. The order is * not well defined. *

* This may include attributes that are used internally by the library and are not supposed to * be changed by application programmers. * * @param groupPath The path of the group to get the members for. * @param readLinkTargets If true, the link targets will be read for symbolic * links. * @throws IllegalArgumentException If groupPath is not a group. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public List getAllGroupMemberInformation(final String groupPath, boolean readLinkTargets); // ///////////////////// // Types // ///////////////////// /** * Returns the data type variant of objectPath, or null, if no type * variant is defined for this objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data type variant or null. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public HDF5DataTypeVariant tryGetTypeVariant(final String objectPath); /** * Returns the data type variant of attributeName of object objectPath, or * null, if no type variant is defined for this objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data type variant or null. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public HDF5DataTypeVariant tryGetTypeVariant(final String objectPath, String attributeName); /** * Returns the path of the data type of the data set objectPath, or null * , if this data set is not of a named data type. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public String tryGetDataTypePath(final String objectPath); /** * Returns the path of the data type, or null, if type is not * a named data type. * @deprecated Use the corresponding method in {@link IHDF5Reader#object()} instead. */ @Deprecated public String tryGetDataTypePath(HDF5DataType type); // ********************* // Opaque // ********************* /** * Returns the tag of the opaque data type associated with objectPath, or * null, if objectPath is not of an opaque data type (i.e. if * reader.getDataSetInformation(objectPath).getTypeInformation().getDataClass() != HDF5DataClass.OPAQUE * ). * * @param objectPath The name (including path information) of the data set object in the file. * @return The tag of the opaque data type, or null. * @deprecated Use the corresponding method in {@link IHDF5Reader#opaque()} instead. */ @Deprecated public String tryGetOpaqueTag(final String objectPath); /** * Returns the opaque data type or null, if objectPath is not of such a * data type. * * @param objectPath The name (including path information) of the data set object in the file. * @return The opaque data type, or null. * @deprecated Use the corresponding method in {@link IHDF5Reader#opaque()} instead. */ @Deprecated public HDF5OpaqueType tryGetOpaqueType(final String objectPath); /** * Gets the (unchanged) byte array values of an attribute attributeName of object * objectPath. * * @deprecated Use the corresponding method in {@link IHDF5Reader#opaque()} instead. */ @Deprecated public byte[] getAttributeAsByteArray(final String objectPath, final String attributeName); /** * Reads the data set objectPath as byte array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#opaque()} instead. */ @Deprecated public byte[] readAsByteArray(final String objectPath); /** * Reads a block from data set objectPath as byte array (of rank 1). * Must not be called for data sets of rank other than 1 and must not be called on Strings! * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size in numbers of elements (this will be the length of the * byte[] returned, divided by the size of one element). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @return The data block read from the data set. * @throws HDF5JavaException If the data set is not of rank 1 or is a String. * @deprecated Use the corresponding method in {@link IHDF5Reader#opaque()} instead. */ @Deprecated public byte[] readAsByteArrayBlock(final String objectPath, final int blockSize, final long blockNumber) throws HDF5JavaException; /** * Reads a block from data set objectPath as byte array (of rank 1). * Must not be called for data sets of rank other than 1 and must not be called on Strings! * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size in numbers of elements (this will be the length of the * byte[] returned, divided by the size of one element). * @param offset The offset of the block to read as number of elements (starting with 0). * @return The data block read from the data set. * @throws HDF5JavaException If the data set is not of rank 1. * @deprecated Use the corresponding method in {@link IHDF5Reader#opaque()} instead. */ @Deprecated public byte[] readAsByteArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset) throws HDF5JavaException; /** * Reads a block from data set objectPath as byte array (of rank 1) into * buffer. * Must not be called for data sets of rank other than 1 and must not be called on Strings! * * @param objectPath The name (including path information) of the data set object in the file. * @param buffer The buffer to read the values in. * @param blockSize The block size in numbers of elements (this will be the length of the * byte[] returned, divided by the size of one element). * @param offset The offset of the block in the data set as number of elements (zero-based). * @param memoryOffset The offset of the block in buffer as number of elements * (zero-based). * @return The effective block size. * @throws HDF5JavaException If the data set is not of rank 1. * @deprecated Use the corresponding method in {@link IHDF5Reader#opaque()} instead. */ @Deprecated public int readAsByteArrayToBlockWithOffset(final String objectPath, final byte[] buffer, final int blockSize, final long offset, final int memoryOffset) throws HDF5JavaException; /** * Provides all natural blocks of this one-dimensional data set to iterate over. * Must not be called for data sets of rank other than 1 and must not be called on Strings! * * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1. * @deprecated Use the corresponding method in {@link IHDF5Reader#opaque()} instead. */ @Deprecated public Iterable> getAsByteArrayNaturalBlocks(final String dataSetPath) throws HDF5JavaException; // ********************* // Boolean // ********************* /** * Reads a boolean attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. * @throws HDF5JavaException If the attribute is not a boolean type. * @deprecated Use the corresponding method in {@link IHDF5Reader#bool()}. */ @Deprecated public boolean getBooleanAttribute(final String objectPath, final String attributeName) throws HDF5JavaException; /** * Reads a Boolean value from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a boolean type. */ public boolean readBoolean(final String objectPath) throws HDF5JavaException; /** * Reads a bit field (which can be considered the equivalent to a boolean array of rank 1) from * the data set objectPath and returns it as a Java {@link BitSet}. *

* Note that the storage form of the bit array is a long[]. However, it is marked * in HDF5 to be interpreted bit-wise. Thus a data set written by * {@link IHDF5LongWriter#writeArray(String, long[])} cannot be read back by this method but * will throw a {@link HDF5DatatypeInterfaceException}. * * @param objectPath The name (including path information) of the data set object in the file. * @return The {@link BitSet} read from the data set. * @throws HDF5DatatypeInterfaceException If the objectPath is not of bit field type. */ public BitSet readBitField(final String objectPath) throws HDF5DatatypeInterfaceException; /** * Reads a block of a bit field (which can be considered the equivalent to a boolean array of * rank 1) from the data set objectPath and returns it as a Java {@link BitSet}. *

* Note that the storage form of the bit array is a long[]. However, it is marked * in HDF5 to be interpreted bit-wise. Thus a data set written by * {@link IHDF5LongWriter#writeArray(String, long[])} cannot be read back by this method but * will throw a {@link HDF5DatatypeInterfaceException}. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The size of the block (in 64 bit words) to read. * @param blockNumber The number of the block to read. * @return The {@link BitSet} read from the data set. * @throws HDF5DatatypeInterfaceException If the objectPath is not of bit field type. * @deprecated Use the corresponding method in {@link IHDF5Reader#bool()}. */ @Deprecated public BitSet readBitFieldBlock(final String objectPath, final int blockSize, final long blockNumber); /** * Reads a block of a bit field (which can be considered the equivalent to a boolean array of * rank 1) from the data set objectPath and returns it as a Java {@link BitSet}. *

* Note that the storage form of the bit array is a long[]. However, it is marked * in HDF5 to be interpreted bit-wise. Thus a data set written by * {@link IHDF5LongWriter#writeArray(String, long[])} cannot be read back by this method but * will throw a {@link HDF5DatatypeInterfaceException}. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The size of the block (in 64 bit words) to read. * @param offset The offset of the block (in 64 bit words) to start reading from. * @return The {@link BitSet} read from the data set. * @throws HDF5DatatypeInterfaceException If the objectPath is not of bit field type. * @deprecated Use the corresponding method in {@link IHDF5Reader#bool()}. */ @Deprecated public BitSet readBitFieldBlockWithOffset(final String objectPath, final int blockSize, final long offset); /** * Returns true if the bitIndex of the bit field dataset * objectPath is set, false otherwise. *

* Will also return false, if bitIndex is outside of the bitfield * dataset. * * @deprecated Use the corresponding method in {@link IHDF5Reader#bool()}. */ @Deprecated public boolean isBitSetInBitField(final String objectPath, final int bitIndex); // ********************* // Byte // ********************* // ///////////////////// // Attributes // ///////////////////// /** * Reads a byte attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int8()}. */ @Deprecated public byte getByteAttribute(final String objectPath, final String attributeName); /** * Reads a byte[] attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int8()}. */ @Deprecated public byte[] getByteArrayAttribute(final String objectPath, final String attributeName); /** * Reads a multi-dimensional array byte attribute named attributeName * from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute array value read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int8()}. */ @Deprecated public MDByteArray getByteMDArrayAttribute(final String objectPath, final String attributeName); /** * Reads a byte matrix attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute matrix value read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int8()}. */ @Deprecated public byte[][] getByteMatrixAttribute(final String objectPath, final String attributeName) throws HDF5JavaException; // ///////////////////// // Data Sets // ///////////////////// /** * Reads a byte value from the data set objectPath. This method doesn't * check the data space but simply reads the first value. * * @param objectPath The name (including path information) of the data set object in the file. * @return The value read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int8()}. */ @Deprecated public byte readByte(final String objectPath); /** * Reads a byte array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int8()}. */ @Deprecated public byte[] readByteArray(final String objectPath); /** * Reads a multi-dimensional byte array data set objectPath into a given * array in memory. * * @param objectPath The name (including path information) of the data set object in the file. * @param array The array to read the data into. * @param memoryOffset The offset in the array to write the data to. * @return The effective dimensions of the block in array that was filled. * @deprecated Use the corresponding method in {@link IHDF5Reader#int8()}. */ @Deprecated public int[] readToByteMDArrayWithOffset(final String objectPath, final MDByteArray array, final int[] memoryOffset); /** * Reads a block of the multi-dimensional byte array data set objectPath * into a given array in memory. * * @param objectPath The name (including path information) of the data set object in the file. * @param array The array to read the data into. * @param blockDimensions The size of the block to read along each axis. * @param offset The offset of the block in the data set. * @param memoryOffset The offset of the block in the array to write the data to. * @return The effective dimensions of the block in array that was filled. * @deprecated Use the corresponding method in {@link IHDF5Reader#int8()}. */ @Deprecated public int[] readToByteMDArrayBlockWithOffset(final String objectPath, final MDByteArray array, final int[] blockDimensions, final long[] offset, final int[] memoryOffset); /** * Reads a block from a byte array (of rank 1) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the byte[] returned * if the data set is long enough). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @return The data read from the data set. The length will be min(size - blockSize*blockNumber, * blockSize). * @deprecated Use the corresponding method in {@link IHDF5Reader#int8()}. */ @Deprecated public byte[] readByteArrayBlock(final String objectPath, final int blockSize, final long blockNumber); /** * Reads a block from byte array (of rank 1) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the byte[] * returned). * @param offset The offset of the block in the data set to start reading from (starting with * 0). * @return The data block read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int8()}. */ @Deprecated public byte[] readByteArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset); /** * Reads a byte matrix (array of arrays) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @throws HDF5JavaException If the data set objectPath is not of rank 2. * @deprecated Use the corresponding method in {@link IHDF5Reader#int8()}. */ @Deprecated public byte[][] readByteMatrix(final String objectPath) throws HDF5JavaException; /** * Reads a byte matrix (array of arrays) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSizeX The size of the block in the x dimension. * @param blockSizeY The size of the block in the y dimension. * @param blockNumberX The block number in the x dimension (offset: multiply with * blockSizeX). * @param blockNumberY The block number in the y dimension (offset: multiply with * blockSizeY). * @return The data block read from the data set. * @throws HDF5JavaException If the data set objectPath is not of rank 2. * @deprecated Use the corresponding method in {@link IHDF5Reader#int8()}. */ @Deprecated public byte[][] readByteMatrixBlock(final String objectPath, final int blockSizeX, final int blockSizeY, final long blockNumberX, final long blockNumberY) throws HDF5JavaException; /** * Reads a byte matrix (array of arrays) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSizeX The size of the block in the x dimension. * @param blockSizeY The size of the block in the y dimension. * @param offsetX The offset in x dimension in the data set to start reading from. * @param offsetY The offset in y dimension in the data set to start reading from. * @return The data block read from the data set. * @throws HDF5JavaException If the data set objectPath is not of rank 2. * @deprecated Use the corresponding method in {@link IHDF5Reader#int8()}. */ @Deprecated public byte[][] readByteMatrixBlockWithOffset(final String objectPath, final int blockSizeX, final int blockSizeY, final long offsetX, final long offsetY) throws HDF5JavaException; /** * Reads a multi-dimensional byte array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int8()}. */ @Deprecated public MDByteArray readByteMDArray(final String objectPath); /** * Reads a multi-dimensional byte array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @return The data block read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int8()}. */ @Deprecated public MDByteArray readByteMDArrayBlock(final String objectPath, final int[] blockDimensions, final long[] blockNumber); /** * Reads a multi-dimensional byte array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @return The data block read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int8()}. */ @Deprecated public MDByteArray readByteMDArrayBlockWithOffset(final String objectPath, final int[] blockDimensions, final long[] offset); /** * Provides all natural blocks of this one-dimensional data set to iterate over. * * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1. * @deprecated Use the corresponding method in {@link IHDF5Reader#int8()}. */ @Deprecated public Iterable> getByteArrayNaturalBlocks(final String dataSetPath) throws HDF5JavaException; /** * Provides all natural blocks of this multi-dimensional data set to iterate over. * * @see HDF5MDDataBlock * @deprecated Use the corresponding method in {@link IHDF5Reader#int8()}. */ @Deprecated public Iterable> getByteMDArrayNaturalBlocks( final String dataSetPath); // ********************* // Short // ********************* // ///////////////////// // Attributes // ///////////////////// /** * Reads a short attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int16()}. */ @Deprecated public short getShortAttribute(final String objectPath, final String attributeName); /** * Reads a short[] attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int16()}. */ @Deprecated public short[] getShortArrayAttribute(final String objectPath, final String attributeName); /** * Reads a multi-dimensional array short attribute named attributeName * from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute array value read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int16()}. */ @Deprecated public MDShortArray getShortMDArrayAttribute(final String objectPath, final String attributeName); /** * Reads a short matrix attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute matrix value read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int16()}. */ @Deprecated public short[][] getShortMatrixAttribute(final String objectPath, final String attributeName) throws HDF5JavaException; // ///////////////////// // Data Sets // ///////////////////// /** * Reads a short value from the data set objectPath. This method doesn't * check the data space but simply reads the first value. * * @param objectPath The name (including path information) of the data set object in the file. * @return The value read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int16()}. */ @Deprecated public short readShort(final String objectPath); /** * Reads a short array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int16()}. */ @Deprecated public short[] readShortArray(final String objectPath); /** * Reads a multi-dimensional short array data set objectPath into a * given array in memory. * * @param objectPath The name (including path information) of the data set object in the file. * @param array The array to read the data into. * @param memoryOffset The offset in the array to write the data to. * @return The effective dimensions of the block in array that was filled. * @deprecated Use the corresponding method in {@link IHDF5Reader#int16()}. */ @Deprecated public int[] readToShortMDArrayWithOffset(final String objectPath, final MDShortArray array, final int[] memoryOffset); /** * Reads a block of the multi-dimensional short array data set * objectPath into a given array in memory. * * @param objectPath The name (including path information) of the data set object in the file. * @param array The array to read the data into. * @param blockDimensions The size of the block to read along each axis. * @param offset The offset of the block in the data set. * @param memoryOffset The offset of the block in the array to write the data to. * @return The effective dimensions of the block in array that was filled. * @deprecated Use the corresponding method in {@link IHDF5Reader#int16()}. */ @Deprecated public int[] readToShortMDArrayBlockWithOffset(final String objectPath, final MDShortArray array, final int[] blockDimensions, final long[] offset, final int[] memoryOffset); /** * Reads a block from a short array (of rank 1) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the short[] returned * if the data set is long enough). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @return The data read from the data set. The length will be min(size - blockSize*blockNumber, * blockSize). * @deprecated Use the corresponding method in {@link IHDF5Reader#int16()}. */ @Deprecated public short[] readShortArrayBlock(final String objectPath, final int blockSize, final long blockNumber); /** * Reads a block from short array (of rank 1) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the short[] * returned). * @param offset The offset of the block in the data set to start reading from (starting with * 0). * @return The data block read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int16()}. */ @Deprecated public short[] readShortArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset); /** * Reads a short matrix (array of arrays) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @throws HDF5JavaException If the data set objectPath is not of rank 2. * @deprecated Use the corresponding method in {@link IHDF5Reader#int16()}. */ @Deprecated public short[][] readShortMatrix(final String objectPath) throws HDF5JavaException; /** * Reads a short matrix (array of arrays) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSizeX The size of the block in the x dimension. * @param blockSizeY The size of the block in the y dimension. * @param blockNumberX The block number in the x dimension (offset: multiply with * blockSizeX). * @param blockNumberY The block number in the y dimension (offset: multiply with * blockSizeY). * @return The data block read from the data set. * @throws HDF5JavaException If the data set objectPath is not of rank 2. * @deprecated Use the corresponding method in {@link IHDF5Reader#int16()}. */ @Deprecated public short[][] readShortMatrixBlock(final String objectPath, final int blockSizeX, final int blockSizeY, final long blockNumberX, final long blockNumberY) throws HDF5JavaException; /** * Reads a short matrix (array of arrays) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSizeX The size of the block in the x dimension. * @param blockSizeY The size of the block in the y dimension. * @param offsetX The offset in x dimension in the data set to start reading from. * @param offsetY The offset in y dimension in the data set to start reading from. * @return The data block read from the data set. * @throws HDF5JavaException If the data set objectPath is not of rank 2. * @deprecated Use the corresponding method in {@link IHDF5Reader#int16()}. */ @Deprecated public short[][] readShortMatrixBlockWithOffset(final String objectPath, final int blockSizeX, final int blockSizeY, final long offsetX, final long offsetY) throws HDF5JavaException; /** * Reads a multi-dimensional short array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int16()}. */ @Deprecated public MDShortArray readShortMDArray(final String objectPath); /** * Reads a multi-dimensional short array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @return The data block read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int16()}. */ @Deprecated public MDShortArray readShortMDArrayBlock(final String objectPath, final int[] blockDimensions, final long[] blockNumber); /** * Reads a multi-dimensional short array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @return The data block read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int16()}. */ @Deprecated public MDShortArray readShortMDArrayBlockWithOffset(final String objectPath, final int[] blockDimensions, final long[] offset); /** * Provides all natural blocks of this one-dimensional data set to iterate over. * * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1. * @deprecated Use the corresponding method in {@link IHDF5Reader#int16()}. */ @Deprecated public Iterable> getShortArrayNaturalBlocks(final String dataSetPath) throws HDF5JavaException; /** * Provides all natural blocks of this multi-dimensional data set to iterate over. * * @see HDF5MDDataBlock * @deprecated Use the corresponding method in {@link IHDF5Reader#int16()}. */ @Deprecated public Iterable> getShortMDArrayNaturalBlocks( final String dataSetPath); // ********************* // Int // ********************* // ///////////////////// // Attributes // ///////////////////// /** * Reads a int attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int32()}. */ @Deprecated public int getIntAttribute(final String objectPath, final String attributeName); /** * Reads a int[] attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int32()}. */ @Deprecated public int[] getIntArrayAttribute(final String objectPath, final String attributeName); /** * Reads a multi-dimensional array int attribute named attributeName * from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute array value read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int32()}. */ @Deprecated public MDIntArray getIntMDArrayAttribute(final String objectPath, final String attributeName); /** * Reads a int matrix attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute matrix value read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int32()}. */ @Deprecated public int[][] getIntMatrixAttribute(final String objectPath, final String attributeName) throws HDF5JavaException; // ///////////////////// // Data Sets // ///////////////////// /** * Reads a int value from the data set objectPath. This method doesn't * check the data space but simply reads the first value. * * @param objectPath The name (including path information) of the data set object in the file. * @return The value read from the data set. */ public int readInt(final String objectPath); /** * Reads a int array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. */ public int[] readIntArray(final String objectPath); /** * Reads a multi-dimensional int array data set objectPath into a given * array in memory. * * @param objectPath The name (including path information) of the data set object in the file. * @param array The array to read the data into. * @param memoryOffset The offset in the array to write the data to. * @return The effective dimensions of the block in array that was filled. * @deprecated Use the corresponding method in {@link IHDF5Reader#int32()}. */ @Deprecated public int[] readToIntMDArrayWithOffset(final String objectPath, final MDIntArray array, final int[] memoryOffset); /** * Reads a block of the multi-dimensional int array data set objectPath * into a given array in memory. * * @param objectPath The name (including path information) of the data set object in the file. * @param array The array to read the data into. * @param blockDimensions The size of the block to read along each axis. * @param offset The offset of the block in the data set. * @param memoryOffset The offset of the block in the array to write the data to. * @return The effective dimensions of the block in array that was filled. * @deprecated Use the corresponding method in {@link IHDF5Reader#int32()}. */ @Deprecated public int[] readToIntMDArrayBlockWithOffset(final String objectPath, final MDIntArray array, final int[] blockDimensions, final long[] offset, final int[] memoryOffset); /** * Reads a block from a int array (of rank 1) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the int[] returned * if the data set is long enough). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @return The data read from the data set. The length will be min(size - blockSize*blockNumber, * blockSize). * @deprecated Use the corresponding method in {@link IHDF5Reader#int32()}. */ @Deprecated public int[] readIntArrayBlock(final String objectPath, final int blockSize, final long blockNumber); /** * Reads a block from int array (of rank 1) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the int[] returned). * @param offset The offset of the block in the data set to start reading from (starting with * 0). * @return The data block read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int32()}. */ @Deprecated public int[] readIntArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset); /** * Reads a int matrix (array of arrays) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @throws HDF5JavaException If the data set objectPath is not of rank 2. */ public int[][] readIntMatrix(final String objectPath) throws HDF5JavaException; /** * Reads a int matrix (array of arrays) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSizeX The size of the block in the x dimension. * @param blockSizeY The size of the block in the y dimension. * @param blockNumberX The block number in the x dimension (offset: multiply with * blockSizeX). * @param blockNumberY The block number in the y dimension (offset: multiply with * blockSizeY). * @return The data block read from the data set. * @throws HDF5JavaException If the data set objectPath is not of rank 2. * @deprecated Use the corresponding method in {@link IHDF5Reader#int32()}. */ @Deprecated public int[][] readIntMatrixBlock(final String objectPath, final int blockSizeX, final int blockSizeY, final long blockNumberX, final long blockNumberY) throws HDF5JavaException; /** * Reads a int matrix (array of arrays) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSizeX The size of the block in the x dimension. * @param blockSizeY The size of the block in the y dimension. * @param offsetX The offset in x dimension in the data set to start reading from. * @param offsetY The offset in y dimension in the data set to start reading from. * @return The data block read from the data set. * @throws HDF5JavaException If the data set objectPath is not of rank 2. * @deprecated Use the corresponding method in {@link IHDF5Reader#int32()}. */ @Deprecated public int[][] readIntMatrixBlockWithOffset(final String objectPath, final int blockSizeX, final int blockSizeY, final long offsetX, final long offsetY) throws HDF5JavaException; /** * Reads a multi-dimensional int array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int32()}. */ @Deprecated public MDIntArray readIntMDArray(final String objectPath); /** * Reads a multi-dimensional int array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @return The data block read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int32()}. */ @Deprecated public MDIntArray readIntMDArrayBlock(final String objectPath, final int[] blockDimensions, final long[] blockNumber); /** * Reads a multi-dimensional int array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @return The data block read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int32()}. */ @Deprecated public MDIntArray readIntMDArrayBlockWithOffset(final String objectPath, final int[] blockDimensions, final long[] offset); /** * Provides all natural blocks of this one-dimensional data set to iterate over. * * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1. * @deprecated Use the corresponding method in {@link IHDF5Reader#int32()}. */ @Deprecated public Iterable> getIntArrayNaturalBlocks(final String dataSetPath) throws HDF5JavaException; /** * Provides all natural blocks of this multi-dimensional data set to iterate over. * * @see HDF5MDDataBlock * @deprecated Use the corresponding method in {@link IHDF5Reader#int32()}. */ @Deprecated public Iterable> getIntMDArrayNaturalBlocks(final String dataSetPath); // ********************* // Long // ********************* // ///////////////////// // Attributes // ///////////////////// /** * Reads a long attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int64()}. */ @Deprecated public long getLongAttribute(final String objectPath, final String attributeName); /** * Reads a long[] attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int64()}. */ @Deprecated public long[] getLongArrayAttribute(final String objectPath, final String attributeName); /** * Reads a multi-dimensional array long attribute named attributeName * from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute array value read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int64()}. */ @Deprecated public MDLongArray getLongMDArrayAttribute(final String objectPath, final String attributeName); /** * Reads a long matrix attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute matrix value read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int64()}. */ @Deprecated public long[][] getLongMatrixAttribute(final String objectPath, final String attributeName) throws HDF5JavaException; // ///////////////////// // Data Sets // ///////////////////// /** * Reads a long value from the data set objectPath. This method doesn't * check the data space but simply reads the first value. * * @param objectPath The name (including path information) of the data set object in the file. * @return The value read from the data set. */ public long readLong(final String objectPath); /** * Reads a long array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. */ public long[] readLongArray(final String objectPath); /** * Reads a multi-dimensional long array data set objectPath into a given * array in memory. * * @param objectPath The name (including path information) of the data set object in the file. * @param array The array to read the data into. * @param memoryOffset The offset in the array to write the data to. * @return The effective dimensions of the block in array that was filled. * @deprecated Use the corresponding method in {@link IHDF5Reader#int64()}. */ @Deprecated public int[] readToLongMDArrayWithOffset(final String objectPath, final MDLongArray array, final int[] memoryOffset); /** * Reads a block of the multi-dimensional long array data set objectPath * into a given array in memory. * * @param objectPath The name (including path information) of the data set object in the file. * @param array The array to read the data into. * @param blockDimensions The size of the block to read along each axis. * @param offset The offset of the block in the data set. * @param memoryOffset The offset of the block in the array to write the data to. * @return The effective dimensions of the block in array that was filled. * @deprecated Use the corresponding method in {@link IHDF5Reader#int64()}. */ @Deprecated public int[] readToLongMDArrayBlockWithOffset(final String objectPath, final MDLongArray array, final int[] blockDimensions, final long[] offset, final int[] memoryOffset); /** * Reads a block from a long array (of rank 1) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the long[] returned * if the data set is long enough). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @return The data read from the data set. The length will be min(size - blockSize*blockNumber, * blockSize). * @deprecated Use the corresponding method in {@link IHDF5Reader#int64()}. */ @Deprecated public long[] readLongArrayBlock(final String objectPath, final int blockSize, final long blockNumber); /** * Reads a block from long array (of rank 1) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the long[] * returned). * @param offset The offset of the block in the data set to start reading from (starting with * 0). * @return The data block read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int64()}. */ @Deprecated public long[] readLongArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset); /** * Reads a long matrix (array of arrays) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @throws HDF5JavaException If the data set objectPath is not of rank 2. */ public long[][] readLongMatrix(final String objectPath) throws HDF5JavaException; /** * Reads a long matrix (array of arrays) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSizeX The size of the block in the x dimension. * @param blockSizeY The size of the block in the y dimension. * @param blockNumberX The block number in the x dimension (offset: multiply with * blockSizeX). * @param blockNumberY The block number in the y dimension (offset: multiply with * blockSizeY). * @return The data block read from the data set. * @throws HDF5JavaException If the data set objectPath is not of rank 2. * @deprecated Use the corresponding method in {@link IHDF5Reader#int64()}. */ @Deprecated public long[][] readLongMatrixBlock(final String objectPath, final int blockSizeX, final int blockSizeY, final long blockNumberX, final long blockNumberY) throws HDF5JavaException; /** * Reads a long matrix (array of arrays) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSizeX The size of the block in the x dimension. * @param blockSizeY The size of the block in the y dimension. * @param offsetX The offset in x dimension in the data set to start reading from. * @param offsetY The offset in y dimension in the data set to start reading from. * @return The data block read from the data set. * @throws HDF5JavaException If the data set objectPath is not of rank 2. * @deprecated Use the corresponding method in {@link IHDF5Reader#int64()}. */ @Deprecated public long[][] readLongMatrixBlockWithOffset(final String objectPath, final int blockSizeX, final int blockSizeY, final long offsetX, final long offsetY) throws HDF5JavaException; /** * Reads a multi-dimensional long array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int64()}. */ @Deprecated public MDLongArray readLongMDArray(final String objectPath); /** * Reads a multi-dimensional long array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @return The data block read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int64()}. */ @Deprecated public MDLongArray readLongMDArrayBlock(final String objectPath, final int[] blockDimensions, final long[] blockNumber); /** * Reads a multi-dimensional long array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @return The data block read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#int64()}. */ @Deprecated public MDLongArray readLongMDArrayBlockWithOffset(final String objectPath, final int[] blockDimensions, final long[] offset); /** * Provides all natural blocks of this one-dimensional data set to iterate over. * * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1. * @deprecated Use the corresponding method in {@link IHDF5Reader#int64()}. */ @Deprecated public Iterable> getLongArrayNaturalBlocks(final String dataSetPath) throws HDF5JavaException; /** * Provides all natural blocks of this multi-dimensional data set to iterate over. * * @see HDF5MDDataBlock * @deprecated Use the corresponding method in {@link IHDF5Reader#int64()}. */ @Deprecated public Iterable> getLongMDArrayNaturalBlocks( final String dataSetPath); // ********************* // Float // ********************* // ///////////////////// // Attributes // ///////////////////// /** * Reads a float attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#float32()}. */ @Deprecated public float getFloatAttribute(final String objectPath, final String attributeName); /** * Reads a float[] attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#float32()}. */ @Deprecated public float[] getFloatArrayAttribute(final String objectPath, final String attributeName); /** * Reads a multi-dimensional array float attribute named attributeName * from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute array value read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#float32()}. */ @Deprecated public MDFloatArray getFloatMDArrayAttribute(final String objectPath, final String attributeName); /** * Reads a float matrix attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute matrix value read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#float32()}. */ @Deprecated public float[][] getFloatMatrixAttribute(final String objectPath, final String attributeName) throws HDF5JavaException; // ///////////////////// // Data Sets // ///////////////////// /** * Reads a float value from the data set objectPath. This method doesn't * check the data space but simply reads the first value. * * @param objectPath The name (including path information) of the data set object in the file. * @return The value read from the data set. */ public float readFloat(final String objectPath); /** * Reads a float array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. */ public float[] readFloatArray(final String objectPath); /** * Reads a multi-dimensional float array data set objectPath into a * given array in memory. * * @param objectPath The name (including path information) of the data set object in the file. * @param array The array to read the data into. * @param memoryOffset The offset in the array to write the data to. * @return The effective dimensions of the block in array that was filled. * @deprecated Use the corresponding method in {@link IHDF5Reader#float32()}. */ @Deprecated public int[] readToFloatMDArrayWithOffset(final String objectPath, final MDFloatArray array, final int[] memoryOffset); /** * Reads a block of the multi-dimensional float array data set * objectPath into a given array in memory. * * @param objectPath The name (including path information) of the data set object in the file. * @param array The array to read the data into. * @param blockDimensions The size of the block to read along each axis. * @param offset The offset of the block in the data set. * @param memoryOffset The offset of the block in the array to write the data to. * @return The effective dimensions of the block in array that was filled. * @deprecated Use the corresponding method in {@link IHDF5Reader#float32()}. */ @Deprecated public int[] readToFloatMDArrayBlockWithOffset(final String objectPath, final MDFloatArray array, final int[] blockDimensions, final long[] offset, final int[] memoryOffset); /** * Reads a block from a float array (of rank 1) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the float[] returned * if the data set is long enough). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @return The data read from the data set. The length will be min(size - blockSize*blockNumber, * blockSize). * @deprecated Use the corresponding method in {@link IHDF5Reader#float32()}. */ @Deprecated public float[] readFloatArrayBlock(final String objectPath, final int blockSize, final long blockNumber); /** * Reads a block from float array (of rank 1) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the float[] * returned). * @param offset The offset of the block in the data set to start reading from (starting with * 0). * @return The data block read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#float32()}. */ @Deprecated public float[] readFloatArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset); /** * Reads a float matrix (array of arrays) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @throws HDF5JavaException If the data set objectPath is not of rank 2. */ public float[][] readFloatMatrix(final String objectPath) throws HDF5JavaException; /** * Reads a float matrix (array of arrays) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSizeX The size of the block in the x dimension. * @param blockSizeY The size of the block in the y dimension. * @param blockNumberX The block number in the x dimension (offset: multiply with * blockSizeX). * @param blockNumberY The block number in the y dimension (offset: multiply with * blockSizeY). * @return The data block read from the data set. * @throws HDF5JavaException If the data set objectPath is not of rank 2. * @deprecated Use the corresponding method in {@link IHDF5Reader#float32()}. */ @Deprecated public float[][] readFloatMatrixBlock(final String objectPath, final int blockSizeX, final int blockSizeY, final long blockNumberX, final long blockNumberY) throws HDF5JavaException; /** * Reads a float matrix (array of arrays) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSizeX The size of the block in the x dimension. * @param blockSizeY The size of the block in the y dimension. * @param offsetX The offset in x dimension in the data set to start reading from. * @param offsetY The offset in y dimension in the data set to start reading from. * @return The data block read from the data set. * @throws HDF5JavaException If the data set objectPath is not of rank 2. * @deprecated Use the corresponding method in {@link IHDF5Reader#float32()}. */ @Deprecated public float[][] readFloatMatrixBlockWithOffset(final String objectPath, final int blockSizeX, final int blockSizeY, final long offsetX, final long offsetY) throws HDF5JavaException; /** * Reads a multi-dimensional float array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#float32()}. */ @Deprecated public MDFloatArray readFloatMDArray(final String objectPath); /** * Reads a multi-dimensional float array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @return The data block read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#float32()}. */ @Deprecated public MDFloatArray readFloatMDArrayBlock(final String objectPath, final int[] blockDimensions, final long[] blockNumber); /** * Reads a multi-dimensional float array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @return The data block read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#float32()}. */ @Deprecated public MDFloatArray readFloatMDArrayBlockWithOffset(final String objectPath, final int[] blockDimensions, final long[] offset); /** * Provides all natural blocks of this one-dimensional data set to iterate over. * * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1. * @deprecated Use the corresponding method in {@link IHDF5Reader#float32()}. */ @Deprecated public Iterable> getFloatArrayNaturalBlocks(final String dataSetPath) throws HDF5JavaException; /** * Provides all natural blocks of this multi-dimensional data set to iterate over. * * @see HDF5MDDataBlock * @deprecated Use the corresponding method in {@link IHDF5Reader#float32()}. */ @Deprecated public Iterable> getFloatMDArrayNaturalBlocks( final String dataSetPath); // ********************* // Double // ********************* // ///////////////////// // Attributes // ///////////////////// /** * Reads a double attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#float64()}. */ @Deprecated public double getDoubleAttribute(final String objectPath, final String attributeName); /** * Reads a double[] attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#float64()}. */ @Deprecated public double[] getDoubleArrayAttribute(final String objectPath, final String attributeName); /** * Reads a multi-dimensional array double attribute named attributeName * from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute array value read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#float64()}. */ @Deprecated public MDDoubleArray getDoubleMDArrayAttribute(final String objectPath, final String attributeName); /** * Reads a double matrix attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute matrix value read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#float64()}. */ @Deprecated public double[][] getDoubleMatrixAttribute(final String objectPath, final String attributeName) throws HDF5JavaException; // ///////////////////// // Data Sets // ///////////////////// /** * Reads a double value from the data set objectPath. This method * doesn't check the data space but simply reads the first value. * * @param objectPath The name (including path information) of the data set object in the file. * @return The value read from the data set. */ public double readDouble(final String objectPath); /** * Reads a double array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. */ public double[] readDoubleArray(final String objectPath); /** * Reads a multi-dimensional double array data set objectPath into a * given array in memory. * * @param objectPath The name (including path information) of the data set object in the file. * @param array The array to read the data into. * @param memoryOffset The offset in the array to write the data to. * @return The effective dimensions of the block in array that was filled. * @deprecated Use the corresponding method in {@link IHDF5Reader#float64()}. */ @Deprecated public int[] readToDoubleMDArrayWithOffset(final String objectPath, final MDDoubleArray array, final int[] memoryOffset); /** * Reads a block of the multi-dimensional double array data set * objectPath into a given array in memory. * * @param objectPath The name (including path information) of the data set object in the file. * @param array The array to read the data into. * @param blockDimensions The size of the block to read along each axis. * @param offset The offset of the block in the data set. * @param memoryOffset The offset of the block in the array to write the data to. * @return The effective dimensions of the block in array that was filled. * @deprecated Use the corresponding method in {@link IHDF5Reader#float64()}. */ @Deprecated public int[] readToDoubleMDArrayBlockWithOffset(final String objectPath, final MDDoubleArray array, final int[] blockDimensions, final long[] offset, final int[] memoryOffset); /** * Reads a block from a double array (of rank 1) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the double[] * returned if the data set is long enough). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @return The data read from the data set. The length will be min(size - blockSize*blockNumber, * blockSize). * @deprecated Use the corresponding method in {@link IHDF5Reader#float64()}. */ @Deprecated public double[] readDoubleArrayBlock(final String objectPath, final int blockSize, final long blockNumber); /** * Reads a block from double array (of rank 1) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the double[] * returned). * @param offset The offset of the block in the data set to start reading from (starting with * 0). * @return The data block read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#float64()}. */ @Deprecated public double[] readDoubleArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset); /** * Reads a double matrix (array of arrays) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @throws HDF5JavaException If the data set objectPath is not of rank 2. */ public double[][] readDoubleMatrix(final String objectPath) throws HDF5JavaException; /** * Reads a double matrix (array of arrays) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSizeX The size of the block in the x dimension. * @param blockSizeY The size of the block in the y dimension. * @param blockNumberX The block number in the x dimension (offset: multiply with * blockSizeX). * @param blockNumberY The block number in the y dimension (offset: multiply with * blockSizeY). * @return The data block read from the data set. * @throws HDF5JavaException If the data set objectPath is not of rank 2. * @deprecated Use the corresponding method in {@link IHDF5Reader#float64()}. */ @Deprecated public double[][] readDoubleMatrixBlock(final String objectPath, final int blockSizeX, final int blockSizeY, final long blockNumberX, final long blockNumberY) throws HDF5JavaException; /** * Reads a double matrix (array of arrays) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSizeX The size of the block in the x dimension. * @param blockSizeY The size of the block in the y dimension. * @param offsetX The offset in x dimension in the data set to start reading from. * @param offsetY The offset in y dimension in the data set to start reading from. * @return The data block read from the data set. * @throws HDF5JavaException If the data set objectPath is not of rank 2. * @deprecated Use the corresponding method in {@link IHDF5Reader#float64()}. */ @Deprecated public double[][] readDoubleMatrixBlockWithOffset(final String objectPath, final int blockSizeX, final int blockSizeY, final long offsetX, final long offsetY) throws HDF5JavaException; /** * Reads a multi-dimensional double array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#float64()}. */ @Deprecated public MDDoubleArray readDoubleMDArray(final String objectPath); /** * Reads a multi-dimensional double array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @return The data block read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#float64()}. */ @Deprecated public MDDoubleArray readDoubleMDArrayBlock(final String objectPath, final int[] blockDimensions, final long[] blockNumber); /** * Reads a multi-dimensional double array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @return The data block read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#float64()}. */ @Deprecated public MDDoubleArray readDoubleMDArrayBlockWithOffset(final String objectPath, final int[] blockDimensions, final long[] offset); /** * Provides all natural blocks of this one-dimensional data set to iterate over. * * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1. * @deprecated Use the corresponding method in {@link IHDF5Reader#float64()}. */ @Deprecated public Iterable> getDoubleArrayNaturalBlocks(final String dataSetPath) throws HDF5JavaException; /** * Provides all natural blocks of this multi-dimensional data set to iterate over. * * @see HDF5MDDataBlock * @deprecated Use the corresponding method in {@link IHDF5Reader#float64()}. */ @Deprecated public Iterable> getDoubleMDArrayNaturalBlocks( final String dataSetPath); // ********************* // String // ********************* // ///////////////////// // Attributes // ///////////////////// /** * Reads a string attribute named attributeName from the object * objectPath. Considers '\0' as end of string. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#string()} instead. */ @Deprecated public String getStringAttribute(final String objectPath, final String attributeName); /** * Reads a string array attribute named attributeName from the object * objectPath. Considers '\0' as end of string. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#string()} instead. */ @Deprecated public String[] getStringArrayAttribute(final String objectPath, final String attributeName); /** * Reads a multi-dimensional string array attribute named attributeName from the * object objectPath. Considers '\0' as end of string. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#string()} instead. */ @Deprecated public MDArray getStringMDArrayAttribute(final String objectPath, final String attributeName); // ///////////////////// // Data Sets // ///////////////////// /** * Reads a string from the data set objectPath. Considers '\0' as end of string. This * needs to be a string type. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a string type. */ public String readString(final String objectPath) throws HDF5JavaException; /** * Reads a string array (of rank 1) from the data set objectPath. The elements of * this data set need to be a string type. Considers '\0' as end of string. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a string type. */ public String[] readStringArray(final String objectPath) throws HDF5JavaException; /** * Reads a block of a string array (of rank 1) from the data set objectPath. The * elements of this data set need to be a string type. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The size of the block to read from the data set. * @param blockNumber The number of the block to read from the data set (the offset is * blockSize * blockNumber). * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a string type. * @deprecated Use the corresponding method in {@link IHDF5Reader#string()} instead. */ @Deprecated public String[] readStringArrayBlock(final String objectPath, final int blockSize, final long blockNumber); /** * Reads a block of a string array (of rank 1) from the data set objectPath. The * elements of this data set need to be a string type. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The size of the block to read from the data set. * @param offset The offset of the block in the data set. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a string type. * @deprecated Use the corresponding method in {@link IHDF5Reader#string()} instead. */ @Deprecated public String[] readStringArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset); /** * Reads a string array (of rank N) from the data set objectPath. The elements of * this data set need to be a string type. Considers '\0' as end of string. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a string type. * @deprecated Use the corresponding method in {@link IHDF5Reader#string()} instead. */ @Deprecated public MDArray readStringMDArray(final String objectPath); /** * Reads a block of a string array (of rank N) from the data set objectPath. The * elements of this data set need to be a string type. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The dimensions (along each axis) of the block to read from the data * set. * @param blockNumber The number of the block to read from the data set (the offset in each * dimension i is blockSize[i] * blockNumber[i]). * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a string type. * @deprecated Use the corresponding method in {@link IHDF5Reader#string()} instead. */ @Deprecated public MDArray readStringMDArrayBlock(final String objectPath, final int[] blockDimensions, final long[] blockNumber); /** * Reads a block of a string array (of rank N) from the data set objectPath. The * elements of this data set need to be a string type. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The dimensions (along each axis) of the block to read from the data * set. * @param offset The offset of the block in the data set. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a string type. * @deprecated Use the corresponding method in {@link IHDF5Reader#string()} instead. */ @Deprecated public MDArray readStringMDArrayBlockWithOffset(final String objectPath, final int[] blockDimensions, final long[] offset); /** * Provides all natural blocks of this one-dimensional string data set to iterate over. * * @param objectPath The name (including path information) of the data set object in the file. * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1. * @deprecated Use the corresponding method in {@link IHDF5Reader#string()} instead. */ @Deprecated public Iterable> getStringArrayNaturalBlocks(final String objectPath) throws HDF5JavaException; /** * Provides all natural blocks of this multi-dimensional string data set to iterate over. * * @see HDF5MDDataBlock * @deprecated Use the corresponding method in {@link IHDF5Reader#string()} instead. */ @Deprecated public Iterable>> getStringMDArrayNaturalBlocks( final String objectPath); // ********************* // Date & Time // ********************* // ///////////////////// // Attributes // ///////////////////// /** * Returns true, if the attribute attributeName of data set * objectPath is a time stamp and false otherwise. * * @deprecated Use the corresponding method in {@link IHDF5Reader#time()} instead. */ @Deprecated public boolean isTimeStamp(final String objectPath, String attributeName) throws HDF5JavaException; /** * Reads a time stamp attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The time stamp as number of milliseconds since January 1, 1970, 00:00:00 GMT. * @throws HDF5JavaException If the attribute attributeName of objct * objectPath is not defined as type variant * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. * @deprecated Use the corresponding method in {@link IHDF5Reader#time()} instead. */ @Deprecated public long getTimeStampAttribute(final String objectPath, final String attributeName); /** * Reads a time stamp array attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The time stamp array; each element is a number of milliseconds since January 1, 1970, * 00:00:00 GMT. * @throws HDF5JavaException If the attribute attributeName of objct * objectPath is not defined as type variant * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. * @deprecated Use the corresponding method in {@link IHDF5Reader#time()} instead. */ @Deprecated public long[] getTimeStampArrayAttribute(final String objectPath, final String attributeName); /** * Reads a time stamp attribute named attributeName from the data set * objectPath and returns it as a Date. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The time stamp as number of milliseconds since January 1, 1970, 00:00:00 GMT. * @throws HDF5JavaException If the attribute attributeName of objct * objectPath is not defined as type variant * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. * @deprecated Use the corresponding method in {@link IHDF5Reader#time()} instead. */ @Deprecated public Date getDateAttribute(final String objectPath, final String attributeName); /** * Reads a time stamp array attribute named attributeName from the data set * objectPath and returns it as a Date[]. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The time stamp as number of milliseconds since January 1, 1970, 00:00:00 GMT. * @throws HDF5JavaException If the attribute attributeName of objct * objectPath is not defined as type variant * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. * @deprecated Use the corresponding method in {@link IHDF5Reader#time()} instead. */ @Deprecated public Date[] getDateArrayAttribute(final String objectPath, final String attributeName); /** * Returns true, if the attribute attributeName of data set * objectPath is a time duration and false otherwise. * * @deprecated Use the corresponding method in {@link IHDF5Reader#duration()} instead. */ @Deprecated public boolean isTimeDuration(final String objectPath, String attributeName) throws HDF5JavaException; /** * Reads a time duration attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The time duration. * @throws HDF5JavaException If the objectPath is not tagged as a type variant that * corresponds to a time duration. * @deprecated Use the corresponding method in {@link IHDF5Reader#duration()} instead. */ @Deprecated public HDF5TimeDuration getTimeDurationAttribute(final String objectPath, final String attributeName); /** * Reads a time duration array attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The time duration. * @throws HDF5JavaException If the objectPath is not tagged as a type variant that * corresponds to a time duration. * @deprecated Use the corresponding method in {@link IHDF5Reader#duration()} instead. */ @Deprecated public HDF5TimeDurationArray getTimeDurationArrayAttribute(final String objectPath, final String attributeName); /** * Returns the time unit, if the attribute given by attributeName of object * objectPath is a time duration and null otherwise. * * @deprecated Use the corresponding method in {@link IHDF5Reader#duration()} instead. */ @Deprecated public HDF5TimeUnit tryGetTimeUnit(final String objectPath, final String attributeName) throws HDF5JavaException; // ///////////////////// // Data Sets // ///////////////////// /** * Returns true, if the data set given by objectPath is a time stamp and * false otherwise. * * @deprecated Use the corresponding method in {@link IHDF5Reader#time()} instead. */ @Deprecated public boolean isTimeStamp(final String objectPath) throws HDF5JavaException; /** * Returns true, if the data set given by objectPath is a time duration * and false otherwise. * * @deprecated Use the corresponding method in {@link IHDF5Reader#duration()} instead. */ @Deprecated public boolean isTimeDuration(final String objectPath) throws HDF5JavaException; /** * Returns the time unit, if the data set given by objectPath is a time duration and * null otherwise. * * @deprecated Use the corresponding method in {@link IHDF5Reader#duration()} instead. */ @Deprecated public HDF5TimeUnit tryGetTimeUnit(final String objectPath) throws HDF5JavaException; /** * Reads a time stamp value from the data set objectPath. The time stamp is stored as * a long value in the HDF5 file. It needs to be tagged as type variant * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. * * @param objectPath The name (including path information) of the data set object in the file. * @return The time stamp as number of milliseconds since January 1, 1970, 00:00:00 GMT. * @throws HDF5JavaException If the objectPath is not defined as type variant * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. * @deprecated Use the corresponding method in {@link IHDF5Reader#time()} instead. */ @Deprecated public long readTimeStamp(final String objectPath) throws HDF5JavaException; /** * Reads a time stamp array from the data set objectPath. The time stamp is stored as * a long value in the HDF5 file. It needs to be tagged as type variant * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. * * @param objectPath The name (including path information) of the data set object in the file. * @return The time stamp as number of milliseconds since January 1, 1970, 00:00:00 GMT. * @throws HDF5JavaException If the objectPath is not defined as type variant * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. * @deprecated Use the corresponding method in {@link IHDF5Reader#time()} instead. */ @Deprecated public long[] readTimeStampArray(final String objectPath) throws HDF5JavaException; /** * Reads a block of a time stamp array (of rank 1) from the data set objectPath. The * time stamp is stored as a long value in the HDF5 file. It needs to be tagged as * type variant {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the long[] returned * if the data set is long enough). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @return The data read from the data set. The length will be min(size - blockSize*blockNumber, * blockSize). * @deprecated Use the corresponding method in {@link IHDF5Reader#time()} instead. */ @Deprecated public long[] readTimeStampArrayBlock(final String objectPath, final int blockSize, final long blockNumber); /** * Reads a block of a time stamp array (of rank 1) from the data set objectPath. The * time stamp is stored as a long value in the HDF5 file. It needs to be tagged as * type variant {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the long[] * returned). * @param offset The offset of the block in the data set to start reading from (starting with * 0). * @return The data block read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#time()} instead. */ @Deprecated public long[] readTimeStampArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset); /** * Provides all natural blocks of this one-dimensional data set of time stamps to iterate over. * * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1. * @deprecated Use the corresponding method in {@link IHDF5Reader#time()} instead. */ @Deprecated public Iterable> getTimeStampArrayNaturalBlocks(final String dataSetPath) throws HDF5JavaException; /** * Reads a time stamp value from the data set objectPath and returns it as a * {@link Date}. The time stamp is stored as a long value in the HDF5 file. It * needs to be tagged as type variant * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. * * @param objectPath The name (including path information) of the data set object in the file. * @return The time stamp as {@link Date}. * @throws HDF5JavaException If the objectPath does not denote a time stamp. */ public Date readDate(final String objectPath) throws HDF5JavaException; /** * Reads a time stamp array (of rank 1) from the data set objectPath and returns it * as an array of {@link Date}s. The time stamp array is stored as a an array of * long values in the HDF5 file. It needs to be tagged as type variant * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. * * @param objectPath The name (including path information) of the data set object in the file. * @return The time stamp as {@link Date}. * @throws HDF5JavaException If the objectPath does not denote a time stamp. */ public Date[] readDateArray(final String objectPath) throws HDF5JavaException; /** * Reads a time duration value and its unit from the data set objectPath. It needs to * be tagged as one of the type variants that indicate a time duration, for example * {@link HDF5DataTypeVariant#TIME_DURATION_SECONDS}. *

* This tagging is done by the writer when using * {@link IHDF5Writer#writeTimeDuration(String, HDF5TimeDuration)} or can be done by calling * {@link IHDF5Writer#setTypeVariant(String, HDF5DataTypeVariant)}. * * @param objectPath The name (including path information) of the data set object in the file. * @return The time duration and its unit. * @throws HDF5JavaException If the objectPath is not tagged as a type variant that * corresponds to a time duration. */ public HDF5TimeDuration readTimeDuration(final String objectPath) throws HDF5JavaException; /** * Reads a time duration value and its unit from the data set objectPath, converts it * to the given timeUnit and returns it as long. It needs to be tagged * as one of the type variants that indicate a time duration, for example * {@link HDF5DataTypeVariant#TIME_DURATION_SECONDS}. *

* This tagging is done by the writer when using * {@link IHDF5Writer#writeTimeDuration(String, long, HDF5TimeUnit)} or can be done by calling * {@link IHDF5Writer#setTypeVariant(String, HDF5DataTypeVariant)}, most conveniantly by code * like * * 

     * writer.addTypeVariant("/dataSetPath", HDF5TimeUnit.SECONDS.getTypeVariant());
     *
* * @param objectPath The name (including path information) of the data set object in the file. * @return The time duration and its unit. * @throws HDF5JavaException If the objectPath is not tagged as a type variant that * corresponds to a time duration. * @deprecated Use {@link IHDF5TimeDurationReader#read(String)} instead. */ @Deprecated public HDF5TimeDuration readTimeDurationAndUnit(final String objectPath) throws HDF5JavaException; /** * Reads a time duration value from the data set objectPath, converts it to the given * timeUnit and returns it as long. It needs to be tagged as one of the * type variants that indicate a time duration, for example * {@link HDF5DataTypeVariant#TIME_DURATION_SECONDS}. *

* This tagging is done by the writer when using * {@link IHDF5Writer#writeTimeDuration(String, long, HDF5TimeUnit)} or can be done by calling * {@link IHDF5Writer#setTypeVariant(String, HDF5DataTypeVariant)}, most conveniantly by code * like * * 

     * writer.addTypeVariant("/dataSetPath", HDF5TimeUnit.SECONDS.getTypeVariant());
     *
* * @param objectPath The name (including path information) of the data set object in the file. * @param timeUnit The time unit that the duration should be converted to. * @return The time duration in the given unit. * @throws HDF5JavaException If the objectPath is not tagged as a type variant that * corresponds to a time duration. * @deprecated Use {@link IHDF5TimeDurationReader#read(String)} and * {@link HDF5TimeUnit#convert(HDF5TimeDuration)} instead. */ @Deprecated public long readTimeDuration(final String objectPath, final HDF5TimeUnit timeUnit) throws HDF5JavaException; /** * Reads a time duration array from the data set objectPath. It needs to be tagged as * one of the type variants that indicate a time duration, for example * {@link HDF5DataTypeVariant#TIME_DURATION_SECONDS}. *

* See {@link #readTimeDuration(String, HDF5TimeUnit)} for how the tagging is done. * * @param objectPath The name (including path information) of the data set object in the file. * @return The time duration in seconds. * @throws HDF5JavaException If the objectPath is not tagged as a type variant that * corresponds to a time duration. */ public HDF5TimeDurationArray readTimeDurationArray(final String objectPath) throws HDF5JavaException; /** * Reads a time duration array from the data set objectPathand returns it as a * HDF5TimeDuration[]. It needs to be tagged as one of the type variants that * indicate a time duration, for example {@link HDF5DataTypeVariant#TIME_DURATION_SECONDS}. *

* See {@link #readTimeDuration(String, HDF5TimeUnit)} for how the tagging is done. * * @param objectPath The name (including path information) of the data set object in the file. * @return The time durations in their respective time unit. * @throws HDF5JavaException If the objectPath is not tagged as a type variant that * corresponds to a time duration. * @see #readTimeDurationArray(String, HDF5TimeUnit) * @deprecated Use {@link IHDF5TimeDurationReader#readArray(String)} instead. */ @Deprecated public HDF5TimeDuration[] readTimeDurationAndUnitArray(final String objectPath) throws HDF5JavaException; /** * Reads a time duration array from the data set objectPath, converts it to the given * timeUnit and returns it as a long[] array. It needs to be tagged as * one of the type variants that indicate a time duration, for example * {@link HDF5DataTypeVariant#TIME_DURATION_SECONDS}. *

* See {@link #readTimeDuration(String, HDF5TimeUnit)} for how the tagging is done. * * @param objectPath The name (including path information) of the data set object in the file. * @param timeUnit The time unit that the duration should be converted to. * @return The time duration in the given unit. * @throws HDF5JavaException If the objectPath is not tagged as a type variant that * corresponds to a time duration. * @deprecated Use {@link IHDF5TimeDurationReader#readArray(String)} and * {@link HDF5TimeUnit#convert(HDF5TimeDurationArray)} instead. */ @Deprecated public long[] readTimeDurationArray(final String objectPath, final HDF5TimeUnit timeUnit) throws HDF5JavaException; /** * Reads a block of a time duration array (of rank 1) from the data set objectPath. * It needs to be tagged as one of the type variants that indicate a time duration, for example * {@link HDF5DataTypeVariant#TIME_DURATION_SECONDS}. *

* See {@link #readTimeDuration(String, HDF5TimeUnit)} for how the tagging is done. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the long[] returned * if the data set is long enough). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @return The data read from the data set. The length will be * min(size - blockSize*blockNumber, * blockSize). * @throws HDF5JavaException If the objectPath is not tagged as a type variant that * corresponds to a time duration. * @deprecated Use the corresponding method in {@link IHDF5Reader#duration()} instead. */ @Deprecated public HDF5TimeDurationArray readTimeDurationArrayBlock(final String objectPath, final int blockSize, final long blockNumber) throws HDF5JavaException; /** * Reads a block of a time duration array (of rank 1) from the data set objectPath. * The time durations are stored as a long[] value in the HDF5 file. It needs to be * tagged as one of the type variants that indicate a time duration, for example * {@link HDF5DataTypeVariant#TIME_DURATION_SECONDS}. *

* See {@link #readTimeDuration(String, HDF5TimeUnit)} for how the tagging is done. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the long[] returned * if the data set is long enough). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @param timeUnit The time unit that the duration should be converted to. * @return The data read from the data set. The length will be * min(size - blockSize*blockNumber, * blockSize). * @throws HDF5JavaException If the objectPath is not tagged as a type variant that * corresponds to a time duration. * @deprecated Use {@link IHDF5TimeDurationReader#readArrayBlock(String, int, long)} and * {@link HDF5TimeUnit#convert(long[], HDF5TimeUnit)} instead. */ @Deprecated public long[] readTimeDurationArrayBlock(final String objectPath, final int blockSize, final long blockNumber, final HDF5TimeUnit timeUnit) throws HDF5JavaException; /** * Reads a block of a time duration array (of rank 1) from the data set objectPath. * It needs to be tagged as one of the type variants that indicate a time duration, for example * {@link HDF5DataTypeVariant#TIME_DURATION_SECONDS}. *

* See {@link #readTimeDuration(String, HDF5TimeUnit)} for how the tagging is done. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the long[] * returned). * @param offset The offset of the block in the data set to start reading from (starting with * 0). * @return The data block read from the data set. * @throws HDF5JavaException If the objectPath is not tagged as a type variant that * corresponds to a time duration. * @deprecated Use the corresponding method in {@link IHDF5Reader#duration()} instead. */ @Deprecated public HDF5TimeDurationArray readTimeDurationArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset) throws HDF5JavaException; /** * Reads a block of a time duration array (of rank 1) from the data set objectPath. * The time durations are stored as a long[] value in the HDF5 file. It needs to be * tagged as one of the type variants that indicate a time duration, for example * {@link HDF5DataTypeVariant#TIME_DURATION_SECONDS}. *

* See {@link #readTimeDuration(String, HDF5TimeUnit)} for how the tagging is done. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the long[] * returned). * @param offset The offset of the block in the data set to start reading from (starting with * 0). * @param timeUnit The time unit that the duration should be converted to. * @return The data block read from the data set. * @throws HDF5JavaException If the objectPath is not tagged as a type variant that * corresponds to a time duration. * @deprecated Use {@link IHDF5TimeDurationReader#readArrayBlockWithOffset(String, int, long)} * and {@link HDF5TimeUnit#convert(HDF5TimeDurationArray)} instead. */ @Deprecated public long[] readTimeDurationArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset, final HDF5TimeUnit timeUnit) throws HDF5JavaException; /** * Reads a block of a time duration array (of rank 1) from the data set objectPath. * The time durations are stored as a HDF5TimeDuration[] value in the HDF5 file. It * needs to be tagged as one of the type variants that indicate a time duration, for example * {@link HDF5DataTypeVariant#TIME_DURATION_SECONDS}. *

* See {@link #readTimeDuration(String, HDF5TimeUnit)} for how the tagging is done. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the long[] returned * if the data set is long enough). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @return The data read from the data set. The length will be * min(size - blockSize*blockNumber, * blockSize). * @throws HDF5JavaException If the objectPath is not tagged as a type variant that * corresponds to a time duration. * @deprecated Use {@link IHDF5TimeDurationReader#readArrayBlock(String, int, long)} and * {@link HDF5TimeUnit#convert(HDF5TimeDuration[])} instead. */ @Deprecated public HDF5TimeDuration[] readTimeDurationAndUnitArrayBlock(final String objectPath, final int blockSize, final long blockNumber) throws HDF5JavaException; /** * Reads a block of a time duration array (of rank 1) from the data set objectPath. * The time durations are stored as a HDF5TimeDuration[] value in the HDF5 file. It * needs to be tagged as one of the type variants that indicate a time duration, for example * {@link HDF5DataTypeVariant#TIME_DURATION_SECONDS}. *

* See {@link #readTimeDuration(String, HDF5TimeUnit)} for how the tagging is done. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the long[] * returned). * @param offset The offset of the block in the data set to start reading from (starting with * 0). * @return The data block read from the data set. * @throws HDF5JavaException If the objectPath is not tagged as a type variant that * corresponds to a time duration. * @deprecated Use {@link IHDF5TimeDurationReader#readArrayBlockWithOffset(String, int, long)} * and {@link HDF5TimeUnit#convert(HDF5TimeDuration[])} instead. */ @Deprecated public HDF5TimeDuration[] readTimeDurationAndUnitArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset) throws HDF5JavaException; /** * Provides all natural blocks of this one-dimensional data set of time durations to iterate * over. * * @param objectPath The name (including path information) of the data set object in the file. * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of a time duration data type or not of rank * 1. * @deprecated Use the corresponding method in {@link IHDF5Reader#duration()} instead. */ @Deprecated public Iterable> getTimeDurationArrayNaturalBlocks( final String objectPath) throws HDF5JavaException; /** * Provides all natural blocks of this one-dimensional data set of time durations to iterate * over. * * @param objectPath The name (including path information) of the data set object in the file. * @param timeUnit The time unit that the duration should be converted to. * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of a time duration data type or not of rank * 1. * @deprecated Use {@link IHDF5TimeDurationReader#getArrayNaturalBlocks(String)} and * {@link HDF5TimeUnit#convert(long[], HDF5TimeUnit)} instead. */ @Deprecated public Iterable> getTimeDurationArrayNaturalBlocks( final String objectPath, final HDF5TimeUnit timeUnit) throws HDF5JavaException; /** * Provides all natural blocks of this one-dimensional data set of time durations to iterate * over. * * @param objectPath The name (including path information) of the data set object in the file. * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of a time duration data type or not of rank * 1. * @deprecated Use {@link IHDF5TimeDurationReader#getArrayNaturalBlocks(String)} instead. */ @Deprecated public Iterable> getTimeDurationAndUnitArrayNaturalBlocks( final String objectPath) throws HDF5JavaException; // ********************* // Reference // ********************* // ////////////////////////////// // Specific to object references // ////////////////////////////// /** * Resolves the path of a reference which has been read without name resolution. * * @param reference Reference encoded as string. * @return The path in the HDF5 file. * @see #readObjectReferenceArray(String, boolean) * @throws HDF5JavaException if reference is not a string-encoded reference. * @deprecated Use the corresponding method in {@link IHDF5Reader#reference()}. */ @Deprecated public String resolvePath(final String reference) throws HDF5JavaException; // ///////////////////// // Attributes // ///////////////////// /** * Reads an object reference attribute named attributeName from the object * objectPath, resolving the name of the object.
* Note that resolving the name of the object is a time consuming operation. If you don't * need the name, but want to dereference the dataset, you don't need to resolve the name if the * reader / writer is configured for auto-dereferencing (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}). * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The path of the object that the reference refers to, or an empty string, if the * object reference refers to an unnamed object. * @deprecated Use the corresponding method in {@link IHDF5Reader#reference()}. */ @Deprecated public String getObjectReferenceAttribute(final String objectPath, final String attributeName); /** * Reads an object reference attribute named attributeName from the object * objectPath.
* Note: if the reader has been configured to automatically resolve references (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}), a reference can be provided in all * places where an object path is expected. This is considerably faster than resolving the * name/path of the reference if the name/path by itself is not needed. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @param resolveName If true, resolves the name of the object referenced, * otherwise returns the references itself. * @return The path of the object that the reference refers to, or an empty string, if the * object reference refers to an unnamed object. * @deprecated Use the corresponding method in {@link IHDF5Reader#reference()}. */ @Deprecated public String getObjectReferenceAttribute(final String objectPath, final String attributeName, final boolean resolveName); /** * Reads a 1D object reference array attribute named attributeName from the object * objectPath, resolving the names of the objects.
* Note that resolving the name of the object is a time consuming operation. If you don't * need the name, but want to dereference the dataset, you don't need to resolve the name if the * reader / writer is configured for auto-dereferencing (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}). * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The paths of the objects that the references refers to. Each string may be empty, if * the corresponding object reference refers to an unnamed object. * @deprecated Use the corresponding method in {@link IHDF5Reader#reference()}. */ @Deprecated public String[] getObjectReferenceArrayAttribute(final String objectPath, final String attributeName); /** * Reads a 1D object reference array attribute named attributeName from the object * objectPath.
* Note: if the reader has been configured to automatically resolve references (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}), a reference can be provided in all * places where an object path is expected. This is considerably faster than resolving the * name/path of the reference if the name/path by itself is not needed. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @param resolveName If true, resolves the names of the objects referenced, * otherwise returns the references itself. * @return The paths of the objects that the references refers to. Each string may be empty, if * the corresponding object reference refers to an unnamed object. * @deprecated Use the corresponding method in {@link IHDF5Reader#reference()}. */ @Deprecated public String[] getObjectReferenceArrayAttribute(final String objectPath, final String attributeName, final boolean resolveName); /** * Reads an object reference array attribute named attributeName from the object * objectPath, resolving the names of the objects.
* Note that resolving the name of the object is a time consuming operation. If you don't * need the name, but want to dereference the dataset, you don't need to resolve the name if the * reader / writer is configured for auto-dereferencing (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}). * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The paths of the objects that the references refers to. Each string may be empty, if * the corresponding object reference refers to an unnamed object. * @deprecated Use the corresponding method in {@link IHDF5Reader#reference()}. */ @Deprecated public MDArray getObjectReferenceMDArrayAttribute(final String objectPath, final String attributeName); /** * Reads an object reference array attribute named attributeName from the object * objectPath.
* Note: if the reader has been configured to automatically resolve references (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}), a reference can be provided in all * places where an object path is expected. This is considerably faster than resolving the * name/path of the reference if the name/path by itself is not needed. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @param resolveName If true, resolves the names of the objects referenced, * otherwise returns the references itself. * @return The paths of the objects that the references refers to. Each string may be empty, if * the corresponding object reference refers to an unnamed object. * @deprecated Use the corresponding method in {@link IHDF5Reader#reference()}. */ @Deprecated public MDArray getObjectReferenceMDArrayAttribute(final String objectPath, final String attributeName, boolean resolveName); // ///////////////////// // Data Sets // ///////////////////// /** * Reads an object reference from the object objectPath, resolving the name of the * object.
* Note that resolving the name of the object is a time consuming operation. If you don't * need the name, but want to dereference the dataset, you don't need to resolve the name if the * reader / writer is configured for auto-dereferencing (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}). * * @param objectPath The name (including path information) of the data set object in the file. * @return The path of the object that the reference refers to, or an empty string, if the * object reference refers to an unnamed object. * @deprecated Use the corresponding method in {@link IHDF5Reader#reference()}. */ @Deprecated public String readObjectReference(final String objectPath); /** * Reads an object reference from the object objectPath.
* Note: if the reader has been configured to automatically resolve references (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}), a reference can be provided in all * places where an object path is expected. This is considerably faster than resolving the * name/path of the reference if the name/path by itself is not needed. * * @param objectPath The name (including path information) of the data set object in the file. * @param resolveName If true, resolves the name of the object referenced, * otherwise returns the references itself. * @return The path of the object that the reference refers to, or an empty string, if the * object reference refers to an unnamed object. * @deprecated Use the corresponding method in {@link IHDF5Reader#reference()}. */ @Deprecated public String readObjectReference(final String objectPath, final boolean resolveName); /** * Reads an array of object references from the object objectPath, resolving the * names of the objects.
* Note that resolving the name of the object is a time consuming operation. If you don't * need the name, but want to dereference the dataset, you don't need to resolve the name if the * reader / writer is configured for auto-dereferencing (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}). * * @param objectPath The name (including path information) of the data set object in the file. * @return The array of the paths of objects that the references refers to. Each string may be * empty, if the corresponding object reference refers to an unnamed object. * @deprecated Use the corresponding method in {@link IHDF5Reader#reference()}. */ @Deprecated public String[] readObjectReferenceArray(final String objectPath); /** * Reads an array of object references from the object objectPath.
* Note: if the reader has been configured to automatically resolve references (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}), a reference can be provided in all * places where an object path is expected. This is considerably faster than resolving the * name/path of the reference if the name/path by itself is not needed. * * @param objectPath The name (including path information) of the data set object in the file. * @param resolveName If true, resolves the names of the objects referenced, * otherwise returns the references itself. * @return The array of the paths of objects that the references refers to. Each string may be * empty, if the corresponding object reference refers to an unnamed object. * @deprecated Use the corresponding method in {@link IHDF5Reader#reference()}. */ @Deprecated public String[] readObjectReferenceArray(final String objectPath, boolean resolveName); /** * Reads a block from an array (of rank 1) of object references from the data set * objectPath, resolving the names of the objects.
* Note that resolving the name of the object is a time consuming operation. If you don't * need the name, but want to dereference the dataset, you don't need to resolve the name if the * reader / writer is configured for auto-dereferencing (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}). * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the long[] returned * if the data set is long enough). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @return The referenced data set paths read from the data set. The length will be min(size - * blockSize*blockNumber, blockSize). * @deprecated Use the corresponding method in {@link IHDF5Reader#reference()}. */ @Deprecated public String[] readObjectReferenceArrayBlock(final String objectPath, final int blockSize, final long blockNumber); /** * Reads a block from an array (of rank 1) of object references from the data set * objectPath.
* Note: if the reader has been configured to automatically resolve references (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}), a reference can be provided in all * places where an object path is expected. This is considerably faster than resolving the * name/path of the reference if the name/path by itself is not needed. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the long[] returned * if the data set is long enough). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @param resolveName If true, resolves the names of the objects referenced, * otherwise returns the references itself. * @return The referenced data set paths read from the data set. The length will be min(size - * blockSize*blockNumber, blockSize). * @deprecated Use the corresponding method in {@link IHDF5Reader#reference()}. */ @Deprecated public String[] readObjectReferenceArrayBlock(final String objectPath, final int blockSize, final long blockNumber, final boolean resolveName); /** * Reads a block from an array (of rank 1) of object references from the data set * objectPath, resolving the names of the objects.
* Note that resolving the name of the object is a time consuming operation. If you don't * need the name, but want to dereference the dataset, you don't need to resolve the name if the * reader / writer is configured for auto-dereferencing (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}). * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the long[] * returned). * @param offset The offset of the block in the data set to start reading from (starting with * 0). * @return The referenced data set paths block read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#reference()}. */ @Deprecated public String[] readObjectReferenceArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset); /** * Reads a block from an array (of rank 1) of object references from the data set * objectPath.
* Note: if the reader has been configured to automatically resolve references (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}), a reference can be provided in all * places where an object path is expected. This is considerably faster than resolving the * name/path of the reference if the name/path by itself is not needed. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the long[] * returned). * @param offset The offset of the block in the data set to start reading from (starting with * 0). * @param resolveName If true, resolves the names of the objects referenced, * otherwise returns the references itself. * @return The referenced data set paths block read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#reference()}. */ @Deprecated public String[] readObjectReferenceArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset, final boolean resolveName); /** * Reads an array (or rank N) of object references from the object objectPath, * resolving the names of the objects.
* Note that resolving the name of the object is a time consuming operation. If you don't * need the name, but want to dereference the dataset, you don't need to resolve the name if the * reader / writer is configured for auto-dereferencing (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}). * * @param objectPath The name (including path information) of the data set object in the file. * @return The multi-dimensional array of the paths of objects that the references refers to. * Each string may be empty, if the corresponding object reference refers to an unnamed * object. * @deprecated Use the corresponding method in {@link IHDF5Reader#reference()}. */ @Deprecated public MDArray readObjectReferenceMDArray(final String objectPath); /** * Reads an array (or rank N) of object references from the object objectPath.
* Note: if the reader has been configured to automatically resolve references (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}), a reference can be provided in all * places where an object path is expected. This is considerably faster than resolving the * name/path of the reference if the name/path by itself is not needed. * * @param objectPath The name (including path information) of the data set object in the file. * @param resolveName If true, resolves the names of the objects referenced, * otherwise returns the references itself. * @return The multi-dimensional array of the paths of objects that the references refers to. * Each string may be empty, if the corresponding object reference refers to an unnamed * object. * @deprecated Use the corresponding method in {@link IHDF5Reader#reference()}. */ @Deprecated public MDArray readObjectReferenceMDArray(final String objectPath, boolean resolveName); /** * Reads a multi-dimensional array of object references from the data set objectPath, * resolving the names of the objects.
* Note that resolving the name of the object is a time consuming operation. If you don't * need the name, but want to dereference the dataset, you don't need to resolve the name if the * reader / writer is configured for auto-dereferencing (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}). * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @return The referenced data set paths block read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#reference()}. */ @Deprecated public MDArray readObjectReferenceMDArrayBlock(final String objectPath, final int[] blockDimensions, final long[] blockNumber); /** * Reads a multi-dimensional array of object references from the data set objectPath.
* Note: if the reader has been configured to automatically resolve references (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}), a reference can be provided in all * places where an object path is expected. This is considerably faster than resolving the * name/path of the reference if the name/path by itself is not needed. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @param resolveName If true, resolves the names of the objects referenced, * otherwise returns the references itself. * @return The referenced data set paths block read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#reference()}. */ @Deprecated public MDArray readObjectReferenceMDArrayBlock(final String objectPath, final int[] blockDimensions, final long[] blockNumber, final boolean resolveName); /** * Reads a multi-dimensional array of object references from the data set objectPath, * resolving the names of the objects.
* Note that resolving the name of the object is a time consuming operation. If you don't * need the name, but want to dereference the dataset, you don't need to resolve the name if the * reader / writer is configured for auto-dereferencing (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}). * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @return The referenced data set paths block read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#reference()}. */ @Deprecated public MDArray readObjectReferenceMDArrayBlockWithOffset(final String objectPath, final int[] blockDimensions, final long[] offset); /** * Reads a multi-dimensional array of object references from the data set objectPath.
* Note: if the reader has been configured to automatically resolve references (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}), a reference can be provided in all * places where an object path is expected. This is considerably faster than resolving the * name/path of the reference if the name/path by itself is not needed. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @param resolveName If true, resolves the names of the objects referenced, * otherwise returns the references itself. * @return The referenced data set paths block read from the data set. * @deprecated Use the corresponding method in {@link IHDF5Reader#reference()}. */ @Deprecated public MDArray readObjectReferenceMDArrayBlockWithOffset(final String objectPath, final int[] blockDimensions, final long[] offset, final boolean resolveName); /** * Provides all natural blocks of this one-dimensional data set to iterate over. * * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1. * @deprecated Use the corresponding method in {@link IHDF5Reader#reference()}. */ @Deprecated public Iterable> getObjectReferenceArrayNaturalBlocks( final String dataSetPath); /** * Provides all natural blocks of this one-dimensional data set to iterate over. * * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1. * @deprecated Use the corresponding method in {@link IHDF5Reader#reference()}. */ @Deprecated public Iterable> getObjectReferenceArrayNaturalBlocks( final String dataSetPath, final boolean resolveName); /** * Provides all natural blocks of this multi-dimensional data set to iterate over. * * @see HDF5MDDataBlock * @deprecated Use the corresponding method in {@link IHDF5Reader#reference()}. */ @Deprecated public Iterable>> getObjectReferenceMDArrayNaturalBlocks( final String dataSetPath); /** * Provides all natural blocks of this multi-dimensional data set to iterate over. * * @see HDF5MDDataBlock * @deprecated Use the corresponding method in {@link IHDF5Reader#reference()}. */ @Deprecated public Iterable>> getObjectReferenceMDArrayNaturalBlocks( final String dataSetPath, final boolean resolveName); /** * Returns the full reader for compounds. * * @deprecated Use {@link IHDF5Reader#compound()} instead. */ // ********************* // Compounds // ********************* @Deprecated public IHDF5CompoundReader compounds(); // ********************* // Enums // ********************* /** * Returns the full reader for enums. * * @deprecated Use {@link IHDF5Reader#enumeration()} instead. */ @Deprecated public IHDF5EnumReader enums(); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5LegacyWriter.java000066400000000000000000007710351256564762100273630ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.io.Flushable; import java.util.BitSet; import java.util.Date; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ncsa.hdf.hdf5lib.exceptions.HDF5SymbolTableException; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDByteArray; import ch.systemsx.cisd.base.mdarray.MDDoubleArray; import ch.systemsx.cisd.base.mdarray.MDFloatArray; import ch.systemsx.cisd.base.mdarray.MDIntArray; import ch.systemsx.cisd.base.mdarray.MDLongArray; import ch.systemsx.cisd.base.mdarray.MDShortArray; import ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator.FileFormat; /** * The legacy interface for writing HDF5 files. Do not use in any new code as it will be removed in * a future version of JHDF5. * * @author Bernd Rinn */ @Deprecated public interface IHDF5LegacyWriter extends IHDF5EnumBasicWriter, IHDF5CompoundBasicWriter { // ********************* // File level // ********************* // ///////////////////// // Configuration // ///////////////////// /** * Returns true, if the {@link IHDF5WriterConfigurator} was not configured * with {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}, that is if extendable data * types are used for new data sets. * * @deprecated Use the corresponding method in {@link IHDF5Writer#file()} instead. */ @Deprecated public boolean isUseExtendableDataTypes(); /** * Returns the {@link FileFormat} compatibility setting for this writer. * * @deprecated Use the corresponding method in {@link IHDF5Writer#file()} instead. */ @Deprecated public FileFormat getFileFormat(); // ///////////////////// // Flushing and Syncing // ///////////////////// /** * Flushes the cache to disk (without discarding it). Note that this may or may not trigger a * fsync(2), depending on the {@link IHDF5WriterConfigurator.SyncMode} used. * * @deprecated Use the corresponding method in {@link IHDF5Writer#file()} instead. */ @Deprecated public void flush(); /** * Flushes the cache to disk (without discarding it) and synchronizes the file with the * underlying storage using a method like fsync(2), regardless of what * {@link IHDF5WriterConfigurator.SyncMode} has been set for this file. *

* This method blocks until fsync(2) has returned. * * @deprecated Use the corresponding method in {@link IHDF5Writer#file()} instead. */ @Deprecated public void flushSyncBlocking(); /** * Adds a {@link Flushable} to the set of flushables. This set is flushed when {@link #flush()} * or {@link #flushSyncBlocking()} are called and before the writer is closed. *

* This function is supposed to be used for in-memory caching structures that need to make it * into the HDF5 file. *

* If the flushable implements * {@link ch.systemsx.cisd.base.exceptions.IErrorStrategy}, in case of an exception in * {@link Flushable#flush()}, the method * {@link ch.systemsx.cisd.base.exceptions.IErrorStrategy#dealWithError(Throwable)} will be * called to decide how do deal with the exception. * * @param flushable The {@link Flushable} to add. Needs to fulfill the {@link Object#hashCode()} * contract. * @return true if the set of flushables did not already contain the specified * element. * @deprecated Use the corresponding method in {@link IHDF5Writer#file()} instead. */ @Deprecated public boolean addFlushable(Flushable flushable); /** * Removes a {@link Flushable} from the set of flushables. * * @param flushable The {@link Flushable} to remove. Needs to fulfill the * {@link Object#hashCode()} contract. * @return true if the set of flushables contained the specified element. * @deprecated Use the corresponding method in {@link IHDF5Writer#file()} instead. */ @Deprecated public boolean removeFlushable(Flushable flushable); // *********************** // Objects, Links, Groups // *********************** /** * Creates a hard link. * * @param currentPath The name of the data set (including path information) to create a link to. * @param newPath The name (including path information) of the link to create. * @deprecated Use the corresponding method in {@link IHDF5Writer#object()} instead. */ @Deprecated public void createHardLink(String currentPath, String newPath); /** * Creates a soft link. * * @param targetPath The name of the data set (including path information) to create a link to. * @param linkPath The name (including path information) of the link to create. * @deprecated Use the corresponding method in {@link IHDF5Writer#object()} instead. */ @Deprecated public void createSoftLink(String targetPath, String linkPath); /** * Creates or updates a soft link. *

* Note: This method will never overwrite a data set, but only a symbolic link. * * @param targetPath The name of the data set (including path information) to create a link to. * @param linkPath The name (including path information) of the link to create. * @deprecated Use the corresponding method in {@link IHDF5Writer#object()} instead. */ @Deprecated public void createOrUpdateSoftLink(String targetPath, String linkPath); /** * Creates an external link, that is a link to a data set in another HDF5 file, the * target . *

* Note: This method is only allowed when the {@link IHDF5WriterConfigurator} was not * configured to enforce strict HDF5 1.6 compatibility. * * @param targetFileName The name of the file where the data set resides that should be linked. * @param targetPath The name of the data set (including path information) in the * targetFileName to create a link to. * @param linkPath The name (including path information) of the link to create. * @throws IllegalStateException If the {@link IHDF5WriterConfigurator} was configured to * enforce strict HDF5 1.6 compatibility. * @deprecated Use the corresponding method in {@link IHDF5Writer#object()} instead. */ @Deprecated public void createExternalLink(String targetFileName, String targetPath, String linkPath) throws IllegalStateException; /** * Creates or updates an external link, that is a link to a data set in another HDF5 file, the * target . *

* Note: This method will never overwrite a data set, but only a symbolic link. *

* Note: This method is only allowed when the {@link IHDF5WriterConfigurator} was not * configured to enforce strict HDF5 1.6 compatibility. * * @param targetFileName The name of the file where the data set resides that should be linked. * @param targetPath The name of the data set (including path information) in the * targetFileName to create a link to. * @param linkPath The name (including path information) of the link to create. * @throws IllegalStateException If the {@link IHDF5WriterConfigurator} was configured to * enforce strict HDF5 1.6 compatibility. * @deprecated Use the corresponding method in {@link IHDF5Writer#object()} instead. */ @Deprecated public void createOrUpdateExternalLink(String targetFileName, String targetPath, String linkPath) throws IllegalStateException; /** * Moves or renames a link in the file atomically. * * @throws HDF5SymbolTableException If oldLinkPath does not exist or if * newLinkPath already exists. * @deprecated Use the corresponding method in {@link IHDF5Writer#object()} instead. */ @Deprecated public void move(String oldLinkPath, String newLinkPath) throws HDF5SymbolTableException; // ///////////////////// // Group // ///////////////////// /** * Creates a group with path objectPath in the HDF5 file. *

* All intermediate groups will be created as well, if they do not already exist. * * @param groupPath The path of the group to create. * @deprecated Use the corresponding method in {@link IHDF5Writer#object()} instead. */ @Deprecated public void createGroup(final String groupPath); /** * Creates a group with path objectPath in the HDF5 file, giving the library a hint * about the size (sizeHint). If you have this information in advance, it will be * more efficient to tell it the library rather than to let the library figure out itself, but * the hint must not be misunderstood as a limit. *

* All intermediate groups will be created as well, if they do not already exist. *

* Note: This method creates an "old-style group", that is the type of group of HDF5 1.6 and * earlier. * * @param groupPath The path of the group to create. * @param sizeHint The estimated size of all group entries (in bytes). * @deprecated Use the corresponding method in {@link IHDF5Writer#object()} instead. */ @Deprecated public void createGroup(final String groupPath, final int sizeHint); /** * Creates a group with path objectPath in the HDF5 file, giving the library hints * about when to switch between compact and dense. Setting appropriate values may improve * performance. *

* All intermediate groups will be created as well, if they do not already exist. *

* Note: This method creates a "new-style group", that is the type of group of HDF5 1.8 and * above. Thus it will fail, if the writer is configured to enforce HDF5 1.6 compatibility. * * @param groupPath The path of the group to create. * @param maxCompact When the group grows to more than this number of entries, the library will * convert the group style from compact to dense. * @param minDense When the group shrinks below this number of entries, the library will convert * the group style from dense to compact. * @deprecated Use the corresponding method in {@link IHDF5Writer#object()} instead. */ @Deprecated public void createGroup(final String groupPath, final int maxCompact, final int minDense); // ///////////////////// // Data Sets // ///////////////////// /** * Sets the data set size of a one-dimensional data set to newSize. Note that this * method can only be applied to extendable data sets. * * @throws HDF5JavaException If the data set objectPath is not extendable. * @deprecated Use the corresponding method in {@link IHDF5Writer#object()} instead. */ @Deprecated public void setDataSetSize(final String objectPath, final long newSize); /** * Sets the data set size of a multi-dimensional data set to newDimensions. Note that * this method can only be applied to extendable data sets. * * @throws HDF5JavaException If the data set objectPath is not extendable. * @deprecated Use the corresponding method in {@link IHDF5Writer#object()} instead. */ @Deprecated public void setDataSetDimensions(final String objectPath, final long[] newDimensions); // ///////////////////// // Types // ///////////////////// /** * Sets a typeVariant of object objectPath. * * @param objectPath The name of the object to add the type variant to. * @param typeVariant The type variant to add. * @deprecated Use the corresponding method in {@link IHDF5Writer#object()} instead. */ @Deprecated public void setTypeVariant(final String objectPath, final HDF5DataTypeVariant typeVariant); /** * Sets a typeVariant of attribute attributeName of object * objectPath. * * @param objectPath The name of the object. * @param attributeName The name of attribute to add the type variant to. * @param typeVariant The type variant to add. * @deprecated Use the corresponding method in {@link IHDF5Writer#object()} instead. */ @Deprecated public void setTypeVariant(final String objectPath, final String attributeName, final HDF5DataTypeVariant typeVariant); /** * Deletes the typeVariant from objectPath. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to delete the type variant from. * @deprecated Use the corresponding method in {@link IHDF5Writer#object()} instead. */ @Deprecated public void deleteTypeVariant(final String objectPath); /** * Deletes the typeVariant from attributeName of objectPath. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object. * @param attributeName The name of the attribute to delete the type variant from. * @deprecated Use the corresponding method in {@link IHDF5Writer#object()} instead. */ @Deprecated public void deleteTypeVariant(final String objectPath, final String attributeName); // ///////////////////// // Attributes // ///////////////////// /** * Deletes an attribute. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to delete the attribute from. * @param name The name of the attribute to delete. * @deprecated Use the corresponding method in {@link IHDF5Writer#object()} instead. */ @Deprecated public void deleteAttribute(final String objectPath, final String name); // ********************* // Opaque // ********************* /** * Writes out an opaque data type described by tag and defined by a byte * array (of rank 1). *

* Note that there is no dedicated method for reading opaque types. Use the method * {@link IHDF5OpaqueReader#readArray(String)} instead. * * @param objectPath The name (including path information) of the data set object in the file. * @param tag The tag of the data set. * @param data The data to write. Must not be null. * @deprecated Use the corresponding method in {@link IHDF5Writer#opaque()} instead. */ @Deprecated public void writeOpaqueByteArray(final String objectPath, final String tag, final byte[] data); /** * Writes out an opaque data type described by tag and defined by a byte * array (of rank 1). *

* Note that there is no dedicated method for reading opaque types. Use the method * {@link IHDF5OpaqueReader#readArray(String)} instead. * * @param objectPath The name (including path information) of the data set object in the file. * @param tag The tag of the data set. * @param data The data to write. Must not be null. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#opaque()} instead. */ @Deprecated public void writeOpaqueByteArray(final String objectPath, final String tag, final byte[] data, final HDF5GenericStorageFeatures features); /** * Creates an opaque data set that will be represented as a byte array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the byte array to create. * @param blockSize The size of on block (for block-wise IO) * @return The {@link HDF5OpaqueType} that can be used in methods * {@link #writeOpaqueByteArrayBlock(String, HDF5OpaqueType, byte[], long)} and * {@link #writeOpaqueByteArrayBlockWithOffset(String, HDF5OpaqueType, byte[], int, long)} * to represent this opaque type. * @deprecated Use the corresponding method in {@link IHDF5Writer#opaque()} instead. */ @Deprecated public HDF5OpaqueType createOpaqueByteArray(final String objectPath, final String tag, final long size, final int blockSize); /** * Creates an opaque data set that will be represented as a byte array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the byte array to create. This will be the total size for * non-extendable data sets and the size of one chunk for extendable (chunked) data * sets. For extendable data sets the initial size of the array will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. * @return The {@link HDF5OpaqueType} that can be used in methods * {@link #writeOpaqueByteArrayBlock(String, HDF5OpaqueType, byte[], long)} and * {@link #writeOpaqueByteArrayBlockWithOffset(String, HDF5OpaqueType, byte[], int, long)} * to represent this opaque type. * @deprecated Use the corresponding method in {@link IHDF5Writer#opaque()} instead. */ @Deprecated public HDF5OpaqueType createOpaqueByteArray(final String objectPath, final String tag, final int size); /** * Creates an opaque data set that will be represented as a byte array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the byte array to create. * @param blockSize The size of on block (for block-wise IO) * @param features The storage features of the data set. * @return The {@link HDF5OpaqueType} that can be used in methods * {@link #writeOpaqueByteArrayBlock(String, HDF5OpaqueType, byte[], long)} and * {@link #writeOpaqueByteArrayBlockWithOffset(String, HDF5OpaqueType, byte[], int, long)} * to represent this opaque type. * @deprecated Use the corresponding method in {@link IHDF5Writer#opaque()} instead. */ @Deprecated public HDF5OpaqueType createOpaqueByteArray(final String objectPath, final String tag, final long size, final int blockSize, final HDF5GenericStorageFeatures features); /** * Creates an opaque data set that will be represented as a byte array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the byte array to create. This will be the total size for * non-extendable data sets and the size of one chunk for extendable (chunked) data * sets. For extendable data sets the initial size of the array will be 0, see * {@link HDF5GenericStorageFeatures}. * @param features The storage features of the data set. * @return The {@link HDF5OpaqueType} that can be used in methods * {@link #writeOpaqueByteArrayBlock(String, HDF5OpaqueType, byte[], long)} and * {@link #writeOpaqueByteArrayBlockWithOffset(String, HDF5OpaqueType, byte[], int, long)} * to represent this opaque type. * @deprecated Use the corresponding method in {@link IHDF5Writer#opaque()} instead. */ @Deprecated public HDF5OpaqueType createOpaqueByteArray(final String objectPath, final String tag, final int size, final HDF5GenericStorageFeatures features); /** * Writes out a block of an opaque data type represented by a byte array (of rank * 1). The data set needs to have been created by * {@link #createOpaqueByteArray(String, String, long, int, HDF5GenericStorageFeatures)} * beforehand. *

* Note: For best performance, the block size in this method should be chosen to be equal * to the blockSize argument of the * {@link #createOpaqueByteArray(String, String, long, int, HDF5GenericStorageFeatures)} call * that was used to created the data set. *

* Note that there is no dedicated method for reading opaque types. Use the method * {@link IHDF5OpaqueReader#readArrayBlock(String, int, long)} instead. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumber The number of the block to write. * @deprecated Use the corresponding method in {@link IHDF5Writer#opaque()} instead. */ @Deprecated public void writeOpaqueByteArrayBlock(final String objectPath, final HDF5OpaqueType dataType, final byte[] data, final long blockNumber); /** * Writes out a block of an opaque data type represented by a byte array (of rank * 1). The data set needs to have been created by * {@link #createOpaqueByteArray(String, String, long, int, HDF5GenericStorageFeatures)} * beforehand. *

* Use this method instead of * {@link #writeOpaqueByteArrayBlock(String, HDF5OpaqueType, byte[], long)} if the total size of * the data set is not a multiple of the block size. *

* Note: For best performance, the typical dataSize in this method should be * chosen to be equal to the blockSize argument of the * {@link #createOpaqueByteArray(String, String, long, int, HDF5GenericStorageFeatures)} call * that was used to created the data set. *

* Note that there is no dedicated method for reading opaque types. Use the method * {@link IHDF5OpaqueReader#readArrayBlockWithOffset(String, int, long)} instead. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param dataSize The (real) size of data (needs to be <= data.length * ) * @param offset The offset in the data set to start writing to. * @deprecated Use the corresponding method in {@link IHDF5Writer#opaque()} instead. */ @Deprecated public void writeOpaqueByteArrayBlockWithOffset(final String objectPath, final HDF5OpaqueType dataType, final byte[] data, final int dataSize, final long offset); // ********************* // Boolean // ********************* /** * Sets a boolean attribute to the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#bool()}. */ @Deprecated public void setBooleanAttribute(final String objectPath, final String name, final boolean value); /** * Writes out a boolean value. * * @param objectPath The name (including path information) of the data set object in the file. * @param value The value of the data set. */ public void writeBoolean(final String objectPath, final boolean value); /** * Writes out a bit field ((which can be considered the equivalent to a boolean array of rank * 1), provided as a Java {@link BitSet}. *

* Note that the storage form of the bit array is a long[]. However, it is marked * in HDF5 to be interpreted bit-wise. Thus a data set written by this method cannot be read * back by {@link IHDF5LongReader#readArray(String)} but will throw a * {@link ncsa.hdf.hdf5lib.exceptions.HDF5DatatypeInterfaceException}. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ public void writeBitField(final String objectPath, final BitSet data); /** * Writes out a bit field ((which can be considered the equivalent to a boolean array of rank * 1), provided as a Java {@link BitSet}. *

* Note that the storage form of the bit array is a long[]. However, it is marked * in HDF5 to be interpreted bit-wise. Thus a data set written by this method cannot be read * back by {@link IHDF5LongReader#readArray(String)} but will throw a * {@link ncsa.hdf.hdf5lib.exceptions.HDF5DatatypeInterfaceException}. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#bool()}. */ @Deprecated public void writeBitField(final String objectPath, final BitSet data, final HDF5GenericStorageFeatures features); /** * Creates a bit field (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size (in 64 bit words) of the bit field to create. This will be the total * size for non-extendable data sets and the size of one chunk for extendable * (chunked) data sets. For extendable data sets the initial size of the array will * be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. * @deprecated Use the corresponding method in {@link IHDF5Writer#bool()}. */ @Deprecated public void createBitField(final String objectPath, final int size); /** * Creates a bit field (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size (in 64 bit words) of the bit field to create. When using extendable data * sets ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no * data set smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). * @deprecated Use the corresponding method in {@link IHDF5Writer#bool()}. */ @Deprecated public void createBitField(final String objectPath, final long size, final int blockSize); /** * Creates a bit field array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size (in 64 bit words) of the bit field to create. This will be the total * size for non-extendable data sets and the size of one chunk for extendable * (chunked) data sets. For extendable data sets the initial size of the array will * be 0, see {@link HDF5IntStorageFeatures}. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#bool()}. */ @Deprecated public void createBitField(final String objectPath, final int size, final HDF5IntStorageFeatures features); /** * Creates a bit field (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size (in 64 bit words) of the bit field to create. When using extendable data * sets ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no * data set smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) * and features is HDF5IntStorageFeature.INTNO_COMPRESSION. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#bool()}. */ @Deprecated public void createBitField(final String objectPath, final long size, final int blockSize, final HDF5IntStorageFeatures features); /** * Writes out a block of a bit field (of rank 1). The data set needs to have been created by * {@link #createBitField(String, long, int, HDF5IntStorageFeatures)} beforehand. *

* Note: For best performance, the block size in this method should be chosen to be equal * to the blockSize argument of the * {@link #createBitField(String, long, int, HDF5IntStorageFeatures)} call that was used to * create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param dataSize The (real) size of data * @param blockNumber The number of the block to write. * @deprecated Use the corresponding method in {@link IHDF5Writer#bool()}. */ @Deprecated public void writeBitFieldBlock(final String objectPath, final BitSet data, final int dataSize, final long blockNumber); /** * Writes out a block of a long array (of rank 1). The data set needs to have been * created by {@link #createBitField(String, long, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeBitFieldBlock(String, BitSet, int, long)} if the * total size of the data set is not a multiple of the block size. *

* Note: For best performance, the typical dataSize in this method should be * chosen to be equal to the blockSize argument of the * {@link #createBitField(String, long, int, HDF5IntStorageFeatures)} call that was used to * create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param dataSize The (real) size of data * @param offset The offset in the data set to start writing to. * @deprecated Use the corresponding method in {@link IHDF5Writer#bool()}. */ @Deprecated public void writeBitFieldBlockWithOffset(final String objectPath, BitSet data, final int dataSize, final long offset); // ********************* // Byte // ********************* // ///////////////////// // Attributes // ///////////////////// /** * Set a byte attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#int8()}. */ @Deprecated public void setByteAttribute(final String objectPath, final String name, final byte value); /** * Set a byte[] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#int8()}. */ @Deprecated public void setByteArrayAttribute(final String objectPath, final String name, final byte[] value); /** * Set a multi-dimensional code>byte attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#int8()}. */ @Deprecated public void setByteMDArrayAttribute(final String objectPath, final String name, final MDByteArray value); /** * Set a byte[][] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#int8()}. */ @Deprecated public void setByteMatrixAttribute(final String objectPath, final String name, final byte[][] value); // ///////////////////// // Data Sets // ///////////////////// /** * Writes out a byte value. * * @param objectPath The name (including path information) of the data set object in the file. * @param value The value to write. * @deprecated Use the corresponding method in {@link IHDF5Writer#int8()}. */ @Deprecated public void writeByte(final String objectPath, final byte value); /** * Writes out a byte array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ public void writeByteArray(final String objectPath, final byte[] data); /** * Writes out a byte array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#int8()}. */ @Deprecated public void writeByteArray(final String objectPath, final byte[] data, final HDF5IntStorageFeatures features); /** * Creates a byte array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the byte array to create. This will be the total size for * non-extendable data sets and the size of one chunk for extendable (chunked) data * sets. For extendable data sets the initial size of the array will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. * @deprecated Use the corresponding method in {@link IHDF5Writer#int8()}. */ @Deprecated public void createByteArray(final String objectPath, final int size); /** * Creates a byte array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the byte array to create. When using extendable data sets ((see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data set * smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). * @deprecated Use the corresponding method in {@link IHDF5Writer#int8()}. */ @Deprecated public void createByteArray(final String objectPath, final long size, final int blockSize); /** * Creates a byte array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the byte array to create. This will be the total size for * non-extendable data sets and the size of one chunk for extendable (chunked) data * sets. For extendable data sets the initial size of the array will be 0, see * {@link HDF5IntStorageFeatures}. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#int8()}. */ @Deprecated public void createByteArray(final String objectPath, final int size, final HDF5IntStorageFeatures features); /** * Creates a byte array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the byte array to create. When using extendable data sets ((see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data set * smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) * and features is HDF5IntStorageFeature.INTNO_COMPRESSION. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#int8()}. */ @Deprecated public void createByteArray(final String objectPath, final long size, final int blockSize, final HDF5IntStorageFeatures features); /** * Writes out a block of a byte array (of rank 1). The data set needs to have been * created by {@link #createByteArray(String, long, int, HDF5IntStorageFeatures)} beforehand. *

* Note: For best performance, the block size in this method should be chosen to be equal * to the blockSize argument of the * {@link #createByteArray(String, long, int, HDF5IntStorageFeatures)} call that was used to * create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumber The number of the block to write. * @deprecated Use the corresponding method in {@link IHDF5Writer#int8()}. */ @Deprecated public void writeByteArrayBlock(final String objectPath, final byte[] data, final long blockNumber); /** * Writes out a block of a byte array (of rank 1). The data set needs to have been * created by {@link #createByteArray(String, long, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeByteArrayBlock(String, byte[], long)} if the total * size of the data set is not a multiple of the block size. *

* Note: For best performance, the typical dataSize in this method should be * chosen to be equal to the blockSize argument of the * {@link #createByteArray(String, long, int, HDF5IntStorageFeatures)} call that was used to * create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param dataSize The (real) size of data (needs to be <= data.length * ) * @param offset The offset in the data set to start writing to. * @deprecated Use the corresponding method in {@link IHDF5Writer#int8()}. */ @Deprecated public void writeByteArrayBlockWithOffset(final String objectPath, final byte[] data, final int dataSize, final long offset); /** * Writes out a byte matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @deprecated Use the corresponding method in {@link IHDF5Writer#int8()}. */ @Deprecated public void writeByteMatrix(final String objectPath, final byte[][] data); /** * Writes out a byte matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#int8()}. */ @Deprecated public void writeByteMatrix(final String objectPath, final byte[][] data, final HDF5IntStorageFeatures features); /** * Creates a byte matrix (array of rank 2). The initial size of the matrix is 0. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. * @deprecated Use the corresponding method in {@link IHDF5Writer#int8()}. */ @Deprecated public void createByteMatrix(final String objectPath, final int blockSizeX, final int blockSizeY); /** * Creates a byte matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the byte matrix to create. * @param sizeY The size of the y dimension of the byte matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. * @deprecated Use the corresponding method in {@link IHDF5Writer#int8()}. */ @Deprecated public void createByteMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY); /** * Creates a byte matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the byte matrix to create. * @param sizeY The size of the y dimension of the byte matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#int8()}. */ @Deprecated public void createByteMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY, final HDF5IntStorageFeatures features); /** * Writes out a block of a byte matrix (array of rank 2). The data set needs to * have been created by * {@link #createByteMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of * {@link #createByteMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} if the total * size of the data set is not a multiple of the block size. *

* Note: For best performance, the size of data in this method should match * the blockSizeX/Y arguments of the * {@link #createByteMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} call that was * used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumberX The block number in the x dimension (offset: multiply with * data.length). * @param blockNumberY The block number in the y dimension (offset: multiply with * data[0.length). * @deprecated Use the corresponding method in {@link IHDF5Writer#int8()}. */ @Deprecated public void writeByteMatrixBlock(final String objectPath, final byte[][] data, final long blockNumberX, final long blockNumberY); /** * Writes out a block of a byte matrix (array of rank 2). The data set needs to * have been created by * {@link #createByteMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeByteMatrixBlock(String, byte[][], long, long)} if the * total size of the data set is not a multiple of the block size. *

* Note: For best performance, the typical dataSize in this method should be * chosen to be equal to the blockSize argument of the * {@link #createByteMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} call that was * used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. * @deprecated Use the corresponding method in {@link IHDF5Writer#int8()}. */ @Deprecated public void writeByteMatrixBlockWithOffset(final String objectPath, final byte[][] data, final long offsetX, final long offsetY); /** * Writes out a block of a byte matrix (array of rank 2). The data set needs to * have been created by * {@link #createByteMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeByteMatrixBlock(String, byte[][], long, long)} if the * total size of the data set is not a multiple of the block size. *

* Note: For best performance, the typical dataSize in this method should be * chosen to be equal to the blockSize argument of the * {@link #createByteMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} call that was * used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param dataSizeX The (real) size of data along the x axis (needs to be * <= data.length ) * @param dataSizeY The (real) size of data along the y axis (needs to be * <= data[0].length ) * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. * @deprecated Use the corresponding method in {@link IHDF5Writer#int8()}. */ @Deprecated public void writeByteMatrixBlockWithOffset(final String objectPath, final byte[][] data, final int dataSizeX, final int dataSizeY, final long offsetX, final long offsetY); /** * Writes out a multi-dimensional byte array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @deprecated Use the corresponding method in {@link IHDF5Writer#int8()}. */ @Deprecated public void writeByteMDArray(final String objectPath, final MDByteArray data); /** * Writes out a multi-dimensional byte array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#int8()}. */ @Deprecated public void writeByteMDArray(final String objectPath, final MDByteArray data, final HDF5IntStorageFeatures features); /** * Creates a multi-dimensional byte array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the byte array to create. This will be the total * dimensions for non-extendable data sets and the dimensions of one chunk (extent * along each axis) for extendable (chunked) data sets. For extendable data sets the * initial size of the array along each axis will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. * @deprecated Use the corresponding method in {@link IHDF5Writer#int8()}. */ @Deprecated public void createByteMDArray(final String objectPath, final int[] dimensions); /** * Creates a multi-dimensional byte array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. * @deprecated Use the corresponding method in {@link IHDF5Writer#int8()}. */ @Deprecated public void createByteMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions); /** * Creates a multi-dimensional byte array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. Will be the total dimensions for * non-extendable data sets and the dimensions of one chunk for extendable (chunked) * data sets For extendable data sets the initial size of the array along each axis * will be 0, see {@link HDF5IntStorageFeatures}. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#int8()}. */ @Deprecated public void createByteMDArray(final String objectPath, final int[] dimensions, final HDF5IntStorageFeatures features); /** * Creates a multi-dimensional byte array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#int8()}. */ @Deprecated public void createByteMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions, final HDF5IntStorageFeatures features); /** * Writes out a block of a multi-dimensional byte array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). * @deprecated Use the corresponding method in {@link IHDF5Writer#int8()}. */ @Deprecated public void writeByteMDArrayBlock(final String objectPath, final MDByteArray data, final long[] blockNumber); /** * Writes out a block of a multi-dimensional byte array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. * @deprecated Use the corresponding method in {@link IHDF5Writer#int8()}. */ @Deprecated public void writeByteMDArrayBlockWithOffset(final String objectPath, final MDByteArray data, final long[] offset); /** * Writes out a block of a multi-dimensional byte array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param blockDimensions The dimensions of the block to write to the data set. * @param offset The offset of the block in the data set to start writing to in each dimension. * @param memoryOffset The offset of the block in the data array. * @deprecated Use the corresponding method in {@link IHDF5Writer#int8()}. */ @Deprecated public void writeByteMDArrayBlockWithOffset(final String objectPath, final MDByteArray data, final int[] blockDimensions, final long[] offset, final int[] memoryOffset); // ********************* // Short // ********************* // ///////////////////// // Attributes // ///////////////////// /** * Set a short attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#int16()}. */ @Deprecated public void setShortAttribute(final String objectPath, final String name, final short value); /** * Set a short[] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#int16()}. */ @Deprecated public void setShortArrayAttribute(final String objectPath, final String name, final short[] value); /** * Set a multi-dimensional code>short attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#int16()}. */ @Deprecated public void setShortMDArrayAttribute(final String objectPath, final String name, final MDShortArray value); /** * Set a short[][] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#int16()}. */ @Deprecated public void setShortMatrixAttribute(final String objectPath, final String name, final short[][] value); // ///////////////////// // Data Sets // ///////////////////// /** * Writes out a short value. * * @param objectPath The name (including path information) of the data set object in the file. * @param value The value to write. * @deprecated Use the corresponding method in {@link IHDF5Writer#int16()}. */ @Deprecated public void writeShort(final String objectPath, final short value); /** * Writes out a short array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @deprecated Use the corresponding method in {@link IHDF5Writer#int16()}. */ @Deprecated public void writeShortArray(final String objectPath, final short[] data); /** * Writes out a short array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#int16()}. */ @Deprecated public void writeShortArray(final String objectPath, final short[] data, final HDF5IntStorageFeatures features); /** * Creates a short array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the short array to create. This will be the total size for * non-extendable data sets and the size of one chunk for extendable (chunked) data * sets. For extendable data sets the initial size of the array will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. * @deprecated Use the corresponding method in {@link IHDF5Writer#int16()}. */ @Deprecated public void createShortArray(final String objectPath, final int size); /** * Creates a short array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the short array to create. When using extendable data sets ((see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data set * smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). * @deprecated Use the corresponding method in {@link IHDF5Writer#int16()}. */ @Deprecated public void createShortArray(final String objectPath, final long size, final int blockSize); /** * Creates a short array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the short array to create. This will be the total size for * non-extendable data sets and the size of one chunk for extendable (chunked) data * sets. For extendable data sets the initial size of the array will be 0, see * {@link HDF5IntStorageFeatures}. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#int16()}. */ @Deprecated public void createShortArray(final String objectPath, final int size, final HDF5IntStorageFeatures features); /** * Creates a short array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the short array to create. When using extendable data sets ((see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data set * smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) * and features is HDF5IntStorageFeature.INTNO_COMPRESSION. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#int16()}. */ @Deprecated public void createShortArray(final String objectPath, final long size, final int blockSize, final HDF5IntStorageFeatures features); /** * Writes out a block of a short array (of rank 1). The data set needs to have been * created by {@link #createShortArray(String, long, int, HDF5IntStorageFeatures)} beforehand. *

* Note: For best performance, the block size in this method should be chosen to be equal * to the blockSize argument of the * {@link #createShortArray(String, long, int, HDF5IntStorageFeatures)} call that was used to * create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumber The number of the block to write. * @deprecated Use the corresponding method in {@link IHDF5Writer#int16()}. */ @Deprecated public void writeShortArrayBlock(final String objectPath, final short[] data, final long blockNumber); /** * Writes out a block of a short array (of rank 1). The data set needs to have been * created by {@link #createShortArray(String, long, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeShortArrayBlock(String, short[], long)} if the total * size of the data set is not a multiple of the block size. *

* Note: For best performance, the typical dataSize in this method should be * chosen to be equal to the blockSize argument of the * {@link #createShortArray(String, long, int, HDF5IntStorageFeatures)} call that was used to * create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param dataSize The (real) size of data (needs to be <= data.length * ) * @param offset The offset in the data set to start writing to. * @deprecated Use the corresponding method in {@link IHDF5Writer#int16()}. */ @Deprecated public void writeShortArrayBlockWithOffset(final String objectPath, final short[] data, final int dataSize, final long offset); /** * Writes out a short matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @deprecated Use the corresponding method in {@link IHDF5Writer#int16()}. */ @Deprecated public void writeShortMatrix(final String objectPath, final short[][] data); /** * Writes out a short matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#int16()}. */ @Deprecated public void writeShortMatrix(final String objectPath, final short[][] data, final HDF5IntStorageFeatures features); /** * Creates a short matrix (array of rank 2). The initial size of the matrix is 0. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. * @deprecated Use the corresponding method in {@link IHDF5Writer#int16()}. */ @Deprecated public void createShortMatrix(final String objectPath, final int blockSizeX, final int blockSizeY); /** * Creates a short matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the short matrix to create. * @param sizeY The size of the y dimension of the short matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. * @deprecated Use the corresponding method in {@link IHDF5Writer#int16()}. */ @Deprecated public void createShortMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY); /** * Creates a short matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the short matrix to create. * @param sizeY The size of the y dimension of the short matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#int16()}. */ @Deprecated public void createShortMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY, final HDF5IntStorageFeatures features); /** * Writes out a block of a short matrix (array of rank 2). The data set needs to * have been created by * {@link #createShortMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of * {@link #createShortMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} if the total * size of the data set is not a multiple of the block size. *

* Note: For best performance, the size of data in this method should match * the blockSizeX/Y arguments of the * {@link #createShortMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} call that * was used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumberX The block number in the x dimension (offset: multiply with * data.length). * @param blockNumberY The block number in the y dimension (offset: multiply with * data[0.length). * @deprecated Use the corresponding method in {@link IHDF5Writer#int16()}. */ @Deprecated public void writeShortMatrixBlock(final String objectPath, final short[][] data, final long blockNumberX, final long blockNumberY); /** * Writes out a block of a short matrix (array of rank 2). The data set needs to * have been created by * {@link #createShortMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeShortMatrixBlock(String, short[][], long, long)} if * the total size of the data set is not a multiple of the block size. *

* Note: For best performance, the typical dataSize in this method should be * chosen to be equal to the blockSize argument of the * {@link #createShortMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} call that * was used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. * @deprecated Use the corresponding method in {@link IHDF5Writer#int16()}. */ @Deprecated public void writeShortMatrixBlockWithOffset(final String objectPath, final short[][] data, final long offsetX, final long offsetY); /** * Writes out a block of a short matrix (array of rank 2). The data set needs to * have been created by * {@link #createShortMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeShortMatrixBlock(String, short[][], long, long)} if * the total size of the data set is not a multiple of the block size. *

* Note: For best performance, the typical dataSize in this method should be * chosen to be equal to the blockSize argument of the * {@link #createShortMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} call that * was used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param dataSizeX The (real) size of data along the x axis (needs to be * <= data.length ) * @param dataSizeY The (real) size of data along the y axis (needs to be * <= data[0].length ) * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. * @deprecated Use the corresponding method in {@link IHDF5Writer#int16()}. */ @Deprecated public void writeShortMatrixBlockWithOffset(final String objectPath, final short[][] data, final int dataSizeX, final int dataSizeY, final long offsetX, final long offsetY); /** * Writes out a multi-dimensional short array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @deprecated Use the corresponding method in {@link IHDF5Writer#int16()}. */ @Deprecated public void writeShortMDArray(final String objectPath, final MDShortArray data); /** * Writes out a multi-dimensional short array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#int16()}. */ @Deprecated public void writeShortMDArray(final String objectPath, final MDShortArray data, final HDF5IntStorageFeatures features); /** * Creates a multi-dimensional short array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the short array to create. This will be the total * dimensions for non-extendable data sets and the dimensions of one chunk (extent * along each axis) for extendable (chunked) data sets. For extendable data sets the * initial size of the array along each axis will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. * @deprecated Use the corresponding method in {@link IHDF5Writer#int16()}. */ @Deprecated public void createShortMDArray(final String objectPath, final int[] dimensions); /** * Creates a multi-dimensional short array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. * @deprecated Use the corresponding method in {@link IHDF5Writer#int16()}. */ @Deprecated public void createShortMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions); /** * Creates a multi-dimensional short array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. Will be the total dimensions for * non-extendable data sets and the dimensions of one chunk for extendable (chunked) * data sets For extendable data sets the initial size of the array along each axis * will be 0, see {@link HDF5IntStorageFeatures}. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#int16()}. */ @Deprecated public void createShortMDArray(final String objectPath, final int[] dimensions, final HDF5IntStorageFeatures features); /** * Creates a multi-dimensional short array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#int16()}. */ @Deprecated public void createShortMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions, final HDF5IntStorageFeatures features); /** * Writes out a block of a multi-dimensional short array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). * @deprecated Use the corresponding method in {@link IHDF5Writer#int16()}. */ @Deprecated public void writeShortMDArrayBlock(final String objectPath, final MDShortArray data, final long[] blockNumber); /** * Writes out a block of a multi-dimensional short array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. * @deprecated Use the corresponding method in {@link IHDF5Writer#int16()}. */ @Deprecated public void writeShortMDArrayBlockWithOffset(final String objectPath, final MDShortArray data, final long[] offset); /** * Writes out a block of a multi-dimensional short array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param blockDimensions The dimensions of the block to write to the data set. * @param offset The offset of the block in the data set to start writing to in each dimension. * @param memoryOffset The offset of the block in the data array. * @deprecated Use the corresponding method in {@link IHDF5Writer#int16()}. */ @Deprecated public void writeShortMDArrayBlockWithOffset(final String objectPath, final MDShortArray data, final int[] blockDimensions, final long[] offset, final int[] memoryOffset); // ********************* // Int // ********************* // ///////////////////// // Attributes // ///////////////////// /** * Set a int attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#int32()}. */ @Deprecated public void setIntAttribute(final String objectPath, final String name, final int value); /** * Set a int[] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#int32()}. */ @Deprecated public void setIntArrayAttribute(final String objectPath, final String name, final int[] value); /** * Set a multi-dimensional code>int attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#int32()}. */ @Deprecated public void setIntMDArrayAttribute(final String objectPath, final String name, final MDIntArray value); /** * Set a int[][] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setIntMatrixAttribute(final String objectPath, final String name, final int[][] value); // ///////////////////// // Data Sets // ///////////////////// /** * Writes out a int value. * * @param objectPath The name (including path information) of the data set object in the file. * @param value The value to write. */ public void writeInt(final String objectPath, final int value); /** * Writes out a int array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ public void writeIntArray(final String objectPath, final int[] data); /** * Writes out a int array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#int32()}. */ @Deprecated public void writeIntArray(final String objectPath, final int[] data, final HDF5IntStorageFeatures features); /** * Creates a int array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the int array to create. This will be the total size for * non-extendable data sets and the size of one chunk for extendable (chunked) data * sets. For extendable data sets the initial size of the array will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. * @deprecated Use the corresponding method in {@link IHDF5Writer#int32()}. */ @Deprecated public void createIntArray(final String objectPath, final int size); /** * Creates a int array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the int array to create. When using extendable data sets ((see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data set * smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). * @deprecated Use the corresponding method in {@link IHDF5Writer#int32()}. */ @Deprecated public void createIntArray(final String objectPath, final long size, final int blockSize); /** * Creates a int array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the int array to create. This will be the total size for * non-extendable data sets and the size of one chunk for extendable (chunked) data * sets. For extendable data sets the initial size of the array will be 0, see * {@link HDF5IntStorageFeatures}. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#int32()}. */ @Deprecated public void createIntArray(final String objectPath, final int size, final HDF5IntStorageFeatures features); /** * Creates a int array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the int array to create. When using extendable data sets ((see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data set * smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) * and features is HDF5IntStorageFeature.INTNO_COMPRESSION. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#int32()}. */ @Deprecated public void createIntArray(final String objectPath, final long size, final int blockSize, final HDF5IntStorageFeatures features); /** * Writes out a block of a int array (of rank 1). The data set needs to have been * created by {@link #createIntArray(String, long, int, HDF5IntStorageFeatures)} beforehand. *

* Note: For best performance, the block size in this method should be chosen to be equal * to the blockSize argument of the * {@link #createIntArray(String, long, int, HDF5IntStorageFeatures)} call that was used to * create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumber The number of the block to write. * @deprecated Use the corresponding method in {@link IHDF5Writer#int32()}. */ @Deprecated public void writeIntArrayBlock(final String objectPath, final int[] data, final long blockNumber); /** * Writes out a block of a int array (of rank 1). The data set needs to have been * created by {@link #createIntArray(String, long, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeIntArrayBlock(String, int[], long)} if the total size * of the data set is not a multiple of the block size. *

* Note: For best performance, the typical dataSize in this method should be * chosen to be equal to the blockSize argument of the * {@link #createIntArray(String, long, int, HDF5IntStorageFeatures)} call that was used to * create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param dataSize The (real) size of data (needs to be <= data.length * ) * @param offset The offset in the data set to start writing to. * @deprecated Use the corresponding method in {@link IHDF5Writer#int32()}. */ @Deprecated public void writeIntArrayBlockWithOffset(final String objectPath, final int[] data, final int dataSize, final long offset); /** * Writes out a int matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ public void writeIntMatrix(final String objectPath, final int[][] data); /** * Writes out a int matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#int32()}. */ @Deprecated public void writeIntMatrix(final String objectPath, final int[][] data, final HDF5IntStorageFeatures features); /** * Creates a int matrix (array of rank 2). The initial size of the matrix is 0. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. * @deprecated Use the corresponding method in {@link IHDF5Writer#int32()}. */ @Deprecated public void createIntMatrix(final String objectPath, final int blockSizeX, final int blockSizeY); /** * Creates a int matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the int matrix to create. * @param sizeY The size of the y dimension of the int matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. * @deprecated Use the corresponding method in {@link IHDF5Writer#int32()}. */ @Deprecated public void createIntMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY); /** * Creates a int matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the int matrix to create. * @param sizeY The size of the y dimension of the int matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#int32()}. */ @Deprecated public void createIntMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY, final HDF5IntStorageFeatures features); /** * Writes out a block of a int matrix (array of rank 2). The data set needs to have * been created by * {@link #createIntMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of * {@link #createIntMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} if the total * size of the data set is not a multiple of the block size. *

* Note: For best performance, the size of data in this method should match * the blockSizeX/Y arguments of the * {@link #createIntMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} call that was * used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumberX The block number in the x dimension (offset: multiply with * data.length). * @param blockNumberY The block number in the y dimension (offset: multiply with * data[0.length). * @deprecated Use the corresponding method in {@link IHDF5Writer#int32()}. */ @Deprecated public void writeIntMatrixBlock(final String objectPath, final int[][] data, final long blockNumberX, final long blockNumberY); /** * Writes out a block of a int matrix (array of rank 2). The data set needs to have * been created by * {@link #createIntMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeIntMatrixBlock(String, int[][], long, long)} if the * total size of the data set is not a multiple of the block size. *

* Note: For best performance, the typical dataSize in this method should be * chosen to be equal to the blockSize argument of the * {@link #createIntMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} call that was * used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. * @deprecated Use the corresponding method in {@link IHDF5Writer#int32()}. */ @Deprecated public void writeIntMatrixBlockWithOffset(final String objectPath, final int[][] data, final long offsetX, final long offsetY); /** * Writes out a block of a int matrix (array of rank 2). The data set needs to have * been created by * {@link #createIntMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeIntMatrixBlock(String, int[][], long, long)} if the * total size of the data set is not a multiple of the block size. *

* Note: For best performance, the typical dataSize in this method should be * chosen to be equal to the blockSize argument of the * {@link #createIntMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} call that was * used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param dataSizeX The (real) size of data along the x axis (needs to be * <= data.length ) * @param dataSizeY The (real) size of data along the y axis (needs to be * <= data[0].length ) * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. * @deprecated Use the corresponding method in {@link IHDF5Writer#int32()}. */ @Deprecated public void writeIntMatrixBlockWithOffset(final String objectPath, final int[][] data, final int dataSizeX, final int dataSizeY, final long offsetX, final long offsetY); /** * Writes out a multi-dimensional int array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @deprecated Use the corresponding method in {@link IHDF5Writer#int32()}. */ @Deprecated public void writeIntMDArray(final String objectPath, final MDIntArray data); /** * Writes out a multi-dimensional int array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#int32()}. */ @Deprecated public void writeIntMDArray(final String objectPath, final MDIntArray data, final HDF5IntStorageFeatures features); /** * Creates a multi-dimensional int array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the int array to create. This will be the total * dimensions for non-extendable data sets and the dimensions of one chunk (extent * along each axis) for extendable (chunked) data sets. For extendable data sets the * initial size of the array along each axis will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. * @deprecated Use the corresponding method in {@link IHDF5Writer#int32()}. */ @Deprecated public void createIntMDArray(final String objectPath, final int[] dimensions); /** * Creates a multi-dimensional int array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. * @deprecated Use the corresponding method in {@link IHDF5Writer#int32()}. */ @Deprecated public void createIntMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions); /** * Creates a multi-dimensional int array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. Will be the total dimensions for * non-extendable data sets and the dimensions of one chunk for extendable (chunked) * data sets For extendable data sets the initial size of the array along each axis * will be 0, see {@link HDF5IntStorageFeatures}. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#int32()}. */ @Deprecated public void createIntMDArray(final String objectPath, final int[] dimensions, final HDF5IntStorageFeatures features); /** * Creates a multi-dimensional int array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#int32()}. */ @Deprecated public void createIntMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions, final HDF5IntStorageFeatures features); /** * Writes out a block of a multi-dimensional int array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). * @deprecated Use the corresponding method in {@link IHDF5Writer#int32()}. */ @Deprecated public void writeIntMDArrayBlock(final String objectPath, final MDIntArray data, final long[] blockNumber); /** * Writes out a block of a multi-dimensional int array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. * @deprecated Use the corresponding method in {@link IHDF5Writer#int32()}. */ @Deprecated public void writeIntMDArrayBlockWithOffset(final String objectPath, final MDIntArray data, final long[] offset); /** * Writes out a block of a multi-dimensional int array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param blockDimensions The dimensions of the block to write to the data set. * @param offset The offset of the block in the data set to start writing to in each dimension. * @param memoryOffset The offset of the block in the data array. * @deprecated Use the corresponding method in {@link IHDF5Writer#int32()}. */ @Deprecated public void writeIntMDArrayBlockWithOffset(final String objectPath, final MDIntArray data, final int[] blockDimensions, final long[] offset, final int[] memoryOffset); // ********************* // Long // ********************* // ///////////////////// // Attributes // ///////////////////// /** * Set a long attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#int64()}. */ @Deprecated public void setLongAttribute(final String objectPath, final String name, final long value); /** * Set a long[] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#int64()}. */ @Deprecated public void setLongArrayAttribute(final String objectPath, final String name, final long[] value); /** * Set a multi-dimensional code>long attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#int64()}. */ @Deprecated public void setLongMDArrayAttribute(final String objectPath, final String name, final MDLongArray value); /** * Set a long[][] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#int64()}. */ @Deprecated public void setLongMatrixAttribute(final String objectPath, final String name, final long[][] value); // ///////////////////// // Data Sets // ///////////////////// /** * Writes out a long value. * * @param objectPath The name (including path information) of the data set object in the file. * @param value The value to write. */ public void writeLong(final String objectPath, final long value); /** * Writes out a long array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ public void writeLongArray(final String objectPath, final long[] data); /** * Writes out a long array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#int64()}. */ @Deprecated public void writeLongArray(final String objectPath, final long[] data, final HDF5IntStorageFeatures features); /** * Creates a long array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the long array to create. This will be the total size for * non-extendable data sets and the size of one chunk for extendable (chunked) data * sets. For extendable data sets the initial size of the array will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. * @deprecated Use the corresponding method in {@link IHDF5Writer#int64()}. */ @Deprecated public void createLongArray(final String objectPath, final int size); /** * Creates a long array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the long array to create. When using extendable data sets ((see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data set * smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). * @deprecated Use the corresponding method in {@link IHDF5Writer#int64()}. */ @Deprecated public void createLongArray(final String objectPath, final long size, final int blockSize); /** * Creates a long array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the long array to create. This will be the total size for * non-extendable data sets and the size of one chunk for extendable (chunked) data * sets. For extendable data sets the initial size of the array will be 0, see * {@link HDF5IntStorageFeatures}. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#int64()}. */ @Deprecated public void createLongArray(final String objectPath, final int size, final HDF5IntStorageFeatures features); /** * Creates a long array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the long array to create. When using extendable data sets ((see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data set * smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) * and features is HDF5IntStorageFeature.INTNO_COMPRESSION. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#int64()}. */ @Deprecated public void createLongArray(final String objectPath, final long size, final int blockSize, final HDF5IntStorageFeatures features); /** * Writes out a block of a long array (of rank 1). The data set needs to have been * created by {@link #createLongArray(String, long, int, HDF5IntStorageFeatures)} beforehand. *

* Note: For best performance, the block size in this method should be chosen to be equal * to the blockSize argument of the * {@link #createLongArray(String, long, int, HDF5IntStorageFeatures)} call that was used to * create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumber The number of the block to write. * @deprecated Use the corresponding method in {@link IHDF5Writer#int64()}. */ @Deprecated public void writeLongArrayBlock(final String objectPath, final long[] data, final long blockNumber); /** * Writes out a block of a long array (of rank 1). The data set needs to have been * created by {@link #createLongArray(String, long, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeLongArrayBlock(String, long[], long)} if the total * size of the data set is not a multiple of the block size. *

* Note: For best performance, the typical dataSize in this method should be * chosen to be equal to the blockSize argument of the * {@link #createLongArray(String, long, int, HDF5IntStorageFeatures)} call that was used to * create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param dataSize The (real) size of data (needs to be <= data.length * ) * @param offset The offset in the data set to start writing to. * @deprecated Use the corresponding method in {@link IHDF5Writer#int64()}. */ @Deprecated public void writeLongArrayBlockWithOffset(final String objectPath, final long[] data, final int dataSize, final long offset); /** * Writes out a long matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ public void writeLongMatrix(final String objectPath, final long[][] data); /** * Writes out a long matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#int64()}. */ @Deprecated public void writeLongMatrix(final String objectPath, final long[][] data, final HDF5IntStorageFeatures features); /** * Creates a long matrix (array of rank 2). The initial size of the matrix is 0. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. * @deprecated Use the corresponding method in {@link IHDF5Writer#int64()}. */ @Deprecated public void createLongMatrix(final String objectPath, final int blockSizeX, final int blockSizeY); /** * Creates a long matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the long matrix to create. * @param sizeY The size of the y dimension of the long matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. * @deprecated Use the corresponding method in {@link IHDF5Writer#int64()}. */ @Deprecated public void createLongMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY); /** * Creates a long matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the long matrix to create. * @param sizeY The size of the y dimension of the long matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#int64()}. */ @Deprecated public void createLongMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY, final HDF5IntStorageFeatures features); /** * Writes out a block of a long matrix (array of rank 2). The data set needs to * have been created by * {@link #createLongMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of * {@link #createLongMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} if the total * size of the data set is not a multiple of the block size. *

* Note: For best performance, the size of data in this method should match * the blockSizeX/Y arguments of the * {@link #createLongMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} call that was * used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumberX The block number in the x dimension (offset: multiply with * data.length). * @param blockNumberY The block number in the y dimension (offset: multiply with * data[0.length). * @deprecated Use the corresponding method in {@link IHDF5Writer#int64()}. */ @Deprecated public void writeLongMatrixBlock(final String objectPath, final long[][] data, final long blockNumberX, final long blockNumberY); /** * Writes out a block of a long matrix (array of rank 2). The data set needs to * have been created by * {@link #createLongMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeLongMatrixBlock(String, long[][], long, long)} if the * total size of the data set is not a multiple of the block size. *

* Note: For best performance, the typical dataSize in this method should be * chosen to be equal to the blockSize argument of the * {@link #createLongMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} call that was * used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. * @deprecated Use the corresponding method in {@link IHDF5Writer#int64()}. */ @Deprecated public void writeLongMatrixBlockWithOffset(final String objectPath, final long[][] data, final long offsetX, final long offsetY); /** * Writes out a block of a long matrix (array of rank 2). The data set needs to * have been created by * {@link #createLongMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeLongMatrixBlock(String, long[][], long, long)} if the * total size of the data set is not a multiple of the block size. *

* Note: For best performance, the typical dataSize in this method should be * chosen to be equal to the blockSize argument of the * {@link #createLongMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} call that was * used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param dataSizeX The (real) size of data along the x axis (needs to be * <= data.length ) * @param dataSizeY The (real) size of data along the y axis (needs to be * <= data[0].length ) * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. * @deprecated Use the corresponding method in {@link IHDF5Writer#int64()}. */ @Deprecated public void writeLongMatrixBlockWithOffset(final String objectPath, final long[][] data, final int dataSizeX, final int dataSizeY, final long offsetX, final long offsetY); /** * Writes out a multi-dimensional long array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @deprecated Use the corresponding method in {@link IHDF5Writer#int64()}. */ @Deprecated public void writeLongMDArray(final String objectPath, final MDLongArray data); /** * Writes out a multi-dimensional long array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#int64()}. */ @Deprecated public void writeLongMDArray(final String objectPath, final MDLongArray data, final HDF5IntStorageFeatures features); /** * Creates a multi-dimensional long array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the long array to create. This will be the total * dimensions for non-extendable data sets and the dimensions of one chunk (extent * along each axis) for extendable (chunked) data sets. For extendable data sets the * initial size of the array along each axis will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. * @deprecated Use the corresponding method in {@link IHDF5Writer#int64()}. */ @Deprecated public void createLongMDArray(final String objectPath, final int[] dimensions); /** * Creates a multi-dimensional long array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. * @deprecated Use the corresponding method in {@link IHDF5Writer#int64()}. */ @Deprecated public void createLongMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions); /** * Creates a multi-dimensional long array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. Will be the total dimensions for * non-extendable data sets and the dimensions of one chunk for extendable (chunked) * data sets For extendable data sets the initial size of the array along each axis * will be 0, see {@link HDF5IntStorageFeatures}. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#int64()}. */ @Deprecated public void createLongMDArray(final String objectPath, final int[] dimensions, final HDF5IntStorageFeatures features); /** * Creates a multi-dimensional long array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#int64()}. */ @Deprecated public void createLongMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions, final HDF5IntStorageFeatures features); /** * Writes out a block of a multi-dimensional long array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). * @deprecated Use the corresponding method in {@link IHDF5Writer#int64()}. */ @Deprecated public void writeLongMDArrayBlock(final String objectPath, final MDLongArray data, final long[] blockNumber); /** * Writes out a block of a multi-dimensional long array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. * @deprecated Use the corresponding method in {@link IHDF5Writer#int64()}. */ @Deprecated public void writeLongMDArrayBlockWithOffset(final String objectPath, final MDLongArray data, final long[] offset); /** * Writes out a block of a multi-dimensional long array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param blockDimensions The dimensions of the block to write to the data set. * @param offset The offset of the block in the data set to start writing to in each dimension. * @param memoryOffset The offset of the block in the data array. * @deprecated Use the corresponding method in {@link IHDF5Writer#int64()}. */ @Deprecated public void writeLongMDArrayBlockWithOffset(final String objectPath, final MDLongArray data, final int[] blockDimensions, final long[] offset, final int[] memoryOffset); // ********************* // Float // ********************* // ///////////////////// // Attributes // ///////////////////// /** * Set a float attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#float32()}. */ @Deprecated public void setFloatAttribute(final String objectPath, final String name, final float value); /** * Set a float[] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#float32()}. */ @Deprecated public void setFloatArrayAttribute(final String objectPath, final String name, final float[] value); /** * Set a multi-dimensional code>float attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#float32()}. */ @Deprecated public void setFloatMDArrayAttribute(final String objectPath, final String name, final MDFloatArray value); /** * Set a float[][] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#float32()}. */ @Deprecated public void setFloatMatrixAttribute(final String objectPath, final String name, final float[][] value); // ///////////////////// // Data Sets // ///////////////////// /** * Writes out a float value. * * @param objectPath The name (including path information) of the data set object in the file. * @param value The value to write. */ public void writeFloat(final String objectPath, final float value); /** * Writes out a float array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ public void writeFloatArray(final String objectPath, final float[] data); /** * Writes out a float array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#float32()}. */ @Deprecated public void writeFloatArray(final String objectPath, final float[] data, final HDF5FloatStorageFeatures features); /** * Creates a float array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the float array to create. This will be the total size for * non-extendable data sets and the size of one chunk for extendable (chunked) data * sets. For extendable data sets the initial size of the array will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. * @deprecated Use the corresponding method in {@link IHDF5Writer#float32()}. */ @Deprecated public void createFloatArray(final String objectPath, final int size); /** * Creates a float array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the float array to create. When using extendable data sets ((see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data set * smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). * @deprecated Use the corresponding method in {@link IHDF5Writer#float32()}. */ @Deprecated public void createFloatArray(final String objectPath, final long size, final int blockSize); /** * Creates a float array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the float array to create. This will be the total size for * non-extendable data sets and the size of one chunk for extendable (chunked) data * sets. For extendable data sets the initial size of the array will be 0, see * {@link HDF5FloatStorageFeatures}. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#float32()}. */ @Deprecated public void createFloatArray(final String objectPath, final int size, final HDF5FloatStorageFeatures features); /** * Creates a float array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the float array to create. When using extendable data sets ((see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data set * smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) * and features is * HDF5FloatStorageFeature.FLOATNO_COMPRESSION. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#float32()}. */ @Deprecated public void createFloatArray(final String objectPath, final long size, final int blockSize, final HDF5FloatStorageFeatures features); /** * Writes out a block of a float array (of rank 1). The data set needs to have been * created by {@link #createFloatArray(String, long, int, HDF5FloatStorageFeatures)} beforehand. *

* Note: For best performance, the block size in this method should be chosen to be equal * to the blockSize argument of the * {@link #createFloatArray(String, long, int, HDF5FloatStorageFeatures)} call that was used to * create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumber The number of the block to write. * @deprecated Use the corresponding method in {@link IHDF5Writer#float32()}. */ @Deprecated public void writeFloatArrayBlock(final String objectPath, final float[] data, final long blockNumber); /** * Writes out a block of a float array (of rank 1). The data set needs to have been * created by {@link #createFloatArray(String, long, int, HDF5FloatStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeFloatArrayBlock(String, float[], long)} if the total * size of the data set is not a multiple of the block size. *

* Note: For best performance, the typical dataSize in this method should be * chosen to be equal to the blockSize argument of the * {@link #createFloatArray(String, long, int, HDF5FloatStorageFeatures)} call that was used to * create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param dataSize The (real) size of data (needs to be <= data.length * ) * @param offset The offset in the data set to start writing to. * @deprecated Use the corresponding method in {@link IHDF5Writer#float32()}. */ @Deprecated public void writeFloatArrayBlockWithOffset(final String objectPath, final float[] data, final int dataSize, final long offset); /** * Writes out a float matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ public void writeFloatMatrix(final String objectPath, final float[][] data); /** * Writes out a float matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#float32()}. */ @Deprecated public void writeFloatMatrix(final String objectPath, final float[][] data, final HDF5FloatStorageFeatures features); /** * Creates a float matrix (array of rank 2). The initial size of the matrix is 0. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. * @deprecated Use the corresponding method in {@link IHDF5Writer#float32()}. */ @Deprecated public void createFloatMatrix(final String objectPath, final int blockSizeX, final int blockSizeY); /** * Creates a float matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the float matrix to create. * @param sizeY The size of the y dimension of the float matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. * @deprecated Use the corresponding method in {@link IHDF5Writer#float32()}. */ @Deprecated public void createFloatMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY); /** * Creates a float matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the float matrix to create. * @param sizeY The size of the y dimension of the float matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#float32()}. */ @Deprecated public void createFloatMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY, final HDF5FloatStorageFeatures features); /** * Writes out a block of a float matrix (array of rank 2). The data set needs to * have been created by * {@link #createFloatMatrix(String, long, long, int, int, HDF5FloatStorageFeatures)} * beforehand. *

* Use this method instead of * {@link #createFloatMatrix(String, long, long, int, int, HDF5FloatStorageFeatures)} if the * total size of the data set is not a multiple of the block size. *

* Note: For best performance, the size of data in this method should match * the blockSizeX/Y arguments of the * {@link #createFloatMatrix(String, long, long, int, int, HDF5FloatStorageFeatures)} call that * was used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumberX The block number in the x dimension (offset: multiply with * data.length). * @param blockNumberY The block number in the y dimension (offset: multiply with * data[0.length). * @deprecated Use the corresponding method in {@link IHDF5Writer#float32()}. */ @Deprecated public void writeFloatMatrixBlock(final String objectPath, final float[][] data, final long blockNumberX, final long blockNumberY); /** * Writes out a block of a float matrix (array of rank 2). The data set needs to * have been created by * {@link #createFloatMatrix(String, long, long, int, int, HDF5FloatStorageFeatures)} * beforehand. *

* Use this method instead of {@link #writeFloatMatrixBlock(String, float[][], long, long)} if * the total size of the data set is not a multiple of the block size. *

* Note: For best performance, the typical dataSize in this method should be * chosen to be equal to the blockSize argument of the * {@link #createFloatMatrix(String, long, long, int, int, HDF5FloatStorageFeatures)} call that * was used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. * @deprecated Use the corresponding method in {@link IHDF5Writer#float32()}. */ @Deprecated public void writeFloatMatrixBlockWithOffset(final String objectPath, final float[][] data, final long offsetX, final long offsetY); /** * Writes out a block of a float matrix (array of rank 2). The data set needs to * have been created by * {@link #createFloatMatrix(String, long, long, int, int, HDF5FloatStorageFeatures)} * beforehand. *

* Use this method instead of {@link #writeFloatMatrixBlock(String, float[][], long, long)} if * the total size of the data set is not a multiple of the block size. *

* Note: For best performance, the typical dataSize in this method should be * chosen to be equal to the blockSize argument of the * {@link #createFloatMatrix(String, long, long, int, int, HDF5FloatStorageFeatures)} call that * was used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param dataSizeX The (real) size of data along the x axis (needs to be * <= data.length ) * @param dataSizeY The (real) size of data along the y axis (needs to be * <= data[0].length ) * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. * @deprecated Use the corresponding method in {@link IHDF5Writer#float32()}. */ @Deprecated public void writeFloatMatrixBlockWithOffset(final String objectPath, final float[][] data, final int dataSizeX, final int dataSizeY, final long offsetX, final long offsetY); /** * Writes out a multi-dimensional float array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @deprecated Use the corresponding method in {@link IHDF5Writer#float32()}. */ @Deprecated public void writeFloatMDArray(final String objectPath, final MDFloatArray data); /** * Writes out a multi-dimensional float array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#float32()}. */ @Deprecated public void writeFloatMDArray(final String objectPath, final MDFloatArray data, final HDF5FloatStorageFeatures features); /** * Creates a multi-dimensional float array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the float array to create. This will be the total * dimensions for non-extendable data sets and the dimensions of one chunk (extent * along each axis) for extendable (chunked) data sets. For extendable data sets the * initial size of the array along each axis will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. * @deprecated Use the corresponding method in {@link IHDF5Writer#float32()}. */ @Deprecated public void createFloatMDArray(final String objectPath, final int[] dimensions); /** * Creates a multi-dimensional float array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. * @deprecated Use the corresponding method in {@link IHDF5Writer#float32()}. */ @Deprecated public void createFloatMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions); /** * Creates a multi-dimensional float array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. Will be the total dimensions for * non-extendable data sets and the dimensions of one chunk for extendable (chunked) * data sets For extendable data sets the initial size of the array along each axis * will be 0, see {@link HDF5FloatStorageFeatures}. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#float32()}. */ @Deprecated public void createFloatMDArray(final String objectPath, final int[] dimensions, final HDF5FloatStorageFeatures features); /** * Creates a multi-dimensional float array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#float32()}. */ @Deprecated public void createFloatMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions, final HDF5FloatStorageFeatures features); /** * Writes out a block of a multi-dimensional float array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). * @deprecated Use the corresponding method in {@link IHDF5Writer#float32()}. */ @Deprecated public void writeFloatMDArrayBlock(final String objectPath, final MDFloatArray data, final long[] blockNumber); /** * Writes out a block of a multi-dimensional float array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. * @deprecated Use the corresponding method in {@link IHDF5Writer#float32()}. */ @Deprecated public void writeFloatMDArrayBlockWithOffset(final String objectPath, final MDFloatArray data, final long[] offset); /** * Writes out a block of a multi-dimensional float array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param blockDimensions The dimensions of the block to write to the data set. * @param offset The offset of the block in the data set to start writing to in each dimension. * @param memoryOffset The offset of the block in the data array. * @deprecated Use the corresponding method in {@link IHDF5Writer#float32()}. */ @Deprecated public void writeFloatMDArrayBlockWithOffset(final String objectPath, final MDFloatArray data, final int[] blockDimensions, final long[] offset, final int[] memoryOffset); // ********************* // Double // ********************* // ///////////////////// // Attributes // ///////////////////// /** * Set a double attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#float64()}. */ @Deprecated public void setDoubleAttribute(final String objectPath, final String name, final double value); /** * Set a double[] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#float64()}. */ @Deprecated public void setDoubleArrayAttribute(final String objectPath, final String name, final double[] value); /** * Set a multi-dimensional code>double attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#float64()}. */ @Deprecated public void setDoubleMDArrayAttribute(final String objectPath, final String name, final MDDoubleArray value); /** * Set a double[][] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#float64()}. */ @Deprecated public void setDoubleMatrixAttribute(final String objectPath, final String name, final double[][] value); // ///////////////////// // Data Sets // ///////////////////// /** * Writes out a double value. * * @param objectPath The name (including path information) of the data set object in the file. * @param value The value to write. */ public void writeDouble(final String objectPath, final double value); /** * Writes out a double array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ public void writeDoubleArray(final String objectPath, final double[] data); /** * Writes out a double array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#float64()}. */ @Deprecated public void writeDoubleArray(final String objectPath, final double[] data, final HDF5FloatStorageFeatures features); /** * Creates a double array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the double array to create. This will be the total size for * non-extendable data sets and the size of one chunk for extendable (chunked) data * sets. For extendable data sets the initial size of the array will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. * @deprecated Use the corresponding method in {@link IHDF5Writer#float64()}. */ @Deprecated public void createDoubleArray(final String objectPath, final int size); /** * Creates a double array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the double array to create. When using extendable data sets ((see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data set * smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). * @deprecated Use the corresponding method in {@link IHDF5Writer#float64()}. */ @Deprecated public void createDoubleArray(final String objectPath, final long size, final int blockSize); /** * Creates a double array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the double array to create. This will be the total size for * non-extendable data sets and the size of one chunk for extendable (chunked) data * sets. For extendable data sets the initial size of the array will be 0, see * {@link HDF5FloatStorageFeatures}. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#float64()}. */ @Deprecated public void createDoubleArray(final String objectPath, final int size, final HDF5FloatStorageFeatures features); /** * Creates a double array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the double array to create. When using extendable data sets ((see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data set * smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) * and features is * HDF5FloatStorageFeature.FLOATNO_COMPRESSION. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#float64()}. */ @Deprecated public void createDoubleArray(final String objectPath, final long size, final int blockSize, final HDF5FloatStorageFeatures features); /** * Writes out a block of a double array (of rank 1). The data set needs to have * been created by {@link #createDoubleArray(String, long, int, HDF5FloatStorageFeatures)} * beforehand. *

* Note: For best performance, the block size in this method should be chosen to be equal * to the blockSize argument of the * {@link #createDoubleArray(String, long, int, HDF5FloatStorageFeatures)} call that was used to * create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumber The number of the block to write. * @deprecated Use the corresponding method in {@link IHDF5Writer#float64()}. */ @Deprecated public void writeDoubleArrayBlock(final String objectPath, final double[] data, final long blockNumber); /** * Writes out a block of a double array (of rank 1). The data set needs to have * been created by {@link #createDoubleArray(String, long, int, HDF5FloatStorageFeatures)} * beforehand. *

* Use this method instead of {@link #writeDoubleArrayBlock(String, double[], long)} if the * total size of the data set is not a multiple of the block size. *

* Note: For best performance, the typical dataSize in this method should be * chosen to be equal to the blockSize argument of the * {@link #createDoubleArray(String, long, int, HDF5FloatStorageFeatures)} call that was used to * create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param dataSize The (real) size of data (needs to be <= data.length * ) * @param offset The offset in the data set to start writing to. * @deprecated Use the corresponding method in {@link IHDF5Writer#float64()}. */ @Deprecated public void writeDoubleArrayBlockWithOffset(final String objectPath, final double[] data, final int dataSize, final long offset); /** * Writes out a double matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ public void writeDoubleMatrix(final String objectPath, final double[][] data); /** * Writes out a double matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#float64()}. */ @Deprecated public void writeDoubleMatrix(final String objectPath, final double[][] data, final HDF5FloatStorageFeatures features); /** * Creates a double matrix (array of rank 2). The initial size of the matrix is 0. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. * @deprecated Use the corresponding method in {@link IHDF5Writer#float64()}. */ @Deprecated public void createDoubleMatrix(final String objectPath, final int blockSizeX, final int blockSizeY); /** * Creates a double matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the double matrix to create. * @param sizeY The size of the y dimension of the double matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. * @deprecated Use the corresponding method in {@link IHDF5Writer#float64()}. */ @Deprecated public void createDoubleMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY); /** * Creates a double matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the double matrix to create. * @param sizeY The size of the y dimension of the double matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#float64()}. */ @Deprecated public void createDoubleMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY, final HDF5FloatStorageFeatures features); /** * Writes out a block of a double matrix (array of rank 2). The data set needs to * have been created by * {@link #createDoubleMatrix(String, long, long, int, int, HDF5FloatStorageFeatures)} * beforehand. *

* Use this method instead of * {@link #createDoubleMatrix(String, long, long, int, int, HDF5FloatStorageFeatures)} if the * total size of the data set is not a multiple of the block size. *

* Note: For best performance, the size of data in this method should match * the blockSizeX/Y arguments of the * {@link #createDoubleMatrix(String, long, long, int, int, HDF5FloatStorageFeatures)} call that * was used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumberX The block number in the x dimension (offset: multiply with * data.length). * @param blockNumberY The block number in the y dimension (offset: multiply with * data[0.length). * @deprecated Use the corresponding method in {@link IHDF5Writer#float64()}. */ @Deprecated public void writeDoubleMatrixBlock(final String objectPath, final double[][] data, final long blockNumberX, final long blockNumberY); /** * Writes out a block of a double matrix (array of rank 2). The data set needs to * have been created by * {@link #createDoubleMatrix(String, long, long, int, int, HDF5FloatStorageFeatures)} * beforehand. *

* Use this method instead of {@link #writeDoubleMatrixBlock(String, double[][], long, long)} if * the total size of the data set is not a multiple of the block size. *

* Note: For best performance, the typical dataSize in this method should be * chosen to be equal to the blockSize argument of the * {@link #createDoubleMatrix(String, long, long, int, int, HDF5FloatStorageFeatures)} call that * was used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. * @deprecated Use the corresponding method in {@link IHDF5Writer#float64()}. */ @Deprecated public void writeDoubleMatrixBlockWithOffset(final String objectPath, final double[][] data, final long offsetX, final long offsetY); /** * Writes out a block of a double matrix (array of rank 2). The data set needs to * have been created by * {@link #createDoubleMatrix(String, long, long, int, int, HDF5FloatStorageFeatures)} * beforehand. *

* Use this method instead of {@link #writeDoubleMatrixBlock(String, double[][], long, long)} if * the total size of the data set is not a multiple of the block size. *

* Note: For best performance, the typical dataSize in this method should be * chosen to be equal to the blockSize argument of the * {@link #createDoubleMatrix(String, long, long, int, int, HDF5FloatStorageFeatures)} call that * was used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param dataSizeX The (real) size of data along the x axis (needs to be * <= data.length ) * @param dataSizeY The (real) size of data along the y axis (needs to be * <= data[0].length ) * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. * @deprecated Use the corresponding method in {@link IHDF5Writer#float64()}. */ @Deprecated public void writeDoubleMatrixBlockWithOffset(final String objectPath, final double[][] data, final int dataSizeX, final int dataSizeY, final long offsetX, final long offsetY); /** * Writes out a multi-dimensional double array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ public void writeDoubleMDArray(final String objectPath, final MDDoubleArray data); /** * Writes out a multi-dimensional double array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#float64()}. */ @Deprecated public void writeDoubleMDArray(final String objectPath, final MDDoubleArray data, final HDF5FloatStorageFeatures features); /** * Creates a multi-dimensional double array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the double array to create. This will be the total * dimensions for non-extendable data sets and the dimensions of one chunk (extent * along each axis) for extendable (chunked) data sets. For extendable data sets the * initial size of the array along each axis will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. * @deprecated Use the corresponding method in {@link IHDF5Writer#float64()}. */ @Deprecated public void createDoubleMDArray(final String objectPath, final int[] dimensions); /** * Creates a multi-dimensional double array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. * @deprecated Use the corresponding method in {@link IHDF5Writer#float64()}. */ @Deprecated public void createDoubleMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions); /** * Creates a multi-dimensional double array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. Will be the total dimensions for * non-extendable data sets and the dimensions of one chunk for extendable (chunked) * data sets For extendable data sets the initial size of the array along each axis * will be 0, see {@link HDF5FloatStorageFeatures}. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#float64()}. */ @Deprecated public void createDoubleMDArray(final String objectPath, final int[] dimensions, final HDF5FloatStorageFeatures features); /** * Creates a multi-dimensional double array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#float64()}. */ @Deprecated public void createDoubleMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions, final HDF5FloatStorageFeatures features); /** * Writes out a block of a multi-dimensional double array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). * @deprecated Use the corresponding method in {@link IHDF5Writer#float64()}. */ @Deprecated public void writeDoubleMDArrayBlock(final String objectPath, final MDDoubleArray data, final long[] blockNumber); /** * Writes out a block of a multi-dimensional double array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. * @deprecated Use the corresponding method in {@link IHDF5Writer#float64()}. */ @Deprecated public void writeDoubleMDArrayBlockWithOffset(final String objectPath, final MDDoubleArray data, final long[] offset); /** * Writes out a block of a multi-dimensional double array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param blockDimensions The dimensions of the block to write to the data set. * @param offset The offset of the block in the data set to start writing to in each dimension. * @param memoryOffset The offset of the block in the data array. * @deprecated Use the corresponding method in {@link IHDF5Writer#float64()}. */ @Deprecated public void writeDoubleMDArrayBlockWithOffset(final String objectPath, final MDDoubleArray data, final int[] blockDimensions, final long[] offset, final int[] memoryOffset); // ********************* // String // ********************* // ///////////////////// // Attributes // ///////////////////// /** * Sets a string attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void setStringAttribute(final String objectPath, final String name, final String value); /** * Sets a string attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @param maxLength The maximal length of the value. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void setStringAttribute(final String objectPath, final String name, final String value, final int maxLength); /** * Sets a string array attribute on the referenced object. The length of the array is taken to * be the longest string in value. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void setStringArrayAttribute(final String objectPath, final String name, final String[] value); /** * Sets a string array attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @param maxLength The maximal length of any element in value. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void setStringArrayAttribute(final String objectPath, final String name, final String[] value, final int maxLength); /** * Sets a multi-dimensional string array attribute on the referenced object. The length of the * array is taken to be the longest string in value. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void setStringMDArrayAttribute(final String objectPath, final String name, final MDArray value); /** * Sets a multi-dimensional string array attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @param maxLength The maximal length of the value. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void setStringMDArrayAttribute(final String objectPath, final String name, final MDArray value, final int maxLength); /** * Sets a string attribute with variable length on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void setStringAttributeVariableLength(final String objectPath, final String name, final String value); // ///////////////////// // Data Sets // ///////////////////// /** * Writes out a String with a fixed maximal length. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param maxLength The maximal length of the data. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void writeString(final String objectPath, final String data, final int maxLength); /** * Writes out a String with a fixed maximal length (which is the length of the * string data). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ public void writeString(final String objectPath, final String data); /** * Writes out a String with a fixed maximal length. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void writeString(final String objectPath, final String data, final HDF5GenericStorageFeatures features); /** * Writes out a String with a fixed maximal length. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param maxLength The maximal length of the data. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void writeString(final String objectPath, final String data, final int maxLength, final HDF5GenericStorageFeatures features); /** * Writes out a String array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void writeStringArray(final String objectPath, final String[] data, final HDF5GenericStorageFeatures features); /** * Writes out a String array (of rank 1). Each element of the array will have a * fixed maximal length which is defined by the longest string in data. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ public void writeStringArray(final String objectPath, final String[] data); /** * Writes out a String array (of rank 1). Each element of the array will have a * fixed maximal length which is given by maxLength. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param maxLength The maximal length of any of the strings in data. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void writeStringArray(final String objectPath, final String[] data, final int maxLength); /** * Writes out a String array (of rank 1). Each element of the array will have a * fixed maximal length which is given by maxLength. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param maxLength The maximal length of any of the strings in data. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void writeStringArray(final String objectPath, final String[] data, final int maxLength, final HDF5GenericStorageFeatures features); /** * Writes out a String array (of rank N). Each element of the array will have a * fixed maximal length which is defined by the longest string in data. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void writeStringMDArray(final String objectPath, final MDArray data); /** * Writes out a String array (of rank N). Each element of the array will have a * fixed maximal length which is defined by the longest string in data. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void writeStringMDArray(final String objectPath, final MDArray data, final HDF5GenericStorageFeatures features); /** * Writes out a String array (of rank N). Each element of the array will have a * fixed maximal length which is given by maxLength. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param maxLength The maximal length of any of the strings in data. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void writeStringMDArray(final String objectPath, final MDArray data, final int maxLength); /** * Writes out a String array (of rank N). Each element of the array will have a * fixed maximal length which is given by maxLength. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param maxLength The maximal length of any of the strings in data. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void writeStringMDArray(final String objectPath, final MDArray data, final int maxLength, final HDF5GenericStorageFeatures features); /** * Creates a String array (of rank 1) for Strings of length maxLength. * * @param objectPath The name (including path information) of the data set object in the file. * @param maxLength The maximal length of one String in the array. * @param size The size of the byte array to create. This will be the total size for * non-extendable data sets and the size of one chunk for extendable (chunked) data * sets. For extendable data sets the initial size of the array will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void createStringArray(final String objectPath, final int maxLength, final int size); /** * Creates a String array (of rank 1) for Strings of length maxLength. * * @param objectPath The name (including path information) of the data set object in the file. * @param maxLength The maximal length of one String in the array. * @param size The size of the String array to create. When using extendable data sets ((see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data set * smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void createStringArray(final String objectPath, final int maxLength, final long size, final int blockSize); /** * Creates a String array (of rank 1) for Strings of length maxLength. * * @param objectPath The name (including path information) of the data set object in the file. * @param maxLength The maximal length of one String in the array. * @param size The size of the array to create. This will be the total size for non-extendable * data sets and the size of one chunk for extendable (chunked) data sets. For * extendable data sets the initial size of the array will be 0, see * {@link HDF5GenericStorageFeatures}. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void createStringArray(final String objectPath, final int maxLength, final int size, final HDF5GenericStorageFeatures features); /** * Creates a String array (of rank 1) for Strings of length maxLength. * * @param objectPath The name (including path information) of the data set object in the file. * @param maxLength The maximal length of one String in the array. * @param size The size of the String array to create. When using extendable data sets ((see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data set * smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void createStringArray(final String objectPath, final int maxLength, final long size, final int blockSize, final HDF5GenericStorageFeatures features); /** * Writes out a block of a String array (of rank 1). The data set needs to have * been created by * {@link #createStringArray(String, int, long, int, HDF5GenericStorageFeatures)} beforehand. *

* Note: For best performance, the block size in this method should be chosen to be equal * to the blockSize argument of the * {@link #createStringArray(String, int, long, int, HDF5GenericStorageFeatures)} call that was * used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumber The number of the block to write. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void writeStringArrayBlock(final String objectPath, final String[] data, final long blockNumber); /** * Writes out a block of a String array (of rank 1). The data set needs to have * been created by * {@link #createStringArray(String, int, long, int, HDF5GenericStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeStringArrayBlock(String, String[], long)} if the * total size of the data set is not a multiple of the block size. *

* Note: For best performance, the block size in this method should be chosen to be equal * to the blockSize argument of the * {@link #createStringArray(String, int, long, int, HDF5GenericStorageFeatures)} call that was * used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param dataSize The (real) size of data (needs to be <= data.length * ) * @param offset The offset in the data set to start writing to. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void writeStringArrayBlockWithOffset(final String objectPath, final String[] data, final int dataSize, final long offset); /** * Creates a String array (of rank N) for Strings of length maxLength. * * @param objectPath The name (including path information) of the data set object in the file. * @param maxLength The maximal length of one String in the array. * @param dimensions The size of the String array to create. When using extendable data sets * ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data * set smaller than this size can be created, however data sets may be larger. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void createStringMDArray(final String objectPath, final int maxLength, final int[] dimensions); /** * Creates a String array (of rank N) for Strings of length maxLength. * * @param objectPath The name (including path information) of the data set object in the file. * @param maxLength The maximal length of one String in the array. * @param dimensions The size of the String array to create. When using extendable data sets * ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data * set smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block in each dimension (for block-wise IO). Ignored if no * extendable data sets are used (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void createStringMDArray(final String objectPath, final int maxLength, final long[] dimensions, final int[] blockSize); /** * Creates a String array (of rank N) for Strings of length maxLength. * * @param objectPath The name (including path information) of the data set object in the file. * @param maxLength The maximal length of one String in the array. * @param dimensions The size of the String array to create. When using extendable data sets * ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data * set smaller than this size can be created, however data sets may be larger. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void createStringMDArray(final String objectPath, final int maxLength, final int[] dimensions, final HDF5GenericStorageFeatures features); /** * Creates a String array (of rank N) for Strings of length maxLength. * * @param objectPath The name (including path information) of the data set object in the file. * @param maxLength The maximal length of one String in the array. * @param dimensions The size of the String array to create. When using extendable data sets * ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data * set smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block in each dimension (for block-wise IO). Ignored if no * extendable data sets are used (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void createStringMDArray(final String objectPath, final int maxLength, final long[] dimensions, final int[] blockSize, final HDF5GenericStorageFeatures features); /** * Writes out a block of a String array (of rank N). The data set needs to have * been created by * {@link #createStringMDArray(String, int, long[], int[], HDF5GenericStorageFeatures)} * beforehand. *

* Note: For best performance, the block size in this method should be chosen to be equal * to the blockSize argument of the * {@link #createStringMDArray(String, int, long[], int[], HDF5GenericStorageFeatures)} call * that was used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumber The number of the block to write in each dimension. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void writeStringMDArrayBlock(final String objectPath, final MDArray data, final long[] blockNumber); /** * Writes out a block of a String array (of rank N). The data set needs to have * been created by * {@link #createStringMDArray(String, int, long[], int[], HDF5GenericStorageFeatures)} * beforehand. *

* Note: For best performance, the block size in this method should be chosen to be equal * to the blockSize argument of the * {@link #createStringMDArray(String, int, long[], int[], HDF5GenericStorageFeatures)} call * that was used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param offset The offset in the data set to start writing to. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void writeStringMDArrayBlockWithOffset(final String objectPath, final MDArray data, final long[] offset); /** * Writes out a String with variable maximal length. *

* The advantage of this method over {@link #writeString(String, String)} is that when writing a * new string later it can have a different (also greater) length. The disadvantage is that it * it is more time consuming to read and write this kind of string and that it can't be * compressed. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void writeStringVariableLength(final String objectPath, final String data); /** * Writes out a String[] where each String of the array has a variable maximal * length. *

* The advantage of this method over {@link #writeStringArray(String, String[])} is that when * writing a new string later it can have a different (also greater) length. The disadvantage is * that it it is more time consuming to read and write this kind of string and that it can't be * compressed. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void writeStringVariableLengthArray(final String objectPath, final String[] data); /** * Writes out a String[] where each String of the array has a variable maximal * length. *

* The advantage of this method over {@link #writeStringArray(String, String[])} is that when * writing a new string later it can have a different (also greater) length. The disadvantage is * that it it is more time consuming to read and write this kind of string and that it can't be * compressed. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void writeStringVariableLengthArray(final String objectPath, final String[] data, final HDF5GenericStorageFeatures features); /** * Creates a String[] where each String of the array has a variable maximal length. * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the byte array to create. This will be the total size for * non-extendable data sets and the size of one chunk for extendable (chunked) data * sets. For extendable data sets the initial size of the array will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void createStringVariableLengthArray(final String objectPath, final int size); /** * Creates a String[] where each String of the array has a variable maximal length. * * @param objectPath The name (including path information) of the data set object in the file. * @param size The intial size of the array. * @param blockSize The size of block in the array. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void createStringVariableLengthArray(final String objectPath, final long size, final int blockSize); /** * Creates a String[] where each String of the array has a variable maximal length. * * @param objectPath The name (including path information) of the data set object in the file. * @param size The initial size of the array. * @param blockSize The size of block in the array. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void createStringVariableLengthArray(final String objectPath, final long size, final int blockSize, final HDF5GenericStorageFeatures features); /** * Creates a String[] where each String of the array has a variable maximal length. * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the byte array to create. This will be the total size for * non-extendable data sets and the size of one chunk for extendable (chunked) data * sets. For extendable data sets the initial size of the array will be 0, see * {@link HDF5GenericStorageFeatures}. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void createStringVariableLengthArray(final String objectPath, final int size, final HDF5GenericStorageFeatures features); /** * Creates a multi-dimensional String array where each String of the array has a * variable maximal length. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The initial dimensions (along each axis) of the array. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void createStringVariableLengthMDArray(final String objectPath, final int[] dimensions, final HDF5GenericStorageFeatures features); /** * Creates a multi-dimensional String array where each String of the array has a * variable maximal length. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The initial dimensions (along each axis) of the array. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void createStringVariableLengthMDArray(final String objectPath, final int[] dimensions); /** * Creates a multi-dimensional String array where each String of the array has a * variable maximal length. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The initial dimensions (along each axis) of the array. * @param blockSize The size of a contiguously stored block (along each axis) in the array. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void createStringVariableLengthMDArray(final String objectPath, final long[] dimensions, final int[] blockSize, final HDF5GenericStorageFeatures features); /** * Creates a multi-dimensional String array where each String of the array has a * variable maximal length. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The initial dimensions (along each axis) of the array. * @param blockSize The size of a contiguously stored block (along each axis) in the array. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void createStringVariableLengthMDArray(final String objectPath, final long[] dimensions, final int[] blockSize); /** * Writes out a String array (of rank N). Each element of the array will have a * variable maximal length. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void writeStringVariableLengthMDArray(final String objectPath, final MDArray data); /** * Writes out a String array (of rank N). Each element of the array will have a * variable maximal length. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#string()} instead. */ @Deprecated public void writeStringVariableLengthMDArray(final String objectPath, final MDArray data, final HDF5GenericStorageFeatures features); // ********************* // Date & Time // ********************* // ///////////////////// // Attributes // ///////////////////// /** * Set a date value as attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param attributeName The name of the attribute. * @param date The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#time()} instead. */ @Deprecated public void setDateAttribute(final String objectPath, final String attributeName, final Date date); /** * Set a date array value as attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param attributeName The name of the attribute. * @param dates The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#time()} instead. */ @Deprecated public void setDateArrayAttribute(final String objectPath, final String attributeName, final Date[] dates); /** * Set a time stamp value as attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param attributeName The name of the attribute. * @param timeStamp The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#time()} instead. */ @Deprecated public void setTimeStampAttribute(final String objectPath, final String attributeName, final long timeStamp); /** * Set a time stamp array value as attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param attributeName The name of the attribute. * @param timeStamps The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#time()} instead. */ @Deprecated public void setTimeStampArrayAttribute(final String objectPath, final String attributeName, final long[] timeStamps); /** * Set a time duration value as attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param attributeName The name of the attribute. * @param timeDuration The value of the attribute. * @param timeUnit The unit of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#time()} instead. */ @Deprecated public void setTimeDurationAttribute(final String objectPath, final String attributeName, final long timeDuration, final HDF5TimeUnit timeUnit); /** * Set a time duration value as attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param attributeName The name of the attribute. * @param timeDuration The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#time()} instead. */ @Deprecated public void setTimeDurationAttribute(final String objectPath, final String attributeName, final HDF5TimeDuration timeDuration); /** * Set a time duration array value as attribute on the referenced object. The smallest time unit * in timeDurations will be used as the time unit of the array. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. *

* Note: Time durations are stored as a long[] array. * * @param objectPath The name of the object to add the attribute to. * @param attributeName The name of the attribute. * @param timeDurations The value of the attribute. * @deprecated Use the corresponding method in {@link IHDF5Writer#time()} instead. */ @Deprecated public void setTimeDurationArrayAttribute(final String objectPath, final String attributeName, final HDF5TimeDurationArray timeDurations); // ///////////////////// // Data Sets // ///////////////////// /** * Writes out a time stamp value. The data set will be tagged as type variant * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. *

* Note: Time stamps are stored as long values. * * @param objectPath The name (including path information) of the data set object in the file. * @param timeStamp The timestamp to write as number of milliseconds since January 1, 1970, * 00:00:00 GMT. * @deprecated Use the corresponding method in {@link IHDF5Writer#time()} instead. */ @Deprecated public void writeTimeStamp(final String objectPath, final long timeStamp); /** * Creates a time stamp array (of rank 1). *

* Note: Time stamps are stored as long values. * * @param objectPath The name (including path information) of the data set object in the file. * @param size The length of the data set to create. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) * and deflate == false. * @deprecated Use the corresponding method in {@link IHDF5Writer#time()} instead. */ @Deprecated public void createTimeStampArray(final String objectPath, final long size, final int blockSize); /** * Creates a time stamp array (of rank 1). *

* Note: Time stamps are stored as long values. * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the byte array to create. This will be the total size for * non-extendable data sets and the size of one chunk for extendable (chunked) data * sets. For extendable data sets the initial size of the array will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. * @deprecated Use the corresponding method in {@link IHDF5Writer#time()} instead. */ @Deprecated public void createTimeStampArray(final String objectPath, final int size); /** * Creates a time stamp array (of rank 1). *

* Note: Time stamps are stored as long values. * * @param objectPath The name (including path information) of the data set object in the file. * @param size The length of the data set to create. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) * and deflate == false. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#time()} instead. */ @Deprecated public void createTimeStampArray(final String objectPath, final long size, final int blockSize, final HDF5GenericStorageFeatures features); /** * Creates a time stamp array (of rank 1). *

* Note: Time stamps are stored as long values. * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the array to create. This will be the total size for non-extendable * data sets and the size of one chunk for extendable (chunked) data sets. For * extendable data sets the initial size of the array will be 0, see * {@link HDF5GenericStorageFeatures}. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#time()} instead. */ @Deprecated public void createTimeStampArray(final String objectPath, final int size, final HDF5GenericStorageFeatures features); /** * Writes out a time stamp array (of rank 1). The data set will be tagged as type variant * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. *

* Note: Time stamps are stored as long values. * * @param objectPath The name (including path information) of the data set object in the file. * @param timeStamps The timestamps to write as number of milliseconds since January 1, 1970, * 00:00:00 GMT. * @deprecated Use the corresponding method in {@link IHDF5Writer#time()} instead. */ @Deprecated public void writeTimeStampArray(final String objectPath, final long[] timeStamps); /** * Writes out a time stamp array (of rank 1). The data set will be tagged as type variant * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. *

* Note: Time stamps are stored as long values. * * @param objectPath The name (including path information) of the data set object in the file. * @param timeStamps The timestamps to write as number of milliseconds since January 1, 1970, * 00:00:00 GMT. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#time()} instead. */ @Deprecated public void writeTimeStampArray(final String objectPath, final long[] timeStamps, final HDF5GenericStorageFeatures features); /** * Writes out a block of a time stamp array (which is stored as a long array of * rank 1). The data set needs to have been created by * {@link #createTimeStampArray(String, long, int, HDF5GenericStorageFeatures)} beforehand. *

* Note: For best performance, the block size in this method should be chosen to be equal * to the blockSize argument of the * {@link IHDF5LongWriter#createArray(String, long, int, HDF5IntStorageFeatures)} call that was * used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumber The number of the block to write. * @deprecated Use the corresponding method in {@link IHDF5Writer#time()} instead. */ @Deprecated public void writeTimeStampArrayBlock(final String objectPath, final long[] data, final long blockNumber); /** * Writes out a block of a time stamp array (which is stored as a long array of * rank 1). The data set needs to have been created by * {@link #createTimeStampArray(String, long, int, HDF5GenericStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeTimeStampArrayBlock(String, long[], long)} if the * total size of the data set is not a multiple of the block size. *

* Note: For best performance, the typical dataSize in this method should be * chosen to be equal to the blockSize argument of the * {@link IHDF5LongWriter#createArray(String, long, int, HDF5IntStorageFeatures)} call that was * used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param dataSize The (real) size of data (needs to be <= data.length * ) * @param offset The offset in the data set to start writing to. * @deprecated Use the corresponding method in {@link IHDF5Writer#time()} instead. */ @Deprecated public void writeTimeStampArrayBlockWithOffset(final String objectPath, final long[] data, final int dataSize, final long offset); /** * Writes out a time stamp value provided as a {@link Date}. *

* Note: The time stamp is stored as long array and tagged as the according * type variant. * * @param objectPath The name (including path information) of the data set object in the file. * @param date The date to write. * @see #writeTimeStamp(String, long) */ public void writeDate(final String objectPath, final Date date); /** * Writes out a {@link Date} array (of rank 1). *

* Note: Time stamps are stored as long[] arrays and tagged as the according * type variant. * * @param objectPath The name (including path information) of the data set object in the file. * @param dates The dates to write. * @see #writeTimeStampArray(String, long[]) */ public void writeDateArray(final String objectPath, final Date[] dates); /** * Writes out a {@link Date} array (of rank 1). *

* Note: Time date is stored as long[] arrays and tagged as the according * type variant. * * @param objectPath The name (including path information) of the data set object in the file. * @param dates The dates to write. * @param features The storage features of the data set. * @see #writeTimeStampArray(String, long[], HDF5GenericStorageFeatures) * @deprecated Use the corresponding method in {@link IHDF5Writer#time()} instead. */ @Deprecated public void writeDateArray(final String objectPath, final Date[] dates, final HDF5GenericStorageFeatures features); /** * Writes out a time duration value in seconds. *

* Note: Time durations are stored as long and tagged as the according * type variant. * * @param objectPath The name (including path information) of the data set object in the file. * @param timeDuration The duration of time to write in seconds. * @deprecated Use {@link IHDF5TimeDurationWriter#write(String, HDF5TimeDuration)} instead. */ @Deprecated public void writeTimeDuration(final String objectPath, final long timeDuration); /** * Writes out a time duration value. *

* Note: Time durations are stored as long[] arrays and tagged as the according * type variant. * * @param objectPath The name (including path information) of the data set object in the file. * @param timeDuration The duration of time to write in the given timeUnit. * @param timeUnit The unit of the time duration. * @deprecated Use the corresponding method in {@link IHDF5Writer#time()} instead. */ @Deprecated public void writeTimeDuration(final String objectPath, final long timeDuration, final HDF5TimeUnit timeUnit); /** * Writes out a time duration value. *

* Note: Time durations are stored as long[] arrays and tagged as the according * type variant. * * @param objectPath The name (including path information) of the data set object in the file. * @param timeDuration The duration of time to write. */ public void writeTimeDuration(final String objectPath, final HDF5TimeDuration timeDuration); /** * Creates a time duration array (of rank 1). *

* Note: Time durations are stored as long values. * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the byte array to create. This will be the total size for * non-extendable data sets and the size of one chunk for extendable (chunked) data * sets. For extendable data sets the initial size of the array will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. * @param timeUnit The unit of the time duration. * @deprecated Use the corresponding method in {@link IHDF5Writer#time()} instead. */ @Deprecated public void createTimeDurationArray(final String objectPath, final int size, final HDF5TimeUnit timeUnit); /** * Creates a time duration array (of rank 1). *

* Note: Time durations are stored as long[] arrays and tagged as the according * type variant. * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the data set to create. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) * and deflate == false. * @param timeUnit The unit of the time duration. * @deprecated Use the corresponding method in {@link IHDF5Writer#time()} instead. */ @Deprecated public void createTimeDurationArray(final String objectPath, final long size, final int blockSize, final HDF5TimeUnit timeUnit); /** * Creates a time duration array (of rank 1). *

* Note: Time durations are stored as long[] arrays and tagged as the according * type variant. * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the data set to create. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) * and deflate == false. * @param timeUnit The unit of the time duration. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#time()} instead. */ @Deprecated public void createTimeDurationArray(final String objectPath, final long size, final int blockSize, final HDF5TimeUnit timeUnit, final HDF5GenericStorageFeatures features); /** * Creates a time duration array (of rank 1). *

* Note: Time durations are stored as long[] arrays and tagged as the according * type variant. * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the array to create. This will be the total size for non-extendable * data sets and the size of one chunk for extendable (chunked) data sets. For * extendable data sets the initial size of the array will be 0, see * {@link HDF5GenericStorageFeatures}. * @param timeUnit The unit of the time duration. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#time()} instead. */ @Deprecated public void createTimeDurationArray(final String objectPath, final int size, final HDF5TimeUnit timeUnit, final HDF5GenericStorageFeatures features); /** * Writes out a time duration array in seconds (of rank 1). * Note: Time durations are stored as long[] arrays and tagged as the according * type variant. *

* Note: Time durations are stored as long[] arrays and tagged as the according * type variant. * * @param objectPath The name (including path information) of the data set object in the file. * @param timeDurations The time durations to write in seconds. * @deprecated Use {@link IHDF5TimeDurationWriter#writeArray(String, HDF5TimeDurationArray)} * instead. */ @Deprecated public void writeTimeDurationArray(final String objectPath, final long[] timeDurations); /** * Writes out a time duration array (of rank 1). *

* Note: Time durations are stored as long[] arrays and tagged as the according * type variant. * * @param objectPath The name (including path information) of the data set object in the file. * @param timeDurations The time durations to write in the given timeUnit. * @param timeUnit The unit of the time duration. * @deprecated Use {@link IHDF5TimeDurationWriter#writeArray(String, HDF5TimeDurationArray)} * instead. */ @Deprecated public void writeTimeDurationArray(final String objectPath, final long[] timeDurations, final HDF5TimeUnit timeUnit); /** * Writes out a time duration array (of rank 1). The smallest time unit in * timeDurations will be used as the time unit of the array. *

* Note: Time durations are stored as long[] arrays and tagged as the according * type variant. * * @param objectPath The name (including path information) of the data set object in the file. * @param timeDurations The time durations to write in the given timeUnit. The array * will be stored in the smallest time unit, durations given in larger time units * will be converted. * @deprecated Use {@link IHDF5TimeDurationWriter#writeArray(String, HDF5TimeDurationArray)} and * {@link HDF5TimeDurationArray#create(HDF5TimeDuration...)} instead. */ @Deprecated public void writeTimeDurationArray(final String objectPath, final HDF5TimeDuration[] timeDurations); /** * Writes out a time duration array (of rank 1). *

* Note: Time durations are stored as long[] arrays and tagged as the according * type variant. * * @param objectPath The name (including path information) of the data set object in the file. * @param timeDurations The time durations to write in the given timeUnit. * @param timeUnit The unit of the time duration. * @param features The storage features of the data set. * @deprecated Use * {@link IHDF5TimeDurationWriter#writeArray(String, HDF5TimeDurationArray, HDF5IntStorageFeatures) * )} instead. */ @Deprecated public void writeTimeDurationArray(final String objectPath, final long[] timeDurations, final HDF5TimeUnit timeUnit, final HDF5IntStorageFeatures features); /** * Writes out a time duration array (of rank 1). *

* Note: Time durations are stored as long[] arrays and tagged as the according * type variant. * * @param objectPath The name (including path information) of the data set object in the file. * @param timeDurations The time durations to write in the given timeUnit. The array * will be stored in the smallest time unit, durations given in larger time units * will be converted. * @deprecated Use * {@link IHDF5TimeDurationWriter#writeArray(String, HDF5TimeDurationArray, HDF5IntStorageFeatures)} * and {@link HDF5TimeDurationArray#create(HDF5TimeDuration...)} instead. */ @Deprecated public void writeTimeDurationArray(final String objectPath, final HDF5TimeDuration[] timeDurations, final HDF5IntStorageFeatures features); /** * Writes out a time duration array (of rank 1). *

* Note: Time durations are stored as long[] arrays and tagged as the according * type variant. * * @param objectPath The name (including path information) of the data set object in the file. * @param timeDurations The time durations to write. */ public void writeTimeDurationArray(final String objectPath, final HDF5TimeDurationArray timeDurations); /** * Writes out a time duration array (of rank 1). *

* Note: Time durations are stored as long[] arrays and tagged as the according * type variant. * * @param objectPath The name (including path information) of the data set object in the file. * @param timeDurations The time durations to write. * @param features The storage features used to store the array. * @deprecated Use the corresponding method in {@link IHDF5Writer#time()} instead. */ @Deprecated public void writeTimeDurationArray(final String objectPath, final HDF5TimeDurationArray timeDurations, final HDF5IntStorageFeatures features); /** * Writes out a block of a time duration array. The data set needs to have been created by * {@link #createTimeDurationArray(String, long, int, HDF5TimeUnit, HDF5GenericStorageFeatures)} * beforehand. *

* Note: For best performance, the block size in this method should be chosen to be equal * to the blockSize argument of the * {@link #createTimeDurationArray(String, long, int, HDF5TimeUnit, HDF5GenericStorageFeatures)} * call that was used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumber The number of the block to write. * @deprecated Use the corresponding method in {@link IHDF5Writer#time()} instead. */ @Deprecated public void writeTimeDurationArrayBlock(final String objectPath, final HDF5TimeDurationArray data, final long blockNumber); /** * Writes out a block of a time duration array. The data set needs to have been created by * {@link #createTimeDurationArray(String, long, int, HDF5TimeUnit, HDF5GenericStorageFeatures)} * beforehand. *

* Use this method instead of * {@link #writeTimeDurationArrayBlock(String, long[], long, HDF5TimeUnit)} if the total size of * the data set is not a multiple of the block size. *

* Note: For best performance, the typical dataSize in this method should be * chosen to be equal to the blockSize argument of the * {@link #createTimeDurationArray(String, long, int, HDF5TimeUnit, HDF5GenericStorageFeatures)} * call that was used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param dataSize The (real) size of data (needs to be <= data.length * ) * @param offset The offset in the data set to start writing to. * @deprecated Use the corresponding method in {@link IHDF5Writer#time()} instead. */ @Deprecated public void writeTimeDurationArrayBlockWithOffset(final String objectPath, final HDF5TimeDurationArray data, final int dataSize, final long offset); /** * Writes out a block of a time duration array (which is stored as a long array of * rank 1). The data set needs to have been created by * {@link #createTimeDurationArray(String, long, int, HDF5TimeUnit, HDF5GenericStorageFeatures)} * beforehand. *

* Note: For best performance, the block size in this method should be chosen to be equal * to the blockSize argument of the * {@link #createTimeDurationArray(String, long, int, HDF5TimeUnit, HDF5GenericStorageFeatures)} * call that was used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumber The number of the block to write. * @deprecated Use * {@link IHDF5TimeDurationWriter#writeArrayBlock(String, HDF5TimeDurationArray, long)} * and {@link HDF5TimeDurationArray#create(HDF5TimeUnit, long...)} instead. */ @Deprecated public void writeTimeDurationArrayBlock(final String objectPath, final long[] data, final long blockNumber, final HDF5TimeUnit timeUnit); /** * Writes out a block of a time duration array (which is stored as a long array of * rank 1). The data set needs to have been created by * {@link #createTimeDurationArray(String, long, int, HDF5TimeUnit, HDF5GenericStorageFeatures)} * beforehand. *

* Use this method instead of * {@link #writeTimeDurationArrayBlock(String, long[], long, HDF5TimeUnit)} if the total size of * the data set is not a multiple of the block size. *

* Note: For best performance, the typical dataSize in this method should be * chosen to be equal to the blockSize argument of the * {@link #createTimeDurationArray(String, long, int, HDF5TimeUnit, HDF5GenericStorageFeatures)} * call that was used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param dataSize The (real) size of data (needs to be <= data.length * ) * @param offset The offset in the data set to start writing to. * @deprecated Use * {@link IHDF5TimeDurationWriter#writeArrayBlockWithOffset(String, HDF5TimeDurationArray, int, long)} * and {@link HDF5TimeDurationArray#create(HDF5TimeUnit, long[])} instead. */ @Deprecated public void writeTimeDurationArrayBlockWithOffset(final String objectPath, final long[] data, final int dataSize, final long offset, final HDF5TimeUnit timeUnit); /** * Writes out a block of a time duration array (which is stored as a long array of * rank 1). The data set needs to have been created by * {@link #createTimeDurationArray(String, long, int, HDF5TimeUnit, HDF5GenericStorageFeatures)} * beforehand. *

* Note: For best performance, the block size in this method should be chosen to be equal * to the blockSize argument of the * {@link #createTimeDurationArray(String, long, int, HDF5TimeUnit, HDF5GenericStorageFeatures)} * call that was used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumber The number of the block to write. * @deprecated Use * {@link IHDF5TimeDurationWriter#writeArrayBlock(String, HDF5TimeDurationArray, long)} * and {@link HDF5TimeDurationArray#create(HDF5TimeDuration[])} instead. */ @Deprecated public void writeTimeDurationArrayBlock(final String objectPath, final HDF5TimeDuration[] data, final long blockNumber); /** * Writes out a block of a time duration array (which is stored as a long array of * rank 1). The data set needs to have been created by * {@link #createTimeDurationArray(String, long, int, HDF5TimeUnit, HDF5GenericStorageFeatures)} * beforehand. *

* Use this method instead of * {@link #writeTimeDurationArrayBlock(String, long[], long, HDF5TimeUnit)} if the total size of * the data set is not a multiple of the block size. *

* Note: For best performance, the typical dataSize in this method should be * chosen to be equal to the blockSize argument of the * {@link #createTimeDurationArray(String, long, int, HDF5TimeUnit, HDF5GenericStorageFeatures)} * call that was used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param dataSize The (real) size of data (needs to be <= data.length * ) * @param offset The offset in the data set to start writing to. * @deprecated Use * {@link IHDF5TimeDurationWriter#writeArrayBlockWithOffset(String, HDF5TimeDurationArray, int, long)} * and {@link HDF5TimeDurationArray#create(HDF5TimeDuration[])}. */ @Deprecated public void writeTimeDurationArrayBlockWithOffset(final String objectPath, final HDF5TimeDuration[] data, final int dataSize, final long offset); // ********************* // Reference // ********************* // ///////////////////// // Attributes // ///////////////////// /** * Sets an object reference attribute to the referenced object. *

* Both the object referenced with objectPath and referencedObjectPath * must exist, that is it need to have been written before by one of the write() or * create() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param referencedObjectPath The path of the object to reference. * @deprecated Use the corresponding method in {@link IHDF5Writer#reference()}. */ @Deprecated public void setObjectReferenceAttribute(final String objectPath, final String name, final String referencedObjectPath); /** * Sets a 1D object reference array attribute to referenced objects. *

* Both the object referenced with objectPath and all * referencedObjectPaths must exist, that is it need to have been written before by * one of the write() or create() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param referencedObjectPaths The paths of the objects to reference. * @deprecated Use the corresponding method in {@link IHDF5Writer#reference()}. */ @Deprecated public void setObjectReferenceArrayAttribute(final String objectPath, final String name, final String[] referencedObjectPaths); /** * Sets an object reference array attribute to referenced objects. *

* Both the object referenced with objectPath and all * referencedObjectPaths must exist, that is it need to have been written before by * one of the write() or create() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param referencedObjectPaths The paths of the objects to reference. * @deprecated Use the corresponding method in {@link IHDF5Writer#reference()}. */ @Deprecated public void setObjectReferenceMDArrayAttribute(final String objectPath, final String name, final MDArray referencedObjectPaths); // ///////////////////// // Data Sets // ///////////////////// /** * Writes an object reference to the referenced object. *

* The object referenced with referencedObjectPath must exist, that is it need to * have been written before by one of the write() or create() methods. * * @param objectPath The name of the object to write. * @param referencedObjectPath The path of the object to reference. * @deprecated Use the corresponding method in {@link IHDF5Writer#reference()}. */ @Deprecated public void writeObjectReference(String objectPath, String referencedObjectPath); /** * Writes an array (of rank 1) of object references. * * @param objectPath The name (including path information) of the data set object in the file. * @param referencedObjectPath The names of the object to write. * @deprecated Use the corresponding method in {@link IHDF5Writer#reference()}. */ @Deprecated public void writeObjectReferenceArray(final String objectPath, final String[] referencedObjectPath); /** * Writes an array (of rank 1) of object references. * * @param objectPath The name (including path information) of the data set object in the file. * @param referencedObjectPath The names of the object to write. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#reference()}. */ @Deprecated public void writeObjectReferenceArray(final String objectPath, final String[] referencedObjectPath, final HDF5IntStorageFeatures features); /** * Creates an array (of rank 1) of object references. * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the array to create. This will be the total size for non-extendable * data sets and the size of one chunk for extendable (chunked) data sets. For * extendable data sets the initial size of the array will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. * @deprecated Use the corresponding method in {@link IHDF5Writer#reference()}. */ @Deprecated public void createObjectReferenceArray(final String objectPath, final int size); /** * Creates an array (of rank 1) of object references. * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the array to create. When using extendable data sets ((see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data set * smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). * @deprecated Use the corresponding method in {@link IHDF5Writer#reference()}. */ @Deprecated public void createObjectReferenceArray(final String objectPath, final long size, final int blockSize); /** * Creates an array (of rank 1) of object references. * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the array to create. This will be the total size for non-extendable * data sets and the size of one chunk for extendable (chunked) data sets. For * extendable data sets the initial size of the array will be 0, see * {@link HDF5IntStorageFeatures}. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#reference()}. */ @Deprecated public void createObjectReferenceArray(final String objectPath, final int size, final HDF5IntStorageFeatures features); /** * Creates an array (of rank 1) of object references. * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the array to create. When using extendable data sets ((see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data set * smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) * and features is HDF5IntStorageFeature.INTNO_COMPRESSION. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#reference()}. */ @Deprecated public void createObjectReferenceArray(final String objectPath, final long size, final int blockSize, final HDF5IntStorageFeatures features); /** * Writes out a block of an array (of rank 1) of object references. The data set needs to have * been created by * {@link #createObjectReferenceArray(String, long, int, HDF5IntStorageFeatures)} beforehand. *

* Note: For best performance, the block size in this method should be chosen to be equal * to the blockSize argument of the * {@link #createObjectReferenceArray(String, long, int, HDF5IntStorageFeatures)} call that was * used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param referencedObjectPaths The paths of the referenced objects to write. The length defines * the block size. Must not be null or of length 0. * @param blockNumber The number of the block to write. * @deprecated Use the corresponding method in {@link IHDF5Writer#reference()}. */ @Deprecated public void writeObjectReferenceArrayBlock(final String objectPath, final String[] referencedObjectPaths, final long blockNumber); /** * Writes out a block of an array (of rank 1) of object references. The data set needs to have * been created by * {@link #createObjectReferenceArray(String, long, int, HDF5IntStorageFeatures)} beforehand. *

* Note: For best performance, the block size in this method should be chosen to be equal * to the blockSize argument of the * {@link #createObjectReferenceArray(String, long, int, HDF5IntStorageFeatures)} call that was * used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param referencedObjectPaths The paths of the referenced objects to write. The length defines * the block size. Must not be null or of length 0. * @param dataSize The (real) size of data (needs to be <= data.length * ) * @param offset The offset in the data set to start writing to. * @deprecated Use the corresponding method in {@link IHDF5Writer#reference()}. */ @Deprecated public void writeObjectReferenceArrayBlockWithOffset(final String objectPath, final String[] referencedObjectPaths, final int dataSize, final long offset); /** * Writes an array (of rank N) of object references. * * @param objectPath The name (including path information) of the data set object in the file. * @param referencedObjectPaths The names of the object to write. * @deprecated Use the corresponding method in {@link IHDF5Writer#reference()}. */ @Deprecated public void writeObjectReferenceMDArray(final String objectPath, final MDArray referencedObjectPaths); /** * Writes an array (of rank N) of object references. * * @param objectPath The name (including path information) of the data set object in the file. * @param referencedObjectPaths The names of the object to write. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#reference()}. */ @Deprecated public void writeObjectReferenceMDArray(final String objectPath, final MDArray referencedObjectPaths, final HDF5IntStorageFeatures features); /** * Creates a multi-dimensional array of object references. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array to create. This will be the total dimensions * for non-extendable data sets and the dimensions of one chunk (extent along each * axis) for extendable (chunked) data sets. For extendable data sets the initial * size of the array along each axis will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. * @deprecated Use the corresponding method in {@link IHDF5Writer#reference()}. */ @Deprecated public void createObjectReferenceMDArray(final String objectPath, final int[] dimensions); /** * Creates a multi-dimensional array of object references. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. * @deprecated Use the corresponding method in {@link IHDF5Writer#reference()}. */ @Deprecated public void createObjectReferenceMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions); /** * Creates a multi-dimensional array of object references. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array to create. This will be the total dimensions * for non-extendable data sets and the dimensions of one chunk (extent along each * axis) for extendable (chunked) data sets. For extendable data sets the initial * size of the array along each axis will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#reference()}. */ @Deprecated public void createObjectReferenceMDArray(final String objectPath, final int[] dimensions, final HDF5IntStorageFeatures features); /** * Creates a multi-dimensional array of object references. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. * @param features The storage features of the data set. * @deprecated Use the corresponding method in {@link IHDF5Writer#reference()}. */ @Deprecated public void createObjectReferenceMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions, final HDF5IntStorageFeatures features); /** * Writes out a block of a multi-dimensional array of object references. * * @param objectPath The name (including path information) of the data set object in the file. * @param referencedObjectPaths The paths of the object references to write. Must not be * null. All columns need to have the same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). * @deprecated Use the corresponding method in {@link IHDF5Writer#reference()}. */ @Deprecated public void writeObjectReferenceMDArrayBlock(final String objectPath, final MDArray referencedObjectPaths, final long[] blockNumber); /** * Writes out a block of a multi-dimensional array of object references. * * @param objectPath The name (including path information) of the data set object in the file. * @param referencedObjectPaths The paths of the object references to write. Must not be * null. * @param offset The offset in the data set to start writing to in each dimension. * @deprecated Use the corresponding method in {@link IHDF5Writer#reference()}. */ @Deprecated public void writeObjectReferenceMDArrayBlockWithOffset(final String objectPath, final MDArray referencedObjectPaths, final long[] offset); /** * Writes out a block of a multi-dimensional array of object references. * * @param objectPath The name (including path information) of the data set object in the file. * @param referencedObjectPaths The paths of the object references to write. Must not be * null. * @param blockDimensions The dimensions of the block to write to the data set. * @param offset The offset of the block in the data set to start writing to in each dimension. * @param memoryOffset The offset of the block in the data array. * @deprecated Use the corresponding method in {@link IHDF5Writer#reference()}. */ @Deprecated public void writeObjectReferenceMDArrayBlockWithOffset(final String objectPath, final MDLongArray referencedObjectPaths, final int[] blockDimensions, final long[] offset, final int[] memoryOffset); // ********************* // Enums // ********************* /** * Returns the full writer for enums. * * @deprecated Use {@link IHDF5Writer#enumeration()} instead. */ @Deprecated public IHDF5EnumWriter enums(); // ********************* // Compounds // ********************* /** * Returns the full writer for compounds. * * @deprecated Use {@link IHDF5Writer#compound()} instead. */ @Deprecated public IHDF5CompoundWriter compounds(); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5LongReader.java000066400000000000000000000424501256564762100267740ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.base.mdarray.MDLongArray; /** * An interface that provides methods for reading long values from HDF5 files. *

* Note: This interface supports block access and sliced access (which is a special cases of * block access) to arrays. The performance of this block access can vary greatly depending on how * the data are layed out in the HDF5 file. For best performance, the block (or slice) dimension should * be chosen to be equal to the chunk dimensions of the array, as in this case the block written / read * are stored as consecutive value in the HDF5 file and one write / read access will suffice. *

* Note: If the values read are unsigned, use the methods in {@link UnsignedIntUtils} to convert * to a larger Java integer type that can hold all values as unsigned. * * @author Bernd Rinn */ public interface IHDF5LongReader { // ///////////////////// // Attributes // ///////////////////// /** * Reads a long attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. */ public long getAttr(String objectPath, String attributeName); /** * Reads a long[] attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. */ public long[] getArrayAttr(String objectPath, String attributeName); /** * Reads a multi-dimensional array long attribute named attributeName * from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute array value read from the data set. */ public MDLongArray getMDArrayAttr(String objectPath, String attributeName); /** * Reads a long matrix attribute named attributeName * from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute matrix value read from the data set. */ public long[][] getMatrixAttr(String objectPath, String attributeName) throws HDF5JavaException; // ///////////////////// // Data Sets // ///////////////////// /** * Reads a long value from the data set objectPath. This method * doesn't check the data space but simply reads the first value. * * @param objectPath The name (including path information) of the data set object in the file. * @return The value read from the data set. */ public long read(String objectPath); /** * Reads a long array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. */ public long[] readArray(String objectPath); /** * Reads a multi-dimensional long array data set objectPath * into a given array in memory. * * @param objectPath The name (including path information) of the data set object in the file. * @param array The array to read the data into. * @param memoryOffset The offset in the array to write the data to. * @return The effective dimensions of the block in array that was filled. */ public int[] readToMDArrayWithOffset(String objectPath, MDLongArray array, int[] memoryOffset); /** * Reads a block of the multi-dimensional long array data set * objectPath into a given array in memory. * * @param objectPath The name (including path information) of the data set object in the file. * @param array The array to read the data into. * @param blockDimensions The size of the block to read along each axis. * @param offset The offset of the block in the data set. * @param memoryOffset The offset of the block in the array to write the data to. * @return The effective dimensions of the block in array that was filled. */ public int[] readToMDArrayBlockWithOffset(String objectPath, MDLongArray array, int[] blockDimensions, long[] offset, int[] memoryOffset); /** * Reads a block from a long array (of rank 1) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the long[] returned * if the data set is long enough). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @return The data read from the data set. The length will be min(size - blockSize*blockNumber, * blockSize). */ public long[] readArrayBlock(String objectPath, int blockSize, long blockNumber); /** * Reads a block from long array (of rank 1) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the long[] * returned). * @param offset The offset of the block in the data set to start reading from (starting with 0). * @return The data block read from the data set. */ public long[] readArrayBlockWithOffset(String objectPath, int blockSize, long offset); /** * Reads a long matrix (array of arrays) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * * @throws HDF5JavaException If the data set objectPath is not of rank 2. */ public long[][] readMatrix(String objectPath) throws HDF5JavaException; /** * Reads a long matrix (array of arrays) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSizeX The size of the block in the x dimension. * @param blockSizeY The size of the block in the y dimension. * @param blockNumberX The block number in the x dimension (offset: multiply with * blockSizeX). * @param blockNumberY The block number in the y dimension (offset: multiply with * blockSizeY). * @return The data block read from the data set. * * @throws HDF5JavaException If the data set objectPath is not of rank 2. */ public long[][] readMatrixBlock(String objectPath, int blockSizeX, int blockSizeY, long blockNumberX, long blockNumberY) throws HDF5JavaException; /** * Reads a long matrix (array of arrays) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSizeX The size of the block in the x dimension. * @param blockSizeY The size of the block in the y dimension. * @param offsetX The offset in x dimension in the data set to start reading from. * @param offsetY The offset in y dimension in the data set to start reading from. * @return The data block read from the data set. * * @throws HDF5JavaException If the data set objectPath is not of rank 2. */ public long[][] readMatrixBlockWithOffset(String objectPath, int blockSizeX, int blockSizeY, long offsetX, long offsetY) throws HDF5JavaException; /** * Reads a multi-dimensional long array from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. */ public MDLongArray readMDArray(String objectPath); /** * Reads a slice of a multi-dimensional long array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDLongArray readMDArraySlice(String objectPath, IndexMap boundIndices); /** * Reads a slice of a multi-dimensional long array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDLongArray readMDArraySlice(String objectPath, long[] boundIndices); /** * Reads a block from a multi-dimensional long array from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @return The data block read from the data set. */ public MDLongArray readMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber); /** * Reads a sliced block from a multi-dimensional long array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDLongArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, IndexMap boundIndices); /** * Reads a sliced block from a multi-dimensional long array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDLongArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, long[] boundIndices); /** * Reads a block from a multi-dimensional long array from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @return The data block read from the data set. */ public MDLongArray readMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset); /** * Reads a sliced block of a multi-dimensional long array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDLongArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, IndexMap boundIndices); /** * Reads a sliced block of a multi-dimensional long array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDLongArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, long[] boundIndices); /** * Provides all natural blocks of this one-dimensional data set to iterate over. * * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1. */ public Iterable> getArrayNaturalBlocks( String dataSetPath) throws HDF5JavaException; /** * Provides all natural blocks of this multi-dimensional data set to iterate over. * * @see HDF5MDDataBlock */ public Iterable> getMDArrayNaturalBlocks( String dataSetPath); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5LongWriter.java000066400000000000000000000712741256564762100270540ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ch.systemsx.cisd.base.mdarray.MDLongArray; /** * An interface that provides methods for writing long values to HDF5 files. *

* Note: This interface supports block access and sliced access (which is a special cases of * block access) to arrays. The performance of this block access can vary greatly depending on how * the data are layed out in the HDF5 file. For best performance, the block (or slice) dimension should * be chosen to be equal to the chunk dimensions of the array, as in this case the block written / read * are stored as consecutive value in the HDF5 file and one write / read access will suffice. *

* Note: If you need to convert from and to unsigned values, use the methods of * {@link UnsignedIntUtils}. * * @author Bernd Rinn */ // Note: It is a trick for keeping backward compatibility to let this interface extend // IHDF5UnsignedLongWriter instead of IHDF5LongReader as it logically should. // Once we remove IHDF5UnsignedLongWriter, uncomment the following line and remove // all @Override annotations and we are fine again. //public interface IHDF5LongWriter extends IHDF5LongReader @SuppressWarnings("deprecation") public interface IHDF5LongWriter extends IHDF5UnsignedLongWriter { // ///////////////////// // Attributes // ///////////////////// /** * Set a long attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ @Override public void setAttr(String objectPath, String name, long value); /** * Set a long[] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ @Override public void setArrayAttr(String objectPath, String name, long[] value); /** * Set a multi-dimensional code>long attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ @Override public void setMDArrayAttr(String objectPath, String name, MDLongArray value); /** * Set a long[][] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ @Override public void setMatrixAttr(String objectPath, String name, long[][] value); // ///////////////////// // Data Sets // ///////////////////// /** * Writes out a long value. * * @param objectPath The name (including path information) of the data set object in the file. * @param value The value to write. */ @Override public void write(String objectPath, long value); /** * Writes out a long array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ @Override public void writeArray(String objectPath, long[] data); /** * Writes out a long array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param features The storage features of the data set. */ @Override public void writeArray(String objectPath, long[] data, HDF5IntStorageFeatures features); /** * Creates a long array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size When the writer is configured to use extendable data types (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be size. When the writer is * configured to enforce a non-extendable data set, the initial size equals the * total size and will be size. */ @Override public void createArray(String objectPath, int size); /** * Creates a long array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the long array to create. When using extendable data sets * ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data * set smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). */ @Override public void createArray(String objectPath, long size, int blockSize); /** * Creates a long array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the long array to create. When requesting a * chunked data set (e.g. {@link HDF5IntStorageFeatures#INT_CHUNKED}), * the initial size of the array will be 0 and the chunk size will be arraySize. * When allowing a chunked data set (e.g. * {@link HDF5IntStorageFeatures#INT_NO_COMPRESSION} when the writer is * not configured to avoid extendable data types, see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be arraySize. When enforcing a * on-extendable data set (e.g. * {@link HDF5IntStorageFeatures#INT_CONTIGUOUS}), the initial size equals * the total size and will be arraySize. * @param features The storage features of the data set. */ @Override public void createArray(String objectPath, int size, HDF5IntStorageFeatures features); /** * Creates a long array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the long array to create. When using extendable data sets * ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data * set smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) and * features is HDF5IntStorageFeature.INT_NO_COMPRESSION. * @param features The storage features of the data set. */ @Override public void createArray(String objectPath, long size, int blockSize, HDF5IntStorageFeatures features); /** * Writes out a block of a long array (of rank 1). The data set needs to have * been created by {@link #createArray(String, long, int, HDF5IntStorageFeatures)} * beforehand. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumber The number of the block to write. */ @Override public void writeArrayBlock(String objectPath, long[] data, long blockNumber); /** * Writes out a block of a long array (of rank 1). The data set needs to have * been created by {@link #createArray(String, long, int, HDF5IntStorageFeatures)} * beforehand. *

* Use this method instead of {@link #writeArrayBlock(String, long[], long)} if the * total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param dataSize The (real) size of data (needs to be <= data.length * ) * @param offset The offset in the data set to start writing to. */ @Override public void writeArrayBlockWithOffset(String objectPath, long[] data, int dataSize, long offset); /** * Writes out a long matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ @Override public void writeMatrix(String objectPath, long[][] data); /** * Writes out a long matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. */ @Override public void writeMatrix(String objectPath, long[][] data, HDF5IntStorageFeatures features); /** * Creates a long matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of one block in the x dimension. See * {@link #createMDArray(String, int[])} on the different * meanings of this parameter. * @param sizeY The size of one block in the y dimension. See * {@link #createMDArray(String, int[])} on the different * meanings of this parameter. */ @Override public void createMatrix(String objectPath, int sizeX, int sizeY); /** * Creates a long matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of one block in the x dimension. See * {@link #createMDArray(String, int[], HDF5IntStorageFeatures)} on the different * meanings of this parameter. * @param sizeY The size of one block in the y dimension. See * {@link #createMDArray(String, int[], HDF5IntStorageFeatures)} on the different * meanings of this parameter. * @param features The storage features of the data set. */ @Override public void createMatrix(String objectPath, int sizeX, int sizeY, HDF5IntStorageFeatures features); /** * Creates a long matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the long matrix to create. * @param sizeY The size of the y dimension of the long matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. */ @Override public void createMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY); /** * Creates a long matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the long matrix to create. * @param sizeY The size of the y dimension of the long matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. * @param features The storage features of the data set. */ @Override public void createMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY, HDF5IntStorageFeatures features); /** * Writes out a block of a long matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of * {@link #createMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} if the total * size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumberX The block number in the x dimension (offset: multiply with * data.length). * @param blockNumberY The block number in the y dimension (offset: multiply with * data[0.length). */ @Override public void writeMatrixBlock(String objectPath, long[][] data, long blockNumberX, long blockNumberY); /** * Writes out a block of a long matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeMatrixBlock(String, long[][], long, long)} if * the total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. */ @Override public void writeMatrixBlockWithOffset(String objectPath, long[][] data, long offsetX, long offsetY); /** * Writes out a block of a long matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeMatrixBlock(String, long[][], long, long)} if * the total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param dataSizeX The (real) size of data along the x axis (needs to be * <= data.length ) * @param dataSizeY The (real) size of data along the y axis (needs to be * <= data[0].length ) * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. */ @Override public void writeMatrixBlockWithOffset(String objectPath, long[][] data, int dataSizeX, int dataSizeY, long offsetX, long offsetY); /** * Writes out a multi-dimensional long array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ @Override public void writeMDArray(String objectPath, MDLongArray data); /** * Writes out a multi-dimensional long array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. */ @Override public void writeMDArray(String objectPath, MDLongArray data, HDF5IntStorageFeatures features); /** * Writes out a slice of a multi-dimensional long array. The slice is defined by * "bound indices", each of which is fixed to a given value. The data object only * contains the free (i.e. non-fixed) indices. *

* Note:The object identified by objectPath needs to exist when this method is * called. This method will not create the array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. */ public void writeMDArraySlice(String objectPath, MDLongArray data, IndexMap boundIndices); /** * Writes out a slice of a multi-dimensional long array. The slice is defined by * "bound indices", each of which is fixed to a given value. The data object only * contains the free (i.e. non-fixed) indices. *

* Note:The object identified by objectPath needs to exist when this method is * called. This method will not create the array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. */ public void writeMDArraySlice(String objectPath, MDLongArray data, long[] boundIndices); /** * Creates a multi-dimensional long array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions When the writer is configured to use extendable data types (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial dimensions * and the dimensions of a chunk of the array will be dimensions. When the * writer is configured to enforce a non-extendable data set, the initial dimensions * equal the dimensions and will be dimensions. */ @Override public void createMDArray(String objectPath, int[] dimensions); /** * Creates a multi-dimensional long array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. */ @Override public void createMDArray(String objectPath, long[] dimensions, int[] blockDimensions); /** * Creates a multi-dimensional long array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the long array to create. When requesting * a chunked data set (e.g. {@link HDF5IntStorageFeatures#INT_CHUNKED}), * the initial size of the array will be 0 and the chunk size will be dimensions. * When allowing a chunked data set (e.g. * {@link HDF5IntStorageFeatures#INT_NO_COMPRESSION} when the writer is * not configured to avoid extendable data types, see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be dimensions. When enforcing a * on-extendable data set (e.g. * {@link HDF5IntStorageFeatures#INT_CONTIGUOUS}), the initial size equals * the total size and will be dimensions. * @param features The storage features of the data set. */ @Override public void createMDArray(String objectPath, int[] dimensions, HDF5IntStorageFeatures features); /** * Creates a multi-dimensional long array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. * @param features The storage features of the data set. */ @Override public void createMDArray(String objectPath, long[] dimensions, int[] blockDimensions, HDF5IntStorageFeatures features); /** * Writes out a block of a multi-dimensional long array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). */ @Override public void writeMDArrayBlock(String objectPath, MDLongArray data, long[] blockNumber); /** * Writes out a sliced block of a multi-dimensional long array. The slice is * defined by "bound indices", each of which is fixed to a given value. The data * object only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. */ public void writeSlicedMDArrayBlock(String objectPath, MDLongArray data, long[] blockNumber, IndexMap boundIndices); /** * Writes out a sliced block of a multi-dimensional long array. The slice is * defined by "bound indices", each of which is fixed to a given value. The data * object only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. */ public void writeSlicedMDArrayBlock(String objectPath, MDLongArray data, long[] blockNumber, long[] boundIndices); /** * Writes out a block of a multi-dimensional long array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. */ @Override public void writeMDArrayBlockWithOffset(String objectPath, MDLongArray data, long[] offset); /** * Writes out a sliced block of a multi-dimensional long array. The slice is * defined by "bound indices", each of which is fixed to a given value. The data * object only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. */ public void writeSlicedMDArrayBlockWithOffset(String objectPath, MDLongArray data, long[] offset, IndexMap boundIndices); /** * Writes out a sliced block of a multi-dimensional long array. The slice is * defined by "bound indices", each of which is fixed to a given value. The data * object only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. */ public void writeSlicedMDArrayBlockWithOffset(String objectPath, MDLongArray data, long[] offset, long[] boundIndices); /** * Writes out a block of a multi-dimensional long array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param blockDimensions The dimensions of the block to write to the data set. * @param offset The offset of the block in the data set to start writing to in each dimension. * @param memoryOffset The offset of the block in the data array. */ @Override public void writeMDArrayBlockWithOffset(String objectPath, MDLongArray data, int[] blockDimensions, long[] offset, int[] memoryOffset); } IHDF5ObjectReadOnlyInfoProviderHandler.java000066400000000000000000000437031256564762100333660ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.util.List; import ch.systemsx.cisd.hdf5.HDF5DataTypeInformation.DataTypeInfoOptions; /** * An interface for getting information on HDF5 objects like links, groups, data sets and data * types. * * @author Bernd Rinn */ public interface IHDF5ObjectReadOnlyInfoProviderHandler { // ///////////////////// // Objects & Links // ///////////////////// /** * Returns the link information for the given objectPath. If objectPath * does not exist, the link information will have a type {@link HDF5ObjectType#NONEXISTENT}. */ public HDF5LinkInformation getLinkInformation(final String objectPath); /** * Returns the object information for the given objectPath. If objectPath * is a symbolic link, this method will return the type of the object that this link points to * rather than the type of the link. If objectPath does not exist, the object * information will have a type {@link HDF5ObjectType#NONEXISTENT} and the other fields will not * be set. */ public HDF5ObjectInformation getObjectInformation(final String objectPath); /** * Returns the type of the given objectPath. If followLink is * false and objectPath is a symbolic link, this method will return the * type of the link rather than the type of the object that the link points to. */ public HDF5ObjectType getObjectType(final String objectPath, boolean followLink); /** * Returns the type of the given objectPath. If objectPath is a symbolic * link, this method will return the type of the object that this link points to rather than the * type of the link, that is, it will follow symbolic links. */ public HDF5ObjectType getObjectType(final String objectPath); /** * Returns true, if objectPath exists and false otherwise. * if followLink is false and objectPath is a symbolic link, * this method will return true regardless of whether the link target exists or * not. */ public boolean exists(final String objectPath, boolean followLink); /** * Returns true, if objectPath exists and false otherwise. * If objectPath is a symbolic link, the method will return true if the * link target exists, that is, this method will follow symbolic links. */ public boolean exists(final String objectPath); /** * Creates and returns an internal (house-keeping) version of objectPath. */ public String toHouseKeepingPath(final String objectPath); /** * Returns true if objectPath denotes an internal (house-keeping) * object. */ public boolean isHouseKeepingObject(final String objectPath); /** * Returns true if the objectPath exists and represents a group and * false otherwise. Note that if followLink is false this * method will return false if objectPath is a symbolic link that points * to a group. */ public boolean isGroup(final String objectPath, boolean followLink); /** * Returns true if the objectPath exists and represents a group and * false otherwise. Note that if objectPath is a symbolic link, this * method will return true if the link target of the symbolic link is a group, that * is, this method will follow symbolic links. */ public boolean isGroup(final String objectPath); /** * Returns true if the objectPath exists and represents a data set and * false otherwise. Note that if followLink is false this * method will return false if objectPath is a symbolic link that points * to a data set. */ public boolean isDataSet(final String objectPath, boolean followLink); /** * Returns true if the objectPath exists and represents a data set and * false otherwise. Note that if objectPath is a symbolic link, this * method will return true if the link target of the symbolic link is a data set, * that is, this method will follow symbolic links. */ public boolean isDataSet(final String objectPath); /** * Returns true if the objectPath exists and represents a data type and * false otherwise. Note that if followLink is false this * method will return false if objectPath is a symbolic link that points * to a data type. */ public boolean isDataType(final String objectPath, boolean followLink); /** * Returns true if the objectPath exists and represents a data type and * false otherwise. Note that if objectPath is a symbolic link, this * method will return true if the link target of the symbolic link is a data type, * that is, this method will follow symbolic links. */ public boolean isDataType(final String objectPath); /** * Returns true if the objectPath exists and represents a soft link and * false otherwise. */ public boolean isSoftLink(final String objectPath); /** * Returns true if the objectPath exists and represents an external link * and false otherwise. */ public boolean isExternalLink(final String objectPath); /** * Returns true if the objectPath exists and represents either a soft * link or an external link and false otherwise. */ public boolean isSymbolicLink(final String objectPath); /** * Returns the target of the symbolic link that objectPath points to, or * null, if objectPath is not a symbolic link. */ public String tryGetSymbolicLinkTarget(final String objectPath); // ///////////////////// // Attributes // ///////////////////// /** * Returns true, if the objectPath has an attribute with name * attributeName. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return true, if the attribute exists for the object. */ public boolean hasAttribute(final String objectPath, final String attributeName); /** * Returns the names of the attributes of the given objectPath. * * @param objectPath The name (including path information) of the object (data set or group) to * return the attributes for. */ public List getAttributeNames(final String objectPath); /** * Returns the names of all attributes of the given objectPath. *

* This may include attributes that are used internally by the library and are not supposed to * be changed by application programmers. * * @param objectPath The name (including path information) of the object (data set or group) to * return the attributes for. */ public List getAllAttributeNames(final String objectPath); /** * Returns the information about a data set as a {@link HDF5DataTypeInformation} object. * * @param objectPath The name (including path information) of the object that has the attribute * to return information about. * @param attributeName The name of the attribute to get information about. */ public HDF5DataTypeInformation getAttributeInformation(final String objectPath, final String attributeName); /** * Returns the information about a data set as a {@link HDF5DataTypeInformation} object. * * @param objectPath The name (including path information) of the object that has the attribute * to return information about. * @param attributeName The name of the attribute to get information about. * @param dataTypeInfoOptions The options on which information to get about the member data * types. */ public HDF5DataTypeInformation getAttributeInformation(final String objectPath, final String attributeName, final DataTypeInfoOptions dataTypeInfoOptions); /** * Returns the information about a data set as a {@link HDF5DataSetInformation} object. It is a * failure condition if the objectPath does not exist or does not identify a data * set. * * @param objectPath The name (including path information) of the data set to return information * about. */ public HDF5DataSetInformation getDataSetInformation(final String objectPath); // ///////////////////// // Data Sets // ///////////////////// /** * Returns the information about a data set as a {@link HDF5DataSetInformation} object. It is a * failure condition if the objectPath does not exist or does not identify a data * set. * * @param objectPath The name (including path information) of the data set to return information * about. * @param dataTypeInfoOptions The options on which information to get about the member data * types. */ public HDF5DataSetInformation getDataSetInformation(final String objectPath, final DataTypeInfoOptions dataTypeInfoOptions); /** * Returns the total size (in bytes) of objectPath. It is a failure condition if the * objectPath does not exist or does not identify a data set. This method follows * symbolic links. */ public long getSize(final String objectPath); /** * Returns the total number of elements of objectPath. It is a failure condition if * the objectPath does not exist or does not identify a data set. This method follows * symbolic links. */ public long getNumberOfElements(final String objectPath); /** * Returns the size of one element of objectPath. It is a failure condition if the * objectPath does not exist or does not identify a data set. This method follows * symbolic links. */ public int getElementSize(final String objectPath); /** * Returns the rank of the space of objectPath (0 if this is a scalar space). It is a * failure condition if the objectPath does not exist or does not identify a data * set. This method follows symbolic links. */ public int getSpaceRank(final String objectPath); /** * Returns the dimensions of the space of objectPath (empty if this is a scalar * space). It is a failure condition if the objectPath does not exist or does not * identify a data set. This method follows symbolic links. */ public long[] getSpaceDimensions(final String objectPath); /** * Returns the rank of the array of objectPath (0 if this is no array type). It is a * failure condition if the objectPath does not exist or does not identify a data * set. This method follows symbolic links. */ public int getArrayRank(final String objectPath); /** * Returns the dimensions of objectPath(empty if this isno array type). It is a * failure condition if the objectPath does not exist or does not identify a data * set. This method follows symbolic links. */ public int[] getArrayDimensions(final String objectPath); /** * Returns the rank of this data set of objectPath. This combines the space rank and * the array rank into one rank. It is a failure condition if the objectPath does not * exist or does not identify a data set. This method follows symbolic links. */ public int getRank(final String objectPath); /** * Returns the dimensions of objectPath. This combines the space dimensions and the * array dimensions into one rank. It is a failure condition if the objectPath does * not exist or does not identify a data set. This method follows symbolic links. */ public long[] getDimensions(final String objectPath); // ///////////////////// // Copies // ///////////////////// /** * Copies the sourceObject to the destinationObject of the HDF5 file * represented by the destinationWriter. If destiantionObject ends with * "/", it will be considered a group and the name of sourceObject will be appended. */ public void copy(String sourceObject, IHDF5Writer destinationWriter, String destinationObject); /** * Copies the sourceObject to the root group of the HDF5 file represented by the * destinationWriter. */ public void copy(String sourceObject, IHDF5Writer destinationWriter); /** * Copies all objects of the file represented by this reader to the root group of the HDF5 file * represented by the destinationWriter. */ public void copyAll(IHDF5Writer destinationWriter); // ///////////////////// // Groups // ///////////////////// /** * Returns the members of groupPath. The order is not well defined. * * @param groupPath The path of the group to get the members for. * @throws IllegalArgumentException If groupPath is not a group. */ public List getGroupMembers(final String groupPath); /** * Returns all members of groupPath, including internal groups that may be used by * the library to do house-keeping. The order is not well defined. * * @param groupPath The path of the group to get the members for. * @throws IllegalArgumentException If groupPath is not a group. */ public List getAllGroupMembers(final String groupPath); /** * Returns the paths of the members of groupPath (including the parent). The order is * not well defined. * * @param groupPath The path of the group to get the member paths for. * @throws IllegalArgumentException If groupPath is not a group. */ public List getGroupMemberPaths(final String groupPath); /** * Returns the link information about the members of groupPath. The order is * not well defined. * * @param groupPath The path of the group to get the members for. * @param readLinkTargets If true, for symbolic links the link targets will be * available via {@link HDF5LinkInformation#tryGetSymbolicLinkTarget()}. * @throws IllegalArgumentException If groupPath is not a group. */ public List getGroupMemberInformation(final String groupPath, boolean readLinkTargets); /** * Returns the link information about all members of groupPath. The order is * not well defined. *

* This may include attributes that are used internally by the library and are not supposed to * be changed by application programmers. * * @param groupPath The path of the group to get the members for. * @param readLinkTargets If true, the link targets will be read for symbolic * links. * @throws IllegalArgumentException If groupPath is not a group. */ public List getAllGroupMemberInformation(final String groupPath, boolean readLinkTargets); // ///////////////////// // Types // ///////////////////// /** * Returns the data type variant of objectPath, or null, if no type * variant is defined for this objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data type variant or null. */ public HDF5DataTypeVariant tryGetTypeVariant(final String objectPath); /** * Returns the data type variant of attributeName of object objectPath, or * null, if no type variant is defined for this objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data type variant or null. */ public HDF5DataTypeVariant tryGetTypeVariant(final String objectPath, String attributeName); /** * Returns the path of the data type of the data set objectPath, or null * , if this data set is not of a named data type. */ public String tryGetDataTypePath(final String objectPath); /** * Returns the path of the data type, or null, if type is not * a named data type. */ public String tryGetDataTypePath(HDF5DataType type); } IHDF5ObjectReadWriteInfoProviderHandler.java000066400000000000000000000231671256564762100335410ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ncsa.hdf.hdf5lib.exceptions.HDF5SymbolTableException; /** * An interface for getting information on and handling HDF5 objects like links, groups, data sets * and data types. * * @author Bernd Rinn */ public interface IHDF5ObjectReadWriteInfoProviderHandler extends IHDF5ObjectReadOnlyInfoProviderHandler { // ///////////////////// // Links // ///////////////////// /** * Creates a hard link. * * @param currentPath The name of the data set (including path information) to create a link to. * @param newPath The name (including path information) of the link to create. */ public void createHardLink(String currentPath, String newPath); /** * Creates a soft link. * * @param targetPath The name of the data set (including path information) to create a link to. * @param linkPath The name (including path information) of the link to create. */ public void createSoftLink(String targetPath, String linkPath); /** * Creates or updates a soft link. *

* Note: This method will never overwrite a data set, but only a symbolic link. * * @param targetPath The name of the data set (including path information) to create a link to. * @param linkPath The name (including path information) of the link to create. */ public void createOrUpdateSoftLink(String targetPath, String linkPath); /** * Creates an external link, that is a link to a data set in another HDF5 file, the * target . *

* Note: This method is only allowed when the {@link IHDF5WriterConfigurator} was not * configured to enforce strict HDF5 1.6 compatibility. * * @param targetFileName The name of the file where the data set resides that should be linked. * @param targetPath The name of the data set (including path information) in the * targetFileName to create a link to. * @param linkPath The name (including path information) of the link to create. * @throws IllegalStateException If the {@link IHDF5WriterConfigurator} was configured to * enforce strict HDF5 1.6 compatibility. */ public void createExternalLink(String targetFileName, String targetPath, String linkPath) throws IllegalStateException; /** * Creates or updates an external link, that is a link to a data set in another HDF5 file, the * target . *

* Note: This method will never overwrite a data set, but only a symbolic link. *

* Note: This method is only allowed when the {@link IHDF5WriterConfigurator} was not * configured to enforce strict HDF5 1.6 compatibility. * * @param targetFileName The name of the file where the data set resides that should be linked. * @param targetPath The name of the data set (including path information) in the * targetFileName to create a link to. * @param linkPath The name (including path information) of the link to create. * @throws IllegalStateException If the {@link IHDF5WriterConfigurator} was configured to * enforce strict HDF5 1.6 compatibility. */ public void createOrUpdateExternalLink(String targetFileName, String targetPath, String linkPath) throws IllegalStateException; /** * Removes an object from the file. If there is more than one link to the object, only the * specified link will be removed. */ public void delete(String objectPath); /** * Moves or renames a link in the file atomically. * * @throws HDF5SymbolTableException If oldLinkPath does not exist or if * newLinkPath already exists. */ public void move(String oldLinkPath, String newLinkPath) throws HDF5SymbolTableException; // ///////////////////// // Group // ///////////////////// /** * Creates a group with path objectPath in the HDF5 file. *

* All intermediate groups will be created as well, if they do not already exist. * * @param groupPath The path of the group to create. */ public void createGroup(final String groupPath); /** * Creates a group with path objectPath in the HDF5 file, giving the library a hint * about the size (sizeHint). If you have this information in advance, it will be * more efficient to tell it the library rather than to let the library figure out itself, but * the hint must not be misunderstood as a limit. *

* All intermediate groups will be created as well, if they do not already exist. *

* Note: This method creates an "old-style group", that is the type of group of HDF5 1.6 and * earlier. * * @param groupPath The path of the group to create. * @param sizeHint The estimated size of all group entries (in bytes). */ public void createGroup(final String groupPath, final int sizeHint); /** * Creates a group with path objectPath in the HDF5 file, giving the library hints * about when to switch between compact and dense. Setting appropriate values may improve * performance. *

* All intermediate groups will be created as well, if they do not already exist. *

* Note: This method creates a "new-style group", that is the type of group of HDF5 1.8 and * above. Thus it will fail, if the writer is configured to enforce HDF5 1.6 compatibility. * * @param groupPath The path of the group to create. * @param maxCompact When the group grows to more than this number of entries, the library will * convert the group style from compact to dense. * @param minDense When the group shrinks below this number of entries, the library will convert * the group style from dense to compact. */ public void createGroup(final String groupPath, final int maxCompact, final int minDense); // ///////////////////// // Data Sets // ///////////////////// /** * Sets the data set size of a one-dimensional data set to newSize. Note that this * method can only be applied to extendable data sets. * * @throws HDF5JavaException If the data set objectPath is not extendable. */ public void setDataSetSize(final String objectPath, final long newSize); /** * Sets the data set size of a multi-dimensional data set to newDimensions. Note that * this method can only be applied to extendable data sets. * * @throws HDF5JavaException If the data set objectPath is not extendable. */ public void setDataSetDimensions(final String objectPath, final long[] newDimensions); // ///////////////////// // Types // ///////////////////// /** * Sets a typeVariant of object objectPath. * * @param objectPath The name of the object to add the type variant to. * @param typeVariant The type variant to add. */ public void setTypeVariant(final String objectPath, final HDF5DataTypeVariant typeVariant); /** * Sets a typeVariant of attribute attributeName of object * objectPath. * * @param objectPath The name of the object. * @param attributeName The name of attribute to add the type variant to. * @param typeVariant The type variant to add. */ public void setTypeVariant(final String objectPath, final String attributeName, final HDF5DataTypeVariant typeVariant); /** * Deletes the typeVariant from objectPath. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to delete the type variant from. */ public void deleteTypeVariant(final String objectPath); /** * Deletes the typeVariant from attributeName of objectPath. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object. * @param attributeName The name of the attribute to delete the type variant from. */ public void deleteTypeVariant(final String objectPath, final String attributeName); // ///////////////////// // Attributes // ///////////////////// /** * Deletes an attribute. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to delete the attribute from. * @param name The name of the attribute to delete. */ public void deleteAttribute(final String objectPath, final String name); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5OpaqueReader.java000066400000000000000000000147641256564762100273360ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; /** * An interface that provides methods for reading any data sets as byte arrays (as 'opaque data', * just like ordinary file systems treat files). This is particularly useful for opaque data types, * which are "black boxes" to the HDF5 library. * * @author Bernd Rinn */ public interface IHDF5OpaqueReader { // ///////////////////////////// // Opaque tags and types // ///////////////////////////// /** * Returns the tag of the opaque data type associated with objectPath, or * null, if objectPath is not of an opaque data type (i.e. if * reader.getDataSetInformation(objectPath).getTypeInformation().getDataClass() != HDF5DataClass.OPAQUE * ). * * @param objectPath The name (including path information) of the data set object in the file. * @return The tag of the opaque data type, or null. */ public String tryGetOpaqueTag(final String objectPath); /** * Returns the opaque data type or null, if objectPath is not of such a * data type. * * @param objectPath The name (including path information) of the data set object in the file. * @return The opaque data type, or null. */ public HDF5OpaqueType tryGetOpaqueType(final String objectPath); // ///////////////////////////// // Reading as byte array // ///////////////////////////// /** * Gets the byte array values of an attribute attributeName of object * objectPath. The bytes read will be in the native byte-order of the machine but * will otherwise be unchanged. */ public byte[] getArrayAttr(final String objectPath, final String attributeName); /** * Reads the data set objectPath as byte array. The bytes read will be in the native * byte-order of the machine and will be ordered 'row-first' in the case of multi-dimensional * data sets, but will otherwise be unchanged. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. */ public byte[] readArray(final String objectPath); /** * Reads a block from data set objectPath as byte array. The bytes read will be in * the native byte-order of the machine, but will otherwise be unchanged. * Must not be called for data sets of rank other than 1 and must not be called on Strings! * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size in numbers of elements (this will be the length of the * byte[] returned, divided by the size of one element). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @return The data block read from the data set. * @throws HDF5JavaException If the data set is not of rank 1 or is a String. */ public byte[] readArrayBlock(final String objectPath, final int blockSize, final long blockNumber) throws HDF5JavaException; /** * Reads a block from data set objectPath as byte array. The bytes read will be in * the native byte-order of the machine, but will otherwise be unchanged. * Must not be called for data sets of rank other than 1 and must not be called on Strings! * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size in numbers of elements (this will be the length of the * byte[] returned, divided by the size of one element). * @param offset The offset of the block to read as number of elements (starting with 0). * @return The data block read from the data set. * @throws HDF5JavaException If the data set is not of rank 1. */ public byte[] readArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset) throws HDF5JavaException; /** * Reads a block from data set objectPath as byte array into buffer. The * bytes read will be in the native byte-order of the machine, but will otherwise be unchanged. * Must not be called for data sets of rank other than 1 and must not be called on Strings! * * @param objectPath The name (including path information) of the data set object in the file. * @param buffer The buffer to read the values in. * @param blockSize The block size in numbers of elements (this will be the length of the * byte[] returned, divided by the size of one element). * @param offset The offset of the block in the data set as number of elements (zero-based). * @param memoryOffset The offset of the block in buffer as number of elements * (zero-based). * @return The effective block size. * @throws HDF5JavaException If the data set is not of rank 1. */ public int readArrayToBlockWithOffset(final String objectPath, final byte[] buffer, final int blockSize, final long offset, final int memoryOffset) throws HDF5JavaException; /** * Provides all natural blocks of this one-dimensional data set to iterate over. The bytes read * will be in the native byte-order of the machine, but will otherwise be unchanged. * Must not be called for data sets of rank other than 1 and must not be called on Strings! * * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1. */ public Iterable> getArrayNaturalBlocks(final String dataSetPath) throws HDF5JavaException; }libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5OpaqueWriter.java000066400000000000000000000215561256564762100274050ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; /** * An interface that provides methods for writing opaque values to HDF5 files. Opaque values are * represented as byte arrays, however, contrary to the methods in {@link IHDF5ByteWriter} there is * no notion on the interpretation of these values. The methods in this writer can be used to store * data sets which are a "black box". Note that there are no dedicated methods for reading opaque * types. Use the methods in {@link IHDF5OpaqueReader} instead which allow you to read any data set * as a byte array. * * @author Bernd Rinn */ public interface IHDF5OpaqueWriter extends IHDF5OpaqueReader { /** * Writes out an opaque data type described by tag and defined by a byte * array (of rank 1). *

* Note that there is no dedicated method for reading opaque types. Use the method * {@link IHDF5OpaqueReader#readArray(String)} instead. * * @param objectPath The name (including path information) of the data set object in the file. * @param tag The tag of the data set. * @param data The data to write. Must not be null. */ public void writeArray(final String objectPath, final String tag, final byte[] data); /** * Writes out an opaque data type described by tag and defined by a byte * array (of rank 1). *

* Note that there is no dedicated method for reading opaque types. Use the method * {@link IHDF5OpaqueReader#readArray(String)} instead. * * @param objectPath The name (including path information) of the data set object in the file. * @param tag The tag of the data set. * @param data The data to write. Must not be null. * @param features The storage features of the data set. */ public void writeArray(final String objectPath, final String tag, final byte[] data, final HDF5GenericStorageFeatures features); /** * Creates an opaque data set that will be represented as a byte array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the byte array to create. * @param blockSize The size of on block (for block-wise IO) * @return The {@link HDF5OpaqueType} that can be used in methods * {@link #writeArrayBlock(String, HDF5OpaqueType, byte[], long)} and * {@link #writeArrayBlockWithOffset(String, HDF5OpaqueType, byte[], int, long)} * to represent this opaque type. */ public HDF5OpaqueType createArray(final String objectPath, final String tag, final long size, final int blockSize); /** * Creates an opaque data set that will be represented as a byte array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the byte array to create. This will be the total size for * non-extendable data sets and the size of one chunk for extendable (chunked) data * sets. For extendable data sets the initial size of the array will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. * @return The {@link HDF5OpaqueType} that can be used in methods * {@link #writeArrayBlock(String, HDF5OpaqueType, byte[], long)} and * {@link #writeArrayBlockWithOffset(String, HDF5OpaqueType, byte[], int, long)} * to represent this opaque type. */ public HDF5OpaqueType createArray(final String objectPath, final String tag, final int size); /** * Creates an opaque data set that will be represented as a byte array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the byte array to create. * @param blockSize The size of on block (for block-wise IO) * @param features The storage features of the data set. * @return The {@link HDF5OpaqueType} that can be used in methods * {@link #writeArrayBlock(String, HDF5OpaqueType, byte[], long)} and * {@link #writeArrayBlockWithOffset(String, HDF5OpaqueType, byte[], int, long)} * to represent this opaque type. */ public HDF5OpaqueType createArray(final String objectPath, final String tag, final long size, final int blockSize, final HDF5GenericStorageFeatures features); /** * Creates an opaque data set that will be represented as a byte array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the byte array to create. This will be the total size for * non-extendable data sets and the size of one chunk for extendable (chunked) data * sets. For extendable data sets the initial size of the array will be 0, see * {@link HDF5GenericStorageFeatures}. * @param features The storage features of the data set. * @return The {@link HDF5OpaqueType} that can be used in methods * {@link #writeArrayBlock(String, HDF5OpaqueType, byte[], long)} and * {@link #writeArrayBlockWithOffset(String, HDF5OpaqueType, byte[], int, long)} * to represent this opaque type. */ public HDF5OpaqueType createArray(final String objectPath, final String tag, final int size, final HDF5GenericStorageFeatures features); /** * Writes out a block of an opaque data type represented by a byte array (of rank * 1). The data set needs to have been created by * {@link #createArray(String, String, long, int, HDF5GenericStorageFeatures)} * beforehand. *

* Note: For best performance, the block size in this method should be chosen to be equal * to the blockSize argument of the * {@link #createArray(String, String, long, int, HDF5GenericStorageFeatures)} call * that was used to created the data set. *

* Note that there is no dedicated method for reading opaque types. Use the method * {@link IHDF5OpaqueReader#readArrayBlock(String, int, long)} instead. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumber The number of the block to write. */ public void writeArrayBlock(final String objectPath, final HDF5OpaqueType dataType, final byte[] data, final long blockNumber); /** * Writes out a block of an opaque data type represented by a byte array (of rank * 1). The data set needs to have been created by * {@link #createArray(String, String, long, int, HDF5GenericStorageFeatures)} * beforehand. *

* Use this method instead of * {@link #writeArrayBlock(String, HDF5OpaqueType, byte[], long)} if the total size of * the data set is not a multiple of the block size. *

* Note: For best performance, the dataSize in this method should be * chosen to be equal to the blockSize argument of the * {@link #createArray(String, String, long, int, HDF5GenericStorageFeatures)} call * that was used to created the data set. *

* Note that there is no dedicated method for reading opaque types. Use the method * {@link IHDF5OpaqueReader#readArrayBlockWithOffset(String, int, long)} instead. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param dataSize The (real) size of data (needs to be <= data.length * ) * @param offset The offset in the data set to start writing to. */ public void writeArrayBlockWithOffset(final String objectPath, final HDF5OpaqueType dataType, final byte[] data, final int dataSize, final long offset); }libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5Reader.java000066400000000000000000000164221256564762100261540ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; /** * An interface for reading HDF5 files (HDF5 1.8.x and older). *

* The interface focuses on ease of use instead of completeness. As a consequence not all features * of HDF5 are supported by this class, however it covers a large subset. In particular all * information written by {@link IHDF5Writer} can be read by this class. *

* The functionality is being made available in two ways: *

    *
  1. {@link IHDF5SimpleReader} contains the most important methods in one interface. If you are * new to the library, this is a good starting point, see the example code below.
    2. *
  2. The hierarchical ("quasi-fluent") API provides the full functionality. It is designed along * the data types supported by JHDF5. *
      *
    • {@link #file()}: File-level information and operations, has e.g. the * {@link IHDF5FileLevelReadOnlyHandler#close()} method.
      • *
    • {@link #object()}: Object-level information, where "objects" can be data sets, links, groups * or data types, following the concept of an HDF5 object. Here you can find for example the method * {@link IHDF5ObjectReadOnlyInfoProviderHandler#getGroupMemberInformation(String, boolean)} which * gives you information on the members of a group and the method * {@link IHDF5ObjectReadOnlyInfoProviderHandler#tryGetSymbolicLinkTarget(String)} for resolving a * symbolic link.
      • *
    • {@link #bool()}: Reader methods for boolean data sets, including bit fields.
      • *
    • {@link #int8()} / {@link #int16()} / {@link #int16()} / {@link #int32()} / {@link #int64()}: * Reader methods for integer data sets, where the number as part of the method name denotes the * size of the integer type. The methods will always read signed integers, if you need unsigned * integers, you need to convert them with one of the methods in {@link UnsignedIntUtils}.
      • *
    • {@link #float32()} / {@link #float64()}: Reader methods for float data sets, where the number * as part of the name sets the size of the float type.
      • *
    • {@link #time()} / {@link #duration()}: Reader methods for time stamp (or date) and for time * duration data sets.
      • *
    • {@link #string()}: Reader methods for string data sets.
      • *
    • {@link #enumeration()}: Reader methods for enumeration data sets.
      • *
    • {@link #compound()}: Reader methods for compound data sets.
      • *
    • {@link #opaque()}: Reader methods for data sets that are "black boxes" to HDF5 which are * called "opaque data sets" in HDF5 jargon. Here you can also find methods of reading arbitrary * data sets as byte arrays.
      • *
    • {@link #reference()}: Reader methods for HDF5 object references. Note that object references, * though similar to hard links and symbolic links on the first glance, are quite different for * HDF5.
      • *
    *
    3. *
*

* Usage example for {@link IHDF5SimpleReader}: * * 

 * IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(new File("test.h5"));
 * float[] f = reader.readFloatArray("/some/path/dataset");
 * String s = reader.getStringAttribute("/some/path/dataset", "some key");
 * reader.close();
 *
* * @author Bernd Rinn */ @SuppressWarnings("deprecation") public interface IHDF5Reader extends IHDF5SimpleReader, IHDF5LegacyReader { // ///////////////////// // File // ///////////////////// /** * Returns the handler for file-level information and status. */ public IHDF5FileLevelReadOnlyHandler file(); // ///////////////////////////////// // Objects, links, groups and types // ///////////////////////////////// /** * Returns an info provider for HDF5 objects like links, groups, data sets and data types. */ public IHDF5ObjectReadOnlyInfoProviderHandler object(); // ///////////////////// // Opaque // ///////////////////// /** * Returns the full reader for reading data sets and attributes as byte arrays ('opaque') and * obtaining opaque types. */ public IHDF5OpaqueReader opaque(); // ///////////////////// // Boolean // ///////////////////// /** * Returns the full reader for boolean values. */ public IHDF5BooleanReader bool(); // ///////////////////// // Bytes // ///////////////////// /** * Returns the full reader for byte / int8. */ public IHDF5ByteReader int8(); /** * Returns the full reader for unsigned byte / uint8. */ public IHDF5ByteReader uint8(); // ///////////////////// // Short // ///////////////////// /** * Returns the full reader for short / int16. */ public IHDF5ShortReader int16(); /** * Returns the full reader for unsigned short / uint16. */ public IHDF5ShortReader uint16(); // ///////////////////// // Int // ///////////////////// /** * Returns the full reader for int / int32. */ public IHDF5IntReader int32(); /** * Returns the full reader for unsigned int / uint32. */ public IHDF5IntReader uint32(); // ///////////////////// // Long // ///////////////////// /** * Returns the full reader for long / int64. */ public IHDF5LongReader int64(); /** * Returns the full reader for unsigned long / uint64. */ public IHDF5LongReader uint64(); // ///////////////////// // Float // ///////////////////// /** * Returns the full reader for float / float32. */ public IHDF5FloatReader float32(); // ///////////////////// // Double // ///////////////////// /** * Returns the full reader for long / float64. */ public IHDF5DoubleReader float64(); // ///////////////////// // Enums // ///////////////////// /** * Returns the full reader for enumerations. */ public IHDF5EnumReader enumeration(); // ///////////////////// // Compounds // ///////////////////// /** * Returns the full reader for compounds. */ public IHDF5CompoundReader compound(); // ///////////////////// // Strings // ///////////////////// /** * Returns the full reader for strings. */ public IHDF5StringReader string(); // ///////////////////// // Date & Time // ///////////////////// /** * Returns the full reader for date and times. */ public IHDF5DateTimeReader time(); /** * Returns the full reader for time durations. */ public IHDF5TimeDurationReader duration(); // ///////////////////// // Object references // ///////////////////// /** * Returns the full reader for object references. */ public IHDF5ReferenceReader reference(); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5ReaderConfigurator.java000066400000000000000000000046121256564762100305350ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; /** * A configurator for a {@link IHDF5Reader}. *

* If you want the reader to perform numeric conversions, call {@link #performNumericConversions()} * before calling {@link #reader()}. * * @author Bernd Rinn */ public interface IHDF5ReaderConfigurator { /** * Returns true, if this platform supports numeric conversions. */ public boolean platformSupportsNumericConversions(); /** * Will try to perform numeric conversions where appropriate if supported by the platform. *

* Numeric conversions can be platform dependent and are not available on all platforms. * Be advised not to rely on numeric conversions if you can help it! */ public IHDF5ReaderConfigurator performNumericConversions(); /** * Sets UTF8 character encoding for all paths and all strings in this file. (The default is * ASCII.) * * @deprecated Should not be used for the reader as it will figure that out by looking at the HDF5 file. */ @Deprecated public IHDF5ReaderConfigurator useUTF8CharacterEncoding(); /** * Switches off automatic dereferencing of unresolved references. Use this when you need to * access file names that start with \0. The down-side of switching off automatic dereferencing * is that you can't provide references as obtained by * {@link IHDF5ReferenceReader#read(String, boolean)} with * resolveName=false in places where a dataset path is required. *
* Note: automatic dereferencing is switched on by default. */ public IHDF5ReaderConfigurator noAutoDereference(); /** * Returns an {@link IHDF5Reader} based on this configuration. */ public IHDF5Reader reader(); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5ReferenceReader.java000066400000000000000000000560741256564762100300020ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.base.mdarray.MDArray; /** * An interface for reading references in HDF5 files. * * @see IHDF5ReferenceWriter * @author Bernd Rinn */ public interface IHDF5ReferenceReader { // ////////////////////////////// // Specific to object references // ////////////////////////////// /** * Resolves the path of a reference which has been read without name resolution. * * @param reference Reference encoded as string. * @return The path in the HDF5 file. * @see #readArray(String, boolean) * @throws HDF5JavaException if reference is not a string-encoded reference. */ public String resolvePath(final String reference) throws HDF5JavaException; // ///////////////////// // Attributes // ///////////////////// /** * Reads an object reference attribute named attributeName from the object * objectPath, resolving the name of the object.
* Note that resolving the name of the object is a time consuming operation. If you don't * need the name, but want to dereference the dataset, you don't need to resolve the name if the * reader / writer is configured for auto-dereferencing (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}). * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The path of the object that the reference refers to, or an empty string, if the * object reference refers to an unnamed object. */ public String getAttr(final String objectPath, final String attributeName); /** * Reads an object reference attribute named attributeName from the object * objectPath.
* Note: if the reader has been configured to automatically resolve references (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}), a reference can be provided in all * places where an object path is expected. This is considerably faster than resolving the * name/path of the reference if the name/path by itself is not needed. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @param resolveName If true, resolves the name of the object referenced, * otherwise returns the references itself. * @return The path of the object that the reference refers to, or an empty string, if the * object reference refers to an unnamed object. */ public String getAttr(final String objectPath, final String attributeName, final boolean resolveName); /** * Reads a 1D object reference array attribute named attributeName from the object * objectPath, resolving the names of the objects.
* Note that resolving the name of the object is a time consuming operation. If you don't * need the name, but want to dereference the dataset, you don't need to resolve the name if the * reader / writer is configured for auto-dereferencing (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}). * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The paths of the objects that the references refers to. Each string may be empty, if * the corresponding object reference refers to an unnamed object. */ public String[] getArrayAttr(final String objectPath, final String attributeName); /** * Reads a 1D object reference array attribute named attributeName from the object * objectPath.
* Note: if the reader has been configured to automatically resolve references (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}), a reference can be provided in all * places where an object path is expected. This is considerably faster than resolving the * name/path of the reference if the name/path by itself is not needed. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @param resolveName If true, resolves the names of the objects referenced, * otherwise returns the references itself. * @return The paths of the objects that the references refers to. Each string may be empty, if * the corresponding object reference refers to an unnamed object. */ public String[] getArrayAttr(final String objectPath, final String attributeName, final boolean resolveName); /** * Reads an object reference array attribute named attributeName from the object * objectPath, resolving the names of the objects.
* Note that resolving the name of the object is a time consuming operation. If you don't * need the name, but want to dereference the dataset, you don't need to resolve the name if the * reader / writer is configured for auto-dereferencing (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}). * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The paths of the objects that the references refers to. Each string may be empty, if * the corresponding object reference refers to an unnamed object. */ public MDArray getMDArrayAttr(final String objectPath, final String attributeName); /** * Reads an object reference array attribute named attributeName from the object * objectPath.
* Note: if the reader has been configured to automatically resolve references (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}), a reference can be provided in all * places where an object path is expected. This is considerably faster than resolving the * name/path of the reference if the name/path by itself is not needed. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @param resolveName If true, resolves the names of the objects referenced, * otherwise returns the references itself. * @return The paths of the objects that the references refers to. Each string may be empty, if * the corresponding object reference refers to an unnamed object. */ public MDArray getMDArrayAttr(final String objectPath, final String attributeName, boolean resolveName); // ///////////////////// // Data Sets // ///////////////////// /** * Reads an object reference from the object objectPath, resolving the name of the * object.
* Note that resolving the name of the object is a time consuming operation. If you don't * need the name, but want to dereference the dataset, you don't need to resolve the name if the * reader / writer is configured for auto-dereferencing (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}). * * @param objectPath The name (including path information) of the data set object in the file. * @return The path of the object that the reference refers to, or an empty string, if the * object reference refers to an unnamed object. */ public String read(final String objectPath); /** * Reads an object reference from the object objectPath.
* Note: if the reader has been configured to automatically resolve references (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}), a reference can be provided in all * places where an object path is expected. This is considerably faster than resolving the * name/path of the reference if the name/path by itself is not needed. * * @param objectPath The name (including path information) of the data set object in the file. * @param resolveName If true, resolves the name of the object referenced, * otherwise returns the references itself. * @return The path of the object that the reference refers to, or an empty string, if the * object reference refers to an unnamed object. */ public String read(final String objectPath, final boolean resolveName); /** * Reads an array of object references from the object objectPath, resolving the * names of the objects.
* Note that resolving the name of the object is a time consuming operation. If you don't * need the name, but want to dereference the dataset, you don't need to resolve the name if the * reader / writer is configured for auto-dereferencing (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}). * * @param objectPath The name (including path information) of the data set object in the file. * @return The array of the paths of objects that the references refers to. Each string may be * empty, if the corresponding object reference refers to an unnamed object. */ public String[] readArray(final String objectPath); /** * Reads an array of object references from the object objectPath.
* Note: if the reader has been configured to automatically resolve references (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}), a reference can be provided in all * places where an object path is expected. This is considerably faster than resolving the * name/path of the reference if the name/path by itself is not needed. * * @param objectPath The name (including path information) of the data set object in the file. * @param resolveName If true, resolves the names of the objects referenced, * otherwise returns the references itself. * @return The array of the paths of objects that the references refers to. Each string may be * empty, if the corresponding object reference refers to an unnamed object. */ public String[] readArray(final String objectPath, boolean resolveName); /** * Reads a block from an array (of rank 1) of object references from the data set * objectPath, resolving the names of the objects.
* Note that resolving the name of the object is a time consuming operation. If you don't * need the name, but want to dereference the dataset, you don't need to resolve the name if the * reader / writer is configured for auto-dereferencing (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}). * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the long[] returned * if the data set is long enough). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @return The referenced data set paths read from the data set. The length will be min(size - * blockSize*blockNumber, blockSize). */ public String[] readArrayBlock(final String objectPath, final int blockSize, final long blockNumber); /** * Reads a block from an array (of rank 1) of object references from the data set * objectPath.
* Note: if the reader has been configured to automatically resolve references (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}), a reference can be provided in all * places where an object path is expected. This is considerably faster than resolving the * name/path of the reference if the name/path by itself is not needed. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the long[] returned * if the data set is long enough). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @param resolveName If true, resolves the names of the objects referenced, * otherwise returns the references itself. * @return The referenced data set paths read from the data set. The length will be min(size - * blockSize*blockNumber, blockSize). */ public String[] readArrayBlock(final String objectPath, final int blockSize, final long blockNumber, final boolean resolveName); /** * Reads a block from an array (of rank 1) of object references from the data set * objectPath, resolving the names of the objects.
* Note that resolving the name of the object is a time consuming operation. If you don't * need the name, but want to dereference the dataset, you don't need to resolve the name if the * reader / writer is configured for auto-dereferencing (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}). * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the long[] * returned). * @param offset The offset of the block in the data set to start reading from (starting with * 0). * @return The referenced data set paths block read from the data set. */ public String[] readArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset); /** * Reads a block from an array (of rank 1) of object references from the data set * objectPath.
* Note: if the reader has been configured to automatically resolve references (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}), a reference can be provided in all * places where an object path is expected. This is considerably faster than resolving the * name/path of the reference if the name/path by itself is not needed. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the long[] * returned). * @param offset The offset of the block in the data set to start reading from (starting with * 0). * @param resolveName If true, resolves the names of the objects referenced, * otherwise returns the references itself. * @return The referenced data set paths block read from the data set. */ public String[] readArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset, final boolean resolveName); /** * Reads an array (or rank N) of object references from the object objectPath, * resolving the names of the objects.
* Note that resolving the name of the object is a time consuming operation. If you don't * need the name, but want to dereference the dataset, you don't need to resolve the name if the * reader / writer is configured for auto-dereferencing (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}). * * @param objectPath The name (including path information) of the data set object in the file. * @return The multi-dimensional array of the paths of objects that the references refers to. * Each string may be empty, if the corresponding object reference refers to an unnamed * object. */ public MDArray readMDArray(final String objectPath); /** * Reads an array (or rank N) of object references from the object objectPath.
* Note: if the reader has been configured to automatically resolve references (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}), a reference can be provided in all * places where an object path is expected. This is considerably faster than resolving the * name/path of the reference if the name/path by itself is not needed. * * @param objectPath The name (including path information) of the data set object in the file. * @param resolveName If true, resolves the names of the objects referenced, * otherwise returns the references itself. * @return The multi-dimensional array of the paths of objects that the references refers to. * Each string may be empty, if the corresponding object reference refers to an unnamed * object. */ public MDArray readMDArray(final String objectPath, boolean resolveName); /** * Reads a multi-dimensional array of object references from the data set objectPath, * resolving the names of the objects.
* Note that resolving the name of the object is a time consuming operation. If you don't * need the name, but want to dereference the dataset, you don't need to resolve the name if the * reader / writer is configured for auto-dereferencing (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}). * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @return The referenced data set paths block read from the data set. */ public MDArray readMDArrayBlock(final String objectPath, final int[] blockDimensions, final long[] blockNumber); /** * Reads a multi-dimensional array of object references from the data set objectPath.
* Note: if the reader has been configured to automatically resolve references (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}), a reference can be provided in all * places where an object path is expected. This is considerably faster than resolving the * name/path of the reference if the name/path by itself is not needed. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @param resolveName If true, resolves the names of the objects referenced, * otherwise returns the references itself. * @return The referenced data set paths block read from the data set. */ public MDArray readMDArrayBlock(final String objectPath, final int[] blockDimensions, final long[] blockNumber, final boolean resolveName); /** * Reads a multi-dimensional array of object references from the data set objectPath, * resolving the names of the objects.
* Note that resolving the name of the object is a time consuming operation. If you don't * need the name, but want to dereference the dataset, you don't need to resolve the name if the * reader / writer is configured for auto-dereferencing (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}). * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @return The referenced data set paths block read from the data set. */ public MDArray readMDArrayBlockWithOffset(final String objectPath, final int[] blockDimensions, final long[] offset); /** * Reads a multi-dimensional array of object references from the data set objectPath.
* Note: if the reader has been configured to automatically resolve references (see * {@link IHDF5ReaderConfigurator#noAutoDereference()}), a reference can be provided in all * places where an object path is expected. This is considerably faster than resolving the * name/path of the reference if the name/path by itself is not needed. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @param resolveName If true, resolves the names of the objects referenced, * otherwise returns the references itself. * @return The referenced data set paths block read from the data set. */ public MDArray readMDArrayBlockWithOffset(final String objectPath, final int[] blockDimensions, final long[] offset, final boolean resolveName); /** * Provides all natural blocks of this one-dimensional data set to iterate over. * * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1. */ public Iterable> getArrayNaturalBlocks(final String dataSetPath); /** * Provides all natural blocks of this one-dimensional data set to iterate over. * * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1. */ public Iterable> getArrayNaturalBlocks(final String dataSetPath, final boolean resolveName); /** * Provides all natural blocks of this multi-dimensional data set to iterate over. * * @see HDF5MDDataBlock */ public Iterable>> getMDArrayNaturalBlocks( final String dataSetPath); /** * Provides all natural blocks of this multi-dimensional data set to iterate over. * * @see HDF5MDDataBlock */ public Iterable>> getMDArrayNaturalBlocks( final String dataSetPath, final boolean resolveName); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5ReferenceWriter.java000066400000000000000000000373161256564762100300520ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDLongArray; /** * An interface for writing references. References can refer to objects or regions of datasets. This * version only supports object references. *

* Note: References are a low-level feature and it is easy to get dangling or even wrong * references by using them. If you have a choice, don't use them, but use links instead. If you * have to use them, e.g. to comply with a pre-defined format definition, use them with care. The * most important fact to know about references is that they don't keep an object alive. Once the * last link to the object is gone, the object is gone as well. The reference will be * dangling. If, at a later time, another object header is written to the same place in the * file, the reference will refer to this new object, which is most likely an undesired effect * (wrong reference). By default JHDF5 itself deletes existing datasets before writing new * content to a dataset of the same name, which may lead to the described problem of dangling or * wrong references without any explicit call to {@link IHDF5Writer#delete(String)}. Thus, HDF5 * files with references should always be opened for writing using the * {@link IHDF5WriterConfigurator#keepDataSetsIfTheyExist()} setting. * * @author Bernd Rinn */ public interface IHDF5ReferenceWriter extends IHDF5ReferenceReader { // ///////////////////// // Attributes // ///////////////////// /** * Sets an object reference attribute to the referenced object. *

* Both the object referenced with objectPath and referencedObjectPath * must exist, that is it need to have been written before by one of the write() or * create() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param referencedObjectPath The path of the object to reference. */ public void setAttr(final String objectPath, final String name, final String referencedObjectPath); /** * Sets a 1D object reference array attribute to referenced objects. *

* Both the object referenced with objectPath and all * referencedObjectPaths must exist, that is it need to have been written before by * one of the write() or create() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param referencedObjectPaths The paths of the objects to reference. */ public void setArrayAttr(final String objectPath, final String name, final String[] referencedObjectPaths); /** * Sets an object reference array attribute to referenced objects. *

* Both the object referenced with objectPath and all * referencedObjectPaths must exist, that is it need to have been written before by * one of the write() or create() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param referencedObjectPaths The paths of the objects to reference. */ public void setMDArrayAttr(final String objectPath, final String name, final MDArray referencedObjectPaths); // ///////////////////// // Data Sets // ///////////////////// /** * Writes an object reference to the referenced object. *

* The object referenced with referencedObjectPath must exist, that is it need to * have been written before by one of the write() or create() methods. * * @param objectPath The name of the object to write. * @param referencedObjectPath The path of the object to reference. */ public void write(String objectPath, String referencedObjectPath); /** * Writes an array (of rank 1) of object references. * * @param objectPath The name (including path information) of the data set object in the file. * @param referencedObjectPath The names of the object to write. */ public void writeArray(final String objectPath, final String[] referencedObjectPath); /** * Writes an array (of rank 1) of object references. * * @param objectPath The name (including path information) of the data set object in the file. * @param referencedObjectPath The names of the object to write. * @param features The storage features of the data set. */ public void writeArray(final String objectPath, final String[] referencedObjectPath, final HDF5IntStorageFeatures features); /** * Creates an array (of rank 1) of object references. * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the array to create. This will be the total size for non-extendable * data sets and the size of one chunk for extendable (chunked) data sets. For * extendable data sets the initial size of the array will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. */ public void createArray(final String objectPath, final int size); /** * Creates an array (of rank 1) of object references. * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the array to create. When using extendable data sets ((see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data set * smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). */ public void createArray(final String objectPath, final long size, final int blockSize); /** * Creates an array (of rank 1) of object references. * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the array to create. This will be the total size for non-extendable * data sets and the size of one chunk for extendable (chunked) data sets. For * extendable data sets the initial size of the array will be 0, see * {@link HDF5IntStorageFeatures}. * @param features The storage features of the data set. */ public void createArray(final String objectPath, final int size, final HDF5IntStorageFeatures features); /** * Creates an array (of rank 1) of object references. * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the array to create. When using extendable data sets ((see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data set * smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) * and features is HDF5IntStorageFeature.INTNO_COMPRESSION. * @param features The storage features of the data set. */ public void createArray(final String objectPath, final long size, final int blockSize, final HDF5IntStorageFeatures features); /** * Writes out a block of an array (of rank 1) of object references. The data set needs to have * been created by {@link #createArray(String, long, int, HDF5IntStorageFeatures)} beforehand. *

* Note: For best performance, the block size in this method should be chosen to be equal * to the blockSize argument of the * {@link #createArray(String, long, int, HDF5IntStorageFeatures)} call that was used to create * the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param referencedObjectPaths The paths of the referenced objects to write. The length defines * the block size. Must not be null or of length 0. * @param blockNumber The number of the block to write. */ public void writeArrayBlock(final String objectPath, final String[] referencedObjectPaths, final long blockNumber); /** * Writes out a block of an array (of rank 1) of object references. The data set needs to have * been created by {@link #createArray(String, long, int, HDF5IntStorageFeatures)} beforehand. *

* Note: For best performance, the block size in this method should be chosen to be equal * to the blockSize argument of the * {@link #createArray(String, long, int, HDF5IntStorageFeatures)} call that was used to create * the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param referencedObjectPaths The paths of the referenced objects to write. The length defines * the block size. Must not be null or of length 0. * @param dataSize The (real) size of data (needs to be <= data.length * ) * @param offset The offset in the data set to start writing to. */ public void writeArrayBlockWithOffset(final String objectPath, final String[] referencedObjectPaths, final int dataSize, final long offset); /** * Writes an array (of rank N) of object references. * * @param objectPath The name (including path information) of the data set object in the file. * @param referencedObjectPaths The names of the object to write. */ public void writeMDArray(final String objectPath, final MDArray referencedObjectPaths); /** * Writes an array (of rank N) of object references. * * @param objectPath The name (including path information) of the data set object in the file. * @param referencedObjectPaths The names of the object to write. * @param features The storage features of the data set. */ public void writeMDArray(final String objectPath, final MDArray referencedObjectPaths, final HDF5IntStorageFeatures features); /** * Creates a multi-dimensional array of object references. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array to create. This will be the total dimensions * for non-extendable data sets and the dimensions of one chunk (extent along each * axis) for extendable (chunked) data sets. For extendable data sets the initial * size of the array along each axis will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. */ public void createMDArray(final String objectPath, final int[] dimensions); /** * Creates a multi-dimensional array of object references. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. */ public void createMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions); /** * Creates a multi-dimensional array of object references. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array to create. This will be the total dimensions * for non-extendable data sets and the dimensions of one chunk (extent along each * axis) for extendable (chunked) data sets. For extendable data sets the initial * size of the array along each axis will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. * @param features The storage features of the data set. */ public void createMDArray(final String objectPath, final int[] dimensions, final HDF5IntStorageFeatures features); /** * Creates a multi-dimensional array of object references. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. * @param features The storage features of the data set. */ public void createMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions, final HDF5IntStorageFeatures features); /** * Writes out a block of a multi-dimensional array of object references. * * @param objectPath The name (including path information) of the data set object in the file. * @param referencedObjectPaths The paths of the object references to write. Must not be * null. All columns need to have the same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). */ public void writeMDArrayBlock(final String objectPath, final MDArray referencedObjectPaths, final long[] blockNumber); /** * Writes out a block of a multi-dimensional array of object references. * * @param objectPath The name (including path information) of the data set object in the file. * @param referencedObjectPaths The paths of the object references to write. Must not be * null. * @param offset The offset in the data set to start writing to in each dimension. */ public void writeMDArrayBlockWithOffset(final String objectPath, final MDArray referencedObjectPaths, final long[] offset); /** * Writes out a block of a multi-dimensional array of object references. * * @param objectPath The name (including path information) of the data set object in the file. * @param referencedObjectPaths The paths of the object references to write. Must not be * null. * @param blockDimensions The dimensions of the block to write to the data set. * @param offset The offset of the block in the data set to start writing to in each dimension. * @param memoryOffset The offset of the block in the data array. */ public void writeMDArrayBlockWithOffset(final String objectPath, final MDLongArray referencedObjectPaths, final int[] blockDimensions, final long[] offset, final int[] memoryOffset); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5ShortReader.java000066400000000000000000000425331256564762100271760ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.base.mdarray.MDShortArray; /** * An interface that provides methods for reading short values from HDF5 files. *

* Note: This interface supports block access and sliced access (which is a special cases of * block access) to arrays. The performance of this block access can vary greatly depending on how * the data are layed out in the HDF5 file. For best performance, the block (or slice) dimension should * be chosen to be equal to the chunk dimensions of the array, as in this case the block written / read * are stored as consecutive value in the HDF5 file and one write / read access will suffice. *

* Note: If the values read are unsigned, use the methods in {@link UnsignedIntUtils} to convert * to a larger Java integer type that can hold all values as unsigned. * * @author Bernd Rinn */ public interface IHDF5ShortReader { // ///////////////////// // Attributes // ///////////////////// /** * Reads a short attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. */ public short getAttr(String objectPath, String attributeName); /** * Reads a short[] attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. */ public short[] getArrayAttr(String objectPath, String attributeName); /** * Reads a multi-dimensional array short attribute named attributeName * from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute array value read from the data set. */ public MDShortArray getMDArrayAttr(String objectPath, String attributeName); /** * Reads a short matrix attribute named attributeName * from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute matrix value read from the data set. */ public short[][] getMatrixAttr(String objectPath, String attributeName) throws HDF5JavaException; // ///////////////////// // Data Sets // ///////////////////// /** * Reads a short value from the data set objectPath. This method * doesn't check the data space but simply reads the first value. * * @param objectPath The name (including path information) of the data set object in the file. * @return The value read from the data set. */ public short read(String objectPath); /** * Reads a short array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. */ public short[] readArray(String objectPath); /** * Reads a multi-dimensional short array data set objectPath * into a given array in memory. * * @param objectPath The name (including path information) of the data set object in the file. * @param array The array to read the data into. * @param memoryOffset The offset in the array to write the data to. * @return The effective dimensions of the block in array that was filled. */ public int[] readToMDArrayWithOffset(String objectPath, MDShortArray array, int[] memoryOffset); /** * Reads a block of the multi-dimensional short array data set * objectPath into a given array in memory. * * @param objectPath The name (including path information) of the data set object in the file. * @param array The array to read the data into. * @param blockDimensions The size of the block to read along each axis. * @param offset The offset of the block in the data set. * @param memoryOffset The offset of the block in the array to write the data to. * @return The effective dimensions of the block in array that was filled. */ public int[] readToMDArrayBlockWithOffset(String objectPath, MDShortArray array, int[] blockDimensions, long[] offset, int[] memoryOffset); /** * Reads a block from a short array (of rank 1) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the short[] returned * if the data set is long enough). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @return The data read from the data set. The length will be min(size - blockSize*blockNumber, * blockSize). */ public short[] readArrayBlock(String objectPath, int blockSize, long blockNumber); /** * Reads a block from short array (of rank 1) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the short[] * returned). * @param offset The offset of the block in the data set to start reading from (starting with 0). * @return The data block read from the data set. */ public short[] readArrayBlockWithOffset(String objectPath, int blockSize, long offset); /** * Reads a short matrix (array of arrays) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * * @throws HDF5JavaException If the data set objectPath is not of rank 2. */ public short[][] readMatrix(String objectPath) throws HDF5JavaException; /** * Reads a short matrix (array of arrays) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSizeX The size of the block in the x dimension. * @param blockSizeY The size of the block in the y dimension. * @param blockNumberX The block number in the x dimension (offset: multiply with * blockSizeX). * @param blockNumberY The block number in the y dimension (offset: multiply with * blockSizeY). * @return The data block read from the data set. * * @throws HDF5JavaException If the data set objectPath is not of rank 2. */ public short[][] readMatrixBlock(String objectPath, int blockSizeX, int blockSizeY, long blockNumberX, long blockNumberY) throws HDF5JavaException; /** * Reads a short matrix (array of arrays) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSizeX The size of the block in the x dimension. * @param blockSizeY The size of the block in the y dimension. * @param offsetX The offset in x dimension in the data set to start reading from. * @param offsetY The offset in y dimension in the data set to start reading from. * @return The data block read from the data set. * * @throws HDF5JavaException If the data set objectPath is not of rank 2. */ public short[][] readMatrixBlockWithOffset(String objectPath, int blockSizeX, int blockSizeY, long offsetX, long offsetY) throws HDF5JavaException; /** * Reads a multi-dimensional short array from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. */ public MDShortArray readMDArray(String objectPath); /** * Reads a slice of a multi-dimensional short array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDShortArray readMDArraySlice(String objectPath, IndexMap boundIndices); /** * Reads a slice of a multi-dimensional short array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDShortArray readMDArraySlice(String objectPath, long[] boundIndices); /** * Reads a block from a multi-dimensional short array from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @return The data block read from the data set. */ public MDShortArray readMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber); /** * Reads a sliced block from a multi-dimensional short array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDShortArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, IndexMap boundIndices); /** * Reads a sliced block from a multi-dimensional short array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDShortArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, long[] boundIndices); /** * Reads a block from a multi-dimensional short array from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @return The data block read from the data set. */ public MDShortArray readMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset); /** * Reads a sliced block of a multi-dimensional short array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDShortArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, IndexMap boundIndices); /** * Reads a sliced block of a multi-dimensional short array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MDShortArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, long[] boundIndices); /** * Provides all natural blocks of this one-dimensional data set to iterate over. * * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1. */ public Iterable> getArrayNaturalBlocks( String dataSetPath) throws HDF5JavaException; /** * Provides all natural blocks of this multi-dimensional data set to iterate over. * * @see HDF5MDDataBlock */ public Iterable> getMDArrayNaturalBlocks( String dataSetPath); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5ShortWriter.java000066400000000000000000000714161256564762100272520ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ch.systemsx.cisd.base.mdarray.MDShortArray; /** * An interface that provides methods for writing short values to HDF5 files. *

* Note: This interface supports block access and sliced access (which is a special cases of * block access) to arrays. The performance of this block access can vary greatly depending on how * the data are layed out in the HDF5 file. For best performance, the block (or slice) dimension should * be chosen to be equal to the chunk dimensions of the array, as in this case the block written / read * are stored as consecutive value in the HDF5 file and one write / read access will suffice. *

* Note: If you need to convert from and to unsigned values, use the methods of * {@link UnsignedIntUtils}. * * @author Bernd Rinn */ // Note: It is a trick for keeping backward compatibility to let this interface extend // IHDF5UnsignedShortWriter instead of IHDF5ShortReader as it logically should. // Once we remove IHDF5UnsignedShortWriter, uncomment the following line and remove // all @Override annotations and we are fine again. //public interface IHDF5ShortWriter extends IHDF5ShortReader @SuppressWarnings("deprecation") public interface IHDF5ShortWriter extends IHDF5UnsignedShortWriter { // ///////////////////// // Attributes // ///////////////////// /** * Set a short attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ @Override public void setAttr(String objectPath, String name, short value); /** * Set a short[] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ @Override public void setArrayAttr(String objectPath, String name, short[] value); /** * Set a multi-dimensional code>short attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ @Override public void setMDArrayAttr(String objectPath, String name, MDShortArray value); /** * Set a short[][] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ @Override public void setMatrixAttr(String objectPath, String name, short[][] value); // ///////////////////// // Data Sets // ///////////////////// /** * Writes out a short value. * * @param objectPath The name (including path information) of the data set object in the file. * @param value The value to write. */ @Override public void write(String objectPath, short value); /** * Writes out a short array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ @Override public void writeArray(String objectPath, short[] data); /** * Writes out a short array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param features The storage features of the data set. */ @Override public void writeArray(String objectPath, short[] data, HDF5IntStorageFeatures features); /** * Creates a short array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size When the writer is configured to use extendable data types (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be size. When the writer is * configured to enforce a non-extendable data set, the initial size equals the * total size and will be size. */ @Override public void createArray(String objectPath, int size); /** * Creates a short array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the short array to create. When using extendable data sets * ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data * set smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). */ @Override public void createArray(String objectPath, long size, int blockSize); /** * Creates a short array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the short array to create. When requesting a * chunked data set (e.g. {@link HDF5IntStorageFeatures#INT_CHUNKED}), * the initial size of the array will be 0 and the chunk size will be arraySize. * When allowing a chunked data set (e.g. * {@link HDF5IntStorageFeatures#INT_NO_COMPRESSION} when the writer is * not configured to avoid extendable data types, see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be arraySize. When enforcing a * on-extendable data set (e.g. * {@link HDF5IntStorageFeatures#INT_CONTIGUOUS}), the initial size equals * the total size and will be arraySize. * @param features The storage features of the data set. */ @Override public void createArray(String objectPath, int size, HDF5IntStorageFeatures features); /** * Creates a short array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the short array to create. When using extendable data sets * ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data * set smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) and * features is HDF5IntStorageFeature.INT_NO_COMPRESSION. * @param features The storage features of the data set. */ @Override public void createArray(String objectPath, long size, int blockSize, HDF5IntStorageFeatures features); /** * Writes out a block of a short array (of rank 1). The data set needs to have * been created by {@link #createArray(String, long, int, HDF5IntStorageFeatures)} * beforehand. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumber The number of the block to write. */ @Override public void writeArrayBlock(String objectPath, short[] data, long blockNumber); /** * Writes out a block of a short array (of rank 1). The data set needs to have * been created by {@link #createArray(String, long, int, HDF5IntStorageFeatures)} * beforehand. *

* Use this method instead of {@link #writeArrayBlock(String, short[], long)} if the * total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param dataSize The (real) size of data (needs to be <= data.length * ) * @param offset The offset in the data set to start writing to. */ @Override public void writeArrayBlockWithOffset(String objectPath, short[] data, int dataSize, long offset); /** * Writes out a short matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ @Override public void writeMatrix(String objectPath, short[][] data); /** * Writes out a short matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. */ @Override public void writeMatrix(String objectPath, short[][] data, HDF5IntStorageFeatures features); /** * Creates a short matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of one block in the x dimension. See * {@link #createMDArray(String, int[])} on the different * meanings of this parameter. * @param sizeY The size of one block in the y dimension. See * {@link #createMDArray(String, int[])} on the different * meanings of this parameter. */ @Override public void createMatrix(String objectPath, int sizeX, int sizeY); /** * Creates a short matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of one block in the x dimension. See * {@link #createMDArray(String, int[], HDF5IntStorageFeatures)} on the different * meanings of this parameter. * @param sizeY The size of one block in the y dimension. See * {@link #createMDArray(String, int[], HDF5IntStorageFeatures)} on the different * meanings of this parameter. * @param features The storage features of the data set. */ @Override public void createMatrix(String objectPath, int sizeX, int sizeY, HDF5IntStorageFeatures features); /** * Creates a short matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the short matrix to create. * @param sizeY The size of the y dimension of the short matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. */ @Override public void createMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY); /** * Creates a short matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the short matrix to create. * @param sizeY The size of the y dimension of the short matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. * @param features The storage features of the data set. */ @Override public void createMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY, HDF5IntStorageFeatures features); /** * Writes out a block of a short matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of * {@link #createMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} if the total * size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumberX The block number in the x dimension (offset: multiply with * data.length). * @param blockNumberY The block number in the y dimension (offset: multiply with * data[0.length). */ @Override public void writeMatrixBlock(String objectPath, short[][] data, long blockNumberX, long blockNumberY); /** * Writes out a block of a short matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeMatrixBlock(String, short[][], long, long)} if * the total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. */ @Override public void writeMatrixBlockWithOffset(String objectPath, short[][] data, long offsetX, long offsetY); /** * Writes out a block of a short matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeMatrixBlock(String, short[][], long, long)} if * the total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param dataSizeX The (real) size of data along the x axis (needs to be * <= data.length ) * @param dataSizeY The (real) size of data along the y axis (needs to be * <= data[0].length ) * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. */ @Override public void writeMatrixBlockWithOffset(String objectPath, short[][] data, int dataSizeX, int dataSizeY, long offsetX, long offsetY); /** * Writes out a multi-dimensional short array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ @Override public void writeMDArray(String objectPath, MDShortArray data); /** * Writes out a multi-dimensional short array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. */ @Override public void writeMDArray(String objectPath, MDShortArray data, HDF5IntStorageFeatures features); /** * Writes out a slice of a multi-dimensional short array. The slice is defined by * "bound indices", each of which is fixed to a given value. The data object only * contains the free (i.e. non-fixed) indices. *

* Note:The object identified by objectPath needs to exist when this method is * called. This method will not create the array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. */ public void writeMDArraySlice(String objectPath, MDShortArray data, IndexMap boundIndices); /** * Writes out a slice of a multi-dimensional short array. The slice is defined by * "bound indices", each of which is fixed to a given value. The data object only * contains the free (i.e. non-fixed) indices. *

* Note:The object identified by objectPath needs to exist when this method is * called. This method will not create the array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. */ public void writeMDArraySlice(String objectPath, MDShortArray data, long[] boundIndices); /** * Creates a multi-dimensional short array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions When the writer is configured to use extendable data types (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial dimensions * and the dimensions of a chunk of the array will be dimensions. When the * writer is configured to enforce a non-extendable data set, the initial dimensions * equal the dimensions and will be dimensions. */ @Override public void createMDArray(String objectPath, int[] dimensions); /** * Creates a multi-dimensional short array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. */ @Override public void createMDArray(String objectPath, long[] dimensions, int[] blockDimensions); /** * Creates a multi-dimensional short array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the short array to create. When requesting * a chunked data set (e.g. {@link HDF5IntStorageFeatures#INT_CHUNKED}), * the initial size of the array will be 0 and the chunk size will be dimensions. * When allowing a chunked data set (e.g. * {@link HDF5IntStorageFeatures#INT_NO_COMPRESSION} when the writer is * not configured to avoid extendable data types, see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be dimensions. When enforcing a * on-extendable data set (e.g. * {@link HDF5IntStorageFeatures#INT_CONTIGUOUS}), the initial size equals * the total size and will be dimensions. * @param features The storage features of the data set. */ @Override public void createMDArray(String objectPath, int[] dimensions, HDF5IntStorageFeatures features); /** * Creates a multi-dimensional short array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. * @param features The storage features of the data set. */ @Override public void createMDArray(String objectPath, long[] dimensions, int[] blockDimensions, HDF5IntStorageFeatures features); /** * Writes out a block of a multi-dimensional short array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). */ @Override public void writeMDArrayBlock(String objectPath, MDShortArray data, long[] blockNumber); /** * Writes out a sliced block of a multi-dimensional short array. The slice is * defined by "bound indices", each of which is fixed to a given value. The data * object only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. */ public void writeSlicedMDArrayBlock(String objectPath, MDShortArray data, long[] blockNumber, IndexMap boundIndices); /** * Writes out a sliced block of a multi-dimensional short array. The slice is * defined by "bound indices", each of which is fixed to a given value. The data * object only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. */ public void writeSlicedMDArrayBlock(String objectPath, MDShortArray data, long[] blockNumber, long[] boundIndices); /** * Writes out a block of a multi-dimensional short array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. */ @Override public void writeMDArrayBlockWithOffset(String objectPath, MDShortArray data, long[] offset); /** * Writes out a sliced block of a multi-dimensional short array. The slice is * defined by "bound indices", each of which is fixed to a given value. The data * object only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. */ public void writeSlicedMDArrayBlockWithOffset(String objectPath, MDShortArray data, long[] offset, IndexMap boundIndices); /** * Writes out a sliced block of a multi-dimensional short array. The slice is * defined by "bound indices", each of which is fixed to a given value. The data * object only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. */ public void writeSlicedMDArrayBlockWithOffset(String objectPath, MDShortArray data, long[] offset, long[] boundIndices); /** * Writes out a block of a multi-dimensional short array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param blockDimensions The dimensions of the block to write to the data set. * @param offset The offset of the block in the data set to start writing to in each dimension. * @param memoryOffset The offset of the block in the data array. */ @Override public void writeMDArrayBlockWithOffset(String objectPath, MDShortArray data, int[] blockDimensions, long[] offset, int[] memoryOffset); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5SimpleReader.java000066400000000000000000000365231256564762100273320ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.io.Closeable; import java.util.BitSet; import java.util.Date; import java.util.List; import ncsa.hdf.hdf5lib.exceptions.HDF5DatatypeInterfaceException; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; /** * A HDF5 reader which contains only the basic methods. If you feel overwhelmed with all the methods * of {@link IHDF5Reader}, then assign the reader to a {@link IHDF5SimpleReader} variable and let * the code completion of your IDE help you find the method you are looking for. *

* Usage: * * 

 * IHDF5SimpleReader reader = HDF5FactoryProvider.get().openForReading(new File("test.h5"));
 * float[] f = reader.readFloatArray("/some/path/dataset");
 * reader.close();
 *
* * @author Bernd Rinn */ public interface IHDF5SimpleReader extends Closeable { /** * Closes this object and the file referenced by this object. This object must not be used after * being closed. */ @Override public void close(); /** * Returns true, if objectPath exists and false otherwise. */ public boolean exists(final String objectPath); /** * Returns true if the objectPath exists and represents a group and * false otherwise. */ public boolean isGroup(final String objectPath); /** * Returns the information about a data set as a {@link HDF5DataSetInformation} object. It is a * failure condition if the dataSetPath does not exist or does not identify a data * set. * * @param dataSetPath The name (including path information) of the data set to return * information about. */ public HDF5DataSetInformation getDataSetInformation(final String dataSetPath); /** * Returns the members of groupPath. The order is not well defined. * * @param groupPath The path of the group to get the members for. * @throws IllegalArgumentException If groupPath is not a group. */ public List getGroupMembers(final String groupPath); /** * Reads the data set objectPath as byte array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. */ public byte[] readAsByteArray(final String objectPath); /** * Reads a Boolean value from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a boolean type. */ public boolean readBoolean(final String objectPath) throws HDF5JavaException; /** * Reads a bit field (which can be considered the equivalent to a boolean array of rank 1) from * the data set objectPath and returns it as a Java {@link BitSet}. *

* Note that the storage form of the bit array is a long[]. However, it is marked * in HDF5 to be interpreted bit-wise. Thus a data set written by * {@link IHDF5LongWriter#writeArray(String, long[])} cannot be read back by this method but * will throw a {@link HDF5DatatypeInterfaceException}. * * @param objectPath The name (including path information) of the data set object in the file. * @return The {@link BitSet} read from the data set. * @throws HDF5DatatypeInterfaceException If the objectPath is not of bit field type. */ public BitSet readBitField(final String objectPath) throws HDF5DatatypeInterfaceException; /** * Reads a int value from the data set objectPath. This method doesn't * check the data space but simply reads the first value. * * @param objectPath The name (including path information) of the data set object in the file. * @return The value read from the data set. */ public int readInt(final String objectPath); /** * Reads a int array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. */ public int[] readIntArray(final String objectPath); /** * Reads a int matrix (array of arrays) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. */ public int[][] readIntMatrix(final String objectPath); /** * Reads a long value from the data set objectPath. This method doesn't * check the data space but simply reads the first value. * * @param objectPath The name (including path information) of the data set object in the file. * @return The value read from the data set. */ public long readLong(final String objectPath); /** * Reads a long array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. */ public long[] readLongArray(final String objectPath); /** * Reads a long matrix (array of arrays) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. */ public long[][] readLongMatrix(final String objectPath); /** * Reads a float value from the data set objectPath. This method doesn't * check the data space but simply reads the first value. * * @param objectPath The name (including path information) of the data set object in the file. * @return The value read from the data set. */ public float readFloat(final String objectPath); /** * Reads a float array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. */ public float[] readFloatArray(final String objectPath); /** * Reads a float matrix (array of arrays) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. */ public float[][] readFloatMatrix(final String objectPath); /** * Reads a double value from the data set objectPath. This method * doesn't check the data space but simply reads the first value. * * @param objectPath The name (including path information) of the data set object in the file. * @return The value read from the data set. */ public double readDouble(final String objectPath); /** * Reads a double array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. */ public double[] readDoubleArray(final String objectPath); /** * Reads a double matrix (array of arrays) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. */ public double[][] readDoubleMatrix(final String objectPath); /** * Reads a date value from the data set objectPath. It needs to have been written by * {@link IHDF5SimpleWriter#writeDate(String, Date)}. * * @param objectPath The name (including path information) of the data set object in the file. * @return The time stamp as {@link Date}. * @throws HDF5JavaException If the objectPath does not denote a time stamp. */ public Date readDate(final String objectPath) throws HDF5JavaException; /** * Reads a date array (of rank 1) from the data set objectPath. It needs to have been * written by {@link IHDF5SimpleWriter#writeDateArray(String, Date[])}. * * @param objectPath The name (including path information) of the data set object in the file. * @return The time stamp as {@link Date}. * @throws HDF5JavaException If the objectPath does not denote a time stamp. */ public Date[] readDateArray(final String objectPath) throws HDF5JavaException; /** * Reads a time duration value from the data set objectPath. It needs to have been * written by {@link IHDF5SimpleWriter#writeTimeDuration(String, HDF5TimeDuration)}. * * @param objectPath The name (including path information) of the data set object in the file. * @return The time duration in seconds. * @throws HDF5JavaException If the objectPath is not tagged as a type variant that * corresponds to a time duration. */ public HDF5TimeDuration readTimeDuration(final String objectPath) throws HDF5JavaException; /** * Reads a time duration array from the data set objectPath. It needs to have been * written by {@link IHDF5SimpleWriter#writeTimeDurationArray(String, HDF5TimeDurationArray)}. * * @param objectPath The name (including path information) of the data set object in the file. * @return The time duration in seconds. * @throws HDF5JavaException If the objectPath is not defined as type variant * {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. */ public HDF5TimeDurationArray readTimeDurationArray(final String objectPath) throws HDF5JavaException; /** * Reads a String from the data set objectPath. Considers '\0' as end of * string. This needs to be a string type. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a string type. */ public String readString(final String objectPath) throws HDF5JavaException; /** * Reads a String array (of rank 1) from the data set objectPath. The * elements of this data set need to be a string type. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. */ public String[] readStringArray(final String objectPath) throws HDF5JavaException; /** * Reads a compound from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param pojoClass The class to return the result in. Use {@link HDF5CompoundDataMap} to get it * in a map, {@link HDF5CompoundDataList} to get it in a list, and * Object[] to get it in an array, or use a pojo (Data Transfer Object), * in which case the compound members will be mapped to Java fields. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set. * @see CompoundType * @see CompoundElement */ public T readCompound(final String objectPath, final Class pojoClass) throws HDF5JavaException; /** * Reads a compound array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param pojoClass The class to return the result in. Use {@link HDF5CompoundDataMap} to get it * in a map, {@link HDF5CompoundDataList} to get it in a list, and * Object[] to get it in an array, or use a pojo (Data Transfer Object), * in which case the compound members will be mapped to Java fields. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a compound data set. * @see CompoundType * @see CompoundElement */ public T[] readCompoundArray(final String objectPath, final Class pojoClass) throws HDF5JavaException; /** * Reads an Enum value from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param enumClass the {@link Enum} class to represent the values of. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not of enumType or if * enumClass is incompatible with the HDF5 enumeration type of * objectPath. */ public > T readEnum(final String objectPath, Class enumClass) throws HDF5JavaException; /** * Reads an Enum value from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set as a String. * @throws HDF5JavaException If the objectPath is not an enum type. */ public String readEnumAsString(final String objectPath) throws HDF5JavaException; /** * Reads an Enum value array from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param enumClass the {@link Enum} class to represent the values of. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not of enumType. */ public > T[] readEnumArray(final String objectPath, Class enumClass) throws HDF5JavaException; /** * Reads an Enum array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set as an array of Strings. * @throws HDF5JavaException If the objectPath is not an enum type. */ public String[] readEnumArrayAsString(final String objectPath) throws HDF5JavaException; } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5SimpleWriter.java000066400000000000000000000307741256564762100274060ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.util.BitSet; import java.util.Date; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; /** * A HDF5 writer which contains only the basic methods. If you feel overwhelmed with all the methods * of {@link IHDF5Writer}, then assign the writer to a {@link IHDF5SimpleWriter} variable and let * the code completion of your IDE help you find the method you are looking for. *

* Usage: * * 

 * float[] f = new float[100];
 * ...
 * IHDF5SimpleWriter writer = HDF5FactoryProvider.get().open(new File("test.h5"));
 * writer.writeFloatArray("/some/path/dataset", f);
 * writer.close();
 *
* * @author Bernd Rinn */ public interface IHDF5SimpleWriter extends IHDF5SimpleReader { /** * Removes an object from the file. If there is more than one link to the object, only the * specified link will be removed. */ public void delete(String objectPath); /** * Writes out a boolean value. * * @param objectPath The name (including path information) of the data set object in the file. * @param value The value of the data set. */ public void writeBoolean(final String objectPath, final boolean value); /** * Writes out a bit field ((which can be considered the equivalent to a boolean array of rank * 1), provided as a Java {@link BitSet}. *

* Note that the storage form of the bit array is a long[]. However, it is marked * in HDF5 to be interpreted bit-wise. Thus a data set written by this method cannot be read * back by {@link #readLongArray(String)} but will throw a * {@link ncsa.hdf.hdf5lib.exceptions.HDF5DatatypeInterfaceException}. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ public void writeBitField(final String objectPath, final BitSet data); /** * Writes out a byte array (of rank 1). Uses a compact storage layout. Should only * be used for small data sets. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ public void writeByteArray(final String objectPath, final byte[] data); /** * Writes out a int value. * * @param objectPath The name (including path information) of the data set object in the file. * @param value The value to write. */ public void writeInt(final String objectPath, final int value); /** * Writes out a int array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ public void writeIntArray(final String objectPath, final int[] data); /** * Writes out a int matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ public void writeIntMatrix(final String objectPath, final int[][] data); /** * Writes out a long value. * * @param objectPath The name (including path information) of the data set object in the file. * @param value The value to write. */ public void writeLong(final String objectPath, final long value); /** * Writes out a long array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ public void writeLongArray(final String objectPath, final long[] data); /** * Writes out a long matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ public void writeLongMatrix(final String objectPath, final long[][] data); /** * Writes out a float value. * * @param objectPath The name (including path information) of the data set object in the file. * @param value The value to write. */ public void writeFloat(final String objectPath, final float value); /** * Writes out a float array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ public void writeFloatArray(final String objectPath, final float[] data); /** * Writes out a float matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ public void writeFloatMatrix(final String objectPath, final float[][] data); /** * Writes out a double value. * * @param objectPath The name (including path information) of the data set object in the file. * @param value The value to write. */ public void writeDouble(final String objectPath, final double value); /** * Writes out a double array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ public void writeDoubleArray(final String objectPath, final double[] data); /** * Writes out a double matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ public void writeDoubleMatrix(final String objectPath, final double[][] data); /** * Writes out a time stamp value provided as a {@link Date}. The data set will be tagged as type * variant {@link HDF5DataTypeVariant#TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH}. *

* Note: This is a convenience method for * * @param objectPath The name (including path information) of the data set object in the file. * @param date The date to write. */ public void writeDate(final String objectPath, final Date date); /** * Writes out a {@link Date} array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param dates The dates to write. */ public void writeDateArray(final String objectPath, final Date[] dates); /** * Writes out a time duration value. *

* Note: Time durations are stored as long[] arrays and tagged as the according * type variant. * * @param objectPath The name (including path information) of the data set object in the file. * @param timeDuration The duration of time to write. */ public void writeTimeDuration(final String objectPath, final HDF5TimeDuration timeDuration); /** * Writes out a time duration array (of rank 1). *

* Note: Time durations are stored as long[] arrays and tagged as the according * type variant. * * @param objectPath The name (including path information) of the data set object in the file. * @param timeDurations The time durations to write. */ public void writeTimeDurationArray(final String objectPath, final HDF5TimeDurationArray timeDurations); /** * Writes out a String with a fixed maximal length. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param maxLength The maximal length of the data. * @deprecated Use {@link #writeString(String, String)} instead. */ @Deprecated public void writeString(final String objectPath, final String data, final int maxLength); /** * Writes out a String with a fixed maximal length. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ public void writeString(final String objectPath, final String data); /** * Writes out a String array (of rank 1). Each element of the array will have a * fixed maximal length which is given by maxLength. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @deprecated Use {@link #writeStringArray(String, String[])} instead. */ @Deprecated public void writeStringArray(final String objectPath, final String[] data, final int maxLength); /** * Writes out a String array (of rank 1). Each element of the array will have a * fixed maximal length which is given by the longest element. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ public void writeStringArray(final String objectPath, final String[] data); /** * Writes out a compound value. The type is inferred based on the values. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The value of the data set. May be a pojo (Data Transfer Object), a * {@link HDF5CompoundDataMap}, {@link HDF5CompoundDataList} or Object[] * . * @see CompoundType * @see CompoundElement */ public void writeCompound(String objectPath, T data); /** * Writes out an array (of rank 1) of compound values. The type is inferred based on the values. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The value of the data set. May be a pojo (Data Transfer Object), a * {@link HDF5CompoundDataMap}, {@link HDF5CompoundDataList} or Object[] * . * @see CompoundType * @see CompoundElement */ public void writeCompoundArray(final String objectPath, final T[] data); /** * Writes out an enum value. * * @param objectPath The name (including path information) of the data set object in the file. * @param value The value of the data set. * @throws HDF5JavaException If the enum type of value is not a type of this file. */ public > void writeEnum(final String objectPath, final Enum value) throws HDF5JavaException; /** * Writes out an array of enum values. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. */ public > void writeEnumArray(String objectPath, Enum[] data); /** * Writes out an array of enum values. * * @param objectPath The name (including path information) of the data set object in the file. * @param options The allowed values of the enumeration type. * @param data The data to write. */ public void writeEnumArray(String objectPath, String[] options, String[] data); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5StringReader.java000066400000000000000000000357711256564762100273530ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.base.mdarray.MDArray; /** * An interface that provides methods for reading String values from HDF5 files. * * @author Bernd Rinn */ public interface IHDF5StringReader { // ///////////////////// // Attributes // ///////////////////// /** * Reads a string attribute named attributeName from the object * objectPath. Considers '\0' as end of string. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. */ public String getAttr(final String objectPath, final String attributeName); /** * Reads a string attribute named attributeName from the object * objectPath. Does not consider '\0' as end of string but reads the full length of * the attribute. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. */ public String getAttrRaw(final String objectPath, final String attributeName); /** * Reads a string array attribute named attributeName from the object * objectPath. Considers '\0' as end of string. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. */ public String[] getArrayAttr(final String objectPath, final String attributeName); /** * Reads a string array attribute named attributeName from the object * objectPath. Does not consider '\0' as end of string but reads the full length. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. */ public String[] getArrayAttrRaw(final String objectPath, final String attributeName); /** * Reads a multi-dimensional string array attribute named attributeName from the * object objectPath. Considers '\0' as end of string. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. */ public MDArray getMDArrayAttr(final String objectPath, final String attributeName); /** * Reads a multi-dimensional string array attribute named attributeName from the * object objectPath. Does not consider '\0' as end of string but reads the full * length. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. */ public MDArray getMDArrayAttrRaw(final String objectPath, final String attributeName); // ///////////////////// // Data Sets // ///////////////////// /** * Reads a string from the data set objectPath. Considers '\0' as end of string. This * needs to be a string type. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a string type. */ public String read(final String objectPath) throws HDF5JavaException; /** * Reads a String from the data set objectPath. Does not consider '\0' * as end of string but reads the full length of the string. This needs to be a string type. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a string type. */ public String readRaw(final String objectPath) throws HDF5JavaException; /** * Reads a string array (of rank 1) from the data set objectPath. The elements of * this data set need to be a string type. Considers '\0' as end of string. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a string type. */ public String[] readArray(final String objectPath) throws HDF5JavaException; /** * Reads a string array (of rank 1) from the data set objectPath. The elements of * this data set need to be a string type. Does not consider '\0' as end of string but reads the * full length. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a string type. */ public String[] readArrayRaw(final String objectPath) throws HDF5JavaException; /** * Reads a block of a string array (of rank 1) from the data set objectPath. The * elements of this data set need to be a string type. Considers '\0' as end of string. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The size of the block to read from the data set. * @param blockNumber The number of the block to read from the data set (the offset is * blockSize * blockNumber). * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a string type. */ public String[] readArrayBlock(final String objectPath, final int blockSize, final long blockNumber); /** * Reads a block of a string array (of rank 1) from the data set objectPath. The * elements of this data set need to be a string type. Does not consider '\0' as end of string * but reads the full length. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The size of the block to read from the data set. * @param blockNumber The number of the block to read from the data set (the offset is * blockSize * blockNumber). * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a string type. */ public String[] readArrayBlockRaw(final String objectPath, final int blockSize, final long blockNumber); /** * Reads a block of a string array (of rank 1) from the data set objectPath. The * elements of this data set need to be a string type. Considers '\0' as end of string. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The size of the block to read from the data set. * @param offset The offset of the block in the data set. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a string type. */ public String[] readArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset); /** * Reads a block of a string array (of rank 1) from the data set objectPath. The * elements of this data set need to be a string type. Does not consider '\0' as end of string * but reads the full length. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The size of the block to read from the data set. * @param offset The offset of the block in the data set. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a string type. */ public String[] readArrayBlockWithOffsetRaw(final String objectPath, final int blockSize, final long offset); /** * Reads a string array (of rank N) from the data set objectPath. The elements of * this data set need to be a string type. Considers '\0' as end of string. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a string type. */ public MDArray readMDArray(final String objectPath); /** * Reads a string array (of rank N) from the data set objectPath. The elements of * this data set need to be a string type. Does not considers '\0' as end of string but reads * the full length. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a string type. */ public MDArray readMDArrayRaw(final String objectPath); /** * Reads a block of a string array (of rank N) from the data set objectPath. The * elements of this data set need to be a string type. Considers '\0' as end of string. * Considers '\0' as end of string. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The dimensions (along each axis) of the block to read from the data * set. * @param blockNumber The number of the block to read from the data set (the offset in each * dimension i is blockSize[i] * blockNumber[i]). * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a string type. */ public MDArray readMDArrayBlock(final String objectPath, final int[] blockDimensions, final long[] blockNumber); /** * Reads a block of a string array (of rank N) from the data set objectPath. The * elements of this data set need to be a string type. Does not consider '\0' as end of string * but reads the full length. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The dimensions (along each axis) of the block to read from the data * set. * @param blockNumber The number of the block to read from the data set (the offset in each * dimension i is blockSize[i] * blockNumber[i]). * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a string type. */ public MDArray readMDArrayBlockRaw(final String objectPath, final int[] blockDimensions, final long[] blockNumber); /** * Reads a block of a string array (of rank N) from the data set objectPath. The * elements of this data set need to be a string type. Considers '\0' as end of string. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The dimensions (along each axis) of the block to read from the data * set. * @param offset The offset of the block in the data set. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a string type. */ public MDArray readMDArrayBlockWithOffset(final String objectPath, final int[] blockDimensions, final long[] offset); /** * Reads a block of a string array (of rank N) from the data set objectPath. The * elements of this data set need to be a string type. Does not consider '\0' as end of string * but reads the full length. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The dimensions (along each axis) of the block to read from the data * set. * @param offset The offset of the block in the data set. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not a string type. */ public MDArray readMDArrayBlockWithOffsetRaw(final String objectPath, final int[] blockDimensions, final long[] offset); /** * Provides all natural blocks of this one-dimensional string data set to iterate over. * Considers '\0' as end of string. * * @param objectPath The name (including path information) of the data set object in the file. * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1. */ public Iterable> getArrayNaturalBlocks(final String objectPath) throws HDF5JavaException; /** * Provides all natural blocks of this one-dimensional string data set to iterate over. Does not * consider '\0' as end of string but reads the full length. * * @param objectPath The name (including path information) of the data set object in the file. * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1. */ public Iterable> getArrayNaturalBlocksRaw(final String objectPath) throws HDF5JavaException; /** * Provides all natural blocks of this multi-dimensional string data set to iterate over. * Considers '\0' as end of string. * * @see HDF5MDDataBlock */ public Iterable>> getMDArrayNaturalBlocks( final String objectPath); /** * Provides all natural blocks of this multi-dimensional string data set to iterate over. Does * not consider '\0' as end of string but reads the full length. * * @see HDF5MDDataBlock */ public Iterable>> getMDArrayNaturalBlocksRaw( final String objectPath); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5StringWriter.java000066400000000000000000000724341256564762100274220ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ch.systemsx.cisd.base.mdarray.MDArray; /** * An interface that provides methods for writing String values to HDF5 files. * * @author Bernd Rinn */ public interface IHDF5StringWriter extends IHDF5StringReader { // ///////////////////// // Attributes // ///////////////////// /** * Sets a string attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setAttr(final String objectPath, final String name, final String value); /** * Sets a string attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @param maxLength The maximal length of the value. */ public void setAttr(final String objectPath, final String name, final String value, final int maxLength); /** * Sets a string array attribute on the referenced object. The length of the array is taken to * be the longest string in value. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setArrayAttr(final String objectPath, final String name, final String[] value); /** * Sets a string array attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @param maxLength The maximal length of any element in value. */ public void setArrayAttr(final String objectPath, final String name, final String[] value, final int maxLength); /** * Sets a multi-dimensional string array attribute on the referenced object. The length of the * array is taken to be the longest string in value. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setMDArrayAttr(final String objectPath, final String name, final MDArray value); /** * Sets a multi-dimensional string array attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. * @param maxLength The maximal length of the value. */ public void setMDArrayAttr(final String objectPath, final String name, final MDArray value, final int maxLength); /** * Sets a string attribute with variable length on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setAttrVL(final String objectPath, final String name, final String value); // ///////////////////// // Data Sets // ///////////////////// /** * Writes out a String with a fixed maximal length. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param maxLength The maximal length of the data. */ public void write(final String objectPath, final String data, final int maxLength); /** * Writes out a String with a fixed maximal length (which is the length of the * string data). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ public void write(final String objectPath, final String data); /** * Writes out a String with a fixed maximal length. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param features The storage features of the data set. */ public void write(final String objectPath, final String data, final HDF5GenericStorageFeatures features); /** * Writes out a String with a fixed maximal length. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param maxLength The maximal length of the data. * @param features The storage features of the data set. */ public void write(final String objectPath, final String data, final int maxLength, final HDF5GenericStorageFeatures features); /** * Writes out a String array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param features The storage features of the data set. */ public void writeArray(final String objectPath, final String[] data, final HDF5GenericStorageFeatures features); /** * Writes out a String array (of rank 1). Each element of the array will have a * fixed maximal length which is defined by the longest string in data. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ public void writeArray(final String objectPath, final String[] data); /** * Writes out a String array (of rank 1). Each element of the array will have a * fixed maximal length which is given by maxLength. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param maxLength The maximal length of any of the strings in data. */ public void writeArray(final String objectPath, final String[] data, final int maxLength); /** * Writes out a String array (of rank 1). Each element of the array will have a * fixed maximal length which is given by maxLength. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param maxLength The maximal length of any of the strings in data. * @param features The storage features of the data set. */ public void writeArray(final String objectPath, final String[] data, final int maxLength, final HDF5GenericStorageFeatures features); /** * Writes out a String array (of rank N). Each element of the array will have a * fixed maximal length which is defined by the longest string in data. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ public void writeMDArray(final String objectPath, final MDArray data); /** * Writes out a String array (of rank N). Each element of the array will have a * fixed maximal length which is defined by the longest string in data. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param features The storage features of the data set. */ public void writeMDArray(final String objectPath, final MDArray data, final HDF5GenericStorageFeatures features); /** * Writes out a String array (of rank N). Each element of the array will have a * fixed maximal length which is given by maxLength. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param maxLength The maximal length of any of the strings in data. */ public void writeMDArray(final String objectPath, final MDArray data, final int maxLength); /** * Writes out a String array (of rank N). Each element of the array will have a * fixed maximal length which is given by maxLength. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param maxLength The maximal length of any of the strings in data. * @param features The storage features of the data set. */ public void writeMDArray(final String objectPath, final MDArray data, final int maxLength, final HDF5GenericStorageFeatures features); /** * Creates a String array (of rank 1) for Strings of length maxLength. * * @param objectPath The name (including path information) of the data set object in the file. * @param maxLength The maximal length of one String in the array. * @param size The size of the byte array to create. This will be the total size for * non-extendable data sets and the size of one chunk for extendable (chunked) data * sets. For extendable data sets the initial size of the array will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. */ public void createArray(final String objectPath, final int maxLength, final int size); /** * Creates a String array (of rank 1) for Strings of length maxLength. * * @param objectPath The name (including path information) of the data set object in the file. * @param maxLength The maximal length of one String in the array. * @param size The size of the String array to create. When using extendable data sets ((see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data set * smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). */ public void createArray(final String objectPath, final int maxLength, final long size, final int blockSize); /** * Creates a String array (of rank 1) for Strings of length maxLength. * * @param objectPath The name (including path information) of the data set object in the file. * @param maxLength The maximal length of one String in the array. * @param size The size of the array to create. This will be the total size for non-extendable * data sets and the size of one chunk for extendable (chunked) data sets. For * extendable data sets the initial size of the array will be 0, see * {@link HDF5GenericStorageFeatures}. */ public void createArray(final String objectPath, final int maxLength, final int size, final HDF5GenericStorageFeatures features); /** * Creates a String array (of rank 1) for Strings of length maxLength. * * @param objectPath The name (including path information) of the data set object in the file. * @param maxLength The maximal length of one String in the array. * @param size The size of the String array to create. When using extendable data sets ((see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data set * smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). * @param features The storage features of the data set. */ public void createArray(final String objectPath, final int maxLength, final long size, final int blockSize, final HDF5GenericStorageFeatures features); /** * Writes out a block of a String array (of rank 1). The data set needs to have * been created by * {@link #createArray(String, int, long, int, HDF5GenericStorageFeatures)} beforehand. *

* Note: For best performance, the block size in this method should be chosen to be equal * to the blockSize argument of the * {@link #createArray(String, int, long, int, HDF5GenericStorageFeatures)} call that was * used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumber The number of the block to write. */ public void writeArrayBlock(final String objectPath, final String[] data, final long blockNumber); /** * Writes out a block of a String array (of rank 1). The data set needs to have * been created by * {@link #createArray(String, int, long, int, HDF5GenericStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeArrayBlock(String, String[], long)} if the * total size of the data set is not a multiple of the block size. *

* Note: For best performance, the block size in this method should be chosen to be equal * to the blockSize argument of the * {@link #createArray(String, int, long, int, HDF5GenericStorageFeatures)} call that was * used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param dataSize The (real) size of data (needs to be <= data.length * ) * @param offset The offset in the data set to start writing to. */ public void writeArrayBlockWithOffset(final String objectPath, final String[] data, final int dataSize, final long offset); /** * Creates a String array (of rank N) for Strings of length maxLength. * * @param objectPath The name (including path information) of the data set object in the file. * @param maxLength The maximal length of one String in the array. * @param dimensions The size of the String array to create. When using extendable data sets * ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data * set smaller than this size can be created, however data sets may be larger. */ public void createMDArray(final String objectPath, final int maxLength, final int[] dimensions); /** * Creates a String array (of rank N) for Strings of length maxLength. * * @param objectPath The name (including path information) of the data set object in the file. * @param maxLength The maximal length of one String in the array. * @param dimensions The size of the String array to create. When using extendable data sets * ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data * set smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block in each dimension (for block-wise IO). Ignored if no * extendable data sets are used (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). */ public void createMDArray(final String objectPath, final int maxLength, final long[] dimensions, final int[] blockSize); /** * Creates a String array (of rank N) for Strings of length maxLength. * * @param objectPath The name (including path information) of the data set object in the file. * @param maxLength The maximal length of one String in the array. * @param dimensions The size of the String array to create. When using extendable data sets * ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data * set smaller than this size can be created, however data sets may be larger. * @param features The storage features of the data set. */ public void createMDArray(final String objectPath, final int maxLength, final int[] dimensions, final HDF5GenericStorageFeatures features); /** * Creates a String array (of rank N) for Strings of length maxLength. * * @param objectPath The name (including path information) of the data set object in the file. * @param maxLength The maximal length of one String in the array. * @param dimensions The size of the String array to create. When using extendable data sets * ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data * set smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block in each dimension (for block-wise IO). Ignored if no * extendable data sets are used (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). * @param features The storage features of the data set. */ public void createMDArray(final String objectPath, final int maxLength, final long[] dimensions, final int[] blockSize, final HDF5GenericStorageFeatures features); /** * Writes out a block of a String array (of rank N). The data set needs to have * been created by * {@link #createMDArray(String, int, long[], int[], HDF5GenericStorageFeatures)} * beforehand. *

* Note: For best performance, the block size in this method should be chosen to be equal * to the blockSize argument of the * {@link #createMDArray(String, int, long[], int[], HDF5GenericStorageFeatures)} call * that was used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumber The number of the block to write in each dimension. */ public void writeMDArrayBlock(final String objectPath, final MDArray data, final long[] blockNumber); /** * Writes out a block of a String array (of rank N). The data set needs to have * been created by * {@link #createMDArray(String, int, long[], int[], HDF5GenericStorageFeatures)} * beforehand. *

* Note: For best performance, the block size in this method should be chosen to be equal * to the blockSize argument of the * {@link #createMDArray(String, int, long[], int[], HDF5GenericStorageFeatures)} call * that was used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param offset The offset in the data set to start writing to. */ public void writeMDArrayBlockWithOffset(final String objectPath, final MDArray data, final long[] offset); /** * Writes out a String with variable maximal length. *

* The advantage of this method over {@link #write(String, String)} is that when writing a * new string later it can have a different (also greater) length. The disadvantage is that it * it is more time consuming to read and write this kind of string and that it can't be * compressed. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ public void writeVL(final String objectPath, final String data); /** * Writes out a String[] where each String of the array has a variable maximal * length. *

* The advantage of this method over {@link #writeArray(String, String[])} is that when * writing a new string later it can have a different (also greater) length. The disadvantage is * that it it is more time consuming to read and write this kind of string and that it can't be * compressed. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ public void writeArrayVL(final String objectPath, final String[] data); /** * Writes out a String[] where each String of the array has a variable maximal * length. *

* The advantage of this method over {@link #writeArray(String, String[])} is that when * writing a new string later it can have a different (also greater) length. The disadvantage is * that it it is more time consuming to read and write this kind of string and that it can't be * compressed. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param features The storage features of the data set. */ public void writeArrayVL(final String objectPath, final String[] data, final HDF5GenericStorageFeatures features); /** * Creates a String[] where each String of the array has a variable maximal length. * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the byte array to create. This will be the total size for * non-extendable data sets and the size of one chunk for extendable (chunked) data * sets. For extendable data sets the initial size of the array will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. */ public void createArrayVL(final String objectPath, final int size); /** * Creates a String[] where each String of the array has a variable maximal length. * * @param objectPath The name (including path information) of the data set object in the file. * @param size The intial size of the array. * @param blockSize The size of block in the array. */ public void createArrayVL(final String objectPath, final long size, final int blockSize); /** * Creates a String[] where each String of the array has a variable maximal length. * * @param objectPath The name (including path information) of the data set object in the file. * @param size The initial size of the array. * @param blockSize The size of block in the array. * @param features The storage features of the data set. */ public void createArrayVL(final String objectPath, final long size, final int blockSize, final HDF5GenericStorageFeatures features); /** * Creates a String[] where each String of the array has a variable maximal length. * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the byte array to create. This will be the total size for * non-extendable data sets and the size of one chunk for extendable (chunked) data * sets. For extendable data sets the initial size of the array will be 0, see * {@link HDF5GenericStorageFeatures}. * @param features The storage features of the data set. */ public void createArrayVL(final String objectPath, final int size, final HDF5GenericStorageFeatures features); /** * Creates a multi-dimensional String array where each String of the array has a * variable maximal length. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The initial dimensions (along each axis) of the array. * @param features The storage features of the data set. */ public void createMDArrayVL(final String objectPath, final int[] dimensions, final HDF5GenericStorageFeatures features); /** * Creates a multi-dimensional String array where each String of the array has a * variable maximal length. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The initial dimensions (along each axis) of the array. */ public void createMDArrayVL(final String objectPath, final int[] dimensions); /** * Creates a multi-dimensional String array where each String of the array has a * variable maximal length. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The initial dimensions (along each axis) of the array. * @param blockSize The size of a contiguously stored block (along each axis) in the array. * @param features The storage features of the data set. */ public void createMDArrayVL(final String objectPath, final long[] dimensions, final int[] blockSize, final HDF5GenericStorageFeatures features); /** * Creates a multi-dimensional String array where each String of the array has a * variable maximal length. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The initial dimensions (along each axis) of the array. * @param blockSize The size of a contiguously stored block (along each axis) in the array. */ public void createMDArrayVL(final String objectPath, final long[] dimensions, final int[] blockSize); /** * Writes out a String array (of rank N). Each element of the array will have a * variable maximal length. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ public void writeMDArrayVL(final String objectPath, final MDArray data); /** * Writes out a String array (of rank N). Each element of the array will have a * variable maximal length. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param features The storage features of the data set. */ public void writeMDArrayVL(final String objectPath, final MDArray data, final HDF5GenericStorageFeatures features); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5TimeDurationReader.java000066400000000000000000000306431256564762100305020ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; /** * An interface that provides methods for reading time duration values from HDF5 files. * * @author Bernd Rinn */ public interface IHDF5TimeDurationReader { // ///////////////////// // Attributes // ///////////////////// /** * Returns true, if the attribute attributeName of data set * objectPath is a time duration and false otherwise. */ public boolean isTimeDuration(String objectPath, String attributeName) throws HDF5JavaException; /** * Returns the time unit, if the attribute given by attributeName of object * objectPath is a time duration and null otherwise. */ public HDF5TimeUnit tryGetTimeUnit(String objectPath, String attributeName) throws HDF5JavaException; /** * Reads a time duration attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The time duration. * @throws HDF5JavaException If the objectPath is not tagged as a type variant that * corresponds to a time duration. */ public HDF5TimeDuration getAttr(String objectPath, String attributeName); /** * Reads a time duration array attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The time duration. * @throws HDF5JavaException If the objectPath is not tagged as a type variant that * corresponds to a time duration. */ public HDF5TimeDurationArray getArrayAttr(String objectPath, String attributeName); /** * Reads a multi-dimension time duration array attribute named attributeName from the * data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The time duration. * @throws HDF5JavaException If the objectPath is not tagged as a type variant that * corresponds to a time duration. */ public HDF5TimeDurationMDArray getMDArrayAttr(String objectPath, String attributeName); // ///////////////////// // Data Sets // ///////////////////// /** * Returns true, if the data set given by objectPath is a time duration * and false otherwise. */ public boolean isTimeDuration(String objectPath) throws HDF5JavaException; /** * Returns the time unit, if the data set given by objectPath is a time duration and * null otherwise. */ public HDF5TimeUnit tryGetTimeUnit(String objectPath) throws HDF5JavaException; /** * Reads a time duration value and its unit from the data set objectPath. It needs to * be tagged as one of the type variants that indicate a time duration, for example * {@link HDF5DataTypeVariant#TIME_DURATION_SECONDS}. *

* This tagging is done by the writer when using * {@link IHDF5Writer#writeTimeDuration(String, HDF5TimeDuration)} or can be done by calling * {@link IHDF5ObjectReadWriteInfoProviderHandler#setTypeVariant(String, HDF5DataTypeVariant)}. * * @param objectPath The name (including path information) of the data set object in the file. * @return The time duration and its unit. * @throws HDF5JavaException If the objectPath is not tagged as a type variant that * corresponds to a time duration. */ public HDF5TimeDuration read(String objectPath) throws HDF5JavaException; /** * Reads a time duration array from the data set objectPath. It needs to be tagged as * one of the type variants that indicate a time duration, for example * {@link HDF5DataTypeVariant#TIME_DURATION_SECONDS}. *

* This tagging is done by the writer when using * {@link IHDF5Writer#writeTimeDuration(String, HDF5TimeDuration)} or can be done by calling * {@link IHDF5ObjectReadWriteInfoProviderHandler#setTypeVariant(String, HDF5DataTypeVariant)}, * most conveniantly by code like * * 

     * writer.addTypeVariant("/dataSetPath", HDF5TimeUnit.SECONDS.getTypeVariant());
     *
* * @param objectPath The name (including path information) of the data set object in the file. * @return The time duration in seconds. * @throws HDF5JavaException If the objectPath is not tagged as a type variant that * corresponds to a time duration. */ public HDF5TimeDurationArray readArray(String objectPath) throws HDF5JavaException; /** * Reads a block of a time duration array (of rank 1) from the data set objectPath. * It needs to be tagged as one of the type variants that indicate a time duration, for example * {@link HDF5DataTypeVariant#TIME_DURATION_SECONDS}. *

* This tagging is done by the writer when using * {@link IHDF5Writer#writeTimeDuration(String, HDF5TimeDuration)} or can be done by calling * {@link IHDF5ObjectReadWriteInfoProviderHandler#setTypeVariant(String, HDF5DataTypeVariant)}, * most conveniently by code like * * 

     * writer.addTypeVariant("/dataSetPath", HDF5TimeUnit.SECONDS.getTypeVariant());
     *
* * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the long[] returned * if the data set is long enough). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @return The data read from the data set. The length will be * min(size - blockSize*blockNumber, * blockSize). * @throws HDF5JavaException If the objectPath is not tagged as a type variant that * corresponds to a time duration. */ public HDF5TimeDurationArray readArrayBlock(String objectPath, int blockSize, long blockNumber) throws HDF5JavaException; /** * Reads a block of a time duration array (of rank 1) from the data set objectPath. * It needs to be tagged as one of the type variants that indicate a time duration, for example * {@link HDF5DataTypeVariant#TIME_DURATION_SECONDS}. *

* This tagging is done by the writer when using * {@link IHDF5Writer#writeTimeDuration(String, HDF5TimeDuration)} or can be done by calling * {@link IHDF5ObjectReadWriteInfoProviderHandler#setTypeVariant(String, HDF5DataTypeVariant)}, * most conveniently by code like * * 

     * writer.addTypeVariant("/dataSetPath", HDF5TimeUnit.SECONDS.getTypeVariant());
     *
* * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the long[] * returned). * @param offset The offset of the block in the data set to start reading from (starting with * 0). * @return The data block read from the data set. * @throws HDF5JavaException If the objectPath is not tagged as a type variant that * corresponds to a time duration. */ public HDF5TimeDurationArray readArrayBlockWithOffset(String objectPath, int blockSize, long offset) throws HDF5JavaException; /** * Provides all natural blocks of this one-dimensional data set of time durations to iterate * over. * * @param objectPath The name (including path information) of the data set object in the file. * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of a time duration data type or not of rank * 1. */ public Iterable> getArrayNaturalBlocks(String objectPath) throws HDF5JavaException; /** * Reads a multi-dimensional array of time durations from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * @throws HDF5JavaException If the objectPath is not tagged as a type variant that * corresponds to a time duration. */ public HDF5TimeDurationMDArray readMDArray(String objectPath) throws HDF5JavaException; /** * Reads a multi-dimensional array of time durations from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @return The data block read from the data set. */ public HDF5TimeDurationMDArray readMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber) throws HDF5JavaException; /** * Reads a multi-dimensional array of time durations from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @return The data block read from the data set. */ public HDF5TimeDurationMDArray readMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset); /** * Reads a multi-dimensional array of time durations from the data set objectPath * into a given array in memory. * * @param objectPath The name (including path information) of the data set object in the file. * @param array The array to read the data into. * @param memoryOffset The offset in the array to write the data to. * @return The effective dimensions of the block in array that was filled. */ public int[] readToMDArrayWithOffset(String objectPath, HDF5TimeDurationMDArray array, int[] memoryOffset); /** * Reads a block of the multi-dimensional long array data set objectPath * into a given array in memory. * * @param objectPath The name (including path information) of the data set object in the file. * @param array The array to read the data into. * @param blockDimensions The size of the block to read along each axis. * @param offset The offset of the block in the data set. * @param memoryOffset The offset of the block in the array to write the data to. * @return The effective dimensions of the block in array that was filled. */ public int[] readToMDArrayBlockWithOffset(String objectPath, HDF5TimeDurationMDArray array, int[] blockDimensions, long[] offset, int[] memoryOffset); /** * Provides all natural blocks of this multi-dimensional data set to iterate over. * * @see HDF5MDDataBlock */ public Iterable> getMDArrayNaturalBlocks( String dataSetPath); }libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5TimeDurationWriter.java000066400000000000000000000411431256564762100305510ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; /** * An interface that provides methods for writing time duration values from HDF5 files. * * @author Bernd Rinn */ public interface IHDF5TimeDurationWriter extends IHDF5TimeDurationReader { // ///////////////////// // Attributes // ///////////////////// /** * Set a time duration value as attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param attributeName The name of the attribute. * @param timeDuration The value of the attribute. * @param timeUnit The unit of the attribute. */ public void setAttr(String objectPath, String attributeName, long timeDuration, HDF5TimeUnit timeUnit); /** * Set a time duration value as attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param attributeName The name of the attribute. * @param timeDuration The value of the attribute. */ public void setAttr(String objectPath, String attributeName, HDF5TimeDuration timeDuration); /** * Set a time duration array value as attribute on the referenced object. The smallest time unit * in timeDurations will be used as the time unit of the array. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. *

* Note: Time durations are stored as a long[] array. * * @param objectPath The name of the object to add the attribute to. * @param attributeName The name of the attribute. * @param timeDurations The value of the attribute. */ public void setArrayAttr(String objectPath, String attributeName, HDF5TimeDurationArray timeDurations); /** * Set a multi-dimensional time duration array value as attribute on the referenced object. The * smallest time unit in timeDurations will be used as the time unit of the array. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. *

* Note: Time durations are stored as a long[] array. * * @param objectPath The name of the object to add the attribute to. * @param attributeName The name of the attribute. * @param timeDurations The value of the attribute. */ public void setMDArrayAttr(String objectPath, String attributeName, HDF5TimeDurationMDArray timeDurations); // ///////////////////// // Data Sets // ///////////////////// /** * Writes out a time duration value. *

* Note: Time durations are stored as long[] arrays and tagged as the according * type variant. * * @param objectPath The name (including path information) of the data set object in the file. * @param timeDuration The duration of time to write in the given timeUnit. * @param timeUnit The unit of the time duration. */ public void write(String objectPath, long timeDuration, HDF5TimeUnit timeUnit); /** * Writes out a time duration value. *

* Note: Time durations are stored as long[] arrays and tagged as the according * type variant. * * @param objectPath The name (including path information) of the data set object in the file. * @param timeDuration The duration of time to write. */ public void write(String objectPath, HDF5TimeDuration timeDuration); /** * Creates a time duration array (of rank 1). *

* Note: Time durations are stored as long values. * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the byte array to create. This will be the total size for * non-extendable data sets and the size of one chunk for extendable (chunked) data * sets. For extendable data sets the initial size of the array will be 0, see * {@link ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator#dontUseExtendableDataTypes}. * @param timeUnit The unit of the time duration. */ public void createArray(String objectPath, int size, HDF5TimeUnit timeUnit); /** * Creates a time duration array (of rank 1). *

* Note: Time durations are stored as long[] arrays and tagged as the according * type variant. * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the data set to create. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) * and deflate == false. * @param timeUnit The unit of the time duration. */ public void createArray(String objectPath, long size, int blockSize, HDF5TimeUnit timeUnit); /** * Creates a time duration array (of rank 1). *

* Note: Time durations are stored as long[] arrays and tagged as the according * type variant. * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the data set to create. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) * and deflate == false. * @param timeUnit The unit of the time duration. * @param features The storage features of the data set. */ public void createArray(String objectPath, long size, int blockSize, HDF5TimeUnit timeUnit, HDF5GenericStorageFeatures features); /** * Creates a time duration array (of rank 1). *

* Note: Time durations are stored as long[] arrays and tagged as the according * type variant. * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the array to create. This will be the total size for non-extendable * data sets and the size of one chunk for extendable (chunked) data sets. For * extendable data sets the initial size of the array will be 0, see * {@link HDF5GenericStorageFeatures}. * @param timeUnit The unit of the time duration. * @param features The storage features of the data set. */ public void createArray(String objectPath, int size, HDF5TimeUnit timeUnit, HDF5GenericStorageFeatures features); /** * Writes out a time duration array (of rank 1). *

* Note: Time durations are stored as long[] arrays and tagged as the according * type variant. * * @param objectPath The name (including path information) of the data set object in the file. * @param timeDurations The time durations to write. */ public void writeArray(String objectPath, HDF5TimeDurationArray timeDurations); /** * Writes out a time duration array (of rank 1). *

* Note: Time durations are stored as long[] arrays and tagged as the according * type variant. * * @param objectPath The name (including path information) of the data set object in the file. * @param timeDurations The time durations to write. * @param features The storage features used to store the array. */ public void writeArray(String objectPath, HDF5TimeDurationArray timeDurations, HDF5IntStorageFeatures features); /** * Writes out a block of a time duration array. The data set needs to have been created by * {@link #createArray(String, long, int, HDF5TimeUnit, HDF5GenericStorageFeatures)} beforehand. *

* Note: For best performance, the block size in this method should be chosen to be equal * to the blockSize argument of the * {@link #createArray(String, long, int, HDF5TimeUnit, HDF5GenericStorageFeatures)} call that * was used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumber The number of the block to write. */ public void writeArrayBlock(String objectPath, HDF5TimeDurationArray data, long blockNumber); /** * Writes out a block of a time duration array. The data set needs to have been created by * {@link #createArray(String, long, int, HDF5TimeUnit, HDF5GenericStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeArrayBlock(String, HDF5TimeDurationArray, long)} if * the total size of the data set is not a multiple of the block size. *

* Note: For best performance, the typical dataSize in this method should be * chosen to be equal to the blockSize argument of the * {@link #createArray(String, long, int, HDF5TimeUnit, HDF5GenericStorageFeatures)} call that * was used to create the data set. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param dataSize The (real) size of data (needs to be <= data.length * ) * @param offset The offset in the data set to start writing to. */ public void writeArrayBlockWithOffset(String objectPath, HDF5TimeDurationArray data, int dataSize, long offset); /** * Writes out a multi-dimensional array of time durations. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. */ public void writeMDArray(String objectPath, HDF5TimeDurationMDArray data, HDF5IntStorageFeatures features); /** * Writes out a multi-dimensional array of time durations. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ public void writeMDArray(String objectPath, HDF5TimeDurationMDArray data); /** * Creates a multi-dimensional array of time durations. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions When the writer is configured to use extendable data types (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial * dimensions and the dimensions of a chunk of the array will be * dimensions. When the writer is configured to enforce a * on-extendable data set, the initial dimensions equal the dimensions and will be * dimensions. */ public void createMDArray(String objectPath, int[] dimensions, HDF5TimeUnit timeUnit); /** * Creates a multi-dimensional array of time durations. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. */ public void createMDArray(String objectPath, long[] dimensions, int[] blockDimensions, HDF5TimeUnit timeUnit); /** * Creates a multi-dimensional array of time durations. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the long array to create. When requesting * a chunked data set (e.g. {@link HDF5IntStorageFeatures#INT_CHUNKED}), * the initial size of the array will be 0 and the chunk size will be dimensions. * When allowing a chunked data set (e.g. * {@link HDF5IntStorageFeatures#INT_NO_COMPRESSION} when the writer is * not configured to avoid extendable data types, see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be dimensions. When enforcing a * on-extendable data set (e.g. * {@link HDF5IntStorageFeatures#INT_CONTIGUOUS}), the initial size equals * the total size and will be dimensions. * @param features The storage features of the data set. */ public void createMDArray(String objectPath, int[] dimensions, HDF5TimeUnit timeUnit, HDF5IntStorageFeatures features); /** * Creates a multi-dimensional array of time durations. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. * @param features The storage features of the data set. */ public void createMDArray(String objectPath, long[] dimensions, int[] blockDimensions, HDF5TimeUnit timeUnit, HDF5IntStorageFeatures features); /** * Writes out a block of a multi-dimensional array of time durations. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). */ public void writeMDArrayBlock(String objectPath, HDF5TimeDurationMDArray data, long[] blockNumber); /** * Writes out a block of a multi-dimensional array of time durations. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. */ public void writeMDArrayBlockWithOffset(String objectPath, HDF5TimeDurationMDArray data, long[] offset); /** * Writes out a block of a multi-dimensional array of time durations. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param blockDimensions The dimensions of the block to write to the data set. * @param offset The offset of the block in the data set to start writing to in each dimension. * @param memoryOffset The offset of the block in the data array. */ public void writeMDArrayBlockWithOffset(String objectPath, HDF5TimeDurationMDArray data, int[] blockDimensions, long[] offset, int[] memoryOffset); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5UnsignedByteWriter.java000066400000000000000000000531011256564762100305420ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ch.systemsx.cisd.base.mdarray.MDByteArray; /** * An interface that provides methods for writing unsigned byte values to HDF5 files. *

* Note: This interface supports block access and sliced access (which is a special cases of * block access) to arrays. The performance of this block access can vary greatly depending on how * the data are layed out in the HDF5 file. For best performance, the block (or slice) dimension should * be chosen to be equal to the chunk dimensions of the array, as in this case the block written / read * are stored as consecutive value in the HDF5 file and one write / read access will suffice. *

* Note: Use the methods in {@link UnsignedIntUtils} to convert from and to unsigned values. * * @deprecated Use {@link IHDF5ByteWriter} instead, it has all methods of this interface. * * @author Bernd Rinn */ @Deprecated public interface IHDF5UnsignedByteWriter extends IHDF5ByteReader { // ///////////////////// // Attributes // ///////////////////// /** * Set a byte attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setAttr(String objectPath, String name, byte value); /** * Set a byte[] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setArrayAttr(String objectPath, String name, byte[] value); /** * Set a multi-dimensional code>byte attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setMDArrayAttr(String objectPath, String name, MDByteArray value); /** * Set a byte[][] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setMatrixAttr(String objectPath, String name, byte[][] value); // ///////////////////// // Data Sets // ///////////////////// /** * Writes out a byte value. * * @param objectPath The name (including path information) of the data set object in the file. * @param value The value to write. */ public void write(String objectPath, byte value); /** * Writes out a byte array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ public void writeArray(String objectPath, byte[] data); /** * Writes out a byte array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param features The storage features of the data set. */ public void writeArray(String objectPath, byte[] data, HDF5IntStorageFeatures features); /** * Creates a byte array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size When the writer is configured to use extendable data types (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be size. When the writer is * configured to enforce a non-extendable data set, the initial size equals the * total size and will be size. */ public void createArray(String objectPath, int size); /** * Creates a byte array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the byte array to create. When using extendable data sets * ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data * set smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). */ public void createArray(String objectPath, long size, int blockSize); /** * Creates a byte array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the byte array to create. When requesting a * chunked data set (e.g. {@link HDF5IntStorageFeatures#INT_CHUNKED}), * the initial size of the array will be 0 and the chunk size will be arraySize. * When allowing a chunked data set (e.g. * {@link HDF5IntStorageFeatures#INT_NO_COMPRESSION} when the writer is * not configured to avoid extendable data types, see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be arraySize. When enforcing a * on-extendable data set (e.g. * {@link HDF5IntStorageFeatures#INT_CONTIGUOUS}), the initial size equals * the total size and will be arraySize. * @param features The storage features of the data set. */ public void createArray(String objectPath, int size, HDF5IntStorageFeatures features); /** * Creates a byte array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the byte array to create. When using extendable data sets * ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data * set smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) and * features is HDF5IntStorageFeature.INT_NO_COMPRESSION. * @param features The storage features of the data set. */ public void createArray(String objectPath, long size, int blockSize, HDF5IntStorageFeatures features); /** * Writes out a block of a byte array (of rank 1). The data set needs to have * been created by {@link #createArray(String, long, int, HDF5IntStorageFeatures)} * beforehand. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumber The number of the block to write. */ public void writeArrayBlock(String objectPath, byte[] data, long blockNumber); /** * Writes out a block of a byte array (of rank 1). The data set needs to have * been created by {@link #createArray(String, long, int, HDF5IntStorageFeatures)} * beforehand. *

* Use this method instead of {@link #writeArrayBlock(String, byte[], long)} if the * total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param dataSize The (real) size of data (needs to be <= data.length * ) * @param offset The offset in the data set to start writing to. */ public void writeArrayBlockWithOffset(String objectPath, byte[] data, int dataSize, long offset); /** * Writes out a byte matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ public void writeMatrix(String objectPath, byte[][] data); /** * Writes out a byte matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. */ public void writeMatrix(String objectPath, byte[][] data, HDF5IntStorageFeatures features); /** * Creates a byte matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of one block in the x dimension. See * {@link #createMDArray(String, int[])} on the different * meanings of this parameter. * @param sizeY The size of one block in the y dimension. See * {@link #createMDArray(String, int[])} on the different * meanings of this parameter. */ public void createMatrix(String objectPath, int sizeX, int sizeY); /** * Creates a byte matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of one block in the x dimension. See * {@link #createMDArray(String, int[], HDF5IntStorageFeatures)} on the different * meanings of this parameter. * @param sizeY The size of one block in the y dimension. See * {@link #createMDArray(String, int[], HDF5IntStorageFeatures)} on the different * meanings of this parameter. * @param features The storage features of the data set. */ public void createMatrix(String objectPath, int sizeX, int sizeY, HDF5IntStorageFeatures features); /** * Creates a byte matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the byte matrix to create. * @param sizeY The size of the y dimension of the byte matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. */ public void createMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY); /** * Creates a byte matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the byte matrix to create. * @param sizeY The size of the y dimension of the byte matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. * @param features The storage features of the data set. */ public void createMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY, HDF5IntStorageFeatures features); /** * Writes out a block of a byte matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of * {@link #createMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} if the total * size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumberX The block number in the x dimension (offset: multiply with * data.length). * @param blockNumberY The block number in the y dimension (offset: multiply with * data[0.length). */ public void writeMatrixBlock(String objectPath, byte[][] data, long blockNumberX, long blockNumberY); /** * Writes out a block of a byte matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeMatrixBlock(String, byte[][], long, long)} if * the total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. */ public void writeMatrixBlockWithOffset(String objectPath, byte[][] data, long offsetX, long offsetY); /** * Writes out a block of a byte matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeMatrixBlock(String, byte[][], long, long)} if * the total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param dataSizeX The (real) size of data along the x axis (needs to be * <= data.length ) * @param dataSizeY The (real) size of data along the y axis (needs to be * <= data[0].length ) * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. */ public void writeMatrixBlockWithOffset(String objectPath, byte[][] data, int dataSizeX, int dataSizeY, long offsetX, long offsetY); /** * Writes out a multi-dimensional byte array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ public void writeMDArray(String objectPath, MDByteArray data); /** * Writes out a multi-dimensional byte array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. */ public void writeMDArray(String objectPath, MDByteArray data, HDF5IntStorageFeatures features); /** * Creates a multi-dimensional byte array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions When the writer is configured to use extendable data types (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial dimensions * and the dimensions of a chunk of the array will be dimensions. When the * writer is configured to enforce a non-extendable data set, the initial dimensions * equal the dimensions and will be dimensions. */ public void createMDArray(String objectPath, int[] dimensions); /** * Creates a multi-dimensional byte array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. */ public void createMDArray(String objectPath, long[] dimensions, int[] blockDimensions); /** * Creates a multi-dimensional byte array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the byte array to create. When requesting * a chunked data set (e.g. {@link HDF5IntStorageFeatures#INT_CHUNKED}), * the initial size of the array will be 0 and the chunk size will be dimensions. * When allowing a chunked data set (e.g. * {@link HDF5IntStorageFeatures#INT_NO_COMPRESSION} when the writer is * not configured to avoid extendable data types, see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be dimensions. When enforcing a * on-extendable data set (e.g. * {@link HDF5IntStorageFeatures#INT_CONTIGUOUS}), the initial size equals * the total size and will be dimensions. * @param features The storage features of the data set. */ public void createMDArray(String objectPath, int[] dimensions, HDF5IntStorageFeatures features); /** * Creates a multi-dimensional byte array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. * @param features The storage features of the data set. */ public void createMDArray(String objectPath, long[] dimensions, int[] blockDimensions, HDF5IntStorageFeatures features); /** * Writes out a block of a multi-dimensional byte array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). */ public void writeMDArrayBlock(String objectPath, MDByteArray data, long[] blockNumber); /** * Writes out a block of a multi-dimensional byte array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. */ public void writeMDArrayBlockWithOffset(String objectPath, MDByteArray data, long[] offset); /** * Writes out a block of a multi-dimensional byte array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param blockDimensions The dimensions of the block to write to the data set. * @param offset The offset of the block in the data set to start writing to in each dimension. * @param memoryOffset The offset of the block in the data array. */ public void writeMDArrayBlockWithOffset(String objectPath, MDByteArray data, int[] blockDimensions, long[] offset, int[] memoryOffset); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5UnsignedIntWriter.java000066400000000000000000000527771256564762100304130ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ch.systemsx.cisd.base.mdarray.MDIntArray; /** * An interface that provides methods for writing unsigned int values to HDF5 files. *

* Note: This interface supports block access and sliced access (which is a special cases of * block access) to arrays. The performance of this block access can vary greatly depending on how * the data are layed out in the HDF5 file. For best performance, the block (or slice) dimension should * be chosen to be equal to the chunk dimensions of the array, as in this case the block written / read * are stored as consecutive value in the HDF5 file and one write / read access will suffice. *

* Note: Use the methods in {@link UnsignedIntUtils} to convert from and to unsigned values. * * @deprecated Use {@link IHDF5IntWriter} instead, it has all methods of this interface. * * @author Bernd Rinn */ @Deprecated public interface IHDF5UnsignedIntWriter extends IHDF5IntReader { // ///////////////////// // Attributes // ///////////////////// /** * Set a int attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setAttr(String objectPath, String name, int value); /** * Set a int[] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setArrayAttr(String objectPath, String name, int[] value); /** * Set a multi-dimensional code>int attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setMDArrayAttr(String objectPath, String name, MDIntArray value); /** * Set a int[][] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setMatrixAttr(String objectPath, String name, int[][] value); // ///////////////////// // Data Sets // ///////////////////// /** * Writes out a int value. * * @param objectPath The name (including path information) of the data set object in the file. * @param value The value to write. */ public void write(String objectPath, int value); /** * Writes out a int array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ public void writeArray(String objectPath, int[] data); /** * Writes out a int array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param features The storage features of the data set. */ public void writeArray(String objectPath, int[] data, HDF5IntStorageFeatures features); /** * Creates a int array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size When the writer is configured to use extendable data types (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be size. When the writer is * configured to enforce a non-extendable data set, the initial size equals the * total size and will be size. */ public void createArray(String objectPath, int size); /** * Creates a int array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the int array to create. When using extendable data sets * ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data * set smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). */ public void createArray(String objectPath, long size, int blockSize); /** * Creates a int array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the int array to create. When requesting a * chunked data set (e.g. {@link HDF5IntStorageFeatures#INT_CHUNKED}), * the initial size of the array will be 0 and the chunk size will be arraySize. * When allowing a chunked data set (e.g. * {@link HDF5IntStorageFeatures#INT_NO_COMPRESSION} when the writer is * not configured to avoid extendable data types, see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be arraySize. When enforcing a * on-extendable data set (e.g. * {@link HDF5IntStorageFeatures#INT_CONTIGUOUS}), the initial size equals * the total size and will be arraySize. * @param features The storage features of the data set. */ public void createArray(String objectPath, int size, HDF5IntStorageFeatures features); /** * Creates a int array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the int array to create. When using extendable data sets * ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data * set smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) and * features is HDF5IntStorageFeature.INT_NO_COMPRESSION. * @param features The storage features of the data set. */ public void createArray(String objectPath, long size, int blockSize, HDF5IntStorageFeatures features); /** * Writes out a block of a int array (of rank 1). The data set needs to have * been created by {@link #createArray(String, long, int, HDF5IntStorageFeatures)} * beforehand. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumber The number of the block to write. */ public void writeArrayBlock(String objectPath, int[] data, long blockNumber); /** * Writes out a block of a int array (of rank 1). The data set needs to have * been created by {@link #createArray(String, long, int, HDF5IntStorageFeatures)} * beforehand. *

* Use this method instead of {@link #writeArrayBlock(String, int[], long)} if the * total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param dataSize The (real) size of data (needs to be <= data.length * ) * @param offset The offset in the data set to start writing to. */ public void writeArrayBlockWithOffset(String objectPath, int[] data, int dataSize, long offset); /** * Writes out a int matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ public void writeMatrix(String objectPath, int[][] data); /** * Writes out a int matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. */ public void writeMatrix(String objectPath, int[][] data, HDF5IntStorageFeatures features); /** * Creates a int matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of one block in the x dimension. See * {@link #createMDArray(String, int[])} on the different * meanings of this parameter. * @param sizeY The size of one block in the y dimension. See * {@link #createMDArray(String, int[])} on the different * meanings of this parameter. */ public void createMatrix(String objectPath, int sizeX, int sizeY); /** * Creates a int matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of one block in the x dimension. See * {@link #createMDArray(String, int[], HDF5IntStorageFeatures)} on the different * meanings of this parameter. * @param sizeY The size of one block in the y dimension. See * {@link #createMDArray(String, int[], HDF5IntStorageFeatures)} on the different * meanings of this parameter. * @param features The storage features of the data set. */ public void createMatrix(String objectPath, int sizeX, int sizeY, HDF5IntStorageFeatures features); /** * Creates a int matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the int matrix to create. * @param sizeY The size of the y dimension of the int matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. */ public void createMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY); /** * Creates a int matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the int matrix to create. * @param sizeY The size of the y dimension of the int matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. * @param features The storage features of the data set. */ public void createMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY, HDF5IntStorageFeatures features); /** * Writes out a block of a int matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of * {@link #createMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} if the total * size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumberX The block number in the x dimension (offset: multiply with * data.length). * @param blockNumberY The block number in the y dimension (offset: multiply with * data[0.length). */ public void writeMatrixBlock(String objectPath, int[][] data, long blockNumberX, long blockNumberY); /** * Writes out a block of a int matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeMatrixBlock(String, int[][], long, long)} if * the total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. */ public void writeMatrixBlockWithOffset(String objectPath, int[][] data, long offsetX, long offsetY); /** * Writes out a block of a int matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeMatrixBlock(String, int[][], long, long)} if * the total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param dataSizeX The (real) size of data along the x axis (needs to be * <= data.length ) * @param dataSizeY The (real) size of data along the y axis (needs to be * <= data[0].length ) * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. */ public void writeMatrixBlockWithOffset(String objectPath, int[][] data, int dataSizeX, int dataSizeY, long offsetX, long offsetY); /** * Writes out a multi-dimensional int array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ public void writeMDArray(String objectPath, MDIntArray data); /** * Writes out a multi-dimensional int array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. */ public void writeMDArray(String objectPath, MDIntArray data, HDF5IntStorageFeatures features); /** * Creates a multi-dimensional int array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions When the writer is configured to use extendable data types (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial dimensions * and the dimensions of a chunk of the array will be dimensions. When the * writer is configured to enforce a non-extendable data set, the initial dimensions * equal the dimensions and will be dimensions. */ public void createMDArray(String objectPath, int[] dimensions); /** * Creates a multi-dimensional int array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. */ public void createMDArray(String objectPath, long[] dimensions, int[] blockDimensions); /** * Creates a multi-dimensional int array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the int array to create. When requesting * a chunked data set (e.g. {@link HDF5IntStorageFeatures#INT_CHUNKED}), * the initial size of the array will be 0 and the chunk size will be dimensions. * When allowing a chunked data set (e.g. * {@link HDF5IntStorageFeatures#INT_NO_COMPRESSION} when the writer is * not configured to avoid extendable data types, see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be dimensions. When enforcing a * on-extendable data set (e.g. * {@link HDF5IntStorageFeatures#INT_CONTIGUOUS}), the initial size equals * the total size and will be dimensions. * @param features The storage features of the data set. */ public void createMDArray(String objectPath, int[] dimensions, HDF5IntStorageFeatures features); /** * Creates a multi-dimensional int array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. * @param features The storage features of the data set. */ public void createMDArray(String objectPath, long[] dimensions, int[] blockDimensions, HDF5IntStorageFeatures features); /** * Writes out a block of a multi-dimensional int array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). */ public void writeMDArrayBlock(String objectPath, MDIntArray data, long[] blockNumber); /** * Writes out a block of a multi-dimensional int array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. */ public void writeMDArrayBlockWithOffset(String objectPath, MDIntArray data, long[] offset); /** * Writes out a block of a multi-dimensional int array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param blockDimensions The dimensions of the block to write to the data set. * @param offset The offset of the block in the data set to start writing to in each dimension. * @param memoryOffset The offset of the block in the data array. */ public void writeMDArrayBlockWithOffset(String objectPath, MDIntArray data, int[] blockDimensions, long[] offset, int[] memoryOffset); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5UnsignedLongWriter.java000066400000000000000000000531011256564762100305360ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ch.systemsx.cisd.base.mdarray.MDLongArray; /** * An interface that provides methods for writing unsigned long values to HDF5 files. *

* Note: This interface supports block access and sliced access (which is a special cases of * block access) to arrays. The performance of this block access can vary greatly depending on how * the data are layed out in the HDF5 file. For best performance, the block (or slice) dimension should * be chosen to be equal to the chunk dimensions of the array, as in this case the block written / read * are stored as consecutive value in the HDF5 file and one write / read access will suffice. *

* Note: Use the methods in {@link UnsignedIntUtils} to convert from and to unsigned values. * * @deprecated Use {@link IHDF5LongWriter} instead, it has all methods of this interface. * * @author Bernd Rinn */ @Deprecated public interface IHDF5UnsignedLongWriter extends IHDF5LongReader { // ///////////////////// // Attributes // ///////////////////// /** * Set a long attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setAttr(String objectPath, String name, long value); /** * Set a long[] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setArrayAttr(String objectPath, String name, long[] value); /** * Set a multi-dimensional code>long attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setMDArrayAttr(String objectPath, String name, MDLongArray value); /** * Set a long[][] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setMatrixAttr(String objectPath, String name, long[][] value); // ///////////////////// // Data Sets // ///////////////////// /** * Writes out a long value. * * @param objectPath The name (including path information) of the data set object in the file. * @param value The value to write. */ public void write(String objectPath, long value); /** * Writes out a long array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ public void writeArray(String objectPath, long[] data); /** * Writes out a long array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param features The storage features of the data set. */ public void writeArray(String objectPath, long[] data, HDF5IntStorageFeatures features); /** * Creates a long array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size When the writer is configured to use extendable data types (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be size. When the writer is * configured to enforce a non-extendable data set, the initial size equals the * total size and will be size. */ public void createArray(String objectPath, int size); /** * Creates a long array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the long array to create. When using extendable data sets * ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data * set smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). */ public void createArray(String objectPath, long size, int blockSize); /** * Creates a long array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the long array to create. When requesting a * chunked data set (e.g. {@link HDF5IntStorageFeatures#INT_CHUNKED}), * the initial size of the array will be 0 and the chunk size will be arraySize. * When allowing a chunked data set (e.g. * {@link HDF5IntStorageFeatures#INT_NO_COMPRESSION} when the writer is * not configured to avoid extendable data types, see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be arraySize. When enforcing a * on-extendable data set (e.g. * {@link HDF5IntStorageFeatures#INT_CONTIGUOUS}), the initial size equals * the total size and will be arraySize. * @param features The storage features of the data set. */ public void createArray(String objectPath, int size, HDF5IntStorageFeatures features); /** * Creates a long array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the long array to create. When using extendable data sets * ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data * set smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) and * features is HDF5IntStorageFeature.INT_NO_COMPRESSION. * @param features The storage features of the data set. */ public void createArray(String objectPath, long size, int blockSize, HDF5IntStorageFeatures features); /** * Writes out a block of a long array (of rank 1). The data set needs to have * been created by {@link #createArray(String, long, int, HDF5IntStorageFeatures)} * beforehand. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumber The number of the block to write. */ public void writeArrayBlock(String objectPath, long[] data, long blockNumber); /** * Writes out a block of a long array (of rank 1). The data set needs to have * been created by {@link #createArray(String, long, int, HDF5IntStorageFeatures)} * beforehand. *

* Use this method instead of {@link #writeArrayBlock(String, long[], long)} if the * total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param dataSize The (real) size of data (needs to be <= data.length * ) * @param offset The offset in the data set to start writing to. */ public void writeArrayBlockWithOffset(String objectPath, long[] data, int dataSize, long offset); /** * Writes out a long matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ public void writeMatrix(String objectPath, long[][] data); /** * Writes out a long matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. */ public void writeMatrix(String objectPath, long[][] data, HDF5IntStorageFeatures features); /** * Creates a long matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of one block in the x dimension. See * {@link #createMDArray(String, int[])} on the different * meanings of this parameter. * @param sizeY The size of one block in the y dimension. See * {@link #createMDArray(String, int[])} on the different * meanings of this parameter. */ public void createMatrix(String objectPath, int sizeX, int sizeY); /** * Creates a long matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of one block in the x dimension. See * {@link #createMDArray(String, int[], HDF5IntStorageFeatures)} on the different * meanings of this parameter. * @param sizeY The size of one block in the y dimension. See * {@link #createMDArray(String, int[], HDF5IntStorageFeatures)} on the different * meanings of this parameter. * @param features The storage features of the data set. */ public void createMatrix(String objectPath, int sizeX, int sizeY, HDF5IntStorageFeatures features); /** * Creates a long matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the long matrix to create. * @param sizeY The size of the y dimension of the long matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. */ public void createMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY); /** * Creates a long matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the long matrix to create. * @param sizeY The size of the y dimension of the long matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. * @param features The storage features of the data set. */ public void createMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY, HDF5IntStorageFeatures features); /** * Writes out a block of a long matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of * {@link #createMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} if the total * size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumberX The block number in the x dimension (offset: multiply with * data.length). * @param blockNumberY The block number in the y dimension (offset: multiply with * data[0.length). */ public void writeMatrixBlock(String objectPath, long[][] data, long blockNumberX, long blockNumberY); /** * Writes out a block of a long matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeMatrixBlock(String, long[][], long, long)} if * the total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. */ public void writeMatrixBlockWithOffset(String objectPath, long[][] data, long offsetX, long offsetY); /** * Writes out a block of a long matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeMatrixBlock(String, long[][], long, long)} if * the total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param dataSizeX The (real) size of data along the x axis (needs to be * <= data.length ) * @param dataSizeY The (real) size of data along the y axis (needs to be * <= data[0].length ) * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. */ public void writeMatrixBlockWithOffset(String objectPath, long[][] data, int dataSizeX, int dataSizeY, long offsetX, long offsetY); /** * Writes out a multi-dimensional long array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ public void writeMDArray(String objectPath, MDLongArray data); /** * Writes out a multi-dimensional long array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. */ public void writeMDArray(String objectPath, MDLongArray data, HDF5IntStorageFeatures features); /** * Creates a multi-dimensional long array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions When the writer is configured to use extendable data types (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial dimensions * and the dimensions of a chunk of the array will be dimensions. When the * writer is configured to enforce a non-extendable data set, the initial dimensions * equal the dimensions and will be dimensions. */ public void createMDArray(String objectPath, int[] dimensions); /** * Creates a multi-dimensional long array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. */ public void createMDArray(String objectPath, long[] dimensions, int[] blockDimensions); /** * Creates a multi-dimensional long array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the long array to create. When requesting * a chunked data set (e.g. {@link HDF5IntStorageFeatures#INT_CHUNKED}), * the initial size of the array will be 0 and the chunk size will be dimensions. * When allowing a chunked data set (e.g. * {@link HDF5IntStorageFeatures#INT_NO_COMPRESSION} when the writer is * not configured to avoid extendable data types, see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be dimensions. When enforcing a * on-extendable data set (e.g. * {@link HDF5IntStorageFeatures#INT_CONTIGUOUS}), the initial size equals * the total size and will be dimensions. * @param features The storage features of the data set. */ public void createMDArray(String objectPath, int[] dimensions, HDF5IntStorageFeatures features); /** * Creates a multi-dimensional long array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. * @param features The storage features of the data set. */ public void createMDArray(String objectPath, long[] dimensions, int[] blockDimensions, HDF5IntStorageFeatures features); /** * Writes out a block of a multi-dimensional long array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). */ public void writeMDArrayBlock(String objectPath, MDLongArray data, long[] blockNumber); /** * Writes out a block of a multi-dimensional long array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. */ public void writeMDArrayBlockWithOffset(String objectPath, MDLongArray data, long[] offset); /** * Writes out a block of a multi-dimensional long array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param blockDimensions The dimensions of the block to write to the data set. * @param offset The offset of the block in the data set to start writing to in each dimension. * @param memoryOffset The offset of the block in the data array. */ public void writeMDArrayBlockWithOffset(String objectPath, MDLongArray data, int[] blockDimensions, long[] offset, int[] memoryOffset); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5UnsignedShortWriter.java000066400000000000000000000532031256564762100307410ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ch.systemsx.cisd.base.mdarray.MDShortArray; /** * An interface that provides methods for writing unsigned short values to HDF5 files. *

* Note: This interface supports block access and sliced access (which is a special cases of * block access) to arrays. The performance of this block access can vary greatly depending on how * the data are layed out in the HDF5 file. For best performance, the block (or slice) dimension should * be chosen to be equal to the chunk dimensions of the array, as in this case the block written / read * are stored as consecutive value in the HDF5 file and one write / read access will suffice. *

* Note: Use the methods in {@link UnsignedIntUtils} to convert from and to unsigned values. * * @deprecated Use {@link IHDF5ShortWriter} instead, it has all methods of this interface. * * @author Bernd Rinn */ @Deprecated public interface IHDF5UnsignedShortWriter extends IHDF5ShortReader { // ///////////////////// // Attributes // ///////////////////// /** * Set a short attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setAttr(String objectPath, String name, short value); /** * Set a short[] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setArrayAttr(String objectPath, String name, short[] value); /** * Set a multi-dimensional code>short attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setMDArrayAttr(String objectPath, String name, MDShortArray value); /** * Set a short[][] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setMatrixAttr(String objectPath, String name, short[][] value); // ///////////////////// // Data Sets // ///////////////////// /** * Writes out a short value. * * @param objectPath The name (including path information) of the data set object in the file. * @param value The value to write. */ public void write(String objectPath, short value); /** * Writes out a short array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ public void writeArray(String objectPath, short[] data); /** * Writes out a short array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param features The storage features of the data set. */ public void writeArray(String objectPath, short[] data, HDF5IntStorageFeatures features); /** * Creates a short array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size When the writer is configured to use extendable data types (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be size. When the writer is * configured to enforce a non-extendable data set, the initial size equals the * total size and will be size. */ public void createArray(String objectPath, int size); /** * Creates a short array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the short array to create. When using extendable data sets * ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data * set smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). */ public void createArray(String objectPath, long size, int blockSize); /** * Creates a short array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the short array to create. When requesting a * chunked data set (e.g. {@link HDF5IntStorageFeatures#INT_CHUNKED}), * the initial size of the array will be 0 and the chunk size will be arraySize. * When allowing a chunked data set (e.g. * {@link HDF5IntStorageFeatures#INT_NO_COMPRESSION} when the writer is * not configured to avoid extendable data types, see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be arraySize. When enforcing a * on-extendable data set (e.g. * {@link HDF5IntStorageFeatures#INT_CONTIGUOUS}), the initial size equals * the total size and will be arraySize. * @param features The storage features of the data set. */ public void createArray(String objectPath, int size, HDF5IntStorageFeatures features); /** * Creates a short array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the short array to create. When using extendable data sets * ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data * set smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) and * features is HDF5IntStorageFeature.INT_NO_COMPRESSION. * @param features The storage features of the data set. */ public void createArray(String objectPath, long size, int blockSize, HDF5IntStorageFeatures features); /** * Writes out a block of a short array (of rank 1). The data set needs to have * been created by {@link #createArray(String, long, int, HDF5IntStorageFeatures)} * beforehand. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumber The number of the block to write. */ public void writeArrayBlock(String objectPath, short[] data, long blockNumber); /** * Writes out a block of a short array (of rank 1). The data set needs to have * been created by {@link #createArray(String, long, int, HDF5IntStorageFeatures)} * beforehand. *

* Use this method instead of {@link #writeArrayBlock(String, short[], long)} if the * total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param dataSize The (real) size of data (needs to be <= data.length * ) * @param offset The offset in the data set to start writing to. */ public void writeArrayBlockWithOffset(String objectPath, short[] data, int dataSize, long offset); /** * Writes out a short matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ public void writeMatrix(String objectPath, short[][] data); /** * Writes out a short matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. */ public void writeMatrix(String objectPath, short[][] data, HDF5IntStorageFeatures features); /** * Creates a short matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of one block in the x dimension. See * {@link #createMDArray(String, int[])} on the different * meanings of this parameter. * @param sizeY The size of one block in the y dimension. See * {@link #createMDArray(String, int[])} on the different * meanings of this parameter. */ public void createMatrix(String objectPath, int sizeX, int sizeY); /** * Creates a short matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of one block in the x dimension. See * {@link #createMDArray(String, int[], HDF5IntStorageFeatures)} on the different * meanings of this parameter. * @param sizeY The size of one block in the y dimension. See * {@link #createMDArray(String, int[], HDF5IntStorageFeatures)} on the different * meanings of this parameter. * @param features The storage features of the data set. */ public void createMatrix(String objectPath, int sizeX, int sizeY, HDF5IntStorageFeatures features); /** * Creates a short matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the short matrix to create. * @param sizeY The size of the y dimension of the short matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. */ public void createMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY); /** * Creates a short matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the short matrix to create. * @param sizeY The size of the y dimension of the short matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. * @param features The storage features of the data set. */ public void createMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY, HDF5IntStorageFeatures features); /** * Writes out a block of a short matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of * {@link #createMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} if the total * size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumberX The block number in the x dimension (offset: multiply with * data.length). * @param blockNumberY The block number in the y dimension (offset: multiply with * data[0.length). */ public void writeMatrixBlock(String objectPath, short[][] data, long blockNumberX, long blockNumberY); /** * Writes out a block of a short matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeMatrixBlock(String, short[][], long, long)} if * the total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. */ public void writeMatrixBlockWithOffset(String objectPath, short[][] data, long offsetX, long offsetY); /** * Writes out a block of a short matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5IntStorageFeatures)} beforehand. *

* Use this method instead of {@link #writeMatrixBlock(String, short[][], long, long)} if * the total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param dataSizeX The (real) size of data along the x axis (needs to be * <= data.length ) * @param dataSizeY The (real) size of data along the y axis (needs to be * <= data[0].length ) * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. */ public void writeMatrixBlockWithOffset(String objectPath, short[][] data, int dataSizeX, int dataSizeY, long offsetX, long offsetY); /** * Writes out a multi-dimensional short array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ public void writeMDArray(String objectPath, MDShortArray data); /** * Writes out a multi-dimensional short array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. */ public void writeMDArray(String objectPath, MDShortArray data, HDF5IntStorageFeatures features); /** * Creates a multi-dimensional short array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions When the writer is configured to use extendable data types (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial dimensions * and the dimensions of a chunk of the array will be dimensions. When the * writer is configured to enforce a non-extendable data set, the initial dimensions * equal the dimensions and will be dimensions. */ public void createMDArray(String objectPath, int[] dimensions); /** * Creates a multi-dimensional short array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. */ public void createMDArray(String objectPath, long[] dimensions, int[] blockDimensions); /** * Creates a multi-dimensional short array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the short array to create. When requesting * a chunked data set (e.g. {@link HDF5IntStorageFeatures#INT_CHUNKED}), * the initial size of the array will be 0 and the chunk size will be dimensions. * When allowing a chunked data set (e.g. * {@link HDF5IntStorageFeatures#INT_NO_COMPRESSION} when the writer is * not configured to avoid extendable data types, see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be dimensions. When enforcing a * on-extendable data set (e.g. * {@link HDF5IntStorageFeatures#INT_CONTIGUOUS}), the initial size equals * the total size and will be dimensions. * @param features The storage features of the data set. */ public void createMDArray(String objectPath, int[] dimensions, HDF5IntStorageFeatures features); /** * Creates a multi-dimensional short array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. * @param features The storage features of the data set. */ public void createMDArray(String objectPath, long[] dimensions, int[] blockDimensions, HDF5IntStorageFeatures features); /** * Writes out a block of a multi-dimensional short array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). */ public void writeMDArrayBlock(String objectPath, MDShortArray data, long[] blockNumber); /** * Writes out a block of a multi-dimensional short array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. */ public void writeMDArrayBlockWithOffset(String objectPath, MDShortArray data, long[] offset); /** * Writes out a block of a multi-dimensional short array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param blockDimensions The dimensions of the block to write to the data set. * @param offset The offset of the block in the data set to start writing to in each dimension. * @param memoryOffset The offset of the block in the data array. */ public void writeMDArrayBlockWithOffset(String objectPath, MDShortArray data, int[] blockDimensions, long[] offset, int[] memoryOffset); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5Writer.java000066400000000000000000000174551256564762100262350ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; /** * An interface for writing HDF5 files (HDF5 1.6.x or HDF5 1.8.x). *

* The interface focuses on ease of use instead of completeness. As a consequence not all features * of HDF5 are supported by this class, however it covers a large subset. *

* The functionality is being made available in two ways: *

    *
  1. {@link IHDF5SimpleWriter} contains the most important methods in one interface. If you are * new to the library, this is a good starting point, see the example code below.
    2. *
  2. The hierarchical ("quasi-fluent") API provides the full functionality. It is designed along * the data types supported by JHDF5. *
      *
    • {@link #file()}: File-level information and operations, has e.g. the * {@link IHDF5FileLevelReadWriteHandler#close()} and {@link IHDF5FileLevelReadWriteHandler#flush()} * methods.
      • *
    • {@link #object()}: Object-level information, where "objects" can be data sets, links, groups * or data types, following the concept of an HDF5 object. Here you can find methods like * {@link IHDF5ObjectReadWriteInfoProviderHandler#createGroup(String)} for creating a new group, or * {@link IHDF5ObjectReadWriteInfoProviderHandler#createSoftLink(String, String)} for creating a * symbolic link.
      • *
    • {@link #bool()}: Writer methods for boolean data sets, including bit fields.
      • *
    • {@link #int8()} / {@link #int16()} / {@link #int16()} / {@link #int32()} / {@link #int64()}: * Writer methods for signed integer data sets, where the number as part of the method name denotes * the size of the integer type.
      • *
    • {@link #uint8()} / {@link #uint16()} / {@link #uint16()} / {@link #uint32()} / * {@link #int64()}: Writer methods for unsigned integer data sets, where the number as part of the * name sets the size of the integer type. While the data sets take signed integer values due to * Java's lack of unsigned integer types, they represent them as unsigned values in the HDF5 * file. See {@link UnsignedIntUtils} for conversion methods, e.g. * uint32().write("myint", UnsignedIntUtils.toInt16(50000)) will write a 16-bit * unsigned integer with value 50000.
      • *
    • {@link #float32()} / {@link #float64()}: Writer methods for float data sets, where the number * as part of the name sets the size of the float type.
      • *
    • {@link #time()} / {@link #duration()}: Writer methods for time stamp (or date) and for time * duration data sets.
      • *
    • {@link #string()}: Writer methods for string data sets.
      • *
    • {@link #enumeration()}: Writer methods for enumeration data sets.
      • *
    • {@link #compound()}: Writer methods for compound data sets.
      • *
    • {@link #opaque()}: Writer methods for data sets that are "black boxes" to HDF5 which are * called "opaque data sets" in HDF5 jargon. Here you can also find methods of reading arbitrary * data sets as byte arrays.
      • *
    • {@link #reference()}: Writer methods for HDF5 object references. Note that object references, * though similar to hard links and symbolic links on the first glance, are quite different for * HDF5.
      • *
    *
    3. *
*

* Simple usage example: * * 

 * float[] f = new float[100];
 * ...
 * IHDF5Writer writer = HDF5FactoryProvider.get().open(new File("test.h5"));
 * writer.writeFloatArray("/some/path/dataset", f);
 * writer.setStringAttribute("some key", "some value");
 * writer.close();
 *
* * @author Bernd Rinn */ @SuppressWarnings("deprecation") public interface IHDF5Writer extends IHDF5Reader, IHDF5SimpleWriter, IHDF5LegacyWriter { // ///////////////////// // File // ///////////////////// /** * Returns the handler for file-level information and status. */ @Override public IHDF5FileLevelReadWriteHandler file(); // ///////////////////////////////// // Objects, links, groups and types // ///////////////////////////////// /** * Returns an info provider and handler for HDF5 objects like links, groups, data sets and data * types. */ @Override public IHDF5ObjectReadWriteInfoProviderHandler object(); // ///////////////////// // Opaque // ///////////////////// /** * Returns the full writer for opaque values. */ @Override public IHDF5OpaqueWriter opaque(); // ///////////////////// // Boolean // ///////////////////// /** * Returns the full writer for boolean values. */ @Override public IHDF5BooleanWriter bool(); // ///////////////////// // Bytes // ///////////////////// /** * Returns the full writer for byte / int8. */ @Override public IHDF5ByteWriter int8(); /** * Returns the full writer for unsigned byte / uint8. */ @Override public IHDF5ByteWriter uint8(); // ///////////////////// // Short // ///////////////////// /** * Returns the full writer for short / int16. */ @Override public IHDF5ShortWriter int16(); /** * Returns the full writer for unsigned short / uint16. */ @Override public IHDF5ShortWriter uint16(); // ///////////////////// // Int // ///////////////////// /** * Returns the full writer for int / int32. */ @Override public IHDF5IntWriter int32(); /** * Returns the full writer for unsigned int / uint32. */ @Override public IHDF5IntWriter uint32(); // ///////////////////// // Long // ///////////////////// /** * Returns the full writer for long / int64. */ @Override public IHDF5LongWriter int64(); /** * Returns the full writer for unsigned long / uint64. */ @Override public IHDF5LongWriter uint64(); // ///////////////////// // Float // ///////////////////// /** * Returns the full writer for float / float32. */ @Override public IHDF5FloatWriter float32(); // ///////////////////// // Double // ///////////////////// /** * Returns the full writer for long / float64. */ @Override public IHDF5DoubleWriter float64(); // ///////////////////// // Enums // ///////////////////// /** * Returns the full writer for enumerations. */ @Override public IHDF5EnumWriter enumeration(); // ///////////////////// // Compounds // ///////////////////// /** * Returns the full reader for compounds. */ @Override public IHDF5CompoundWriter compound(); // ///////////////////// // Strings // ///////////////////// /** * Returns the full writer for strings. */ @Override public IHDF5StringWriter string(); // ///////////////////// // Date & Time // ///////////////////// /** * Returns the full writer for date and times. */ @Override public IHDF5DateTimeWriter time(); /** * Returns the full writer for time durations. */ @Override public IHDF5TimeDurationWriter duration(); // ///////////////////// // Object references // ///////////////////// /** * Returns the full reader for object references. */ @Override public IHDF5ReferenceWriter reference(); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IHDF5WriterConfigurator.java000066400000000000000000000144151256564762100306110ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; /** * The configuration of the writer is done by chaining calls to configuration methods before calling * {@link #writer()}. * * @author Bernd Rinn */ public interface IHDF5WriterConfigurator extends IHDF5ReaderConfigurator { /** * The mode of synchronizing changes (using a method like fsync(2)) to the HDF5 * file with the underlying storage. As fsync(2) is blocking, the synchonization is * by default performed in a separate thread to minimize latency effects on the application. In * order to ensure that fsync(2) is called in the same thread, use one of the * *_BLOCK modes. *

* Note that non-blocking modes can have unexpected interactions with mandatory locks on * Windows. The symptom of that will be that the program holds a lock to the HDF5 file for some * (short) time even after the file has been closed. Thus, on Windows by default a blocking mode * is chosen. */ public enum SyncMode { /** * Do not synchronize at all. */ NO_SYNC, /** * Synchronize whenever {@link IHDF5FileLevelReadWriteHandler#flush()} or * {@link IHDF5FileLevelReadWriteHandler#close()} are called. */ SYNC, /** * Synchronize whenever {@link IHDF5FileLevelReadWriteHandler#flush()} or * {@link IHDF5FileLevelReadWriteHandler#close()} are called. Block until synchronize is * finished. */ SYNC_BLOCK, /** * Synchronize whenever {@link IHDF5FileLevelReadWriteHandler#flush()} is called. Default * on Unix */ SYNC_ON_FLUSH, /** * Synchronize whenever {@link IHDF5FileLevelReadWriteHandler#flush()} is called. Block * until synchronize is finished. Default on Windows. */ SYNC_ON_FLUSH_BLOCK, } /** * Specify file format compatibility settings. */ public enum FileFormat { /** * Enforce compatibility with HDF5 1.6 format. */ STRICTLY_1_6, /** * Start with HDF5 1.6 format, but allow usage of features which require HDF5 1.8 library to * read. Default. */ ALLOW_1_8, /** * Enforce compatibility with HDF5 1.8 format. */ STRICTLY_1_8; /** * Returns true if using HDF5 1.8 features is OK. */ boolean isHDF5_1_8_OK() { return ordinal() > STRICTLY_1_6.ordinal(); } } /** * The file will be truncated to length 0 if it already exists, that is its content will be * deleted. */ public IHDF5WriterConfigurator overwrite(); /** * Use data types which can not be extended later on. This may reduce the initial size of the * HDF5 file. */ public IHDF5WriterConfigurator dontUseExtendableDataTypes(); /** * Use simple data spaces for attributes. */ public IHDF5WriterConfigurator useSimpleDataSpaceForAttributes(); /** * On writing a data set, keep the data set if it exists and only write the new data. This is * equivalent to the _KEEP variants of {@link HDF5GenericStorageFeatures} and makes * this behavior the default. *

* If this setting is not given, an existing data set will be deleted before the data set is * written. *

* Note: If this configuration option is chosen, data types and storage features may only * apply if the written data set does not yet exist. For example, it may lead to a string value * being truncated on write if a string dataset with the same name and shorter length already * exists. */ public IHDF5WriterConfigurator keepDataSetsIfTheyExist(); /** * Sets the file format compatibility for the writer. */ public IHDF5WriterConfigurator fileFormat(FileFormat newFileFormat); /** * Sets the {@link SyncMode}. */ public IHDF5WriterConfigurator syncMode(SyncMode newSyncMode); /** * Will try to perform numeric conversions where appropriate if supported by the platform. *

* Numeric conversions can be platform dependent and are not available on all platforms. * Be advised not to rely on numeric conversions if you can help it! */ @Override public IHDF5WriterConfigurator performNumericConversions(); /** * Sets UTF8 character encoding for all paths and all strings in this file. (The default is * ASCII.) */ @Override public IHDF5WriterConfigurator useUTF8CharacterEncoding(); /** * Switches off automatic dereferencing of unresolved references. Use this when you need to * access file names that start with \0. The down-side of switching off automatic dereferencing * is that you can't provide references as obtained by * {@link IHDF5ReferenceReader#read(String, boolean)} with resolveName=false in * places where a dataset path is required.
* Note: automatic dereferencing is switched on by default. */ @Override public IHDF5WriterConfigurator noAutoDereference(); /** * Sets the suffix that is used to mark and recognize house keeping files and groups. An empty * string ("") encodes for the default, which is two leading and two trailing underscores * ("__NAME__"). */ public IHDF5WriterConfigurator houseKeepingNameSuffix(String houseKeepingNameSuffix); /** * Returns an {@link IHDF5Writer} based on this configuration. */ public IHDF5Writer writer(); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/IndexMap.java000066400000000000000000000025541256564762100257400ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.util.HashMap; /** * A map for storing index to index value mapping. * * @author Bernd Rinn */ public class IndexMap extends HashMap { private static final long serialVersionUID = 1L; /** * Bind index to indexValue. * * @return The map itself (for chained calls). */ public IndexMap bind(int index, long indexValue) { put(index, indexValue); return this; } /** * Bind index to indexValue. * * @return The map itself (for chained calls). */ public IndexMap bind(int index, int indexValue) { put(index, (long) indexValue); return this; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/MatrixUtils.java000066400000000000000000000362001256564762100265130ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.lang.reflect.Array; import java.util.Arrays; import java.util.Map; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.base.mdarray.MDAbstractArray; import ch.systemsx.cisd.base.mdarray.MDArray; /** * Utilities for working with primitive matrices. *

* This is an internal API that should not be expected to be stable between releases! * * @author Bernd Rinn */ final class MatrixUtils { private MatrixUtils() { // Cannot be instantiated } static void checkMDArrayDimensions(final String name, final int[] dimensions, final MDAbstractArray array) { if (Arrays.equals(dimensions, array.dimensions()) == false) { throw new IllegalArgumentException("The member '" + name + "' has dimensions " + Arrays.toString(array.dimensions()) + " but is supposed to have dimensions " + Arrays.toString(dimensions) + "."); } } static void checkMatrixDimensions(final String name, final int[] dimensions, final Object matrix) { final int dimX = Array.getLength(matrix); final int dimY = Array.getLength(Array.get(matrix, 0)); if (dimensions.length != 2 || dimensions[0] != dimX || dimensions[1] != dimY) { throw new IllegalArgumentException("The member '" + name + "' has dimensions [" + dimX + "," + dimY + "]." + " but is supposed to have dimensions " + Arrays.toString(dimensions) + "."); } } static float[] flatten(float[][] matrix) { if (matrix.length == 0) { throw new IllegalArgumentException("Matrix must not have a length of 0."); } final int dimY = matrix.length; final int dimX = matrix[0].length; for (int i = 1; i < dimY; ++i) { if (matrix[i].length != dimX) { throw new IllegalArgumentException( "All rows in matrix need to have the same number of columns."); } } final float[] result = new float[dimX * dimY]; for (int i = 0; i < dimY; ++i) { System.arraycopy(matrix[i], 0, result, i * dimX, dimX); } return result; } static float[][] shapen(float[] matrixData, int[] dims) { final int dimY = dims[0]; final int dimX = dims[1]; final float[][] result = new float[dimY][dimX]; for (int i = 0; i < dimY; ++i) { System.arraycopy(matrixData, i * dimX, result[i], 0, dimX); } return result; } static double[] flatten(double[][] matrix) { if (matrix.length == 0) { throw new IllegalArgumentException("Matrix must not have a length of 0."); } final int dimY = matrix.length; final int dimX = matrix[0].length; for (int i = 1; i < dimY; ++i) { if (matrix[i].length != dimX) { throw new IllegalArgumentException( "All rows in matrix need to have the same number of columns."); } } final double[] result = new double[dimX * dimY]; for (int i = 0; i < dimY; ++i) { System.arraycopy(matrix[i], 0, result, i * dimX, dimX); } return result; } static double[][] shapen(double[] matrixData, int[] dims) { final int dimY = dims[0]; final int dimX = dims[1]; final double[][] result = new double[dimY][dimX]; for (int i = 0; i < dimY; ++i) { System.arraycopy(matrixData, i * dimX, result[i], 0, dimX); } return result; } static int[] flatten(int[][] matrix) { if (matrix.length == 0) { throw new IllegalArgumentException("Matrix must not have a length of 0."); } final int dimY = matrix.length; final int dimX = matrix[0].length; for (int i = 1; i < dimY; ++i) { if (matrix[i].length != dimX) { throw new IllegalArgumentException( "All rows in matrix need to have the same number of columns."); } } final int[] result = new int[dimX * dimY]; for (int i = 0; i < dimY; ++i) { System.arraycopy(matrix[i], 0, result, i * dimX, dimX); } return result; } static int[][] shapen(int[] matrixData, int[] dims) { final int dimY = dims[0]; final int dimX = dims[1]; final int[][] result = new int[dimY][dimX]; for (int i = 0; i < dimY; ++i) { System.arraycopy(matrixData, i * dimX, result[i], 0, dimX); } return result; } static long[] flatten(long[][] matrix) { if (matrix.length == 0) { throw new IllegalArgumentException("Matrix must not have a length of 0."); } final int dimY = matrix.length; final int dimX = matrix[0].length; for (int i = 1; i < dimY; ++i) { if (matrix[i].length != dimX) { throw new IllegalArgumentException( "All rows in matrix need to have the same number of columns."); } } final long[] result = new long[dimX * dimY]; for (int i = 0; i < dimY; ++i) { System.arraycopy(matrix[i], 0, result, i * dimX, dimX); } return result; } static long[][] shapen(long[] matrixData, int[] dims) { final int dimY = dims[0]; final int dimX = dims[1]; final long[][] result = new long[dimY][dimX]; for (int i = 0; i < dimY; ++i) { System.arraycopy(matrixData, i * dimX, result[i], 0, dimX); } return result; } static short[] flatten(short[][] matrix) { if (matrix.length == 0) { throw new IllegalArgumentException("Matrix must not have a length of 0."); } final int dimY = matrix.length; final int dimX = matrix[0].length; for (int i = 1; i < dimY; ++i) { if (matrix[i].length != dimX) { throw new IllegalArgumentException( "All rows in matrix need to have the same number of columns."); } } final short[] result = new short[dimX * dimY]; for (int i = 0; i < dimY; ++i) { System.arraycopy(matrix[i], 0, result, i * dimX, dimX); } return result; } static short[][] shapen(short[] matrixData, int[] dims) { final int dimY = dims[0]; final int dimX = dims[1]; final short[][] result = new short[dimY][dimX]; for (int i = 0; i < dimY; ++i) { System.arraycopy(matrixData, i * dimX, result[i], 0, dimX); } return result; } static byte[] flatten(byte[][] matrix) { if (matrix.length == 0) { throw new IllegalArgumentException("Matrix must not have a length of 0."); } final int dimY = matrix.length; final int dimX = matrix[0].length; for (int i = 1; i < dimY; ++i) { if (matrix[i].length != dimX) { throw new IllegalArgumentException( "All rows in matrix need to have the same number of columns."); } } final byte[] result = new byte[dimX * dimY]; for (int i = 0; i < dimY; ++i) { System.arraycopy(matrix[i], 0, result, i * dimX, dimX); } return result; } static byte[][] shapen(byte[] matrixData, int[] dims) { final int dimY = dims[0]; final int dimX = dims[1]; final byte[][] result = new byte[dimY][dimX]; for (int i = 0; i < dimY; ++i) { System.arraycopy(matrixData, i * dimX, result[i], 0, dimX); } return result; } static boolean incrementIdx(int[] idx, int[] dims, int[] offset) { int d = idx.length - 1; while (++idx[d] >= offset[d] + dims[d]) { idx[d] = offset[d]; if (d == 0) { return false; } else { --d; } } return true; } static int[] concat(int[] array1, int[] array2) { if (array1.length == 0) { return array2; } if (array2.length == 0) { return array1; } final int[] result = new int[array1.length + array2.length]; System.arraycopy(array1, 0, result, 0, array1.length); System.arraycopy(array2, 0, result, array1.length, array2.length); return result; } static long[] concat(long[] array1, int[] array2) { if (array1.length == 0) { return MDArray.toLong(array2); } if (array2.length == 0) { return array1; } final long[] result = new long[array1.length + array2.length]; System.arraycopy(array1, 0, result, 0, array1.length); for (int i = 0; i < array2.length; ++i) { result[array1.length + i] = array2[i]; } return result; } static int cardinalityBoundIndices(Map boundIndices) { return boundIndices.size(); } static int cardinalityBoundIndices(long[] boundIndices) { int card = 0; for (int i = 0; i < boundIndices.length; ++i) { if (boundIndices[i] >= 0) { ++card; } } return card; } static void createFullBlockDimensionsAndOffset(int[] blockDimensions, long[] offsetOrNull, Map boundIndices, final long[] fullDimensions, final int[] fullBlockDimensions, final long[] fullOffset) { createFullBlockDimensionsAndOffset(blockDimensions, offsetOrNull, boundIndices, fullDimensions.length, fullDimensions, fullBlockDimensions, fullOffset); } static void createFullBlockDimensionsAndOffset(int[] blockDimensions, long[] offsetOrNull, Map boundIndices, final int fullRank, final int[] fullBlockDimensions, final long[] fullOffset) { createFullBlockDimensionsAndOffset(blockDimensions, offsetOrNull, boundIndices, fullRank, null, fullBlockDimensions, fullOffset); } static void createFullBlockDimensionsAndOffset(int[] blockDimensions, long[] offsetOrNull, Map boundIndices, final int fullRank, final long[] fullDimensionsOrNull, final int[] fullBlockDimensions, final long[] fullOffset) { int j = 0; for (int i = 0; i < fullRank; ++i) { final Long boundIndexOrNull = boundIndices.get(i); if (boundIndexOrNull == null) { if (blockDimensions[j] < 0 && fullDimensionsOrNull != null) { blockDimensions[j] = (int) fullDimensionsOrNull[i]; } fullBlockDimensions[i] = blockDimensions[j]; fullOffset[i] = (offsetOrNull == null) ? 0 : offsetOrNull[j]; ++j; } else { fullBlockDimensions[i] = 1; fullOffset[i] = boundIndexOrNull; } } } static void createFullBlockDimensionsAndOffset(int[] blockDimensions, long[] offsetOrNull, long[] boundIndices, final long[] fullDimensions, final int[] fullBlockDimensions, final long[] fullOffset) { createFullBlockDimensionsAndOffset(blockDimensions, offsetOrNull, boundIndices, fullDimensions.length, fullDimensions, fullBlockDimensions, fullOffset); } static void createFullBlockDimensionsAndOffset(int[] blockDimensions, long[] offsetOrNull, long[] boundIndices, final int fullRank, final int[] fullBlockDimensions, final long[] fullOffset) { createFullBlockDimensionsAndOffset(blockDimensions, offsetOrNull, boundIndices, fullRank, null, fullBlockDimensions, fullOffset); } static void createFullBlockDimensionsAndOffset(int[] blockDimensions, long[] offsetOrNull, long[] boundIndices, final int fullRank, final long[] fullDimensionsOrNull, final int[] fullBlockDimensions, final long[] fullOffset) { int j = 0; for (int i = 0; i < fullRank; ++i) { final long boundIndex = boundIndices[i]; if (boundIndex < 0) { if (blockDimensions[j] < 0 && fullDimensionsOrNull != null) { blockDimensions[j] = (int) fullDimensionsOrNull[i]; } fullBlockDimensions[i] = blockDimensions[j]; fullOffset[i] = (offsetOrNull == null) ? 0 : offsetOrNull[j]; ++j; } else { fullBlockDimensions[i] = 1; fullOffset[i] = boundIndex; } } } static void checkBoundIndices(String objectPath, long[] dimensions, int cardBoundIndices) throws HDF5JavaException { if (cardBoundIndices > dimensions.length) { throw new HDF5JavaException("Dataset " + objectPath + ": more bound indices (#" + cardBoundIndices + ") than dataset dimensions (#" + dimensions.length + ")"); } } static void checkBoundIndices(String objectPath, long[] dimensions, long[] boundIndices) throws HDF5JavaException { if (dimensions.length != boundIndices.length) { throw new HDF5JavaException("Dataset " + objectPath + ": boundIndices array (#" + boundIndices.length + ") differs from dataset dimensions (#" + dimensions.length + ")"); } } static void checkBoundIndices(String objectPath, long[] dimensions, int[] blockDimensions, int cardBoundIndices) throws HDF5JavaException { if (dimensions.length != blockDimensions.length + cardBoundIndices) { throw new HDF5JavaException("Dataset " + objectPath + ": cardinality of bound indices (#" + cardBoundIndices + ") plus rank of blocks (#" + blockDimensions.length + ") not equal to rank of dataset (#" + dimensions.length + ")"); } } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/PaddingUtils.java000066400000000000000000000043211256564762100266140ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ch.systemsx.cisd.hdf5.hdf5lib.HDFNativeData; /** * A class with methods for padding of memory structures. *

* This is an internal API that should not be expected to be stable between releases! * * @author Bernd Rinn */ class PaddingUtils { private static final int machineWordSize = HDFNativeData.getMachineWordSize(); private PaddingUtils() { // Cannot be instantiated } /** * Compute the padded offset to have aligned access to variables of * elementSize, or the size of the machine word, whatever is smaller. */ static int padOffset(int offset, int elementSize) { if (elementSize > 0) { final int actualElementSize = Math.min(elementSize, machineWordSize); int mod = offset % actualElementSize; return (mod > 0) ? offset + actualElementSize - mod : offset; } else { return offset; } } /** * Compute the maximal element size (in bytes). If the maximal element size is larger than the * size of a machine word on this platform, return the size of a machine word instead. */ static int findMaxElementSize(HDF5MemberByteifyer[] byteifyers) { int maxElementSize = 0; for (HDF5MemberByteifyer b : byteifyers) { maxElementSize = Math.max(maxElementSize, b.getElementSize()); if (maxElementSize >= machineWordSize) { return machineWordSize; } } return maxElementSize; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/ReflectionUtils.java000066400000000000000000000114361256564762100273450ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.lang.reflect.AccessibleObject; import java.lang.reflect.Constructor; import java.lang.reflect.Field; import java.lang.reflect.InvocationTargetException; import java.util.HashMap; import java.util.Map; /** * Utility methods for reflection, used for inferring the mapping between a compound data type and * the fields of a Java class. *

* This is an internal API that should not be expected to be stable between releases! * * @author Bernd Rinn */ public final class ReflectionUtils { private ReflectionUtils() { // Cannot be instantiated } /** * Returns a map from field names to fields for all fields in the given clazz. */ public static Map getFieldMap(final Class clazz) { return getFieldMap(clazz, true); } /** * Returns a map from field names to fields for all fields in the given clazz. * * @param clazz The clazz to get the fields from. * @param excludeNonMappedFields If true, do not include fields to the map which * are not supposed to be mapped to HDF5 members. */ public static Map getFieldMap(final Class clazz, boolean excludeNonMappedFields) { final Map map = new HashMap(); final CompoundType ct = clazz.getAnnotation(CompoundType.class); final boolean includeAllFields = excludeNonMappedFields ? ((ct != null) ? ct.mapAllFields() : true) : true; for (Class c = clazz; c != null; c = c.getSuperclass()) { for (Field f : c.getDeclaredFields()) { final CompoundElement e = f.getAnnotation(CompoundElement.class); if (e != null && org.apache.commons.lang.StringUtils.isNotEmpty(e.memberName())) { map.put(e.memberName(), f); } else if (e != null || includeAllFields) { map.put(f.getName(), f); } } } return map; } /** * Ensures that the given member is accessible even if by definition it is not. */ public static void ensureAccessible(final AccessibleObject memberOrNull) { if (memberOrNull != null && memberOrNull.isAccessible() == false) { memberOrNull.setAccessible(true); } } /** * Creates an object of clazz using the default constructor, making the default * constructor accessible if necessary. */ public static Constructor getDefaultConstructor(final Class clazz) throws SecurityException, NoSuchMethodException, IllegalArgumentException, InstantiationException, IllegalAccessException, InvocationTargetException { final Constructor defaultConstructor = clazz.getDeclaredConstructor(); ensureAccessible(defaultConstructor); return defaultConstructor; } /** * Creates an object of clazz using the default constructor, making the default * constructor accessible if necessary. */ public static T newInstance(final Class clazz) throws SecurityException, NoSuchMethodException, IllegalArgumentException, InstantiationException, IllegalAccessException, InvocationTargetException { final Constructor defaultConstructor = clazz.getDeclaredConstructor(); ensureAccessible(defaultConstructor); return defaultConstructor.newInstance(); } /** * Returns the enum options of the given enumClass. If enumClass is not an * enum class, return an empty array. */ public static String[] getEnumOptions(Class> enumClass) { final Enum[] constants = enumClass.getEnumConstants(); if (constants == null) { return new String[0]; } final String[] options = new String[constants.length]; for (int i = 0; i < options.length; ++i) { options[i] = constants[i].name(); } return options; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/StringUtils.java000066400000000000000000000154571256564762100265300ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.io.UnsupportedEncodingException; /** * Some auxiliary methods for String to Byte conversion. *

* This is an internal API that should not be expected to be stable between releases! * * @author Bernd Rinn */ public final class StringUtils { private StringUtils() { // Not to be instantiated. } /** * Converts string s to a byte array of a 0-terminated string, using * encoding and cutting it to maxLength if necessary. */ public static byte[] toBytes0Term(String s, int maxCharacters, CharacterEncoding encoding) { try { return (cut(s, maxCharacters) + '\0').getBytes(encoding.getCharSetName()); } catch (UnsupportedEncodingException ex) { return (cut(s, maxCharacters) + '\0').getBytes(); } } /** * Converts string s to a byte array of a 0-terminated string, using * encoding. */ public static byte[] toBytes0Term(String s, CharacterEncoding encoding) { try { return (s + '\0').getBytes(encoding.getCharSetName()); } catch (UnsupportedEncodingException ex) { return (s + '\0').getBytes(); } } /** * Converts string s to a byte array of a string, using encoding and * cutting it to maxLength characters. */ static byte[] toBytes(String s, int maxLength, CharacterEncoding encoding) { try { return (cut(s, maxLength)).getBytes(encoding.getCharSetName()); } catch (UnsupportedEncodingException ex) { return (cut(s, maxLength)).getBytes(); } } /** * Converts string s to a byte array of a string, using encoding. */ static byte[] toBytes(String s, CharacterEncoding encoding) { try { return s.getBytes(encoding.getCharSetName()); } catch (UnsupportedEncodingException ex) { return s.getBytes(); } } /** * Converts string array in to a byte array, using * encoding and cutting it to maxLengthin to a byte array of a 0-terminated string, using * encoding and cutting it to maxLengthdata containing a 0-terminated string using * encoding to a string. */ static String fromBytes0Term(byte[] data, CharacterEncoding encoding) { return fromBytes0Term(data, 0, data.length, encoding); } /** * Converts byte array data containing a 0-terminated string at startIdx * using encoding to a string. Does search further than maxEndIdx */ static String fromBytes0Term(byte[] data, int startIdx, int maxEndIdx, CharacterEncoding encoding) { int termIdx; for (termIdx = startIdx; termIdx < maxEndIdx && data[termIdx] != 0; ++termIdx) { } try { return new String(data, startIdx, termIdx - startIdx, encoding.getCharSetName()); } catch (UnsupportedEncodingException ex) { return new String(data, startIdx, termIdx - startIdx); } } /** * Converts the first length bytes of byte array data containing a string * using encoding to a string. */ static String fromBytes(byte[] data, int length, CharacterEncoding encoding) { return fromBytes(data, 0, length, encoding); } /** * Converts byte array data containing a string using encoding to a * string. */ static String fromBytes(byte[] data, CharacterEncoding encoding) { return fromBytes(data, 0, data.length, encoding); } /** * Converts byte array data containing a string from startIdx to * endIdx using encoding to a string. */ static String fromBytes(byte[] data, int startIdx, int endIdx, CharacterEncoding encoding) { try { return new String(data, startIdx, endIdx - startIdx, encoding.getCharSetName()); } catch (UnsupportedEncodingException ex) { return new String(data, startIdx, endIdx - startIdx); } } private static String cut(String s, int maxLength) { if (s.length() > maxLength) { return s.substring(0, maxLength); } else { return s; } } /** * Cuts or pads value to length. */ static byte[] cutOrPadBytes(byte[] value, int length) { if (value.length == length) { return value; } else { final byte[] newValue = new byte[length]; System.arraycopy(value, 0, newValue, 0, Math.min(value.length, length)); return newValue; } } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/UnsignedIntUtils.java000066400000000000000000000106561256564762100275050ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.math.BigInteger; import ch.systemsx.cisd.base.convert.NativeData; import ch.systemsx.cisd.base.convert.NativeData.ByteOrder; /** * Utilities for converting signed integers to unsigned integers and vice versa. * * @author Bernd Rinn */ public final class UnsignedIntUtils { private final static short MAX_UINT_8_P1 = 256; private final static short MAX_UINT_8 = MAX_UINT_8_P1 - 1; private final static int MAX_UINT_16_P1 = 65536; private final static int MAX_UINT_16 = MAX_UINT_16_P1 - 1; private final static long MAX_UINT_32_P1 = 4294967296L; private final static long MAX_UINT_32 = MAX_UINT_32_P1 - 1; private final static BigInteger MAX_UINT_64_P1 = new BigInteger("2").pow(64); private final static BigInteger MAX_UINT_64 = MAX_UINT_64_P1.subtract(BigInteger.ONE); /** * Converts value to int8. * * @throws IllegalArgumentException if value is either negative or too large to fit * into uint8. */ public static byte toInt8(int value) throws IllegalArgumentException { if (value < 0 || value > MAX_UINT_8) { throw new IllegalArgumentException("Value " + Integer.toString(value) + " cannot be converted to uint8."); } return (byte) value; } /** * Converts value as int16. * * @throws IllegalArgumentException if value is either negative or too large to fit * into uint16. */ public static short toInt16(int value) throws IllegalArgumentException { if (value < 0 || value > MAX_UINT_16) { throw new IllegalArgumentException("Value " + Integer.toString(value) + " cannot be converted to uint16."); } return (short) value; } /** * Converts value as int32. * * @throws IllegalArgumentException if value is either negative or too large to fit * into uint32. */ public static int toInt32(long value) throws IllegalArgumentException { if (value < 0 || value > MAX_UINT_32) { throw new IllegalArgumentException("Value " + Long.toString(value) + " cannot be converted to uint32."); } return (int) value; } /** * Converts value as int64. * * @throws IllegalArgumentException if value is either negative or too large to fit * into uint64. */ public static long toInt64(BigInteger value) throws IllegalArgumentException { if (value.compareTo(BigInteger.ZERO) < 0 || value.compareTo(MAX_UINT_64) > 0) { throw new IllegalArgumentException("Value " + value.toString() + " cannot be converted to uint64."); } return value.longValue(); } /** * Converts value to uint8. */ public static short toUint8(byte value) { return (short) (value < 0 ? MAX_UINT_8_P1 + value : value); } /** * Converts value to uint16. */ public static int toUint16(short value) { return value < 0 ? MAX_UINT_16_P1 + value : value; } /** * Converts value to uint32. */ public static long toUint32(int value) { return value < 0 ? MAX_UINT_32_P1 + value : value; } /** * Converts value to uint64. */ public static BigInteger toUint64(long value) { return new BigInteger(1, NativeData.longToByte(new long[] { value }, ByteOrder.BIG_ENDIAN)); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/cleanup/000077500000000000000000000000001256564762100250115ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/cleanup/CleanUpCallable.java000066400000000000000000000031151256564762100306230ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.cleanup; /** * A class that implements the logic of cleaning up a resource even in case of an exception but * re-throws an exception of the clean up procedure only when the main procedure didn't throw one. * CleanUpRunners can be stacked. *

* This is an internal implementation class that is not meant to be used by users of the library. * * @author Bernd Rinn */ public final class CleanUpCallable { /** * Runs a {@link ICallableWithCleanUp} and ensures that all registered clean-ups are performed * afterwards. */ public T call(ICallableWithCleanUp runnable) { final CleanUpRegistry registry = new CleanUpRegistry(); boolean exceptionThrown = true; try { T result = runnable.call(registry); exceptionThrown = false; return result; } finally { registry.cleanUp(exceptionThrown); } } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/cleanup/CleanUpRegistry.java000066400000000000000000000052731256564762100307430ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.cleanup; import java.util.ArrayList; import java.util.List; /** * A class that allows registering items for clean up and that allows to perform the clean up later. *

* This is an internal implementation class that is not meant to be used by users of the library. * * @author Bernd Rinn */ public class CleanUpRegistry implements ICleanUpRegistry { private final List cleanUpList = new ArrayList(); /** * Creates a synchronized version of a {@link CleanUpRegistry}. */ public static CleanUpRegistry createSynchonized() { return new CleanUpRegistry() { @Override public synchronized void registerCleanUp(Runnable cleanUp) { super.registerCleanUp(cleanUp); } @Override public synchronized void cleanUp(boolean suppressExceptions) { super.cleanUp(suppressExceptions); } }; } @Override public void registerCleanUp(Runnable cleanUp) { cleanUpList.add(cleanUp); } /** * Performs all clean-ups registered with {@link #registerCleanUp(Runnable)}. * * @param suppressExceptions If true, all exceptions that happen during clean-up * will be suppressed. */ public void cleanUp(boolean suppressExceptions) { RuntimeException exceptionDuringCleanUp = null; for (int i = cleanUpList.size() - 1; i >= 0; --i) { final Runnable runnable = cleanUpList.get(i); try { runnable.run(); } catch (RuntimeException ex) { if (suppressExceptions == false && exceptionDuringCleanUp == null) { exceptionDuringCleanUp = ex; } } } cleanUpList.clear(); if (exceptionDuringCleanUp != null) { throw exceptionDuringCleanUp; } } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/cleanup/ICallableWithCleanUp.java000066400000000000000000000022121256564762100315650ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.cleanup; /** * A role that calls a method which requires one or more clean-up steps that need to be run reliably * at the end of the method regardless of whether the method is finished normally or whether it * exits with an exception. *

* This is an internal interface that is not meant to be used by users of the library. * * @author Bernd Rinn */ public interface ICallableWithCleanUp { /** Calls the method requiring clean-up. */ public T call(ICleanUpRegistry registry); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/cleanup/ICleanUpRegistry.java000066400000000000000000000021231256564762100310430ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.cleanup; /** * A role that allows to register a clean-up method that is called regardless of whether an * exception occurs or not. *

* This is an internal interface that is not meant to be used by users of the library. * * @author Bernd Rinn */ public interface ICleanUpRegistry { /** * Register a clean-up to run when the main {@link Runnable} has been executed. */ public void registerCleanUp(Runnable cleanUp); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/000077500000000000000000000000001256564762100242215ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/ArchiveEntry.java000066400000000000000000000600661256564762100274770ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import ch.systemsx.cisd.base.unix.FileLinkType; import ch.systemsx.cisd.hdf5.h5ar.HDF5ArchiveUpdater.DataSetInfo; /** * An entry of an archive listing. * * @author Bernd Rinn */ public final class ArchiveEntry { private final String path; private final String parentPath; private final String name; private final String realPath; private final String realParentPath; private final String realName; private final ArchiveEntryCompleteness completeness; private final boolean hasLinkTarget; private final String linkTarget; private final FileLinkType linkType; private final FileLinkType verifiedLinkType; private final long size; private long verifiedSize; private final long lastModified; private final long verifiedLastModified; private int crc32; private boolean knowsChecksum; private int verifiedCrc32; private final int uid; private final int gid; private final IdCache idCache; private final short permissions; private final String errorLineOrNull; ArchiveEntry(String dir, String path, LinkRecord link, IdCache idCache) { this(dir, path, link, idCache, null); } ArchiveEntry(String dir, String path, LinkRecord link, IdCache idCache, String errorLineOrNull) { this.parentPath = (dir != null) ? dir : Utils.getParentPath(path); this.realParentPath = parentPath; this.path = path; this.realPath = path; this.name = link.getLinkName(); this.realName = name; this.idCache = idCache; this.completeness = link.getCompleteness(); this.hasLinkTarget = (link.tryGetLinkTarget() != null); this.linkTarget = hasLinkTarget ? link.tryGetLinkTarget() : "?"; this.linkType = link.getLinkType(); this.verifiedLinkType = link.getVerifiedType(); this.size = link.getSize(); this.verifiedSize = link.getVerifiedSize(); this.lastModified = link.getLastModified(); this.verifiedLastModified = link.getVerifiedLastModified(); this.crc32 = link.getCrc32(); this.knowsChecksum = link.hasCRC32Checksum(); this.verifiedCrc32 = link.getVerifiedCrc32(); this.uid = link.getUid(); this.gid = link.getGid(); this.permissions = link.getPermissions(); this.errorLineOrNull = errorLineOrNull; } ArchiveEntry(ArchiveEntry pathInfo, ArchiveEntry linkInfo) { this.parentPath = pathInfo.parentPath; this.path = pathInfo.path; this.name = pathInfo.name; this.realParentPath = linkInfo.parentPath; this.realPath = linkInfo.realPath; this.realName = linkInfo.name; this.idCache = pathInfo.idCache; this.completeness = linkInfo.completeness; this.hasLinkTarget = linkInfo.hasLinkTarget; this.linkTarget = linkInfo.linkTarget; this.linkType = linkInfo.linkType; this.verifiedLinkType = linkInfo.verifiedLinkType; this.size = linkInfo.size; this.verifiedSize = linkInfo.verifiedSize; this.lastModified = Math.max(pathInfo.lastModified, linkInfo.lastModified); this.verifiedLastModified = Math.max(pathInfo.verifiedLastModified, linkInfo.verifiedLastModified); this.crc32 = linkInfo.crc32; this.knowsChecksum = linkInfo.knowsChecksum; this.verifiedCrc32 = linkInfo.verifiedCrc32; this.uid = linkInfo.uid; this.gid = linkInfo.gid; this.permissions = linkInfo.permissions; this.errorLineOrNull = null; } ArchiveEntry(String errorLineOrNull) { this.errorLineOrNull = errorLineOrNull; this.path = null; this.parentPath = null; this.name = null; this.realPath = null; this.realParentPath = null; this.realName = null; this.idCache = null; this.completeness = null; this.linkTarget = null; this.hasLinkTarget = false; this.linkType = null; this.verifiedLinkType = null; this.size = Utils.UNKNOWN; this.verifiedSize = Utils.UNKNOWN; this.lastModified = Utils.UNKNOWN; this.verifiedLastModified = Utils.UNKNOWN; this.crc32 = 0; this.verifiedCrc32 = 0; this.uid = Utils.UNKNOWN; this.gid = Utils.UNKNOWN; this.permissions = Utils.UNKNOWN_S; } void setDataSetInfo(DataSetInfo dataSetInfo) { this.verifiedSize = dataSetInfo.size; this.crc32 = dataSetInfo.crc32; this.verifiedCrc32 = crc32; this.knowsChecksum = true; } /** * Returns the full path of this entry. */ public String getPath() { return path; } /** * Returns the parent directory of the path of this entry. */ public String getParentPath() { return parentPath; } /** * Returns the name of the path this entry. */ public String getName() { return name; } /** * Returns the real full path of this entry. *

* This will be the same as {@link #getPath()}, except when it originates from a call to * {@link IHDF5ArchiveInfoProvider#tryGetResolvedEntry(String, boolean)} with * keepPath=true where it will be the path of the link target. */ public String getRealPath() { return realPath; } /** * Returns the real parent directory of the path of this entry. *

* This will be the same as {@link #getPath()}, except when it originates from a call to * {@link IHDF5ArchiveInfoProvider#tryGetResolvedEntry(String, boolean)} with * keepPath=true where it will be the parent path of the link target. */ public String getRealParentPath() { return realParentPath; } /** * Returns the name of the path this entry. *

* This will be the same as {@link #getPath()}, except when it originates from a call to * {@link IHDF5ArchiveInfoProvider#tryGetResolvedEntry(String, boolean)} with * keepPath=true where it will be the name of the link target. */ public String getRealName() { return realName; } /** * Returns how complete this entry is. *

* {@link ArchiveEntryCompleteness#BASE} entries can occur if the archive does not contain valid * file attributes, {@link ArchiveEntryCompleteness#LAST_MODIFIED} entries can occur if the * archive has been created or updated on a non-POSIX (read: Microsoft Windows) machine. */ public ArchiveEntryCompleteness getCompleteness() { return completeness; } /** * Returns the link target. May be "?" if the link target has not been readm or if this entry * does not represent a link. * * @see #hasLinkTarget() */ public String getLinkTarget() { return linkTarget; } /** * Returns true, if this entry has a meaningful link target. * * @see #getLinkTarget() */ public boolean hasLinkTarget() { return hasLinkTarget; } /** * Returns the type of this entry. */ public FileLinkType getLinkType() { return linkType; } /** * Returns if this entry is of type {@link FileLinkType#DIRECTORY}. */ public boolean isDirectory() { return linkType == FileLinkType.DIRECTORY; } /** * Returns if this entry is of type {@link FileLinkType#SYMLINK}. */ public boolean isSymLink() { return linkType == FileLinkType.SYMLINK; } /** * Returns if this entry is of type {@link FileLinkType#REGULAR_FILE}. */ public boolean isRegularFile() { return linkType == FileLinkType.REGULAR_FILE; } /** * Returns the size of this entry, if this entry is a regular file, or 0 otherwise. * * @see #isRegularFile() */ public long getSize() { return size; } /** * Returns the date and time of last modification of this entry, measured in seconds since the * epoch (00:00:00 GMT, January 1, 1970), or -1, if this information is not available. */ public long getLastModified() { return lastModified; } /** * Returns a string representation of the date and time of last modification of this entry, or * "?", if this information is not available. */ public String getLastModifiedStr() { return getLastModifiedStr(lastModified); } private static String getLastModifiedStr(long lastModified) { if (lastModified >= 0) { return String.format("%1$tY-%1$tm-%1$td %1$tH:%1$tM:%1$tS", lastModified * Utils.MILLIS_PER_SECOND); } else { return "?"; } } /** * Returns true, if this archive entry has a CRC32 checksum stored. */ public boolean hasChecksum() { return knowsChecksum; } /** * Returns the CRC32 checksum of this entry, or 0, if this information is not available or if * this entry is not a regular file. * * @see #isRegularFile() */ public int getCrc32() { return crc32; } /** * Returns a string representation (using hexadecimal digits) of the CRC32 checksum of this * entry, or "00000000", if this information is not available or if this entry is not a regular * file. * * @see #isRegularFile() */ public String getCrc32Str() { return Utils.crc32ToString(crc32); } /** * Returns a string representation of the user owning this archive entry, or "?", if this * information is not available. *

* Note that the archive only stores the UID and it is the local system which is used to resolve * the UID to a user. */ public String getUser(boolean numeric) { return (uid >= 0) ? idCache.getUser(uid, numeric) : "?"; } /** * Returns the UID of the user owning this archive entry, or -1, if this information is not * available. */ public int getUid() { return uid; } /** * Returns a string representation of the group owning this archive entry, or "?", if this * information is not available. *

* Note that the archive only stores the GID and it is the local system which is used to resolve * the GID to a group. */ public String getGroup(boolean numeric) { return (gid >= 0) ? idCache.getGroup(gid, numeric) : "?"; } /** * Returns the GID of the group owning this archive entry, or -1, if this information is not * available. */ public int getGid() { return gid; } /** * Returns the access permissions of this archive entry, or -1, if this information is not * available. */ public short getPermissions() { return permissions; } /** * Returns a string representation of the access permissions of this archive entry, or "?", if * this information is not available. */ public String getPermissionsString(boolean numeric) { return (permissions >= 0) ? Utils.permissionsToString(permissions, linkType == FileLinkType.DIRECTORY, numeric) : "?"; } /** * Returns the error line saved for this archive entry, or null, if no error line * is available. A non-null error line is one indication of a verification error. *

* Note that the error line may contain additional information when a verification step has * failed on the archive entry. */ public String tryGetErrorLine() { return errorLineOrNull; } /** * Returns the verified type of this entry, or null, if no verification has been * performed on this entry. *

* This information may come from an internal test of the archive (see * {@link ListParameters#isTestArchive()}) or from a verification of the archive against the * filesystem (see {@link VerifyParameters}). */ public FileLinkType tryGetVerifiedLinkType() { return verifiedLinkType; } /** * Returns the verified size of this archive entry, or -1, if this information is not available. */ public long getVerifiedSize() { return verifiedSize; } /** * Returns the verified CRC32 checksum of this archive entry, or 0, if this information is not * available. */ public int getVerifiedCrc32() { return verifiedCrc32; } /** * Returns a string representation (using hexadecimal digits) of the verified CRC32 checksum of * this entry, or "00000000", if this information is not available or if this entry is not a * regular file. * * @see #isRegularFile() */ public String getVerifiedCrc32Str() { return Utils.crc32ToString(verifiedCrc32); } /** * Returns the verified date and time of last modification of this entry, measured in seconds * since the epoch (00:00:00 GMT, January 1, 1970), or -1, if this information is not available. */ public long getVerifiedLastModified() { return verifiedLastModified; } /** * Returns a string representation of the verified date and time of last modification of this * entry, or "?", if this information is not available. */ public String getVerifiedLastModifiedStr() { return getLastModifiedStr(verifiedLastModified); } /** * Returns true, if this entry has verification information on archive integrity. */ public boolean hasVerificationInfo() { return (verifiedLinkType != null || verifiedSize != -1 || verifiedCrc32 != 0 || verifiedLastModified != -1 || errorLineOrNull != null); } /** * Returns true if this archive entry has been verified successfully (or if no * verification information is available). */ public boolean isOK() { return (errorLineOrNull == null) && linkTypeOK() && sizeOK() && lastModifiedOK() && checksumOK(); } /** * Returns true if this the type of this archive entry has been verified * successfully (or if no verification information for the type is available). */ public boolean linkTypeOK() { return (verifiedLinkType == null) || (linkType == verifiedLinkType); } /** * Returns true if this the size of this archive entry has been verified * successfully (or if no verification information for the size is available). */ public boolean sizeOK() { return (verifiedSize == Utils.UNKNOWN) || (size == verifiedSize); } /** * Returns true if this the last modification date of this archive entry has been * verified successfully (or if no verification information for the last modification date is * available). */ public boolean lastModifiedOK() { return (verifiedLastModified == Utils.UNKNOWN) || (lastModified == Utils.UNKNOWN) || (lastModified == verifiedLastModified); } /** * Returns true if this the checksum of this archive entry has been verified * successfully (or if no verification information for the checksum is available). */ public boolean checksumOK() { return (false == knowsChecksum) || (verifiedSize == Utils.UNKNOWN) ||(crc32 == verifiedCrc32); } /** * Returns a status string for this entry. *

* Note that the status will alway be OK if no verification information is * available. * * @see #hasVerificationInfo() */ public String getStatus(boolean verbose) { if (isOK() == false) { if (errorLineOrNull != null) { return "ERROR: " + errorLineOrNull; } else if (linkTypeOK() == false) { return verbose ? String.format( "ERROR: Entry '%s' failed link type test, expected: %s, found: %s.", path, linkType, verifiedLinkType) : "WRONG TYPE"; } else if (sizeOK() == false) { return verbose ? String.format( "ERROR: Entry '%s' failed size test, expected: %d, found: %d.", path, size, verifiedSize) : "WRONG SIZE"; } else if (checksumOK() == false) { return verbose ? String.format( "ERROR: Entry '%s' failed CRC checksum test, expected: %s, found: %s.", path, Utils.crc32ToString(crc32), Utils.crc32ToString(verifiedCrc32)) : "WRONG CRC32"; } else if (lastModifiedOK() == false) { return verbose ? String .format("ERROR: Entry '%s' failed last modification test, expected: %s, found: %s.", path, getLastModifiedStr(), getVerifiedLastModifiedStr()) : "WRONG LASTMODIFICATION"; } } return "OK"; } /** * Returns a (verbose) string description of this entry, including the (brief) verification * status, if available. */ public String describeLink() { return describeLink(true, false, true); } /** * Returns a string description of this entry, including the (brief) verification status, if * available. * * @param verbose If true, the link description will contain all information * available, if false, it will only contain the path information. */ public String describeLink(boolean verbose) { return describeLink(verbose, false, true); } /** * Returns a string description of this entry, including the (brief) verification status, if * available. * * @param verbose If true, the link description will contain all information * available, if false, it will only contain the path information. * @param numeric If true, file ownership and access permissions will be * represented numerically, if false, they will be represented as * strings. Only relevant if verbose is true. */ public String describeLink(boolean verbose, boolean numeric) { return describeLink(verbose, numeric, true); } /** * Returns a string description of this entry. * * @param verbose If true, the link description will contain all information * available, if false, it will only contain the path information. * @param numeric If true, file ownership and access permissions will be * represented numerically, if false, they will be represented as * strings. Only relevant if verbose is true. * @param includeCheck If true (and if verification information is available for * this entry), add a (brief) verification status string. * @see #hasVerificationInfo() */ public String describeLink(boolean verbose, boolean numeric, boolean includeCheck) { final StringBuilder builder = new StringBuilder(); if (verbose == false) { builder.append(path); } else { switch (completeness) { case BASE: if (linkType == FileLinkType.SYMLINK) { builder.append(String.format(" \t%s -> %s", path, linkTarget)); } else if (linkType == FileLinkType.DIRECTORY) { builder.append(String.format(" DIR\t%s", path)); } else { builder.append(String.format("%10d\t%s\t%s%s", size, Utils.crc32ToString(crc32), path, (linkType == FileLinkType.REGULAR_FILE) ? "" : "\t*")); } break; case LAST_MODIFIED: if (linkType == FileLinkType.SYMLINK) { builder.append(String.format( " \t%1$tY-%1$tm-%1$td %1$tH:%1$tM:%1$tS\t%2$s -> %3$s", lastModified * Utils.MILLIS_PER_SECOND, path, linkTarget)); } else if (linkType == FileLinkType.DIRECTORY) { builder.append(String.format( " DIR\t%1$tY-%1$tm-%1$td %1$tH:%1$tM:%1$tS\t%2$s", lastModified * Utils.MILLIS_PER_SECOND, path)); } else { builder.append(String.format( "%10d\t%2$tY-%2$tm-%2$td %2$tH:%2$tM:%2$tS\t%3$s\t%4$s%5$s", size, lastModified * Utils.MILLIS_PER_SECOND, Utils.crc32ToString(crc32), path, (linkType == FileLinkType.REGULAR_FILE) ? "" : "\t*")); } break; case FULL: if (linkType == FileLinkType.SYMLINK) { builder.append(String .format("%s\t%s\t%s\t \t%4$tY-%4$tm-%4$td %4$tH:%4$tM:%4$tS\t \t%5$s -> %6$s", Utils.permissionsToString(permissions, false, numeric), getUser(numeric), getGroup(numeric), lastModified * Utils.MILLIS_PER_SECOND, path, linkTarget)); } else if (linkType == FileLinkType.DIRECTORY) { builder.append(String .format("%s\t%s\t%s\t DIR\t%4$tY-%4$tm-%4$td %4$tH:%4$tM:%4$tS\t \t%5$s", Utils.permissionsToString(permissions, true, numeric), getUser(numeric), getGroup(numeric), lastModified * Utils.MILLIS_PER_SECOND, path)); } else { builder.append(String .format("%s\t%s\t%s\t%10d\t%5$tY-%5$tm-%5$td %5$tH:%5$tM:%5$tS\t%6$s\t%7$s%8$s", Utils.permissionsToString(permissions, false, numeric), getUser(numeric), getGroup(numeric), size, lastModified * Utils.MILLIS_PER_SECOND, Utils.crc32ToString(crc32), path, (linkType == FileLinkType.REGULAR_FILE) ? "" : "\t*")); } break; default: throw new Error("Unknown level of link completeness: " + completeness); } } if (includeCheck && hasVerificationInfo()) { builder.append('\t'); builder.append(getStatus(false)); } return builder.toString(); } @Override public String toString() { return describeLink(); } }libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/ArchiveEntryCompleteness.java000066400000000000000000000017741256564762100320620ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; /** * An enum to specify the completeness of an archive entry. * * @author Bernd Rinn */ public enum ArchiveEntryCompleteness { /** Contains only the path information. */ BASE, /** Contains the path information and the "last modified" timestamp. */ LAST_MODIFIED, /** Contains all information, including user and permission. */ FULL }libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/ArchiveEntryExtractProcessor.java000066400000000000000000000231651256564762100327310ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import java.io.File; import java.io.IOException; import java.io.OutputStream; import java.util.zip.CRC32; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import org.apache.commons.io.FileUtils; import org.apache.commons.io.IOUtils; import ch.systemsx.cisd.base.exceptions.IErrorStrategy; import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked; import ch.systemsx.cisd.base.unix.FileLinkType; import ch.systemsx.cisd.base.unix.Unix; import ch.systemsx.cisd.base.unix.Unix.Stat; import ch.systemsx.cisd.hdf5.IHDF5Reader; /** * A processor that extracts files from an archive to the file system. * * @author Bernd Rinn */ class ArchiveEntryExtractProcessor implements IArchiveEntryProcessor { private static final int ROOT_UID = 0; private final IArchiveEntryVisitor visitorOrNull; private final ArchivingStrategy strategy; private final File rootDirectory; private final String rootPathToStrip; private final byte[] buffer; private final GroupCache groupCache; ArchiveEntryExtractProcessor(IArchiveEntryVisitor visitorOrNull, ArchivingStrategy strategy, File rootDirectory, String rootPathToStrip, byte[] buffer) { this.visitorOrNull = visitorOrNull; this.strategy = strategy; this.rootDirectory = rootDirectory; final String normalizedRootPathToStrip = Utils.normalizePath(rootPathToStrip); this.rootPathToStrip = "/".equals(normalizedRootPathToStrip) ? "" : normalizedRootPathToStrip; this.buffer = buffer; this.groupCache = new GroupCache(); } @Override public boolean process(String dir, String path, LinkRecord link, IHDF5Reader reader, IdCache idCache, IErrorStrategy errorStrategy) throws IOException { if (strategy.doExclude(path, link.isDirectory())) { return false; } final File file = createFile(path); if (link.isDirectory()) { if (file.exists() && file.isDirectory() == false) { file.delete(); } file.mkdirs(); if (file.isDirectory() == false) { errorStrategy.dealWithError(new UnarchivingException(file, new IOException( "Failed to make directory '" + file.getAbsolutePath() + "'."))); } if (visitorOrNull != null) { visitorOrNull.visit(new ArchiveEntry(dir, path, link, idCache)); } } else if (link.tryGetLinkTarget() != null && Unix.isOperational()) { try { file.delete(); final String linkTarget = link.tryGetLinkTarget(); Unix.createSymbolicLink(linkTarget, file.getAbsolutePath()); if (visitorOrNull != null) { visitorOrNull.visit(new ArchiveEntry(dir, path, link, idCache)); } } catch (IOExceptionUnchecked ex) { errorStrategy.dealWithError(new UnarchivingException(file, ex)); } } else { if (link.isSymLink()) { if (Unix.isOperational() == false) { errorStrategy.warning("Warning: extracting symlink as regular file because" + " Unix calls are not available on this system."); } else { errorStrategy.dealWithError(new UnarchivingException(path, new HDF5JavaException("Symlink doesn't have a link target."))); } } else { try { // Here we don't rely on link.getSize() to protect against wrong index entries. final long size = reader.object().getSize(path); final int crc32 = copyFromHDF5(reader, path, size, file); restoreAttributes(file, link); final FileSizeType sizeType = getFileSizeType(file); link.setVerifiedType(sizeType.type); link.setFileVerification(sizeType.size, crc32, file.lastModified() / Utils.MILLIS_PER_SECOND); final ArchiveEntry entry = new ArchiveEntry(dir, path, link, idCache); if (visitorOrNull != null) { visitorOrNull.visit(entry); } if (entry.isOK() == false) { errorStrategy.dealWithError(new UnarchivingException(path, entry .getStatus(true))); } } catch (IOException ex) { errorStrategy.dealWithError(new UnarchivingException(file, ex)); } catch (HDF5Exception ex) { errorStrategy.dealWithError(new UnarchivingException(path, ex)); } } } return true; } @Override public void postProcessDirectory(String dir, String path, LinkRecord link, IHDF5Reader reader, IdCache idCache, IErrorStrategy errorStrategy) throws IOException, HDF5Exception { final File file = createFile(path); restoreAttributes(file, link); } private File createFile(String path) { final String workingPath = path.startsWith(rootPathToStrip) ? path.substring(rootPathToStrip.length()) : path; final File file = new File(rootDirectory, workingPath); return file; } /** * A record for file size and type. * * @author Bernd Rinn */ private static class FileSizeType { final FileLinkType type; final long size; FileSizeType(FileLinkType type, long size) { super(); this.type = type; this.size = size; } } private FileSizeType getFileSizeType(final File file) { if (Unix.isOperational()) { final Stat info = Unix.getLinkInfo(file.getPath(), false); return new FileSizeType(info.getLinkType(), info.getSize()); } else { return new FileSizeType((file.isDirectory()) ? FileLinkType.DIRECTORY : (file.isFile() ? FileLinkType.REGULAR_FILE : FileLinkType.OTHER), file.length()); } } private int copyFromHDF5(final IHDF5Reader reader, final String objectPath, final long size, File destination) throws IOException { final OutputStream output = FileUtils.openOutputStream(destination); final CRC32 crc32 = new CRC32(); try { long offset = 0; while (offset < size) { final int n = reader.opaque().readArrayToBlockWithOffset(objectPath, buffer, buffer.length, offset, 0); offset += n; output.write(buffer, 0, n); crc32.update(buffer, 0, n); } output.close(); // Make sure we don't silence exceptions on closing. } finally { IOUtils.closeQuietly(output); } return (int) crc32.getValue(); } private void restoreAttributes(File file, LinkRecord linkInfoOrNull) { assert file != null; if (linkInfoOrNull != null) { if (linkInfoOrNull.hasLastModified()) { file.setLastModified(linkInfoOrNull.getLastModified() * Utils.MILLIS_PER_SECOND); } if (linkInfoOrNull.hasUnixPermissions() && Unix.isOperational()) { Unix.setAccessMode(file.getPath(), linkInfoOrNull.getPermissions()); if (Unix.getUid() == ROOT_UID) // Are we root? { Unix.setOwner(file.getPath(), linkInfoOrNull.getUid(), linkInfoOrNull.getGid()); } else { if (groupCache.isUserInGroup(linkInfoOrNull.getGid())) { Unix.setOwner(file.getPath(), Unix.getUid(), linkInfoOrNull.getGid()); } } } } } @Override public ArchiverException createException(String objectPath, String detailedMsg) { return new UnarchivingException(objectPath, detailedMsg); } @Override public ArchiverException createException(String objectPath, HDF5Exception cause) { return new UnarchivingException(objectPath, cause); } @Override public ArchiverException createException(String objectPath, RuntimeException cause) { return new UnarchivingException(objectPath, cause); } @Override public ArchiverException createException(File file, IOException cause) { return new UnarchivingException(file, cause); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/ArchiveEntryListProcessor.java000066400000000000000000000111061256564762100322220ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import java.io.File; import java.io.IOException; import java.util.zip.CRC32; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import ch.systemsx.cisd.base.exceptions.IErrorStrategy; import ch.systemsx.cisd.base.unix.FileLinkType; import ch.systemsx.cisd.hdf5.HDF5LinkInformation; import ch.systemsx.cisd.hdf5.IHDF5Reader; import ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants; /** * An {@Link IArchiveEntryProcessor} that performs a file list. * * @author Bernd Rinn */ class ArchiveEntryListProcessor implements IArchiveEntryProcessor { private final IArchiveEntryVisitor visitor; private final byte[] buffer; private final boolean checkArchive; ArchiveEntryListProcessor(IArchiveEntryVisitor visitor, byte[] buffer, boolean checkArchive) { this.visitor = visitor; this.buffer = buffer; this.checkArchive = checkArchive; } @Override public boolean process(String dir, String path, LinkRecord link, IHDF5Reader reader, IdCache idCache, IErrorStrategy errorStrategy) throws IOException { String errorMessage = null; if (checkArchive) { final HDF5LinkInformation info = reader.object().getLinkInformation(path); final FileLinkType verifiedType = Utils.translateType(info.getType()); link.setVerifiedType(verifiedType); if (verifiedType == FileLinkType.REGULAR_FILE) { final long verifiedSize = reader.object().getSize(path); int verifiedCrc32 = 0; try { verifiedCrc32 = calcCRC32Archive(path, verifiedSize, reader); } catch (HDF5Exception ex) { errorMessage = ex.getClass().getSimpleName() + ": " + ex.getMessage(); } link.setFileVerification(verifiedSize, verifiedCrc32, Utils.UNKNOWN); } } visitor.visit(new ArchiveEntry(dir, path, link, idCache, errorMessage)); return true; } @Override public void postProcessDirectory(String dir, String path, LinkRecord link, IHDF5Reader reader, IdCache idCache, IErrorStrategy errorStrategy) throws IOException, HDF5Exception { } private int calcCRC32Archive(String objectPath, long size, IHDF5Reader hdf5Reader) { final CRC32 crc32Digest = new CRC32(); long offset = 0; while (offset < size) { final int n = hdf5Reader.opaque().readArrayToBlockWithOffset(objectPath, buffer, buffer.length, offset, 0); offset += n; crc32Digest.update(buffer, 0, n); } return (int) crc32Digest.getValue(); } @Override public ArchiverException createException(String objectPath, String detailedMsg) { return new ListArchiveException(objectPath, detailedMsg); } @Override public ArchiverException createException(String objectPath, HDF5Exception cause) { if (isTooManySymlinksError(cause)) { return new ListArchiveTooManySymbolicLinksException(objectPath, cause); } return new ListArchiveException(objectPath, cause); } private boolean isTooManySymlinksError(HDF5Exception cause) { return cause instanceof HDF5LibraryException && ((HDF5LibraryException) cause).getMajorErrorNumber() == HDF5Constants.H5E_LINK && "Too many soft links in path".equals(((HDF5LibraryException) cause) .getMinorError()); } @Override public ArchiverException createException(String objectPath, RuntimeException cause) { return new ListArchiveException(objectPath, cause); } @Override public ArchiverException createException(File file, IOException cause) { return new ListArchiveException(file, cause); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/ArchiveEntryVerifyProcessor.java000066400000000000000000000254501256564762100325620ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import java.io.File; import java.io.IOException; import java.io.InputStream; import java.util.Set; import java.util.zip.CRC32; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import org.apache.commons.io.FileUtils; import org.apache.commons.io.IOUtils; import ch.systemsx.cisd.base.exceptions.IErrorStrategy; import ch.systemsx.cisd.base.unix.FileLinkType; import ch.systemsx.cisd.base.unix.Unix; import ch.systemsx.cisd.base.unix.Unix.Stat; import ch.systemsx.cisd.base.utilities.OSUtilities; import ch.systemsx.cisd.hdf5.IHDF5Reader; /** * An {@Link IArchiveEntryProcessor} that performs a verify operation versus a directory on * the file system. * * @author Bernd Rinn */ class ArchiveEntryVerifyProcessor implements IArchiveEntryProcessor { private final IArchiveEntryVisitor visitor; private final File rootDirectoryOnFS; private final Set filesOnFSOrNull; private final String rootDirectoryInArchive; private final byte[] buffer; private final boolean checkAttributes; private final boolean numeric; ArchiveEntryVerifyProcessor(IArchiveEntryVisitor visitor, File rootDirectoryOnFS, Set filesOnFSOrNull, byte[] buffer, boolean checkAttributes, boolean numeric) { this(visitor, rootDirectoryOnFS, filesOnFSOrNull, "", buffer, checkAttributes, numeric); } ArchiveEntryVerifyProcessor(IArchiveEntryVisitor visitor, File rootDirectoryOnFS, Set filesOnFSOrNull, String rootDirectoryInArchive, byte[] buffer, boolean checkAttributes, boolean numeric) { this.visitor = visitor; this.rootDirectoryOnFS = rootDirectoryOnFS; this.filesOnFSOrNull = filesOnFSOrNull; this.rootDirectoryInArchive = Utils.normalizePath(rootDirectoryInArchive); this.buffer = buffer; this.checkAttributes = checkAttributes; this.numeric = numeric; } @Override public boolean process(String dir, String path, LinkRecord link, IHDF5Reader reader, IdCache idCache, IErrorStrategy errorStrategy) throws IOException { final String errorMessage = checkLink(link, path, idCache); visitor.visit(new ArchiveEntry(dir, path, link, idCache, errorMessage)); if (filesOnFSOrNull != null) { filesOnFSOrNull.remove(new File(rootDirectoryOnFS, path)); } return true; } @Override public void postProcessDirectory(String dir, String path, LinkRecord link, IHDF5Reader reader, IdCache idCache, IErrorStrategy errorStrategy) throws IOException, HDF5Exception { } private String checkLink(LinkRecord link, String path, IdCache idCache) throws IOException { if (rootDirectoryInArchive.length() > 0 && path.startsWith(rootDirectoryInArchive) == false) { return "Object '" + path + "' does not start with path prefix '" + rootDirectoryInArchive + "'."; } final String strippedPath = path.substring(rootDirectoryInArchive.length()); final File f = new File(rootDirectoryOnFS, strippedPath); if (exists(f) == false) { link.setVerifiedType(FileLinkType.OTHER); return "Object '" + strippedPath + "' does not exist on file system."; } final String symbolicLinkOrNull = tryGetSymbolicLink(f); if (symbolicLinkOrNull != null) { link.setVerifiedType(FileLinkType.SYMLINK); if (link.isSymLink() == false) { return "Object '" + strippedPath + "' is a " + link.getLinkType() + " in archive, but a symlink on file system."; } if (symbolicLinkOrNull.equals(link.tryGetLinkTarget()) == false) { return "Symlink '" + strippedPath + "' links to '" + link.tryGetLinkTarget() + "' in archive, but to '" + symbolicLinkOrNull + "' on file system"; } } else if (f.isDirectory()) { link.setVerifiedType(FileLinkType.DIRECTORY); if (link.isDirectory() == false) { if (Unix.isOperational() || OSUtilities.isWindows()) { return "Object '" + strippedPath + "' is a " + link.getLinkType() + " in archive, but a directory on file system."; } else { return "Object '" + strippedPath + "' is a " + link.getLinkType() + " in archive, but a directory on file system (error may be " + "inaccurate because Unix system calls are not available.)"; } } } else { link.setVerifiedType(FileLinkType.REGULAR_FILE); if (link.isDirectory()) { return "Object '" + strippedPath + "' is a directory in archive, but a file on file system."; } if (link.isSymLink()) { if (Unix.isOperational() || OSUtilities.isWindows()) { return "Object '" + strippedPath + "' is a symbolic link in archive, but a file on file system."; } else { return "Object '" + strippedPath + "' is a symbolic link in archive, but a file on file system " + "(error may be inaccurate because Unix system calls are not available.)."; } } final long size = f.length(); final int crc32 = calcCRC32Filesystem(f, buffer); link.setFileVerification(size, crc32, f.lastModified() / Utils.MILLIS_PER_SECOND); if (link.getSize() != size) { return "File '" + f.getAbsolutePath() + "' failed size test, expected: " + link.getSize() + ", found: " + size; } if (link.getSize() > 0 && link.getCrc32() == 0) { return "File '" + f.getAbsolutePath() + "': cannot verify (missing CRC checksum)."; } if (link.getCrc32() != crc32) { return "File '" + f.getAbsolutePath() + "' failed CRC checksum test, expected: " + Utils.crc32ToString(link.getCrc32()) + ", found: " + Utils.crc32ToString(crc32) + "."; } } return checkAttributes ? doFilesystemAttributeCheck(f, idCache, link, numeric) : null; } private static boolean exists(final File f) { if (Unix.isOperational()) { return Unix.tryGetLinkInfo(f.getPath(), false) != null; } else { return f.exists(); } } private static String tryGetSymbolicLink(File f) { if (Unix.isOperational()) { return Unix.getLinkInfo(f.getPath()).tryGetSymbolicLink(); } else { return null; } } private static int calcCRC32Filesystem(File source, byte[] buffer) throws IOException { final InputStream input = FileUtils.openInputStream(source); final CRC32 crc32 = new CRC32(); try { int n = 0; while (-1 != (n = input.read(buffer))) { crc32.update(buffer, 0, n); } } finally { IOUtils.closeQuietly(input); } return (int) crc32.getValue(); } private static String doFilesystemAttributeCheck(File file, IdCache idCache, LinkRecord link, boolean numeric) { final StringBuilder sb = new StringBuilder(); if (link.hasLastModified()) { final long expectedLastModifiedMillis = link.getLastModified() * 1000L; final long foundLastModifiedMillis = file.lastModified(); if (expectedLastModifiedMillis != foundLastModifiedMillis) { sb.append(String.format("'last modified time': (expected: " + "%1$tY-%1$tm-%1$td %1$tH:%1$tM:%1$tS, found: " + "%2$tY-%2$tm-%2$td %2$tH:%2$tM:%2$tS) ", expectedLastModifiedMillis, foundLastModifiedMillis)); } } if (link.hasUnixPermissions() && Unix.isOperational()) { final Stat info = Unix.getLinkInfo(file.getPath(), false); if (link.getPermissions() != info.getPermissions() || link.getLinkType() != info.getLinkType()) { sb.append(String.format("'access permissions': (expected: %s, found: %s) ", Utils .permissionsToString(link.getPermissions(), link.isDirectory(), numeric), Utils.permissionsToString(info.getPermissions(), info.getLinkType() == FileLinkType.DIRECTORY, numeric))); } if (link.getUid() != info.getUid() || link.getGid() != info.getGid()) { sb.append(String.format("'ownerwhip': (expected: %s:%s, found: %s:%s", idCache.getUser(link, numeric), idCache.getGroup(link, numeric), idCache.getUser(info, numeric), idCache.getGroup(info, numeric))); } } if (sb.length() == 0) { return null; } else { return "File '" + file.getAbsolutePath() + "': " + sb.toString(); } } @Override public ArchiverException createException(String objectPath, String detailedMsg) { return new VerifyArchiveException(objectPath, detailedMsg); } @Override public ArchiverException createException(String objectPath, HDF5Exception cause) { return new VerifyArchiveException(objectPath, cause); } @Override public ArchiverException createException(String objectPath, RuntimeException cause) { return new VerifyArchiveException(objectPath, cause); } @Override public ArchiverException createException(File file, IOException cause) { return new VerifyArchiveException(file, cause); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/ArchiverException.java000066400000000000000000000052731256564762100305150ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import java.io.File; import java.io.IOException; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked; /** * Base class of exceptions from the archiver. * * @author Bernd Rinn */ public abstract class ArchiverException extends RuntimeException { private final String fileOrObjectPath; private static final long serialVersionUID = 1L; protected ArchiverException(String objectPath, String operationName, String detailedMsg) { super("Error " + operationName + " object '" + objectPath + "': " + detailedMsg, null); this.fileOrObjectPath = objectPath; } protected ArchiverException(String objectPath, String operationName, HDF5Exception cause) { super("Error " + operationName + " object '" + objectPath + "' [" + cause.getClass().getSimpleName() + "]: " + cause.getMessage(), cause); this.fileOrObjectPath = objectPath; } protected ArchiverException(String objectPath, String operationName, RuntimeException cause) { super("Error " + operationName + " object '" + objectPath + "' [" + cause.getClass().getSimpleName() + "]: " + cause.getMessage(), cause); this.fileOrObjectPath = objectPath; } protected ArchiverException(File file, String operationName, IOExceptionUnchecked cause) { this(file, operationName, cause.getCause()); } protected ArchiverException(File file, String operationName, IOException cause) { super("Error " + operationName + " file '" + file + "' [IO]: " + cause.getMessage(), cause); this.fileOrObjectPath = file.getAbsolutePath(); } protected ArchiverException(String filePath, String operationName, IOException cause) { super("Error " + operationName + " on reading input stream for object '" + filePath + "' [IO]: " + cause.getMessage(), cause); this.fileOrObjectPath = filePath; } public final String getFileOrObjectPath() { return fileOrObjectPath; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/ArchivingException.java000066400000000000000000000031771256564762100306650ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import java.io.File; import java.io.IOException; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; /** * Exception thrown when archiving a file / directory fails. * * @author Bernd Rinn */ public class ArchivingException extends ArchiverException { private static final long serialVersionUID = 1L; private static final String OPERATION_NAME = "archiving"; public ArchivingException(String msg) { super("GENERAL", OPERATION_NAME, msg); } public ArchivingException(String objectPath, HDF5Exception cause) { super(objectPath, OPERATION_NAME, cause); } public ArchivingException(File file, IOException cause) { super(file, OPERATION_NAME, cause); } public ArchivingException(String filePath, IOException cause) { super(filePath, OPERATION_NAME, cause); } public ArchivingException(String objectPath, String detailedMsg) { super(objectPath, OPERATION_NAME, detailedMsg); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/ArchivingStrategy.java000066400000000000000000000260211256564762100305220ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import java.util.ArrayList; import java.util.List; import java.util.regex.Pattern; import ch.systemsx.cisd.hdf5.HDF5GenericStorageFeatures; /** * A class that represents a strategy for excluding files from archiving / extracting and for * compressing files in the archive. * * @author Bernd Rinn */ public class ArchivingStrategy { public enum CompressionStrategy { COMPRESS_NOTHING, COMPRESS_ALL, USE_BLACK_WHITE_LISTS } private List fileWhiteListOrNull; private List fileBlackListOrNull; private List dirWhiteListOrNull; private List dirBlackListOrNull; private List compressionWhiteListOrNull; private List compressionBlackListOrNull; private CompressionStrategy compressionStrategy; private boolean sealed; /** * The default strategy: include everything, compress all files except those * known to be already compressed. */ public static final ArchivingStrategy DEFAULT = new ArchivingStrategy() .addToCompressionBlackList(".*\\.zip").addToCompressionBlackList(".*\\.gz") .addToCompressionBlackList(".*\\.bz2").seal(); /** * An alias for the default strategy (kept for backward compatibility). */ public static final ArchivingStrategy DEFAULT_WITH_COMPRESSION = DEFAULT; /** * The default strategy without compression: include everything, compress nothing. */ public static final ArchivingStrategy DEFAULT_NO_COMPRESSION = new ArchivingStrategy().seal(); public ArchivingStrategy() { this.compressionStrategy = CompressionStrategy.COMPRESS_NOTHING; } public ArchivingStrategy(ArchivingStrategy template) { this.fileWhiteListOrNull = template.fileWhiteListOrNull; this.fileBlackListOrNull = template.fileBlackListOrNull; this.dirWhiteListOrNull = template.dirWhiteListOrNull; this.dirBlackListOrNull = template.dirBlackListOrNull; this.compressionStrategy = template.compressionStrategy; this.compressionWhiteListOrNull = template.compressionWhiteListOrNull; this.compressionBlackListOrNull = template.compressionBlackListOrNull; } private List getOrCreateFileWhiteList() { if (fileWhiteListOrNull == null) { fileWhiteListOrNull = new ArrayList(); } return fileWhiteListOrNull; } private List getOrCreateFileBlackList() { if (fileBlackListOrNull == null) { fileBlackListOrNull = new ArrayList(); } return fileBlackListOrNull; } private List getOrCreateDirWhiteList() { if (dirWhiteListOrNull == null) { dirWhiteListOrNull = new ArrayList(); } return dirWhiteListOrNull; } private List getOrCreateDirBlackList() { if (dirBlackListOrNull == null) { dirBlackListOrNull = new ArrayList(); } return dirBlackListOrNull; } private List getOrCreateCompressionWhiteList() { if (compressionWhiteListOrNull == null) { compressionWhiteListOrNull = new ArrayList(); } return compressionWhiteListOrNull; } private List getOrCreateCompressionBlackList() { if (compressionBlackListOrNull == null) { compressionBlackListOrNull = new ArrayList(); } return compressionBlackListOrNull; } private void checkSealed() { if (sealed) { throw new IllegalStateException("ArchivingStrategy is sealed."); } } /** * Add the given pattern to the whitelist of files to include in archiving. */ public ArchivingStrategy addToFileWhiteList(Pattern pattern) { checkSealed(); getOrCreateFileWhiteList().add(pattern); return this; } /** * Add the given pattern to the whitelist of files to include in archiving. */ public ArchivingStrategy addToFileWhiteList(String pattern) { checkSealed(); getOrCreateFileWhiteList().add(Pattern.compile(pattern)); return this; } /** * Add the given pattern to the blacklist of files to exclude from archiving. */ public ArchivingStrategy addToFileBlackList(Pattern pattern) { checkSealed(); getOrCreateFileBlackList().add(pattern); return this; } /** * Add the given pattern to the blacklist of files to exclude from archiving. */ public ArchivingStrategy addToFileBlackList(String pattern) { checkSealed(); getOrCreateFileBlackList().add(Pattern.compile(pattern)); return this; } /** * Add the given pattern to the whitelist of directories to include in archiving. */ public ArchivingStrategy addToDirWhiteList(Pattern pattern) { checkSealed(); getOrCreateDirWhiteList().add(pattern); return this; } /** * Add the given pattern to the whitelist of directories to include in archiving. */ public ArchivingStrategy addToDirWhiteList(String pattern) { checkSealed(); getOrCreateDirWhiteList().add(Pattern.compile(pattern)); return this; } /** * Add the given pattern to the blacklist of directories to exclude from archiving. */ public ArchivingStrategy addToDirBlackList(Pattern pattern) { checkSealed(); getOrCreateDirBlackList().add(pattern); return this; } /** * Add the given pattern to the blacklist of directories to exclude from archiving. */ public ArchivingStrategy addToDirBlackList(String pattern) { checkSealed(); getOrCreateDirBlackList().add(Pattern.compile(pattern)); return this; } /** * Add the given pattern to the whitelist of files to store compressed in archive. */ public ArchivingStrategy addToCompressionWhiteList(Pattern pattern) { checkSealed(); getOrCreateCompressionWhiteList().add(pattern); compressionStrategy = CompressionStrategy.USE_BLACK_WHITE_LISTS; return this; } /** * Add the given pattern to the whitelist of files to store compressed in archive. */ public ArchivingStrategy addToCompressionWhiteList(String pattern) { checkSealed(); getOrCreateCompressionWhiteList().add(Pattern.compile(pattern)); compressionStrategy = CompressionStrategy.USE_BLACK_WHITE_LISTS; return this; } /** * Add the given pattern to the blacklist of files to store compressed in archive. */ public ArchivingStrategy addToCompressionBlackList(Pattern pattern) { checkSealed(); getOrCreateCompressionBlackList().add(pattern); compressionStrategy = CompressionStrategy.USE_BLACK_WHITE_LISTS; return this; } /** * Add the given pattern to the blacklist of files to store compressed in archive. */ public ArchivingStrategy addToCompressionBlackList(String pattern) { checkSealed(); getOrCreateCompressionBlackList().add(Pattern.compile(pattern)); compressionStrategy = CompressionStrategy.USE_BLACK_WHITE_LISTS; return this; } /** * Seal the strategy. After sealing, all attempts to modify the strategy will throw on * {@link IllegalStateException}. */ public ArchivingStrategy seal() { this.sealed = true; return this; } /** * Returns true if this strategy is sealed. * * @see #seal() */ public boolean isSealed() { return sealed; } /** * Store all files compressed in archive. */ public ArchivingStrategy compressAll() { checkSealed(); this.compressionStrategy = CompressionStrategy.COMPRESS_ALL; return this; } /** * Sets, whether all files should be stored compressed in archive (true) or not ( * false). */ public ArchivingStrategy compressAll(boolean compress) { checkSealed(); this.compressionStrategy = compress ? CompressionStrategy.COMPRESS_ALL : CompressionStrategy.COMPRESS_NOTHING; return this; } /** * @deprecated Use {@link #compressAll(boolean)} instead. */ @Deprecated public final void setCompress(boolean compress) { checkSealed(); this.compressionStrategy = compress ? CompressionStrategy.COMPRESS_ALL : CompressionStrategy.COMPRESS_NOTHING; } boolean doExclude(String path, boolean isDirectory) { if (isDirectory) { return match(dirBlackListOrNull, dirWhiteListOrNull, path) == false; } else { return match(fileBlackListOrNull, fileWhiteListOrNull, path) == false; } } HDF5GenericStorageFeatures getStorageFeatureForPath(String path) { return doCompress(path) ? HDF5GenericStorageFeatures.GENERIC_DEFLATE : HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION; } public boolean doCompress(String path) { switch (compressionStrategy) { case COMPRESS_NOTHING: return false; case COMPRESS_ALL: return true; default: return match(compressionBlackListOrNull, compressionWhiteListOrNull, path); } } public CompressionStrategy getCompressionStrategy() { return compressionStrategy; } private static boolean match(Iterable blackListOrNull, Iterable whiteListOrNull, String path) { if (blackListOrNull != null) { for (Pattern p : blackListOrNull) { if (p.matcher(path).matches()) { return false; } } } if (whiteListOrNull == null) { return true; } for (Pattern p : whiteListOrNull) { if (p.matcher(path).matches()) { return true; } } return false; } }libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/DeleteFromArchiveException.java000066400000000000000000000024611256564762100322760ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import java.io.File; import java.io.IOException; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; /** * Exception thrown when deleting a file / directory in an archive fails. * * @author Bernd Rinn */ public class DeleteFromArchiveException extends ArchiverException { private static final long serialVersionUID = 1L; private static final String OPERATION_NAME = "deleting"; public DeleteFromArchiveException(String objectPath, HDF5Exception cause) { super(objectPath, OPERATION_NAME, cause); } public DeleteFromArchiveException(File file, IOException cause) { super(file, OPERATION_NAME, cause); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/DirectoryIndex.java000066400000000000000000000450431256564762100300260ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import static ch.systemsx.cisd.hdf5.HDF5CompoundMemberMapping.mapping; import java.io.File; import java.io.Flushable; import java.util.Arrays; import java.util.Collection; import java.util.Iterator; import java.util.LinkedHashSet; import java.util.LinkedList; import java.util.List; import java.util.Set; import java.util.zip.CRC32; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ch.systemsx.cisd.base.exceptions.IErrorStrategy; import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked; import ch.systemsx.cisd.base.unix.FileLinkType; import ch.systemsx.cisd.hdf5.CharacterEncoding; import ch.systemsx.cisd.hdf5.HDF5CompoundMemberInformation; import ch.systemsx.cisd.hdf5.HDF5CompoundMemberMapping; import ch.systemsx.cisd.hdf5.HDF5CompoundType; import ch.systemsx.cisd.hdf5.HDF5DataTypeInformation.DataTypeInfoOptions; import ch.systemsx.cisd.hdf5.HDF5EnumerationType; import ch.systemsx.cisd.hdf5.HDF5GenericStorageFeatures; import ch.systemsx.cisd.hdf5.HDF5LinkInformation; import ch.systemsx.cisd.hdf5.IHDF5CompoundInformationRetriever; import ch.systemsx.cisd.hdf5.IHDF5Reader; import ch.systemsx.cisd.hdf5.IHDF5Writer; import ch.systemsx.cisd.hdf5.StringUtils; /** * Memory representation of the directory index stored in an HDF5 archive. *

* Can operate in read-only or read-write mode. The mode is automatically determined by the * hdf5Reader provided the constructor: If this is an instance of {@link IHDF5Writer}, * the directory index will be read-write, otherwise read-only. * * @author Bernd Rinn */ class DirectoryIndex implements IDirectoryIndex { private static final String CRC32_ATTRIBUTE_NAME = "CRC32"; private final IHDF5Reader hdf5Reader; private final IHDF5Writer hdf5WriterOrNull; private final String groupPath; private final IErrorStrategy errorStrategy; private final Set flushables; /** * The list of all links in this directory. *

* The order is to have all directories (in alphabetical order) before all files (in * alphabetical order). */ private LinkStore links; private boolean readLinkTargets; private boolean dirty; /** * Converts an array of {@link File}s into a list of {@link LinkRecord}s. The list is optimized * for iterating through it and removing single entries during the iteration. *

* Note that the length of the list will always be the same as the length of entries. * If some stat call failed on an entry, this entry will be null, so * code using the returned list of this method needs to be prepared that this list may contain * null values! * * @return A list of {@link LinkRecord}s in the same order as entries. */ public static List convertFilesToLinks(File[] files, IErrorStrategy errorStrategy) { final List list = new LinkedList(); for (File file : files) { list.add(LinkRecord.tryCreate(file, errorStrategy)); } return list; } private static HDF5EnumerationType getHDF5LinkTypeEnumeration(IHDF5Reader reader) { return reader.enumeration().getType("linkType", getFileLinkTypeValues()); } private static HDF5CompoundType getHDF5LinkCompoundType(IHDF5Reader reader) { return getHDF5LinkCompoundType(reader, getHDF5LinkTypeEnumeration(reader)); } private static HDF5CompoundType getHDF5LinkCompoundType(IHDF5Reader reader, HDF5EnumerationType hdf5LinkTypeEnumeration) { return reader.compound().getType(LinkRecord.class, getMapping(hdf5LinkTypeEnumeration)); } private static String[] getFileLinkTypeValues() { final FileLinkType[] fileLinkTypes = FileLinkType.values(); final String[] values = new String[fileLinkTypes.length]; for (int i = 0; i < values.length; ++i) { values[i] = fileLinkTypes[i].name(); } return values; } private static HDF5CompoundMemberMapping[] getMapping(HDF5EnumerationType linkEnumerationType) { return new HDF5CompoundMemberMapping[] { mapping("linkNameLength"), mapping("linkType").enumType(linkEnumerationType), mapping("size"), mapping("lastModified"), mapping("uid"), mapping("gid"), mapping("permissions"), mapping("checksum").fieldName("crc32") }; } /** * Creates a new directory (group) index. Note that hdf5Reader needs to be an * instance of {@link IHDF5Writer} if you intend to write the index to the archive. */ DirectoryIndex(IHDF5Reader hdf5Reader, String groupPath, IErrorStrategy errorStrategy, boolean readLinkTargets) { assert hdf5Reader != null; assert groupPath != null; this.hdf5Reader = hdf5Reader; this.hdf5WriterOrNull = (hdf5Reader instanceof IHDF5Writer) ? (IHDF5Writer) hdf5Reader : null; if (hdf5WriterOrNull != null) { hdf5WriterOrNull.file().addFlushable(this); } this.groupPath = (groupPath.length() == 0) ? "/" : groupPath; this.errorStrategy = errorStrategy; this.flushables = new LinkedHashSet(); readIndex(readLinkTargets); } @Override public boolean addFlushable(Flushable flushable) { return flushables.add(flushable); } @Override public boolean removeFlushable(Flushable flushable) { return flushables.remove(flushable); } void flushExternals() { for (Flushable f : flushables) { try { f.flush(); } catch (Exception ex) { System.err.println("External flushable throws an exception:"); ex.printStackTrace(); } } } /** * Amend the index with link targets. If the links targets have already been read, this method * is a noop. */ @Override public void amendLinkTargets() { if (readLinkTargets) { return; } links.amendLinkTargets(hdf5Reader, groupPath); readLinkTargets = true; } private String getIndexDataSetName() { return groupPath + "/" + hdf5Reader.object().toHouseKeepingPath("INDEX"); } private String getIndexNamesDataSetName() { return groupPath + "/" + hdf5Reader.object().toHouseKeepingPath("INDEXNAMES"); } /** * (Re-)Reads the directory index from the archive represented by hdf5Reader. */ private void readIndex(boolean withLinkTargets) { boolean readingH5ArIndexWorked = false; try { if (hdf5Reader.exists(getIndexDataSetName()) && hdf5Reader.exists(getIndexNamesDataSetName())) { final HDF5CompoundType linkCompoundType = getHDF5LinkCompoundType(hdf5Reader); final CRC32 crc32Digester = new CRC32(); final String indexDataSetName = getIndexDataSetName(); final HDF5CompoundMemberInformation[] info = linkCompoundType.getCompoundMemberInformation(DataTypeInfoOptions.MINIMAL); final LinkRecord[] work = hdf5Reader.compound().readArray(indexDataSetName, linkCompoundType, new IHDF5CompoundInformationRetriever.IByteArrayInspector() { @Override public void inspect(byte[] byteArray) { updateCRC32(byteArray, linkCompoundType, info, crc32Digester); } }); int crc32 = (int) crc32Digester.getValue(); int crc32Stored = hdf5Reader.int32().getAttr(indexDataSetName, CRC32_ATTRIBUTE_NAME); if (crc32 != crc32Stored) { if (calcLegacy_14_12_0_Checksum(indexDataSetName, linkCompoundType) != crc32Stored) { throw new ListArchiveException(groupPath, "CRC checksum mismatch on index (links). Expected: " + Utils.crc32ToString(crc32Stored) + ", found: " + Utils.crc32ToString(crc32)); } } final String indexNamesDataSetName = getIndexNamesDataSetName(); final String concatenatedNames = hdf5Reader.readString(indexNamesDataSetName); crc32 = calcCrc32(concatenatedNames); crc32Stored = hdf5Reader.int32().getAttr(indexNamesDataSetName, CRC32_ATTRIBUTE_NAME); if (crc32 != crc32Stored) { throw new ListArchiveException(groupPath, "CRC checksum mismatch on index (names). Expected: " + Utils.crc32ToString(crc32Stored) + ", found: " + Utils.crc32ToString(crc32)); } initLinks(work, concatenatedNames, withLinkTargets); links = new LinkStore(work); readingH5ArIndexWorked = true; } } catch (RuntimeException ex) { errorStrategy.dealWithError(new ListArchiveException(groupPath, ex)); } // Fallback: couldn't read the index, reconstructing it from the group information. if (readingH5ArIndexWorked == false) { if (hdf5Reader.object().isGroup(groupPath, false)) { final List hdf5LinkInfos = hdf5Reader.object().getGroupMemberInformation(groupPath, withLinkTargets); final LinkRecord[] work = new LinkRecord[hdf5LinkInfos.size()]; int idx = 0; for (HDF5LinkInformation linfo : hdf5LinkInfos) { final long size = linfo.isDataSet() ? hdf5Reader.object().getSize(linfo.getPath()) : Utils.UNKNOWN; work[idx++] = new LinkRecord(linfo, size); } Arrays.sort(work); links = new LinkStore(work); } else { links = new LinkStore(); } } readLinkTargets = withLinkTargets; dirty = false; } private int calcLegacy_14_12_0_Checksum(final String indexDataSetName, final HDF5CompoundType linkCompoundType) { final CRC32 crc32Digester = new CRC32(); hdf5Reader.compound().readArray(indexDataSetName, linkCompoundType, new IHDF5CompoundInformationRetriever.IByteArrayInspector() { @Override public void inspect(byte[] byteArray) { crc32Digester.update(byteArray); } }); return (int) crc32Digester.getValue(); } private void initLinks(final LinkRecord[] work, final String concatenatedNames, boolean withLinkTargets) { int namePos = 0; for (LinkRecord link : work) { namePos = link.initAfterReading(concatenatedNames, namePos, hdf5Reader, groupPath, withLinkTargets); } } @Override public boolean exists(String name) { return links.exists(name); } @Override public boolean isDirectory(String name) { final LinkRecord link = links.tryGetLink(name); return (link != null) && link.isDirectory(); } /** * Returns the link with {@link LinkRecord#getLinkName()} equal to name, or * null, if there is no such link in the directory index. */ @Override public LinkRecord tryGetLink(String name) { final LinkRecord linkOrNull = links.tryGetLink(name); if (linkOrNull != null) { linkOrNull.resetVerification(); } return linkOrNull; } /** * Returns true, if this class has link targets read. */ @Override public boolean hasLinkTargets() { return readLinkTargets; } // // Iterable // @Override public Iterator iterator() { return links.iterator(); } // // Writing methods // /** * Writes the directory index to the archive represented by hdf5Writer. *

* Works on the list data structure. */ @Override public void flush() { flushExternals(); if (dirty == false) { return; } ensureWriteMode(); try { final StringBuilder concatenatedNames = new StringBuilder(); for (LinkRecord link : links) { link.prepareForWriting(concatenatedNames); } final String indexNamesDataSetName = getIndexNamesDataSetName(); final String concatenatedNamesStr = concatenatedNames.toString(); hdf5WriterOrNull.string().write(indexNamesDataSetName, concatenatedNamesStr, HDF5GenericStorageFeatures.GENERIC_DEFLATE); hdf5WriterOrNull.int32().setAttr(indexNamesDataSetName, CRC32_ATTRIBUTE_NAME, calcCrc32(concatenatedNamesStr)); final String indexDataSetName = getIndexDataSetName(); final CRC32 crc32Digester = new CRC32(); final HDF5CompoundType linkCompoundType = getHDF5LinkCompoundType(hdf5WriterOrNull); final HDF5CompoundMemberInformation[] info = linkCompoundType.getCompoundMemberInformation(DataTypeInfoOptions.MINIMAL); hdf5WriterOrNull.compound().writeArray(indexDataSetName, linkCompoundType, links.getLinkArray(), HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION, new IHDF5CompoundInformationRetriever.IByteArrayInspector() { @Override public void inspect(byte[] byteArray) { updateCRC32(byteArray, linkCompoundType, info, crc32Digester); } }); hdf5WriterOrNull.int32().setAttr(indexDataSetName, CRC32_ATTRIBUTE_NAME, (int) crc32Digester.getValue()); } catch (HDF5Exception ex) { errorStrategy.dealWithError(new ListArchiveException(groupPath, ex)); } dirty = false; } /** * Add entries to the index. Any link that already exists in the index will be * replaced. */ @Override public void updateIndex(LinkRecord[] entries) { ensureWriteMode(); links.update(entries); dirty = true; } /** * Add entries to the index. Any link that already exists in the index will be * replaced. */ @Override public void updateIndex(Collection entries) { ensureWriteMode(); links.update(entries); dirty = true; } /** * Add entry to the index. If it already exists in the index, it will be replaced. */ @Override public void updateIndex(LinkRecord entry) { ensureWriteMode(); links.update(entry); dirty = true; } /** * Removes linkName from the index, if it is in. * * @return true, if linkName was removed. */ @Override public boolean remove(String linkName) { ensureWriteMode(); final boolean storeChanged = links.remove(linkName); dirty |= storeChanged; return storeChanged; } private void ensureWriteMode() { if (hdf5WriterOrNull == null) { throw new IllegalStateException("Cannot write index in read-only mode."); } } private int calcCrc32(String names) { final CRC32 crc32 = new CRC32(); crc32.update(StringUtils.toBytes0Term(names, names.length(), CharacterEncoding.UTF8)); return (int) crc32.getValue(); } private void updateCRC32(byte[] byteArray, final HDF5CompoundType linkCompoundType, final HDF5CompoundMemberInformation[] info, final CRC32 crc32Digester) { final int numberOfRecords = byteArray.length / linkCompoundType.getRecordSizeInMemory(); for (int i = 0; i < numberOfRecords; ++i) { final int recordOfs = i * linkCompoundType.getRecordSizeInMemory(); for (int j = 0; j < info.length; ++j) { final int ofs = recordOfs + info[j].getOffsetInMemory(); final int diskOfs = info[j].getOffsetOnDisk(); final int nextDiskOfs = (j + 1 < info.length) ? info[j + 1].getOffsetOnDisk() : linkCompoundType .getRecordSizeOnDisk(); final int sizeOnDisk = nextDiskOfs - diskOfs; crc32Digester.update(byteArray, ofs, sizeOnDisk); } } } // // Closeable // @Override public void close() throws IOExceptionUnchecked { flush(); if (hdf5WriterOrNull != null) { hdf5WriterOrNull.file().removeFlushable(this); } flushables.clear(); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/DirectoryIndexProvider.java000066400000000000000000000051301256564762100315320ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import java.util.HashMap; import java.util.Map; import ch.systemsx.cisd.base.exceptions.IErrorStrategy; import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked; import ch.systemsx.cisd.hdf5.IHDF5Reader; /** * A provider for {@link DirectoryIndex} objects. * * @author Bernd Rinn */ class DirectoryIndexProvider implements IDirectoryIndexProvider { private final Map cacheMap = new HashMap(); private final IHDF5Reader reader; private final IErrorStrategy errorStrategy; DirectoryIndexProvider(IHDF5Reader reader, IErrorStrategy errorStrategy) { this.reader = reader; this.errorStrategy = errorStrategy; } @Override public synchronized IDirectoryIndex get(String normalizedGroupPath, boolean withLinkTargets) { final String nonEmptyGroupPath = (normalizedGroupPath.length() == 0) ? "/" : normalizedGroupPath; DirectoryIndex index = cacheMap.get(nonEmptyGroupPath); if (index == null) { index = new DirectoryIndex(reader, nonEmptyGroupPath, errorStrategy, withLinkTargets); cacheMap.put(nonEmptyGroupPath, index); } else if (withLinkTargets) { index.amendLinkTargets(); } return index; } @Override public IErrorStrategy getErrorStrategy() { return errorStrategy; } @Override public synchronized void close() throws IOExceptionUnchecked { IOExceptionUnchecked exeptionOrNull = null; for (DirectoryIndex index : cacheMap.values()) { try { index.close(); } catch (IOExceptionUnchecked ex) { if (exeptionOrNull == null) { exeptionOrNull = ex; } } } if (exeptionOrNull != null) { throw exeptionOrNull; } } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/DirectoryIndexUpdater.java000066400000000000000000000064771256564762100313630ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import java.io.File; import ch.systemsx.cisd.base.exceptions.IErrorStrategy; import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked; /** * A class to update the {@link DirectoryIndex} from files on the filesystem. * * @author Bernd Rinn */ final class DirectoryIndexUpdater { private final IDirectoryIndexProvider indexProvider; private final IErrorStrategy errorStrategy; DirectoryIndexUpdater(IDirectoryIndexProvider indexProvider) { this.indexProvider = indexProvider; this.errorStrategy = indexProvider.getErrorStrategy(); } void updateIndicesOnThePath(String rootDir, File path, int crc32, boolean immediateGroupOnly) throws IOExceptionUnchecked { String groupPath = rootDir.endsWith("/") ? rootDir.substring(0, rootDir.length() - 1) : rootDir; final IDirectoryIndex index = indexProvider.get(groupPath, false); final LinkRecord linkOrNull = LinkRecord.tryCreate(path, errorStrategy); if (linkOrNull == null) { throw new IOExceptionUnchecked("Cannot get link information for path '" + path + "'."); } linkOrNull.setCrc32(crc32); index.updateIndex(linkOrNull); if (immediateGroupOnly == false) { final String pathPrefixOnFSOrNull = tryGetPathPrefix(groupPath, path.getAbsolutePath()); String groupName = Utils.getName(groupPath); groupPath = Utils.getParentPath(groupPath); while (groupName.length() > 0) { updateIndex(pathPrefixOnFSOrNull, groupPath, groupName); groupName = Utils.getName(groupPath); groupPath = Utils.getParentPath(groupPath); } } } private void updateIndex(String pathPrefixOnFSOrNull, String groupPath, String groupName) { final IDirectoryIndex index = indexProvider.get(groupPath, false); if (pathPrefixOnFSOrNull == null) { index.updateIndex(new LinkRecord(groupName)); } else { final File groupPathFile = new File(pathPrefixOnFSOrNull, groupName); index.updateIndex(LinkRecord.tryCreate(groupPathFile, errorStrategy)); } } private String tryGetPathPrefix(String root, String filePath) { final String parentPath = Utils.getParentPath(filePath); if (parentPath.endsWith(root) == false) { return null; } final String pathPrefix = parentPath.substring(0, parentPath.length() - root.length()); if (pathPrefix.length() == 0) { return "/"; } else { return pathPrefix; } } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/GroupCache.java000066400000000000000000000037651256564762100271170ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import java.util.HashMap; import java.util.Map; import org.apache.commons.lang.ArrayUtils; import ch.systemsx.cisd.base.unix.Unix; import ch.systemsx.cisd.base.unix.Unix.Group; import ch.systemsx.cisd.base.unix.Unix.Password; /** * Cache for group affiliations of the current user. * * @author Bernd RInn */ class GroupCache { private final Password userOrNull; /** Gid -> Is user member? */ private final Map gidMap = new HashMap(); GroupCache() { this.userOrNull = Unix.isOperational() ? Unix.tryGetUserByUid(Unix.getUid()) : null; } boolean isUserInGroup(int gid) { if (userOrNull == null) { return false; } final Boolean cached = gidMap.get(gid); if (cached != null) { return cached; } final Group groupOrNull = Unix.tryGetGroupByGid(gid); if (groupOrNull != null) { final int idx = ArrayUtils.indexOf(groupOrNull.getGroupMembers(), userOrNull.getUserName()); final Boolean found = idx != ArrayUtils.INDEX_NOT_FOUND ? Boolean.TRUE : Boolean.FALSE; gidMap.put(gid, found); return found; } else { gidMap.put(gid, Boolean.FALSE); return false; } } }libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/HDF5ArchiveDeleter.java000066400000000000000000000051101256564762100303560ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import java.util.List; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ch.systemsx.cisd.hdf5.IHDF5Writer; /** * A class to delete paths from an h5ar archives. * * @author Bernd Rinn */ class HDF5ArchiveDeleter { private final IHDF5Writer hdf5Writer; private final IDirectoryIndexProvider indexProvider; private final IdCache idCache; public HDF5ArchiveDeleter(IHDF5Writer hdf5Writer, IDirectoryIndexProvider indexProvider, IdCache idCache) { this.hdf5Writer = hdf5Writer; this.indexProvider = indexProvider; this.idCache = idCache; } public HDF5ArchiveDeleter delete(List hdf5ObjectPaths, IArchiveEntryVisitor entryVisitorOrNull) { for (String path : hdf5ObjectPaths) { final String normalizedPath = Utils.normalizePath(path); final String group = Utils.getParentPath(normalizedPath); final IDirectoryIndex index = indexProvider.get(group, false); try { final String name = Utils.getName(normalizedPath); LinkRecord link = index.tryGetLink(name); if (link == null) { link = LinkRecord.tryReadFromArchive(hdf5Writer, normalizedPath); } if (link != null) { hdf5Writer.delete(normalizedPath); index.remove(name); if (entryVisitorOrNull != null) { final ArchiveEntry entry = new ArchiveEntry(group, normalizedPath, link, idCache); entryVisitorOrNull.visit(entry); } } } catch (HDF5Exception ex) { indexProvider.getErrorStrategy().dealWithError( new DeleteFromArchiveException(path, ex)); } } return this; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/HDF5ArchiveTraverser.java000066400000000000000000000152421256564762100307560ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import java.io.File; import java.io.IOException; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ch.systemsx.cisd.base.exceptions.IErrorStrategy; import ch.systemsx.cisd.hdf5.IHDF5Reader; /** * A traverser for h5ar archives. * * @author Bernd Rinn */ class HDF5ArchiveTraverser { interface IDirectoryChecker { boolean isDirectoryFollowSymlinks(ArchiveEntry entry); } private final IHDF5Reader hdf5Reader; private final IDirectoryIndexProvider indexProvider; private final IErrorStrategy errorStrategy; private final IdCache idCache; private final IDirectoryChecker directoryChecker; public HDF5ArchiveTraverser(IDirectoryChecker directoryChecker, IHDF5Reader hdf5Reader, IDirectoryIndexProvider indexProvider, IdCache idCache) { this.directoryChecker = directoryChecker; this.hdf5Reader = hdf5Reader; this.indexProvider = indexProvider; this.errorStrategy = indexProvider.getErrorStrategy(); this.idCache = idCache; } public void process(String fileOrDir, boolean recursive, boolean readLinkTargets, boolean followSymlinks, IArchiveEntryProcessor processor) { final String normalizedPath = Utils.normalizePath(fileOrDir); final boolean isDirectory = hdf5Reader.object().isGroup(normalizedPath, followSymlinks); final boolean effectiveReadLinkTargets = readLinkTargets | followSymlinks; final String parentPath = Utils.getParentPath(normalizedPath); LinkRecord link = null; if (parentPath.length() > 0) { link = indexProvider.get(parentPath, effectiveReadLinkTargets).tryGetLink( getNameFromPath(normalizedPath, parentPath)); if (link == null) { errorStrategy.dealWithError(processor.createException(normalizedPath, "Object not found in archive.")); return; } try { if (processor.process(parentPath, normalizedPath, link, hdf5Reader, idCache, errorStrategy) == false) { return; } } catch (IOException ex) { final File f = new File(normalizedPath); errorStrategy.dealWithError(processor.createException(f, ex)); } catch (HDF5Exception ex) { errorStrategy.dealWithError(processor.createException(normalizedPath, ex)); } } if (isDirectory) { processDirectory(normalizedPath, recursive, effectiveReadLinkTargets, followSymlinks, processor); postProcessDirectory(parentPath, normalizedPath, link, processor); } } private String getNameFromPath(final String normalizedPath, final String parentPath) { return normalizedPath.substring(parentPath.length() == 1 ? 1 : parentPath.length() + 1); } private void postProcessDirectory(final String parentPath, final String normalizedPath, LinkRecord linkOrNull, IArchiveEntryProcessor processor) { if (linkOrNull != null) { try { processor.postProcessDirectory(parentPath, normalizedPath, linkOrNull, hdf5Reader, idCache, errorStrategy); } catch (IOException ex) { final File f = new File(normalizedPath); errorStrategy.dealWithError(processor.createException(f, ex)); } catch (HDF5Exception ex) { errorStrategy.dealWithError(processor.createException(normalizedPath, ex)); } } } /** * Provide the entries of normalizedDir to processor. */ private void processDirectory(String normalizedDir, boolean recursive, boolean readLinkTargets, boolean followSymlinks, IArchiveEntryProcessor processor) { if (hdf5Reader.object().exists(normalizedDir, followSymlinks) == false) { if (hdf5Reader.object().exists(normalizedDir, false) == false) { errorStrategy.dealWithError(processor.createException(normalizedDir, "Directory not found in archive.")); } return; } for (LinkRecord link : indexProvider.get(normalizedDir, readLinkTargets)) { final String path = Utils.concatLink(normalizedDir, link.getLinkName()); try { if (processor .process(normalizedDir, path, link, hdf5Reader, idCache, errorStrategy) == false) { continue; } if (recursive && isDirectory(path, link, followSymlinks)) { processDirectory(path, recursive, readLinkTargets, followSymlinks, processor); postProcessDirectory(normalizedDir, path, link, processor); } } catch (IOException ex) { final File f = new File(path); errorStrategy.dealWithError(processor.createException(f, ex)); } catch (HDF5Exception ex) { errorStrategy.dealWithError(processor.createException(path, ex)); } } } private boolean isDirectory(String path, LinkRecord link, boolean followSymlinks) { if (link.isDirectory() == false && followSymlinks) { return directoryChecker.isDirectoryFollowSymlinks(toArchiveEntry(path, link)); } else { return link.isDirectory(); } } private ArchiveEntry toArchiveEntry(String path, LinkRecord linkRecord) { final String normalizedPath = Utils.normalizePath(path); final String parentPath = Utils.getParentPath(normalizedPath); return Utils.tryToArchiveEntry(parentPath, normalizedPath, linkRecord, idCache); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/HDF5ArchiveUpdater.java000066400000000000000000000653751256564762100304210ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import java.io.File; import java.io.Flushable; import java.io.IOException; import java.io.InputStream; import java.util.Iterator; import java.util.List; import java.util.zip.CRC32; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import org.apache.commons.io.FileUtils; import org.apache.commons.io.FilenameUtils; import org.apache.commons.io.IOUtils; import ch.systemsx.cisd.base.exceptions.IErrorStrategy; import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked; import ch.systemsx.cisd.base.io.IOutputStream; import ch.systemsx.cisd.base.unix.FileLinkType; import ch.systemsx.cisd.hdf5.HDF5GenericStorageFeatures; import ch.systemsx.cisd.hdf5.HDF5OpaqueType; import ch.systemsx.cisd.hdf5.IHDF5Writer; import ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator.FileFormat; import ch.systemsx.cisd.hdf5.io.HDF5IOAdapterFactory; /** * A class to create or update h5ar archives. * * @author Bernd Rinn */ class HDF5ArchiveUpdater { private static final String OPAQUE_TAG_FILE = "FILE"; private static final int SIZEHINT_FACTOR = 5; private static final int MIN_GROUP_MEMBER_COUNT_TO_COMPUTE_SIZEHINT = 100; private static final int SMALL_DATASET_LIMIT = 4096; private final IHDF5Writer hdf5Writer; private final IDirectoryIndexProvider indexProvider; private final IErrorStrategy errorStrategy; private final DirectoryIndexUpdater indexUpdater; private final IdCache idCache; private final byte[] buffer; static class DataSetInfo { final long size; final int crc32; DataSetInfo(long size, int crc32) { this.size = size; this.crc32 = crc32; } } private final class H5ARIOutputStream implements IOutputStream, Flushable { private final IOutputStream delegate; private final String directory; private final String path; private final LinkRecord link; private final CRC32 crc32 = new CRC32(); private long size = 0; H5ARIOutputStream(String normalizedDirectory, LinkRecord link, int chunkSize, boolean compress) { this.directory = normalizedDirectory; this.path = Utils.concatLink(this.directory, link.getLinkName()); this.link = link; final HDF5GenericStorageFeatures creationStorageFeature = compress ? HDF5GenericStorageFeatures.GENERIC_DEFLATE : HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION; this.delegate = HDF5IOAdapterFactory.asIOutputStream(hdf5Writer, path, creationStorageFeature, getEffectiveChunkSize(chunkSize), OPAQUE_TAG_FILE); indexProvider.get(normalizedDirectory, false).addFlushable(this); } @Override public void write(int b) throws IOExceptionUnchecked { crc32.update(b); ++size; delegate.write(b); } @Override public void write(byte[] b) throws IOExceptionUnchecked { crc32.update(b); size += b.length; delegate.write(b); } @Override public void write(byte[] b, int off, int len) throws IOExceptionUnchecked { crc32.update(b, off, len); size += len; delegate.write(b, off, len); } @Override public void flush() throws IOExceptionUnchecked { link.setCrc32((int) crc32.getValue()); link.setSize(size); final boolean updateImmediateGroupOnly = hdf5Writer.isGroup(directory); updateIndicesOnThePath(path, link, updateImmediateGroupOnly); delegate.flush(); } @Override public void synchronize() throws IOExceptionUnchecked { delegate.synchronize(); } @Override public void close() throws IOExceptionUnchecked { flush(); delegate.close(); indexProvider.get(path, false).removeFlushable(this); } } public HDF5ArchiveUpdater(IHDF5Writer hdf5Writer, IDirectoryIndexProvider indexProvider, IdCache idCache, byte[] buffer) { this.hdf5Writer = hdf5Writer; this.indexProvider = indexProvider; this.idCache = idCache; this.errorStrategy = indexProvider.getErrorStrategy(); this.indexUpdater = new DirectoryIndexUpdater(indexProvider); this.buffer = buffer; } public HDF5ArchiveUpdater archive(File path, ArchivingStrategy strategy, int chunkSize, boolean keepNameFromPath, IArchiveEntryVisitor entryVisitorOrNull) { final File absolutePath = Utils.normalizePath(path); return archive(keepNameFromPath ? absolutePath.getParentFile() : absolutePath, absolutePath, strategy, chunkSize, entryVisitorOrNull); } public IOutputStream archiveFile(String directory, LinkRecord link, boolean compress, int chunkSize) { if (link.getLinkType() != FileLinkType.REGULAR_FILE) { errorStrategy.dealWithError(new ArchivingException("A regular file is expected here.")); } return new H5ARIOutputStream(Utils.normalizePath(directory), link, chunkSize, compress); } public HDF5ArchiveUpdater archive(String directory, LinkRecord link, InputStream inputOrNull, boolean compress, int chunkSize) { boolean ok = true; final String normalizedDir = Utils.normalizePath(directory); final String hdf5ObjectPath = Utils.concatLink(normalizedDir, link.getLinkName()); final ArchiveEntry entry = new ArchiveEntry(normalizedDir, hdf5ObjectPath, link, idCache); final boolean groupExists = hdf5Writer.isGroup(normalizedDir); if (link.getLinkType() == FileLinkType.DIRECTORY) { if (inputOrNull == null) { ok = archiveEmptyDirectory(normalizedDir, link); } else { errorStrategy.dealWithError(new ArchivingException( "Cannot take InputStream when archiving a directory.")); } } else if (link.getLinkType() == FileLinkType.SYMLINK) { if (inputOrNull == null) { ok = archiveSymLink(entry); } else { errorStrategy.dealWithError(new ArchivingException( "Cannot take InputStream when archiving a symlink.")); } } else if (link.getLinkType() == FileLinkType.REGULAR_FILE) { if (inputOrNull != null) { final HDF5GenericStorageFeatures compression = compress ? HDF5GenericStorageFeatures.GENERIC_DEFLATE : HDF5GenericStorageFeatures.GENERIC_NO_COMPRESSION; try { final DataSetInfo info = copyToHDF5(inputOrNull, hdf5ObjectPath, compression, chunkSize); link.setCrc32(info.crc32); link.setSize(info.size); } catch (IOException ex) { ok = false; errorStrategy.dealWithError(new ArchivingException(hdf5ObjectPath, ex)); } catch (HDF5Exception ex) { ok = false; errorStrategy.dealWithError(new ArchivingException(hdf5ObjectPath, ex)); } } else { errorStrategy.dealWithError(new ArchivingException( "Need to have InputStream when archiving a regular file.")); } } else { errorStrategy.dealWithError(new ArchivingException( "Don't know how to archive file link type " + link.getLinkType())); ok = false; } if (ok) { updateIndicesOnThePath(hdf5ObjectPath, link, groupExists); } return this; } public HDF5ArchiveUpdater archive(String rootDirInArchive, File path, ArchivingStrategy strategy, int chunkSize, IArchiveEntryVisitor entryVisitorOrNull) { final File absolutePath = Utils.normalizePath(path); final String normalizedRootDirInArchive = Utils.normalizePath(rootDirInArchive); final String hdf5ObjectPath = Utils.concatLink(normalizedRootDirInArchive, absolutePath.getName()); final String hdf5GroupPath = Utils.getParentPath(hdf5ObjectPath); final boolean groupExists = hdf5Writer.isGroup(hdf5GroupPath); final boolean ok; int crc32 = 0; final LinkRecord linkOrNull = LinkRecord.tryCreate(absolutePath, errorStrategy); if (linkOrNull == null) { return this; } final ArchiveEntry entry = new ArchiveEntry(normalizedRootDirInArchive, hdf5ObjectPath, linkOrNull, idCache); if (linkOrNull.isSymLink()) { ok = archiveSymLink(entry, absolutePath, entryVisitorOrNull); } else if (absolutePath.isDirectory()) { ok = archiveDirectory(absolutePath, entry, strategy, chunkSize, entryVisitorOrNull); } else if (absolutePath.isFile()) { final DataSetInfo dataSetInfoOrNull = tryArchiveFile(absolutePath, entry, strategy.getStorageFeatureForPath(hdf5ObjectPath), chunkSize, entryVisitorOrNull); ok = (dataSetInfoOrNull != null); if (dataSetInfoOrNull != null) { crc32 = dataSetInfoOrNull.crc32; } } else { ok = false; errorStrategy.dealWithError(new ArchivingException(absolutePath, new IOException( "Path corresponds to neither a file nor a directory."))); } if (ok) { indexUpdater.updateIndicesOnThePath(normalizedRootDirInArchive, absolutePath, crc32, groupExists); } return this; } public HDF5ArchiveUpdater archiveBelow(String rootDirInArchive, File directory, ArchivingStrategy strategy, int chunkSize, IArchiveEntryVisitor entryVisitorOrNull) { final File absoluteDirectory = Utils.normalizePath(directory); if (absoluteDirectory.isDirectory()) { final LinkRecord linkOrNull = LinkRecord.tryCreate(absoluteDirectory, errorStrategy); if (linkOrNull == null) { return this; } final String normalizedRootDirInArchive = Utils.normalizePath(rootDirInArchive); final ArchiveEntry dirEntry = new ArchiveEntry(null, normalizedRootDirInArchive, linkOrNull, idCache); archiveDirectory(absoluteDirectory, dirEntry, strategy, chunkSize, entryVisitorOrNull); } else { errorStrategy.dealWithError(new ArchivingException(absoluteDirectory, new IOException( "Path does not correspond to a directory."))); } return this; } public HDF5ArchiveUpdater archive(File parentDirToStrip, File path, ArchivingStrategy strategy, int chunkSize, IArchiveEntryVisitor entryVisitorOrNull) { final File absoluteParentDirToStrip = Utils.normalizePath(parentDirToStrip); final File absolutePath = Utils.normalizePath(path); final String hdf5ObjectPath = getRelativePath(absoluteParentDirToStrip, absolutePath); final String hdf5GroupPath = Utils.getParentPath(hdf5ObjectPath); final boolean groupExists = (hdf5GroupPath.length() == 0) ? true : hdf5Writer.isGroup(hdf5GroupPath); final boolean ok; int crc32 = 0; final LinkRecord linkOrNull = LinkRecord.tryCreate(absolutePath, errorStrategy); final ArchiveEntry entry = new ArchiveEntry(hdf5GroupPath, hdf5ObjectPath, linkOrNull, idCache); if (linkOrNull != null && linkOrNull.isSymLink()) { ok = archiveSymLink(entry, absolutePath, entryVisitorOrNull); } else if (absolutePath.isDirectory()) { ok = archiveDirectory(absolutePath, entry, strategy, chunkSize, entryVisitorOrNull); } else if (absolutePath.isFile()) { final DataSetInfo dataSetInfoOrNull = tryArchiveFile(absolutePath, entry, strategy.getStorageFeatureForPath(hdf5ObjectPath), chunkSize, entryVisitorOrNull); ok = (dataSetInfoOrNull != null); if (dataSetInfoOrNull != null) { crc32 = dataSetInfoOrNull.crc32; } } else { ok = false; errorStrategy.dealWithError(new ArchivingException(absolutePath, new IOException( "Path corresponds to neither a file nor a directory."))); } if (ok) { updateIndicesOnThePath(absoluteParentDirToStrip, absolutePath, crc32, groupExists); } return this; } private void updateIndicesOnThePath(File parentDirToStrip, File path, int crc32, boolean immediateGroupOnly) { final String rootAbsolute = parentDirToStrip.getAbsolutePath(); File pathProcessing = path; int crc32Processing = crc32; while (true) { File dirProcessingOrNull = pathProcessing.getParentFile(); String dirAbsolute = (dirProcessingOrNull != null) ? dirProcessingOrNull.getAbsolutePath() : ""; if (dirProcessingOrNull == null || dirAbsolute.startsWith(rootAbsolute) == false) { break; } final String hdf5GroupPath = getRelativePath(rootAbsolute, dirAbsolute); final IDirectoryIndex index = indexProvider.get(hdf5GroupPath, false); final LinkRecord linkOrNull = LinkRecord.tryCreate(pathProcessing, errorStrategy); if (linkOrNull != null) { linkOrNull.setCrc32(crc32Processing); crc32Processing = 0; // Directories don't have a checksum index.updateIndex(linkOrNull); } pathProcessing = dirProcessingOrNull; if (immediateGroupOnly) { break; } } } private void updateIndicesOnThePath(String path, LinkRecord link, boolean immediateGroupOnly) { String pathProcessing = Utils.normalizePath(path); if ("/".equals(pathProcessing)) { return; } int crc32 = link.getCrc32(); long size = link.getSize(); long lastModified = link.getLastModified(); short permissions = link.getPermissions(); int uid = link.getUid(); int gid = link.getGid(); FileLinkType fileLinkType = link.getLinkType(); String linkTargetOrNull = link.tryGetLinkTarget(); while (true) { final String hdf5GroupPath = Utils.getParentPath(pathProcessing); final IDirectoryIndex index = indexProvider.get(hdf5GroupPath, false); final String hdf5FileName = Utils.getName(pathProcessing); final LinkRecord linkProcessing = new LinkRecord(hdf5FileName, linkTargetOrNull, fileLinkType, size, lastModified, uid, gid, permissions, crc32); index.updateIndex(linkProcessing); fileLinkType = FileLinkType.DIRECTORY; crc32 = 0; // Directories don't have a checksum size = Utils.UNKNOWN; // Directories don't have a size linkTargetOrNull = null; // Directories don't have a link target pathProcessing = hdf5GroupPath; if (immediateGroupOnly || "/".equals(pathProcessing)) { break; } } } private boolean archiveEmptyDirectory(String parentDirectory, LinkRecord link) { final String hdf5GroupPath = Utils.concatLink(parentDirectory, link.getLinkName()); try { hdf5Writer.object().createGroup(hdf5GroupPath); return true; } catch (HDF5Exception ex) { errorStrategy.dealWithError(new ArchivingException(hdf5GroupPath, ex)); return false; } } private boolean archiveDirectory(File dir, ArchiveEntry dirEntry, ArchivingStrategy strategy, int chunkSize, IArchiveEntryVisitor entryVisitorOrNull) { final File[] fileEntries = dir.listFiles(); if (fileEntries == null) { errorStrategy.dealWithError(new ArchivingException(dir, new IOException( "Cannot read directory"))); return false; } final String hdf5GroupPath = dirEntry.getPath(); if ("/".equals(hdf5GroupPath) == false) try { if (hdf5Writer.file().getFileFormat() != FileFormat.STRICTLY_1_8 && fileEntries.length > MIN_GROUP_MEMBER_COUNT_TO_COMPUTE_SIZEHINT) { // Compute size hint and pre-create group in order to improve performance. int totalLength = computeSizeHint(fileEntries); hdf5Writer.object().createGroup(hdf5GroupPath, totalLength * SIZEHINT_FACTOR); } else { hdf5Writer.object().createGroup(hdf5GroupPath); } } catch (HDF5Exception ex) { errorStrategy.dealWithError(new ArchivingException(hdf5GroupPath, ex)); } final List linkEntries = DirectoryIndex.convertFilesToLinks(fileEntries, errorStrategy); if (entryVisitorOrNull != null) { entryVisitorOrNull.visit(dirEntry); } final Iterator linkIt = linkEntries.iterator(); for (int i = 0; i < fileEntries.length; ++i) { final File file = fileEntries[i]; final LinkRecord link = linkIt.next(); if (link == null) { linkIt.remove(); continue; } final String absoluteEntry = file.getAbsolutePath(); final ArchiveEntry entry = new ArchiveEntry(hdf5GroupPath, Utils.concatLink(hdf5GroupPath, link.getLinkName()), link, idCache); if (entry.isDirectory()) { if (strategy.doExclude(absoluteEntry, true)) { linkIt.remove(); continue; } final boolean ok = archiveDirectory(file, entry, strategy, chunkSize, entryVisitorOrNull); if (ok == false) { linkIt.remove(); } } else { if (strategy.doExclude(absoluteEntry, false)) { linkIt.remove(); continue; } if (entry.isSymLink()) { final boolean ok = archiveSymLink(entry, file, entryVisitorOrNull); if (ok == false) { linkIt.remove(); } } else if (entry.isRegularFile()) { final DataSetInfo dataSetInfoOrNull = tryArchiveFile(file, entry, strategy.getStorageFeatureForPath(entry.getPath()), chunkSize, entryVisitorOrNull); if (dataSetInfoOrNull == null) { linkIt.remove(); } else { link.setSize(dataSetInfoOrNull.size); link.setCrc32(dataSetInfoOrNull.crc32); } } else { errorStrategy.dealWithError(new ArchivingException(file, new IOException( "Path corresponds to neither a file nor a directory."))); } } } final boolean verbose = (entryVisitorOrNull != null); final IDirectoryIndex index = indexProvider.get(hdf5GroupPath, verbose); index.updateIndex(linkEntries); return true; } private boolean archiveSymLink(ArchiveEntry entry) { if (entry.hasLinkTarget() == false) { errorStrategy.dealWithError(new ArchivingException(entry.getName(), new IOException( "Link target not given for symbolic link."))); return false; } return archiveSymLink(entry, null); } private boolean archiveSymLink(ArchiveEntry entry, File file, IArchiveEntryVisitor entryVisitorOrNull) { if (entry.hasLinkTarget() == false) { errorStrategy.dealWithError(new ArchivingException(file, new IOException( "Cannot read link target of symbolic link."))); return false; } return archiveSymLink(entry, entryVisitorOrNull); } private boolean archiveSymLink(ArchiveEntry entry, IArchiveEntryVisitor entryVisitorOrNull) { try { hdf5Writer.object().createSoftLink(entry.getLinkTarget(), entry.getPath()); if (entryVisitorOrNull != null) { entryVisitorOrNull.visit(entry); } } catch (HDF5Exception ex) { errorStrategy.dealWithError(new ArchivingException(entry.getPath(), ex)); return false; } return true; } private static int computeSizeHint(final File[] entries) { int totalLength = 0; for (File entry : entries) { totalLength += entry.getName().length(); } return totalLength; } private DataSetInfo tryArchiveFile(File file, ArchiveEntry entry, HDF5GenericStorageFeatures features, int chunkSize, IArchiveEntryVisitor entryVisitorOrNull) throws ArchivingException { DataSetInfo info = null; try { info = copyToHDF5(file, entry.getPath(), features, chunkSize); entry.setDataSetInfo(info); if (entryVisitorOrNull != null) { entryVisitorOrNull.visit(entry); } } catch (IOException ex) { errorStrategy.dealWithError(new ArchivingException(file, ex)); } catch (HDF5Exception ex) { errorStrategy.dealWithError(new ArchivingException(entry.getPath(), ex)); } return info; } static String getRelativePath(File root, File filePath) { return getRelativePath(root.getAbsolutePath(), filePath.getAbsolutePath()); } static String getRelativePath(String parentDirToBeStripped, String filePath) { if (filePath.startsWith(parentDirToBeStripped) == false && parentDirToBeStripped.startsWith(filePath) == false) { throw new IOExceptionUnchecked("Path '" + filePath + "' does not start with '" + parentDirToBeStripped + "'."); } final String path = (parentDirToBeStripped.length() >= filePath.length()) ? "/" : filePath .substring(parentDirToBeStripped.length()); return FilenameUtils.separatorsToUnix(path); } private DataSetInfo copyToHDF5(final File source, final String objectPath, final HDF5GenericStorageFeatures compression, int chunkSize) throws IOException { final InputStream input = FileUtils.openInputStream(source); try { return copyToHDF5(input, objectPath, compression, chunkSize); } finally { IOUtils.closeQuietly(input); } } private int getEffectiveChunkSize(int chunkSize) { return (chunkSize <= 0 || chunkSize > buffer.length) ? buffer.length : chunkSize; } private DataSetInfo copyToHDF5(final InputStream input, final String objectPath, final HDF5GenericStorageFeatures compression, int chunkSize) throws IOException { final int effectiveBufferLength = getEffectiveChunkSize(chunkSize); final CRC32 crc32 = new CRC32(); HDF5GenericStorageFeatures features = compression; int n = fillBuffer(input, effectiveBufferLength); // Deal with small data sources separately to keep the file size smaller if (n < effectiveBufferLength) { // For data sets roughly up to 4096 bytes the overhead of a chunked data set outweighs // the saving of the compression. if (n <= SMALL_DATASET_LIMIT || features.isDeflating() == false) { features = HDF5GenericStorageFeatures.GENERIC_CONTIGUOUS; } final HDF5OpaqueType type = hdf5Writer.opaque().createArray(objectPath, OPAQUE_TAG_FILE, n, features); hdf5Writer.opaque().writeArrayBlockWithOffset(objectPath, type, buffer, n, 0); crc32.update(buffer, 0, n); return new DataSetInfo(n, (int) crc32.getValue()); } final HDF5OpaqueType type = hdf5Writer.opaque().createArray(objectPath, OPAQUE_TAG_FILE, 0, effectiveBufferLength, compression); long count = 0; while (n > 0) { hdf5Writer.opaque().writeArrayBlockWithOffset(objectPath, type, buffer, n, count); count += n; crc32.update(buffer, 0, n); n = fillBuffer(input, effectiveBufferLength); } return new DataSetInfo(count, (int) crc32.getValue()); } private int fillBuffer(InputStream input, int bufferLength) throws IOException { int ofs = 0; int len = bufferLength; int count = 0; int n = 0; while (len > 0 && -1 != (n = input.read(buffer, ofs, len))) { ofs += n; len -= n; count += n; } return count; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/HDF5Archiver.java000066400000000000000000001004411256564762100272360ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import java.io.ByteArrayInputStream; import java.io.ByteArrayOutputStream; import java.io.Closeable; import java.io.File; import java.io.Flushable; import java.io.IOException; import java.io.InputStream; import java.io.OutputStream; import java.util.ArrayList; import java.util.Collections; import java.util.HashSet; import java.util.List; import java.util.Set; import ch.systemsx.cisd.base.exceptions.IErrorStrategy; import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked; import ch.systemsx.cisd.base.io.AdapterIInputStreamToInputStream; import ch.systemsx.cisd.base.io.AdapterIOutputStreamToOutputStream; import ch.systemsx.cisd.base.io.IInputStream; import ch.systemsx.cisd.base.io.IOutputStream; import ch.systemsx.cisd.hdf5.HDF5DataBlock; import ch.systemsx.cisd.hdf5.HDF5FactoryProvider; import ch.systemsx.cisd.hdf5.IHDF5Reader; import ch.systemsx.cisd.hdf5.IHDF5Writer; import ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator; import ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator.FileFormat; import ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator.SyncMode; import ch.systemsx.cisd.hdf5.h5ar.NewArchiveEntry.NewDirectoryArchiveEntry; import ch.systemsx.cisd.hdf5.h5ar.NewArchiveEntry.NewFileArchiveEntry; import ch.systemsx.cisd.hdf5.h5ar.NewArchiveEntry.NewSymLinkArchiveEntry; import ch.systemsx.cisd.hdf5.io.HDF5IOAdapterFactory; /** * An archiver based on HDF5 as archive format for directory with fast random access to particular * files in the archive. * * @author Bernd Rinn */ final class HDF5Archiver implements Closeable, Flushable, IHDF5Archiver, IHDF5ArchiveInfoProvider { private static final String HOUSEKEEPING_SUFFIX = "\1\0"; public static final int CHUNK_SIZE_AUTO = -1; private final static int MB = 1024 * 1024; final static int BUFFER_SIZE = 10 * MB; private final IHDF5Reader hdf5Reader; private final IHDF5Writer hdf5WriterOrNull; private final boolean closeReaderOnCloseFile; private final IErrorStrategy errorStrategy; private final IDirectoryIndexProvider indexProvider; private final byte[] buffer; private final HDF5ArchiveUpdater updaterOrNull; private final HDF5ArchiveDeleter deleterOrNull; private final HDF5ArchiveTraverser processor; private final IdCache idCache; static IHDF5Reader createHDF5Reader(File archiveFile) { return HDF5FactoryProvider.get().openForReading(archiveFile); } static IHDF5Writer createHDF5Writer(File archiveFile, FileFormat fileFormat, boolean noSync) { final IHDF5WriterConfigurator config = HDF5FactoryProvider.get().configure(archiveFile); config.fileFormat(fileFormat); config.useUTF8CharacterEncoding(); config.houseKeepingNameSuffix(HOUSEKEEPING_SUFFIX); if (noSync == false) { config.syncMode(SyncMode.SYNC); } return config.writer(); } HDF5Archiver(File archiveFile, boolean readOnly) { this(archiveFile, readOnly, false, FileFormat.STRICTLY_1_6, null); } HDF5Archiver(File archiveFile, boolean readOnly, boolean noSync, FileFormat fileFormat, IErrorStrategy errorStrategyOrNull) { this.buffer = new byte[BUFFER_SIZE]; this.closeReaderOnCloseFile = true; this.hdf5WriterOrNull = readOnly ? null : createHDF5Writer(archiveFile, fileFormat, noSync); this.hdf5Reader = (hdf5WriterOrNull != null) ? hdf5WriterOrNull : createHDF5Reader(archiveFile); if (errorStrategyOrNull == null) { this.errorStrategy = IErrorStrategy.DEFAULT_ERROR_STRATEGY; } else { this.errorStrategy = errorStrategyOrNull; } this.indexProvider = new DirectoryIndexProvider(hdf5Reader, errorStrategy); this.idCache = new IdCache(); this.processor = new HDF5ArchiveTraverser(new HDF5ArchiveTraverser.IDirectoryChecker() { @Override public boolean isDirectoryFollowSymlinks(ArchiveEntry entry) { final ArchiveEntry resolvedEntry = tryResolveLink(entry); return (resolvedEntry == null) ? false : resolvedEntry.isDirectory(); } }, hdf5Reader, indexProvider, idCache); if (hdf5WriterOrNull == null) { this.updaterOrNull = null; this.deleterOrNull = null; } else { this.updaterOrNull = new HDF5ArchiveUpdater(hdf5WriterOrNull, indexProvider, idCache, buffer); this.deleterOrNull = new HDF5ArchiveDeleter(hdf5WriterOrNull, indexProvider, idCache); } } HDF5Archiver(IHDF5Reader reader, boolean enforceReadOnly, IErrorStrategy errorStrategyOrNull) { this.buffer = new byte[BUFFER_SIZE]; this.closeReaderOnCloseFile = false; this.hdf5WriterOrNull = (enforceReadOnly == false && reader instanceof IHDF5Writer) ? (IHDF5Writer) reader : null; if (errorStrategyOrNull == null) { this.errorStrategy = IErrorStrategy.DEFAULT_ERROR_STRATEGY; } else { this.errorStrategy = errorStrategyOrNull; } this.hdf5Reader = reader; this.indexProvider = new DirectoryIndexProvider(hdf5Reader, errorStrategy); this.idCache = new IdCache(); this.processor = new HDF5ArchiveTraverser(new HDF5ArchiveTraverser.IDirectoryChecker() { @Override public boolean isDirectoryFollowSymlinks(ArchiveEntry entry) { return tryResolveLink(entry).isDirectory(); } }, hdf5Reader, indexProvider, idCache); if (hdf5WriterOrNull == null) { this.updaterOrNull = null; this.deleterOrNull = null; } else { this.updaterOrNull = new HDF5ArchiveUpdater(hdf5WriterOrNull, indexProvider, idCache, buffer); this.deleterOrNull = new HDF5ArchiveDeleter(hdf5WriterOrNull, indexProvider, idCache); } } // // Closeable // @Override public void close() { if (isClosed() == false) { flush(); } if (closeReaderOnCloseFile) { hdf5Reader.close(); } else { indexProvider.close(); } } @Override public boolean isClosed() { return hdf5Reader.file().isClosed(); } // // Flusheable // @Override public void flush() { if (hdf5WriterOrNull != null) { hdf5WriterOrNull.file().flush(); } } // // IHDF5ArchiveInfo // @Override public boolean exists(String path) { final String normalizedPath = Utils.normalizePath(path); final String parentPath = Utils.getParentPath(normalizedPath); final String name = Utils.getName(normalizedPath); return indexProvider.get(parentPath, false).exists(name); } @Override public boolean isDirectory(String path) { final String normalizedPath = Utils.normalizePath(path); final String parentPath = Utils.getParentPath(normalizedPath); final String name = Utils.getName(normalizedPath); return indexProvider.get(parentPath, false).isDirectory(name); } @Override public boolean isRegularFile(String path) { return isRegularFile(tryGetLink(path, false)); } @Override public boolean isSymLink(String path) { return isSymLink(tryGetLink(path, false)); } @Override public ArchiveEntry tryGetEntry(String path, boolean readLinkTarget) { final String normalizedPath = Utils.normalizePath(path); if ("/".equals(normalizedPath)) { return new ArchiveEntry("", "/", LinkRecord.getLinkRecordForArchiveRoot(hdf5Reader .file().getFile()), idCache); } final String parentPath = Utils.getParentPath(normalizedPath); final String name = Utils.getName(normalizedPath); return Utils.tryToArchiveEntry(parentPath, normalizedPath, indexProvider.get(parentPath, readLinkTarget).tryGetLink(name), idCache); } private LinkRecord tryGetLink(String path, boolean readLinkTargets) { final String normalizedPath = Utils.normalizePath(path); final String parentPath = Utils.getParentPath(normalizedPath); final String name = Utils.getName(normalizedPath); return indexProvider.get(parentPath, readLinkTargets).tryGetLink(name); } @Override public ArchiveEntry tryResolveLink(ArchiveEntry entry) { if (entry == null) { return null; } ArchiveEntry workEntry = entry; String firstPath = null; if (entry.isSymLink()) { Set workPathSet = null; while (workEntry != null && workEntry.isSymLink()) { if (firstPath == null) { firstPath = workEntry.getPath(); } else { if (workPathSet == null) { workPathSet = new HashSet(); workPathSet.add(firstPath); } if (workPathSet.contains(workEntry.getPath())) { // The link targets form a loop, resolve to null. return null; } workPathSet.add(workEntry.getPath()); } String linkTarget; if (workEntry.hasLinkTarget()) { linkTarget = workEntry.getLinkTarget(); } else { workEntry = tryGetEntry(workEntry.getPath(), true); linkTarget = workEntry.getLinkTarget(); } if (linkTarget.startsWith("/") == false) { linkTarget = Utils.concatLink(workEntry.getParentPath(), linkTarget); } linkTarget = Utils.normalizePath(linkTarget); if (linkTarget == null) // impossible link target like '/..' { return null; } workEntry = tryGetEntry(linkTarget, true); } } return workEntry; } @Override public ArchiveEntry tryGetResolvedEntry(String path, boolean keepPath) { final ArchiveEntry entry = tryGetEntry(path, true); ArchiveEntry resolvedEntry = tryResolveLink(entry); if (resolvedEntry == null) { return null; } if (entry != resolvedEntry && keepPath) { resolvedEntry = new ArchiveEntry(entry, resolvedEntry); } return resolvedEntry; } private static boolean isRegularFile(LinkRecord linkOrNull) { return linkOrNull != null && linkOrNull.isRegularFile(); } private static boolean isSymLink(LinkRecord linkOrNull) { return linkOrNull != null && linkOrNull.isSymLink(); } // // IHDF5ArchiveReader // @Override public List list() { return list("/", ListParameters.DEFAULT); } @Override public List list(final String fileOrDir) { return list(fileOrDir, ListParameters.DEFAULT); } @Override public List list(final String fileOrDir, final ListParameters params) { final List result = new ArrayList(100); list(fileOrDir, new IArchiveEntryVisitor() { @Override public void visit(ArchiveEntry entry) { result.add(entry); } }, params); return result; } @Override public List test() { final List result = new ArrayList(100); list("/", new IArchiveEntryVisitor() { @Override public void visit(ArchiveEntry entry) { if (entry.isOK() == false) { result.add(entry); } } }, ListParameters.TEST); return result; } @Override public IHDF5Archiver list(String fileOrDir, IArchiveEntryVisitor visitor) { return list(fileOrDir, visitor, ListParameters.DEFAULT); } @Override public IHDF5Archiver list(final String fileOrDir, final IArchiveEntryVisitor visitor, final ListParameters params) { final String normalizedPath = Utils.normalizePath(fileOrDir); final IArchiveEntryVisitor decoratedVisitor = new IArchiveEntryVisitor() { @Override public void visit(ArchiveEntry entry) { if (params.isIncludeTopLevelDirectoryEntry() == false && normalizedPath.equals(entry.getPath())) { return; } ArchiveEntry workEntry = entry; if (workEntry.isSymLink() && params.isResolveSymbolicLinks()) { workEntry = tryResolveLink(workEntry); if (workEntry == null) { return; } if (workEntry != entry) { workEntry = new ArchiveEntry(entry, workEntry); } } if (params.isSuppressDirectoryEntries() == false || workEntry.isDirectory() == false) { visitor.visit(workEntry); } } }; final ArchiveEntryListProcessor listProcessor = new ArchiveEntryListProcessor(decoratedVisitor, buffer, params.isTestArchive()); processor.process(normalizedPath, params.isRecursive(), params.isReadLinkTargets(), params.isFollowSymbolicLinks(), listProcessor); return this; } @Override public List verifyAgainstFilesystem(File rootDirectoryOnFS) { return verifyAgainstFilesystem("/", rootDirectoryOnFS, VerifyParameters.DEFAULT); } @Override public List verifyAgainstFilesystem(String fileOrDir, File rootDirectoryOnFS) { return verifyAgainstFilesystem(fileOrDir, rootDirectoryOnFS, VerifyParameters.DEFAULT); } @Override public IHDF5Archiver verifyAgainstFilesystem(String fileOrDir, File rootDirectoryOnFS, IArchiveEntryVisitor visitor) { return verifyAgainstFilesystem(fileOrDir, rootDirectoryOnFS, visitor, VerifyParameters.DEFAULT); } @Override public List verifyAgainstFilesystem(String fileOrDir, File rootDirectoryOnFS, VerifyParameters params) { final List verifyErrors = new ArrayList(); verifyAgainstFilesystem(fileOrDir, rootDirectoryOnFS, new IArchiveEntryVisitor() { @Override public void visit(ArchiveEntry entry) { if (entry.isOK() == false) verifyErrors.add(entry); } }, params); return verifyErrors; } @SuppressWarnings("null") @Override public IHDF5Archiver verifyAgainstFilesystem(String fileOrDir, File rootDirectoryOnFS, IArchiveEntryVisitor visitor, IArchiveEntryVisitor missingArchiveEntryVisitorOrNull, VerifyParameters params) { final Set filesOnFSOrNull = (missingArchiveEntryVisitorOrNull != null) ? getFiles(rootDirectoryOnFS, params.isRecursive()) : null; final ArchiveEntryVerifyProcessor verifyProcessor = new ArchiveEntryVerifyProcessor(visitor, rootDirectoryOnFS, filesOnFSOrNull, buffer, params.isVerifyAttributes(), params.isNumeric()); processor.process(fileOrDir, params.isRecursive(), true, false, verifyProcessor); if (filesOnFSOrNull != null && filesOnFSOrNull.isEmpty() == false) { for (File f : filesOnFSOrNull) { missingArchiveEntryVisitorOrNull.visit(new ArchiveEntry(HDF5ArchiveUpdater .getRelativePath(rootDirectoryOnFS, f.getParentFile()), HDF5ArchiveUpdater .getRelativePath(rootDirectoryOnFS, f), LinkRecord.getLinkRecordForLink(f), idCache)); } } return this; } @Override public IHDF5Archiver verifyAgainstFilesystem(String fileOrDir, File rootDirectoryOnFS, IArchiveEntryVisitor visitor, VerifyParameters params) { return verifyAgainstFilesystem(fileOrDir, rootDirectoryOnFS, visitor, null, params); } @SuppressWarnings("null") @Override public IHDF5Archiver verifyAgainstFilesystem(String fileOrDir, File rootDirectoryOnFS, String rootDirectoryInArchive, IArchiveEntryVisitor visitor, IArchiveEntryVisitor missingArchiveEntryVisitorOrNull, VerifyParameters params) { final Set filesOnFSOrNull = (missingArchiveEntryVisitorOrNull != null) ? getFiles(rootDirectoryOnFS, params.isRecursive()) : null; final ArchiveEntryVerifyProcessor verifyProcessor = new ArchiveEntryVerifyProcessor(visitor, rootDirectoryOnFS, filesOnFSOrNull, rootDirectoryInArchive, buffer, params.isVerifyAttributes(), params.isNumeric()); processor.process(fileOrDir, params.isRecursive(), true, false, verifyProcessor); if (filesOnFSOrNull != null && filesOnFSOrNull.isEmpty() == false) { for (File f : filesOnFSOrNull) { missingArchiveEntryVisitorOrNull.visit(new ArchiveEntry(f.getParent(), f.getPath(), LinkRecord.getLinkRecordForLink(f), idCache)); } } return this; } @Override public IHDF5Archiver verifyAgainstFilesystem(String fileOrDir, File rootDirectoryOnFS, String rootDirectoryInArchive, IArchiveEntryVisitor visitor, VerifyParameters params) { return verifyAgainstFilesystem(fileOrDir, rootDirectoryOnFS, rootDirectoryInArchive, visitor, null, params); } @Override public IHDF5Archiver verifyAgainstFilesystem(String fileOrDir, File rootDirectoryOnFS, IArchiveEntryVisitor visitor, IArchiveEntryVisitor missingArchiveEntryVisitor) { return verifyAgainstFilesystem(fileOrDir, rootDirectoryOnFS, visitor, missingArchiveEntryVisitor, VerifyParameters.DEFAULT); } @Override public List verifyAgainstFilesystem(String fileOrDir, File rootDirectoryOnFS, String rootDirectoryInArchive, VerifyParameters params) { final List verifyErrors = new ArrayList(); verifyAgainstFilesystem(fileOrDir, rootDirectoryOnFS, rootDirectoryInArchive, new IArchiveEntryVisitor() { @Override public void visit(ArchiveEntry entry) { if (entry.isOK() == false) { verifyErrors.add(entry); } } }, params); return verifyErrors; } @Override public List verifyAgainstFilesystem(String fileOrDir, File rootDirectoryOnFS, String rootDirectoryInArchive) { return verifyAgainstFilesystem(fileOrDir, rootDirectoryOnFS, rootDirectoryInArchive, VerifyParameters.DEFAULT); } private static Set getFiles(File fsRoot, boolean recursive) { final Set result = new HashSet(); if (recursive && fsRoot.isDirectory()) { addFilesInDir(fsRoot, result); } return result; } private static void addFilesInDir(File dir, Set files) { for (File f : dir.listFiles()) { files.add(f); if (f.isDirectory()) { addFilesInDir(f, files); } } } @Override public IHDF5Archiver extractFile(String path, OutputStream out) throws IOExceptionUnchecked { if (hdf5Reader.object().isDataSet(path) == false) { errorStrategy.dealWithError(new UnarchivingException(path, "not found in archive")); return this; } try { for (HDF5DataBlock block : hdf5Reader.opaque().getArrayNaturalBlocks(path)) { out.write(block.getData()); } } catch (IOException ex) { errorStrategy.dealWithError(new UnarchivingException(new File("stdout"), ex)); } return this; } @Override public byte[] extractFileAsByteArray(String path) throws IOExceptionUnchecked { final ByteArrayOutputStream out = new ByteArrayOutputStream(); extractFile(path, out); return out.toByteArray(); } @Override public IInputStream extractFileAsIInputStream(String path) { if (hdf5Reader.object().isDataSet(path) == false) { errorStrategy.dealWithError(new UnarchivingException(path, "not found in archive")); return null; } return HDF5IOAdapterFactory.asIInputStream(hdf5Reader, path); } @Override public InputStream extractFileAsInputStream(String path) { return new AdapterIInputStreamToInputStream(extractFileAsIInputStream(path)); } @Override public IHDF5Archiver extractToFilesystem(File rootDirectory) throws IllegalStateException { return extractToFilesystemBelowDirectory(rootDirectory, "", "/", ArchivingStrategy.DEFAULT, null); } @Override public IHDF5Archiver extractToFilesystem(File rootDirectory, String path) throws IllegalStateException { return extractToFilesystemBelowDirectory(rootDirectory, "", path, ArchivingStrategy.DEFAULT, null); } @Override public IHDF5Archiver extractToFilesystem(File rootDirectory, String path, IArchiveEntryVisitor visitorOrNull) throws IllegalStateException { return extractToFilesystemBelowDirectory(rootDirectory, "", path, ArchivingStrategy.DEFAULT, visitorOrNull); } @Override public IHDF5Archiver extractToFilesystem(File rootDirectory, String path, ArchivingStrategy strategy, IArchiveEntryVisitor visitorOrNull) throws IllegalStateException { return extractToFilesystemBelowDirectory(rootDirectory, "", path, strategy, visitorOrNull); } @Override public IHDF5Archiver extractToFilesystemBelowDirectory(File rootDirectory, String rootPathInArchive) { return extractToFilesystemBelowDirectory(rootDirectory, rootPathInArchive, "", ArchivingStrategy.DEFAULT, null); } @Override public IHDF5Archiver extractToFilesystemBelowDirectory(File rootDirectory, String rootPathInArchive, IArchiveEntryVisitor visitorOrNull) { return extractToFilesystemBelowDirectory(rootDirectory, rootPathInArchive, "", ArchivingStrategy.DEFAULT, visitorOrNull); } @Override public IHDF5Archiver extractToFilesystemBelowDirectory(File rootDirectory, String rootPathInArchive, ArchivingStrategy strategy, IArchiveEntryVisitor visitorOrNull) { return extractToFilesystemBelowDirectory(rootDirectory, rootPathInArchive, "", strategy, visitorOrNull); } @Override public IHDF5Archiver extractToFilesystemBelowDirectory(File rootDirectory, String rootPathInArchive, String path, ArchivingStrategy strategy, IArchiveEntryVisitor visitorOrNull) throws IllegalStateException { final IArchiveEntryProcessor extractor = new ArchiveEntryExtractProcessor(visitorOrNull, strategy, rootDirectory, rootPathInArchive, buffer); processor.process(Utils.concatLink(rootPathInArchive, path), true, true, false, extractor); return this; } // // IHDF5Archiver // @Override public IHDF5Archiver archiveFromFilesystem(File path) throws IllegalStateException { return archiveFromFilesystem(path, ArchivingStrategy.DEFAULT, false, (IArchiveEntryVisitor) null); } @Override public IHDF5Archiver archiveFromFilesystem(File path, ArchivingStrategy strategy) throws IllegalStateException { return archiveFromFilesystem(path, strategy, false, (IArchiveEntryVisitor) null); } @Override public IHDF5Archiver archiveFromFilesystem(File path, IArchiveEntryVisitor entryVisitorOrNull) throws IllegalStateException { return archiveFromFilesystem(path, ArchivingStrategy.DEFAULT, false, entryVisitorOrNull); } @Override public IHDF5Archiver archiveFromFilesystem(File path, ArchivingStrategy strategy, boolean keepNameFromPath, IArchiveEntryVisitor entryVisitorOrNull) throws IllegalStateException { checkReadWrite(); updaterOrNull .archive(path, strategy, CHUNK_SIZE_AUTO, keepNameFromPath, entryVisitorOrNull); return this; } @Override public IHDF5Archiver archiveFromFilesystem(File parentDirToStrip, File path) throws IllegalStateException { return archiveFromFilesystem(parentDirToStrip, path, ArchivingStrategy.DEFAULT); } @Override public IHDF5Archiver archiveFromFilesystem(File parentDirToStrip, File path, ArchivingStrategy strategy) throws IllegalStateException { return archiveFromFilesystem(parentDirToStrip, path, strategy, null); } @Override public IHDF5Archiver archiveFromFilesystem(File parentDirToStrip, File path, ArchivingStrategy strategy, IArchiveEntryVisitor entryVisitorOrNull) throws IllegalStateException { checkReadWrite(); updaterOrNull .archive(parentDirToStrip, path, strategy, CHUNK_SIZE_AUTO, entryVisitorOrNull); return this; } @Override public IHDF5Archiver archiveFromFilesystem(String rootInArchive, File path) { return archiveFromFilesystem(rootInArchive, path, ArchivingStrategy.DEFAULT, null); } @Override public IHDF5Archiver archiveFromFilesystem(String rootInArchive, File path, ArchivingStrategy strategy) { return archiveFromFilesystem(rootInArchive, path, strategy, null); } @Override public IHDF5Archiver archiveFromFilesystem(String rootInArchive, File path, ArchivingStrategy strategy, IArchiveEntryVisitor entryVisitorOrNull) { checkReadWrite(); updaterOrNull.archive(rootInArchive, path, strategy, CHUNK_SIZE_AUTO, entryVisitorOrNull); return this; } @Override public IHDF5Archiver archiveFromFilesystemBelowDirectory(String rootInArchive, File directory) { return archiveFromFilesystemBelowDirectory(rootInArchive, directory, ArchivingStrategy.DEFAULT, null); } @Override public IHDF5Archiver archiveFromFilesystemBelowDirectory(String rootInArchive, File directory, ArchivingStrategy strategy) { return archiveFromFilesystemBelowDirectory(rootInArchive, directory, strategy, null); } @Override public IHDF5Archiver archiveFromFilesystemBelowDirectory(String rootInArchive, File directory, IArchiveEntryVisitor visitor) { return archiveFromFilesystemBelowDirectory(rootInArchive, directory, ArchivingStrategy.DEFAULT, visitor); } @Override public IHDF5Archiver archiveFromFilesystemBelowDirectory(String rootInArchive, File directory, ArchivingStrategy strategy, IArchiveEntryVisitor entryVisitorOrNull) { checkReadWrite(); updaterOrNull.archiveBelow(rootInArchive, directory, strategy, CHUNK_SIZE_AUTO, entryVisitorOrNull); return this; } @Override public IHDF5Archiver archiveFile(String path, byte[] data) throws IllegalStateException { return archiveFile(NewArchiveEntry.file(path), new ByteArrayInputStream(data)); } @Override public IHDF5Archiver archiveFile(String path, InputStream input) { return archiveFile(NewArchiveEntry.file(path), input); } @Override public IHDF5Archiver archiveFile(NewFileArchiveEntry entry, byte[] data) { return archiveFile(entry, new ByteArrayInputStream(data)); } @Override public OutputStream archiveFileAsOutputStream(NewFileArchiveEntry entry) { return new AdapterIOutputStreamToOutputStream(archiveFileAsIOutputStream(entry)); } @Override public IOutputStream archiveFileAsIOutputStream(NewFileArchiveEntry entry) { checkReadWrite(); final LinkRecord link = new LinkRecord(entry); final IOutputStream stream = updaterOrNull.archiveFile(entry.getParentPath(), link, entry.isCompress(), entry.getChunkSize()); return stream; } @Override public IHDF5Archiver archiveFile(NewFileArchiveEntry entry, InputStream input) { checkReadWrite(); final LinkRecord link = new LinkRecord(entry); updaterOrNull.archive(entry.getParentPath(), link, input, entry.isCompress(), entry.getChunkSize()); entry.setCrc32(link.getCrc32()); return this; } @Override public IHDF5Archiver archiveSymlink(String path, String linkTarget) { return archiveSymlink(NewArchiveEntry.symlink(path, linkTarget)); } @Override public IHDF5Archiver archiveSymlink(NewSymLinkArchiveEntry entry) { checkReadWrite(); final LinkRecord link = new LinkRecord(entry); updaterOrNull.archive(entry.getParentPath(), link, null, false, CHUNK_SIZE_AUTO); return this; } @Override public IHDF5Archiver archiveDirectory(String path) { return archiveDirectory(NewArchiveEntry.directory(path)); } @Override public IHDF5Archiver archiveDirectory(NewDirectoryArchiveEntry entry) throws IllegalStateException, IllegalArgumentException { checkReadWrite(); final LinkRecord link = new LinkRecord(entry); updaterOrNull.archive(entry.getParentPath(), link, null, false, CHUNK_SIZE_AUTO); return this; } @Override public IHDF5Archiver delete(String hdf5ObjectPath) { return delete(Collections.singletonList(hdf5ObjectPath), null); } @Override public IHDF5Archiver delete(List hdf5ObjectPaths) { return delete(hdf5ObjectPaths, null); } @Override public IHDF5Archiver delete(List hdf5ObjectPaths, IArchiveEntryVisitor entryVisitorOrNull) { checkReadWrite(); deleterOrNull.delete(hdf5ObjectPaths, entryVisitorOrNull); return this; } private void checkReadWrite() { if (updaterOrNull == null) { throw new IllegalStateException("Cannot update archive in read-only mode."); } } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/HDF5ArchiverFactory.java000066400000000000000000000205571256564762100305770ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import java.io.File; import ch.systemsx.cisd.base.exceptions.IErrorStrategy; import ch.systemsx.cisd.hdf5.IHDF5Reader; import ch.systemsx.cisd.hdf5.IHDF5Writer; import ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator.FileFormat; /** * A factory for {@link IHDF5Archiver} * * @author Bernd Rinn */ public class HDF5ArchiverFactory { /** * Opens an HDF5 archive file for writing and reading. * * @param file The archive file to open. If the archive file does not yet exist, it will be * created. */ public static IHDF5Archiver open(File file) { return new HDF5Archiver(file, false); } /** * Opens an HDF5 archive file for writing and reading. * * @param file The archive file to open. If the archive file does not yet exist, it will be * created. * @param errorStrategyOrNull The {@link IErrorStrategy} to use on errors when accessing the * archive. May be null, in which case every error just causes an * exception. */ public static IHDF5Archiver open(File file, IErrorStrategy errorStrategyOrNull) { return new HDF5Archiver(file, false, false, FileFormat.STRICTLY_1_6, errorStrategyOrNull); } /** * Opens an HDF5 archive file for writing and reading. * * @param file The archive file to open. If the archive file does not yet exist, it will be * created. * @param noSync if true, no sync call will be performed on closing * the file. * @param fileFormat The HDF5 file format to use for the archive. * @param errorStrategyOrNull The {@link IErrorStrategy} to use on errors when accessing the * archive. May be null, in which case every error just causes an * exception. */ public static IHDF5Archiver open(File file, boolean noSync, FileFormat fileFormat, IErrorStrategy errorStrategyOrNull) { return new HDF5Archiver(file, false, noSync, fileFormat, errorStrategyOrNull); } /** * Opens an HDF5 archive file named filePath for writing and reading. * * @param filePath The path of the archive file to open. If the archive file does not yet exist, * it will be created. */ public static IHDF5Archiver open(String filePath) { return new HDF5Archiver(new File(filePath), false); } /** * Opens an HDF5 archive file named filePath for writing and reading. * * @param filePath The path of the archive file to open. If the archive file does not yet exist, * it will be created. * @param errorStrategyOrNull The {@link IErrorStrategy} to use on errors when accessing the * archive. May be null, in which case every error just causes an * exception. */ public static IHDF5Archiver open(String filePath, IErrorStrategy errorStrategyOrNull) { return new HDF5Archiver(new File(filePath), false, false, FileFormat.STRICTLY_1_6, errorStrategyOrNull); } /** * Opens an HDF5 archive file named filePath for writing and reading. * * @param filePath The path of the archive file to open. If the archive file does not yet exist, * it will be created. * @param noSync if true, no sync call will be performed on closing * the file. * @param fileFormat The HDF5 file format to use for the archive. * @param errorStrategyOrNull The {@link IErrorStrategy} to use on errors when accessing the * archive. May be null, in which case every error just causes an * exception. */ public static IHDF5Archiver open(String filePath, boolean noSync, FileFormat fileFormat, IErrorStrategy errorStrategyOrNull) { return new HDF5Archiver(new File(filePath), false, noSync, fileFormat, errorStrategyOrNull); } /** * Opens an HDF5 archive file based on an HDF writer for writing and reading. * * @param writer The HDF5 writer to base the archive file on. Closing the archive writer will * not close the HDF5 writer. */ public static IHDF5Archiver open(IHDF5Writer writer) { return new HDF5Archiver(writer, false, null); } /** * Opens an HDF5 archive file based on an HDF writer for writing and reading. * * @param writer The HDF5 writer to base the archive file on. Closing the archive writer will * not close the HDF5 writer. It is recommended that you configure the * writer with IHDF5WriterConfigurator.houseKeepingNameSuffix("\\1\\0)") * so that internal house-keeping files cannot overwrite archived files. . * @param errorStrategy The {@link IErrorStrategy} to use on errors when accessing the archive. */ public static IHDF5Archiver open(IHDF5Writer writer, IErrorStrategy errorStrategy) { return new HDF5Archiver(writer, false, errorStrategy); } /** * Opens an HDF5 archive file for reading. * * @param file The archive file to open. It is an error if the archive file does not exist. */ public static IHDF5ArchiveReader openForReading(File file) { return new HDF5Archiver(file, true); } /** * Opens an HDF5 archive file for reading. * * @param file The archive file to open. It is an error if the archive file does not exist. * @param errorStrategy The {@link IErrorStrategy} to use on errors when accessing the archive. */ public static IHDF5ArchiveReader openForReading(File file, IErrorStrategy errorStrategy) { return new HDF5Archiver(file, true, true, FileFormat.STRICTLY_1_6, errorStrategy); } /** * Opens an HDF5 archive file named filePath for reading. * * @param filePath The path of the archive file to open. It is an error if the archive file does * not exist. */ public static IHDF5ArchiveReader openForReading(String filePath) { return new HDF5Archiver(new File(filePath), true); } /** * Opens an HDF5 archive file named filePath for reading. * * @param filePath The path of the archive file to open. It is an error if the archive file does * not exist. * @param errorStrategy The {@link IErrorStrategy} to use on errors when accessing the archive. */ public static IHDF5ArchiveReader openForReading(String filePath, IErrorStrategy errorStrategy) { return new HDF5Archiver(new File(filePath), true, true, FileFormat.STRICTLY_1_6, errorStrategy); } /** * Opens an HDF5 archive file based on an HDF5 reader. * * @param reader The HDF5 reader to use as the source of the archive. Closing the archive reader * will not close the HDF5 reader. * @param errorStrategy The {@link IErrorStrategy} to use on errors when accessing the archive. */ public static IHDF5ArchiveReader openForReading(IHDF5Reader reader, IErrorStrategy errorStrategy) { return new HDF5Archiver(reader, true, errorStrategy); } /** * Opens an HDF5 archive file based on an HDF5 reader. * * @param reader The HDF5 reader to use as the source of the archive. Closing the archive reader * will not close the HDF5 reader. */ public static IHDF5ArchiveReader openForReading(IHDF5Reader reader) { return new HDF5Archiver(reader, true, null); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/HDF5ArchiverMain.java000066400000000000000000000573551256564762100300620ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import java.io.File; import java.io.FileDescriptor; import java.io.FileOutputStream; import java.util.ArrayList; import java.util.List; import java.util.concurrent.atomic.AtomicInteger; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import org.apache.commons.io.FilenameUtils; import ch.systemsx.cisd.args4j.Argument; import ch.systemsx.cisd.args4j.CmdLineException; import ch.systemsx.cisd.args4j.CmdLineParser; import ch.systemsx.cisd.args4j.ExampleMode; import ch.systemsx.cisd.args4j.Option; import ch.systemsx.cisd.base.exceptions.IErrorStrategy; import ch.systemsx.cisd.hdf5.BuildAndEnvironmentInfo; import ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator.FileFormat; /** * The main class of the HDF5 based archiver. * * @author Bernd Rinn */ public class HDF5ArchiverMain { private static final String FILE_EXTENSION_H5 = ".h5"; private static final String FILE_EXTENSION_H5AR = ".h5ar"; private enum Command { ARCHIVE(new String[] { "A", "AR", "ARCHIVE" }, false), CAT(new String[] { "C", "CT", "CAT" }, true), EXTRACT(new String[] { "E", "EX", "EXTRACT" }, true), DELETE(new String[] { "D", "RM", "DELETE", "REMOVE" }, false), LIST(new String[] { "L", "LS", "LIST" }, true), VERIFY(new String[] { "V", "VF", "VERIFY" }, true), HELP(new String[] { "H", "HELP" }, true); String[] forms; boolean readOnly; Command(String[] forms, boolean readOnly) { this.forms = forms; this.readOnly = readOnly; } boolean isReadOnly() { return readOnly; } static Command parse(String commandStr) { final String commandStrU = commandStr.toUpperCase(); for (Command cmd : values()) { for (String frm : cmd.forms) { if (frm.equals(commandStrU)) { return cmd; } } } return HELP; } } private final static IErrorStrategy ERROR_STRATEGY_CONTINUE = new IErrorStrategy() { @Override public void dealWithError(Throwable th) throws ArchiverException { System.err.println(th.getMessage()); } @Override public void warning(String message) { System.err.println(message); } }; @Argument private List arguments; private Command command; private File archiveFile; private final boolean initializationOK; @Option(name = "i", longName = "include", metaVar = "REGEX", skipForExample = true, usage = "Regex of files to include") private List fileWhiteList = new ArrayList(); @Option(name = "e", longName = "exclude", metaVar = "REGEX", usage = "Regex of files to exclude") private List fileBlackList = new ArrayList(); @Option(name = "I", longName = "include-dirs", metaVar = "REGEX", skipForExample = true, usage = "Regex of directories to include") private List dirWhiteList = new ArrayList(); @Option(name = "E", longName = "exclude-dirs", metaVar = "REGEX", skipForExample = true, usage = "Regex of directories to exclude") private List dirBlackList = new ArrayList(); @Option(name = "c", longName = "compress", metaVar = "REGEX", skipForExample = true, usage = "Regex of files to compress") private List compressionWhiteList = new ArrayList(); @Option(name = "nc", longName = "no-compression", metaVar = "REGEX", skipForExample = true, usage = "Regex of files not to compress") private List compressionBlackList = new ArrayList(); @Option(name = "C", longName = "compress-all", usage = "Compress all files") private Boolean compressAll = null; @Option(name = "r", longName = "root-dir", metaVar = "DIR", usage = "Root directory for archiving / extracting / verifying") private File rootOrNull; @Option(name = "D", longName = "suppress-directories", usage = "Supress output for directories itself for LIST and VERIFY") private boolean suppressDirectoryEntries = false; @Option(name = "R", longName = "recursive", usage = "Recursive LIST and VERIFY") private boolean recursive = false; @Option(name = "v", longName = "verbose", usage = "Verbose output (all operations)") private boolean verbose = false; @Option(name = "q", longName = "quiet", usage = "Quiet operation (only error output)") private boolean quiet = false; @Option(name = "n", longName = "numeric", usage = "Use numeric values for mode, uid and gid for LIST and VERIFY") private boolean numeric = false; @Option(name = "t", longName = "test-checksums", usage = "Test CRC32 checksums of files in archive for LIST") private boolean testAgainstChecksums = false; @Option(name = "a", longName = "verify-attributes", usage = "Consider file attributes for VERIFY") private boolean verifyAttributes = false; @Option(name = "m", longName = "check-missing-files", usage = "Check for files present on the filesystem but missing from the archive for VERIFY") private boolean checkMissingFile = false; @Option(longName = "file-format", skipForExample = true, usage = "Specifies the file format version when creating an archive (N=1 -> HDF51.6 (default), N=2 -> HDF51.8)") private int fileFormat = 1; @Option(longName = "stop-on-error", skipForExample = true, usage = "Stop on first error and give detailed error report") private boolean stopOnError = false; @Option(longName = "no-sync", skipForExample = true, usage = "Do not sync to disk before program exits (write mode only)") private boolean noSync = false; private HDF5Archiver archiver; /** * The command line parser. */ private final CmdLineParser parser = new CmdLineParser(this); private HDF5ArchiverMain(String[] args) { try { parser.parseArgument(args); } catch (CmdLineException ex) { System.err.printf("Error when parsing command line: '%s'\n", ex.getMessage()); printHelp(true); initializationOK = false; return; } if (arguments == null || arguments.size() < 2) { printHelp(true); initializationOK = false; return; } command = Command.parse(arguments.get(0)); if (command == null || command == Command.HELP) { printHelp(true); initializationOK = false; return; } if (arguments.get(1).endsWith(FILE_EXTENSION_H5) || arguments.get(1).endsWith(FILE_EXTENSION_H5AR)) { archiveFile = new File(arguments.get(1)); } else { archiveFile = new File(arguments.get(1) + FILE_EXTENSION_H5AR); if (command.isReadOnly() && archiveFile.exists() == false) { archiveFile = new File(arguments.get(1) + FILE_EXTENSION_H5); if (command.isReadOnly() && archiveFile.exists() == false) { archiveFile = new File(arguments.get(1)); } } } if (command.isReadOnly() && archiveFile.exists() == false) { System.err.println("Archive '" + archiveFile.getAbsolutePath() + "' does not exist."); initializationOK = false; return; } if (quiet && verbose) { System.err.println("Cannot be quiet and verbose at the same time."); initializationOK = false; return; } initializationOK = true; } @Option(longName = "version", skipForExample = true, usage = "Prints out the version information") void printVersion(final boolean exit) { System.err.println("HDF5 archiver version " + BuildAndEnvironmentInfo.INSTANCE.getFullVersion()); if (exit) { System.exit(0); } } private boolean helpPrinted = false; @Option(longName = "help", skipForExample = true, usage = "Shows this help text") void printHelp(final boolean dummy) { if (helpPrinted) { return; } parser.printHelp("h5ar", "[option [...]]", "[ARCHIVE [...] | " + "CAT [...] | " + "EXTRACT [ [...]] | " + "DELETE [...] | " + "LIST | VERIFY ]", ExampleMode.NONE); System.err.println("ARCHIVE: add files on the file system to an archive"); System.err.println("CAT: extract files from an archive to stdout"); System.err.println("EXTRACT: extract files from an archive to the file system"); System.err.println("DELETE: delete files from an archive"); System.err.println("LIST: list files in an archive"); System.err .println("VERIFY: verify the existence and integrity of files on the file system vs. the content of an archive"); System.err .println("Command aliases: ARCHIVE: A, AR; CAT: C, CT; EXTRACT: E, EX; DELETE: D, REMOVE, RM; LIST: L, LS; VERIFY: V, VF"); System.err.println("Example: h5ar" + parser.printExample(ExampleMode.ALL) + " ARCHIVE archive.h5ar ."); helpPrinted = true; } private boolean createArchiver() { final FileFormat fileFormatEnum = (fileFormat == 1) ? FileFormat.STRICTLY_1_6 : FileFormat.STRICTLY_1_8; try { archiver = new HDF5Archiver(archiveFile, command.isReadOnly(), noSync, fileFormatEnum, stopOnError ? IErrorStrategy.DEFAULT_ERROR_STRATEGY : ERROR_STRATEGY_CONTINUE); } catch (HDF5JavaException ex) { // Problem opening the archive file: non readable / writable System.err.println("Error opening archive file: " + ex.getMessage()); return false; } catch (HDF5LibraryException ex) { // Problem opening the archive file: corrupt file System.err.println("Error opening archive file: corrupt file [" + ex.getClass().getSimpleName() + ": " + ex.getMessage() + "]"); return false; } return true; } private ArchivingStrategy createArchivingStrategy() { final ArchivingStrategy strategy = new ArchivingStrategy(compressionBlackList.isEmpty() ? ArchivingStrategy.DEFAULT : ArchivingStrategy.DEFAULT_NO_COMPRESSION); if (compressAll != null) { strategy.compressAll(compressAll); } for (String pattern : fileWhiteList) { strategy.addToFileWhiteList(pattern); } for (String pattern : fileBlackList) { strategy.addToFileBlackList(pattern); } for (String pattern : dirWhiteList) { strategy.addToDirWhiteList(pattern); } for (String pattern : dirBlackList) { strategy.addToDirBlackList(pattern); } for (String pattern : fileWhiteList) { strategy.addToFileWhiteList(pattern); } for (String pattern : compressionWhiteList) { strategy.addToCompressionWhiteList(pattern); } for (String pattern : compressionBlackList) { strategy.addToCompressionBlackList(pattern); } return strategy; } private File getFSRoot() { return (rootOrNull == null) ? new File(".") : rootOrNull; } private static class ListingVisitor implements IArchiveEntryVisitor { private final boolean verifying; private final boolean quiet; private final boolean verbose; private final boolean numeric; private final boolean suppressDirectoryEntries; private int checkSumFailures; ListingVisitor(boolean verifying, boolean quiet, boolean verbose, boolean numeric) { this(verifying, quiet, verbose, numeric, false); } ListingVisitor(boolean verifying, boolean quiet, boolean verbose, boolean numeric, boolean suppressDirectoryEntries) { this.verifying = verifying; this.quiet = quiet; this.verbose = verbose; this.numeric = numeric; this.suppressDirectoryEntries = suppressDirectoryEntries; } @Override public void visit(ArchiveEntry entry) { if (suppressDirectoryEntries && entry.isDirectory()) { return; } if (verifying) { final boolean ok = entry.isOK(); if (quiet == false) { System.out.println(entry.describeLink(verbose, numeric, true)); } if (ok == false) { System.err.println(entry.getStatus(true)); ++checkSumFailures; } } else { if (quiet == false) { System.out.println(entry.describeLink(verbose, numeric, false)); } } } boolean isOK(int missingFiles) { if (verifying && (checkSumFailures + missingFiles > 0)) { System.err.println(checkSumFailures + missingFiles + " file(s) failed the test."); return false; } else { return true; } } } boolean run() { if (initializationOK == false) { return false; } try { switch (command) { case ARCHIVE: { if (arguments.size() == 2) { System.err.println("Nothing to archive."); break; } if (createArchiver() == false) { break; } final ArchivingStrategy strategy = createArchivingStrategy(); if (verbose) { System.out.printf("Archiving to file '%s', file system root: '%s'\n", archiveFile, getFSRoot()); } if (rootOrNull != null) { for (int i = 2; i < arguments.size(); ++i) { if (verbose) { System.out.printf(" Adding entry: '%s'\n", arguments.get(i)); } archiver.archiveFromFilesystem(rootOrNull, new File(rootOrNull, arguments.get(i)), strategy, verbose ? IArchiveEntryVisitor.NONVERBOSE_VISITOR : null); } } else { for (int i = 2; i < arguments.size(); ++i) { if (verbose) { System.out.printf(" Adding entry: '%s'\n", arguments.get(i)); } archiver.archiveFromFilesystem(new File(arguments.get(i)), strategy, true, verbose ? IArchiveEntryVisitor.NONVERBOSE_VISITOR : null); } } break; } case CAT: { if (createArchiver() == false) { break; } if (arguments.size() == 2) { System.err.println("Nothing to cat."); break; } else { for (int i = 2; i < arguments.size(); ++i) { archiver.extractFile(arguments.get(i), new FileOutputStream( FileDescriptor.out)); } } break; } case EXTRACT: { if (createArchiver() == false) { break; } final ArchivingStrategy strategy = createArchivingStrategy(); if (verbose) { System.out.printf("Extracting from file '%s', file system root: '%s'\n", archiveFile, getFSRoot()); } if (arguments.size() == 2) { if (verbose) { System.out.println(" Extracting entry: '/'"); } archiver.extractToFilesystem(getFSRoot(), "/", strategy, verbose ? IArchiveEntryVisitor.DEFAULT_VISITOR : quiet ? null : IArchiveEntryVisitor.NONVERBOSE_VISITOR); } else { for (int i = 2; i < arguments.size(); ++i) { if (verbose) { System.out.printf(" Extracting entry: '%s'\n", arguments.get(i)); } final String unixPath = FilenameUtils.separatorsToUnix(arguments.get(i)); archiver.extractToFilesystem(getFSRoot(), unixPath, strategy, verbose ? IArchiveEntryVisitor.DEFAULT_VISITOR : quiet ? null : IArchiveEntryVisitor.NONVERBOSE_VISITOR); } } break; } case DELETE: { if (arguments.size() == 2) { System.err.println("Nothing to delete."); break; } if (createArchiver() == false) { break; } if (verbose) { System.out.printf("Deleting from file '%s'\n", archiveFile); for (String entry : arguments.subList(2, arguments.size())) { System.out.printf(" Deleting entry: '%s'\n", entry); } } archiver.delete(arguments.subList(2, arguments.size()), verbose ? IArchiveEntryVisitor.NONVERBOSE_VISITOR : null); break; } case VERIFY: { if (createArchiver() == false) { break; } if (verbose) { System.out.printf("Verifying file '%s', file system root: '%s'\n", archiveFile, getFSRoot()); } final String fileOrDir = (arguments.size() > 2) ? arguments.get(2) : "/"; final AtomicInteger missingFileCount = new AtomicInteger(); final IArchiveEntryVisitor missingFileVisitorOrNull = checkMissingFile ? new IArchiveEntryVisitor() { @Override public void visit(ArchiveEntry entry) { final String errMsg = "ERROR: Object '" + entry.getName() + "' does not exist in archive."; if (verbose) { System.out.println(entry.describeLink(true, false, false) + "\t" + errMsg); } else if (quiet == false) { System.out.println(entry.getPath() + "\t" + errMsg); } System.err.println(errMsg); missingFileCount.incrementAndGet(); } } : null; final ListingVisitor visitor = new ListingVisitor(true, quiet, verbose, numeric); archiver.verifyAgainstFilesystem(fileOrDir, getFSRoot(), visitor, missingFileVisitorOrNull, VerifyParameters.build().recursive(recursive) .numeric(numeric).verifyAttributes(verifyAttributes).get()); return visitor.isOK(missingFileCount.get()); } case LIST: { if (createArchiver() == false) { break; } if (verbose) { System.out.printf("Listing file '%s'\n", archiveFile); } final String fileOrDir = (arguments.size() > 2) ? arguments.get(2) : "/"; final ListingVisitor visitor = new ListingVisitor(testAgainstChecksums, quiet, verbose, numeric, suppressDirectoryEntries); archiver.list(fileOrDir, visitor, ListParameters.build().recursive(recursive) .readLinkTargets(verbose).testArchive(testAgainstChecksums).get()); return visitor.isOK(0); } case HELP: // Can't happen any more at this point break; } return true; } finally { if (archiver != null) { archiver.close(); } } } public static void main(String[] args) { final HDF5ArchiverMain main = new HDF5ArchiverMain(args); if (main.run() == false) { System.exit(1); } } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/IArchiveEntryProcessor.java000066400000000000000000000060651256564762100315070ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import java.io.File; import java.io.IOException; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ch.systemsx.cisd.base.exceptions.IErrorStrategy; import ch.systemsx.cisd.hdf5.IHDF5Reader; /** * A processor for an archive entry. * * @author Bernd Rinn */ interface IArchiveEntryProcessor { /** * Performs any kind of processing of the given link. * * @param dir The directory the current link is in. * @param path The path of the current link (including the link name) * @param link The link in the archive. * @param reader The HDF5 reader. * @param idCache The cached map of user and group ids to names. * @param errorStrategy The strategy object for errors. * @return true for continuing processing this link, false * to skip over this entry (only relevant for directory links). */ public boolean process(String dir, String path, LinkRecord link, IHDF5Reader reader, IdCache idCache, IErrorStrategy errorStrategy) throws IOException, HDF5Exception; /** * Performs any kind of post-processing of a directory. This is called after all files in the * directory have been processed. * * @param dir The directory the current link is in. * @param path The path of the current link (including the link name) * @param link The link in the archive. * @param reader The HDF5 reader. * @param idCache The cached map of user and group ids to names. * @param errorStrategy The strategy object for errors. */ public void postProcessDirectory(String dir, String path, LinkRecord link, IHDF5Reader reader, IdCache idCache, IErrorStrategy errorStrategy) throws IOException, HDF5Exception; /** * Creates the appropriate exception class for this processor. */ public ArchiverException createException(String objectPath, String detailedMsg); /** * Creates the appropriate exception class for this processor. */ public ArchiverException createException(String objectPath, HDF5Exception cause); /** * Creates the appropriate exception class for this processor. */ public ArchiverException createException(String objectPath, RuntimeException cause); /** * Creates the appropriate exception class for this processor. */ public ArchiverException createException(File file, IOException cause); } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/IArchiveEntryVisitor.java000066400000000000000000000025561256564762100311700ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; /** * A role to visit {@link ArchiveEntry}s. * * @author Bernd Rinn */ public interface IArchiveEntryVisitor { public final static IArchiveEntryVisitor DEFAULT_VISITOR = new IArchiveEntryVisitor() { @Override public void visit(ArchiveEntry entry) { System.out.println(entry.describeLink()); } }; public final static IArchiveEntryVisitor NONVERBOSE_VISITOR = new IArchiveEntryVisitor() { @Override public void visit(ArchiveEntry entry) { System.out.println(entry.describeLink(false)); } }; /** * Called for each archive entry which is visited. */ public void visit(ArchiveEntry entry); }libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/IDirectoryIndex.java000066400000000000000000000060451256564762100301360ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import java.io.Closeable; import java.io.Flushable; import java.util.Collection; import java.util.Iterator; import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked; import ch.systemsx.cisd.hdf5.IHDF5Writer; /** * Memory representation of the directory index stored in an HDF5 archive. *

* Can operate in read-only or read-write mode. The mode is automatically determined by the * hdf5Reader provided the constructor: If this is an instance of {@link IHDF5Writer}, * the directory index will be read-write, otherwise read-only. * * @author Bernd Rinn */ interface IDirectoryIndex extends Iterable, Closeable, Flushable { /** * Amend the index with link targets. If the links targets have already been read, this method * is a noop. */ public void amendLinkTargets(); public boolean exists(String name); public boolean isDirectory(String name); /** * Returns the link with {@link LinkRecord#getLinkName()} equal to name, or * null, if there is no such link in the directory index. */ public LinkRecord tryGetLink(String name); /** * Returns true, if this class has link targets read. */ public boolean hasLinkTargets(); @Override public Iterator iterator(); /** * Writes the directory index to the archive represented by hdf5Writer. *

* Works on the list data structure. */ @Override public void flush(); /** * Add entries to the index. Any link that already exists in the index will be * replaced. */ public void updateIndex(LinkRecord[] entries); /** * Add entries to the index. Any link that already exists in the index will be * replaced. */ public void updateIndex(Collection entries); /** * Add entry to the index. If it already exists in the index, it will be replaced. */ public void updateIndex(LinkRecord entry); /** * Removes linkName from the index, if it is in. * * @return true, if linkName was removed. */ public boolean remove(String linkName); public boolean addFlushable(Flushable flushable); public boolean removeFlushable(Flushable flushable); @Override public void close() throws IOExceptionUnchecked; }libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/IDirectoryIndexProvider.java000066400000000000000000000020341256564762100316430ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import java.io.Closeable; import ch.systemsx.cisd.base.exceptions.IErrorStrategy; /** * A provider for {@link DirectoryIndex} objects. * * @author Bernd Rinn */ interface IDirectoryIndexProvider extends Closeable { public IDirectoryIndex get(String normalizedGroupPath, boolean withLinkTargets); public IErrorStrategy getErrorStrategy(); @Override public void close(); }libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/IHDF5ArchiveInfoProvider.java000066400000000000000000000127161256564762100315230ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import java.util.List; /** * An info provider for HDF5 archives. * * @author Bernd Rinn */ public interface IHDF5ArchiveInfoProvider { // // Information about individual entries // /** * Returns true, if an entry path exists in the archive. * * @param path The path to obtain information for. */ public boolean exists(String path); /** * Returns true, if a directory entry path exists in the archive. * * @param path The path to obtain information for. */ public boolean isDirectory(String path); /** * Returns true, if a regular file entry path exists in the archive. * * @param path The path to obtain information for. */ public boolean isRegularFile(String path); /** * Returns true, if a symbolic link entry path exists in the archive. * * @param path The path to obtain information for. */ public boolean isSymLink(String path); /** * Returns an archive entry for path, or null, if the archive has no * archive entry for this path. * * @param path The path to obtain information for. * @param readLinkTarget If true and if the entry is a symbolic link entry, read * the link target. */ public ArchiveEntry tryGetEntry(String path, boolean readLinkTarget); /** * Resolves the symbolic link of entry, if any. * * @param entry The archive entry to resolve. * @return The resolved link, if entry is a symbolic link that links to an existing * file or directory target, null if entry is a symbolic link * that links to a non-existing target, or entry, if this is not a link. */ public ArchiveEntry tryResolveLink(ArchiveEntry entry); /** * Returns the archive entry for path. If path is a symbolic link, the * entry will be resolved to the real file or directory in the archive, or null, if * the link target doesn't exist. * * @param path The path in the archive to get the entry for. * @param keepPath If true, the resolved entry will keep the path, i.e. * the returned entry of a symlink will look like a hard link. If false, * the returned entry will be the entry of the resolved path. * @return The resolved link, if path denotes a file, directory, or symbolic link * that links to an existing file or directory target, null if * path denotes a symbolic link that links to a non-existing target. */ public ArchiveEntry tryGetResolvedEntry(String path, boolean keepPath); // // Listing // /** * Returns the list of all entries in the archive recursively. * * @return The list of archive entries. */ public List list(); /** * Returns the list of all entries below fileOrDir in the archive recursively. * * @param fileOrDir The file to list or the directory to list the entries from recursively. * @return The list of archive entries. */ public List list(String fileOrDir); /** * Returns the list of entries below fileOrDir in the archive. * * @param fileOrDir The file to list or the directory to list the entries from. * @param params the parameters to modify the listing behavior. * @return The list of archive entries. */ public List list(String fileOrDir, ListParameters params); /** * Returns the list of all entries below fileOrDir in the archive recursively. * * @param fileOrDir The file to list or the directory to list the entries from recursively. * @param visitor The archive entry visitor to call for each entry. * @return This archive info provider. */ public IHDF5ArchiveInfoProvider list(String fileOrDir, IArchiveEntryVisitor visitor); /** * Returns the list of entries below fileOrDir in the archive. * * @param fileOrDir The file to list or the directory to list the entries from. * @param visitor The archive entry visitor to call for each entry. * @param params the parameters to modify the listing behavior. * @return This archive info provider. */ public IHDF5ArchiveInfoProvider list(String fileOrDir, IArchiveEntryVisitor visitor, ListParameters params); /** * Performs an integrity of the archive. * * @return All entries which failed the integrity check. */ public List test(); }libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/IHDF5ArchiveReader.java000066400000000000000000000440251256564762100303150ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import java.io.File; import java.io.InputStream; import java.io.OutputStream; import java.util.List; import ch.systemsx.cisd.base.io.IInputStream; /** * An interface for an HDF5 archive reader. * * @author Bernd Rinn */ public interface IHDF5ArchiveReader extends IHDF5ArchiveInfoProvider { /** * Closes this object and the file referenced by this object. This object must not be used after * being closed. Calling this method for a second time is a no-op. */ public void close(); /** * Returns true if this archive reader has been already closed. */ public boolean isClosed(); // // Verification // /** * Verifies the content of the archive against the filesystem. * * @param fileOrDir The file or directory entry in the archive to verify. May be empty, in which * case all entries below rootDirectoryInArchive are verified. * @param rootDirectoryOnFS The root directory on the file system that should be added to each * entry in the archive when comparing. * @param rootDirectoryInArchive The root directory in the archive to start verify from. It will * be stripped from each entry before rootDirectoryOnFS is added. * @param visitor The entry visitor to call for each entry. Call {@link ArchiveEntry#isOK()} to * check whether verification was successful. * @param missingArchiveEntryVisitor The entry visitor to call for each file that exists on the * filesystem, but is missing in the archive. * @param params The parameters to determine behavior of the verification process. * @return This archive reader. */ public IHDF5ArchiveReader verifyAgainstFilesystem(String fileOrDir, File rootDirectoryOnFS, String rootDirectoryInArchive, IArchiveEntryVisitor visitor, IArchiveEntryVisitor missingArchiveEntryVisitor, VerifyParameters params); /** * Verifies the content of the archive against the filesystem. * * @param fileOrDir The file or directory entry in the archive to verify. May be empty, in which * case all entries below rootDirectoryInArchive are verified. * @param rootDirectoryOnFS The root directory on the file system that should be added to each * entry in the archive when comparing. * @param rootDirectoryInArchive The root directory in the archive to start verify from. It will * be stripped from each entry before rootDirectoryOnFS is added. * @param visitor The entry visitor to call for each entry. Call {@link ArchiveEntry#isOK()} to * check whether verification was successful. * @param params The parameters to determine behavior of the verification process. * @return This archive reader. */ public IHDF5ArchiveReader verifyAgainstFilesystem(String fileOrDir, File rootDirectoryOnFS, String rootDirectoryInArchive, IArchiveEntryVisitor visitor, VerifyParameters params); /** * Verifies the content of the complete archive against the filesystem. * * @param fileOrDir The file or directory entry in the archive to verify. May be empty, in which * case all entries below rootDirectoryInArchive are verified. * @param rootDirectoryOnFS The root directory on the file system that should be added to each * entry in the archive when comparing. * @param visitor The entry visitor to call for each entry. Call {@link ArchiveEntry#isOK()} to * check whether verification was successful. * @param missingArchiveEntryVisitor The entry visitor to call for each file that exists on the * filesystem, but is missing in the archive. * @param params The parameters to determine behavior of the verification process. * @return This archive reader. */ public IHDF5ArchiveReader verifyAgainstFilesystem(String fileOrDir, File rootDirectoryOnFS, IArchiveEntryVisitor visitor, IArchiveEntryVisitor missingArchiveEntryVisitor, VerifyParameters params); /** * Verifies the content of the complete archive against the filesystem. * * @param fileOrDir The file or directory entry in the archive to verify. May be empty, in which * case all entries below rootDirectoryInArchive are verified. * @param rootDirectoryOnFS The root directory on the file system that should be added to each * entry in the archive when comparing. * @param visitor The entry visitor to call for each entry. Call {@link ArchiveEntry#isOK()} to * check whether verification was successful. * @param params The parameters to determine behavior of the verification process. * @return This archive reader. */ public IHDF5ArchiveReader verifyAgainstFilesystem(String fileOrDir, File rootDirectoryOnFS, IArchiveEntryVisitor visitor, VerifyParameters params); /** * Verifies the content of the complete archive against the filesystem. * * @param fileOrDir The file or directory entry in the archive to verify. May be empty, in which * case all entries below rootDirectoryInArchive are verified. * @param rootDirectoryOnFS The root directory on the file system that should be added to each * entry in the archive when comparing. * @param visitor The entry visitor to call for each entry. Call {@link ArchiveEntry#isOK()} to * check whether verification was successful. * @param missingArchiveEntryVisitor The entry visitor to call for each file that exists on the * filesystem, but is missing in the archive. * @return This archive reader. */ public IHDF5ArchiveReader verifyAgainstFilesystem(String fileOrDir, File rootDirectoryOnFS, IArchiveEntryVisitor visitor, IArchiveEntryVisitor missingArchiveEntryVisitor); /** * Verifies the content of the complete archive against the filesystem. * * @param fileOrDir The file or directory entry in the archive to verify. May be empty, in which * case all entries below rootDirectoryInArchive are verified. * @param rootDirectoryOnFS The root directory on the file system that should be added to each * entry in the archive when comparing. * @param visitor The entry visitor to call for each entry. Call {@link ArchiveEntry#isOK()} to * check whether verification was successful. * @return This archive reader. */ public IHDF5ArchiveReader verifyAgainstFilesystem(String fileOrDir, File rootDirectoryOnFS, IArchiveEntryVisitor visitor); /** * Verifies the content of the archive against the filesystem. * * @param fileOrDir The file or directory entry in the archive to verify. May be empty, in which * case all entries below rootDirectoryInArchive are verified. * @param rootDirectoryOnFS The root directory on the file system that should be added to each * entry in the archive when comparing. * @param rootDirectoryInArchive The root directory in the archive to start verify from. It will * be stripped from each entry before rootDirectoryOnFS is added. * @param params The parameters to determine behavior of the verification process. * @return The list of archive entries which failed verification. */ public List verifyAgainstFilesystem(String fileOrDir, File rootDirectoryOnFS, String rootDirectoryInArchive, VerifyParameters params); /** * Verifies the content of the archive against the filesystem. * * @param fileOrDir The file or directory entry in the archive to verify. May be empty, in which * case all entries below rootDirectoryInArchive are verified. * @param rootDirectoryOnFS The root directory on the file system that should be added to each * entry in the archive when comparing. * @param params The parameters to determine behavior of the verification process. * @return The list of archive entries which failed verification. */ public List verifyAgainstFilesystem(String fileOrDir, File rootDirectoryOnFS, VerifyParameters params); /** * Verifies the content of the archive against the filesystem. * * @param fileOrDir The file or directory entry in the archive to verify. May be empty, in which * case all entries below rootDirectoryInArchive are verified. * @param rootDirectoryOnFS The root directory on the file system that should be added to each * entry in the archive when comparing. * @return The list of archive entries which failed verification. */ public List verifyAgainstFilesystem(String fileOrDir, File rootDirectoryOnFS); /** * Verifies the content of the complete archive against the filesystem. * * @param rootDirectoryOnFS The root directory on the file system that should be added to each * entry in the archive when comparing. * @return The list of archive entries which failed verification. */ public List verifyAgainstFilesystem(File rootDirectoryOnFS); /** * Verifies the content of the archive against the filesystem. * * @param fileOrDir The file or directory entry in the archive to verify. May be empty, in which * case all entries below rootDirectoryInArchive are verified. * @param rootDirectoryOnFS The root directory on the file system that should be added to each * entry in the archive when comparing. * @param rootDirectoryInArchive The root directory in the archive to start verify from. It will * be stripped from each entry before rootDirectoryOnFS is added. */ public List verifyAgainstFilesystem(String fileOrDir, File rootDirectoryOnFS, String rootDirectoryInArchive); // // Extraction // /** * Extract the content of a file in the archive to an {@link OutputStream}. * * @param path The path of the file to extract the content of. * @param out The output stream to extract the content to. * @return This archive reader. */ public IHDF5ArchiveReader extractFile(String path, OutputStream out); /** * Extract the content of a file in the archive to a byte array. * * @param path The path of the file to extract the content of. * @return The byte array representing the content of the file. */ public byte[] extractFileAsByteArray(String path); /** * Extract the content of a file in the archive as an {@link IInputStream}. * * @param path The path of the file to extract the content of. * @return The input stream interface. If an error occurs and the * {@link ch.systemsx.cisd.base.exceptions.IErrorStrategy} of the archive reader does * not re-throw the exception, the return value will be null on errors. */ public IInputStream extractFileAsIInputStream(String path); /** * Extract the content of a file in the archive as an {@link InputStream}. * * @param path The path of the file to extract the content of. * @return The input stream. If an error occurs and the * {@link ch.systemsx.cisd.base.exceptions.IErrorStrategy} of the archive reader does * not re-throw the exception, the return value will be null on errors. */ public InputStream extractFileAsInputStream(String path); /** * Extracts the complete archive to the file system. * * @param rootDirectory The directory in the file system to use as root directory for the * extracted archive path. * @return This archive reader. */ public IHDF5ArchiveReader extractToFilesystem(File rootDirectory); /** * Extracts a path from the archive to the file system. * * @param rootDirectory The directory in the file system to use as root directory for the * extracted archive path. * @param path The path in the archive to extract. This path will be kept unchanged when * extracted. * @return This archive reader. */ public IHDF5ArchiveReader extractToFilesystem(File rootDirectory, String path); /** * Extracts a path from the archive to the file system. * * @param rootDirectory The directory in the file system to use as root directory for the * extracted archive path. * @param path The path in the archive to extract. This path will be kept unchanged when * extracted. * @param visitorOrNull The entry visitor to call for each entry. Call * {@link ArchiveEntry#isOK()} to check whether verification was successful. May be * null. * @return This archive reader. */ public IHDF5ArchiveReader extractToFilesystem(File rootDirectory, String path, IArchiveEntryVisitor visitorOrNull); /** * Extracts a path from the archive to the file system. * * @param rootDirectory The directory in the file system to use as root directory for the * extracted archive path. * @param path The path in the archive to extract. This path will be kept unchanged when * extracted. * @param strategy The strategy to determine which files and directories to extract and which * ones to suppress. * @param visitorOrNull The entry visitor to call for each entry. Call * {@link ArchiveEntry#isOK()} to check whether verification was successful. May be * null. * @return This archive reader. */ public IHDF5ArchiveReader extractToFilesystem(File rootDirectory, String path, ArchivingStrategy strategy, IArchiveEntryVisitor visitorOrNull); /** * Extracts all paths below a given directory path from the archive to the file system. * * @param rootDirectory The directory in the file system to use as root directory for the * extracted archive path. * @param rootInArchive The root path in the archive to extract. This path will be stripped when * extracted. * @return This archive reader. */ public IHDF5ArchiveReader extractToFilesystemBelowDirectory(File rootDirectory, String rootInArchive); /** * Extracts all paths below a given directory path from the archive to the file system. * * @param rootDirectory The directory in the file system to use as root directory for the * extracted archive path. * @param rootInArchive The root path in the archive to extract. This path will be stripped when * extracted. * @param visitorOrNull The entry visitor to call for each entry. Call * {@link ArchiveEntry#isOK()} to check whether verification was successful. May be * null. * @return This archive reader. */ public IHDF5ArchiveReader extractToFilesystemBelowDirectory(File rootDirectory, String rootInArchive, IArchiveEntryVisitor visitorOrNull); /** * Extracts all paths below a given directory path from the archive to the file system. * * @param rootDirectory The directory in the file system to use as root directory for the * extracted archive path. * @param rootInArchive The root path in the archive to extract. This path will be stripped when * extracted. * @param strategy The strategy to determine which files and directories to extract and which * ones to suppress. * @param visitorOrNull The entry visitor to call for each entry. Call * {@link ArchiveEntry#isOK()} to check whether verification was successful. May be * null. * @return This archive reader. */ public IHDF5ArchiveReader extractToFilesystemBelowDirectory(File rootDirectory, String rootInArchive, ArchivingStrategy strategy, IArchiveEntryVisitor visitorOrNull); /** * Extracts a path from the archive below a given directory path to the file system. * * @param rootDirectory The directory in the file system to use as root directory for the * extracted archive path. * @param rootInArchive The root path in the archive to extract. This path will be stripped when * extracted. * @param path The path in the archive to extract, relative to rootPathInArchive. * This path will be kept unchanged when extracted. * @param strategy The strategy to determine which files and directories to extract and which * ones to suppress. * @param visitorOrNull The entry visitor to call for each entry. Call * {@link ArchiveEntry#isOK()} to check whether verification was successful. May be * null. * @return This archive reader. */ public IHDF5ArchiveReader extractToFilesystemBelowDirectory(File rootDirectory, String rootInArchive, String path, ArchivingStrategy strategy, IArchiveEntryVisitor visitorOrNull); }libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/IHDF5Archiver.java000066400000000000000000000457731256564762100273670ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import java.io.File; import java.io.IOException; import java.io.InputStream; import java.io.OutputStream; import java.util.List; import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked; import ch.systemsx.cisd.base.io.IOutputStream; import ch.systemsx.cisd.hdf5.h5ar.NewArchiveEntry.NewDirectoryArchiveEntry; import ch.systemsx.cisd.hdf5.h5ar.NewArchiveEntry.NewFileArchiveEntry; import ch.systemsx.cisd.hdf5.h5ar.NewArchiveEntry.NewSymLinkArchiveEntry; /** * An interface for the HDF5 archiver. * * @author Bernd Rinn */ public interface IHDF5Archiver extends IHDF5ArchiveReader { /** * Flush the underlying HDF5 writer. */ public void flush() throws IOException; /** * Archive the path from the filesystem. * * @param path The file or directory to archive. Everything below this path is archived. */ public IHDF5Archiver archiveFromFilesystem(File path) throws IllegalStateException; /** * Archive the path from the filesystem. * * @param path The file or directory to archive. Everything below this path is archived. * @param strategy The archiving strategy to use. This strategy object determines which files to * include and to exclude and which files to compress. */ public IHDF5Archiver archiveFromFilesystem(File path, ArchivingStrategy strategy); /** * Archive the path from the filesystem. * * @param path The file or directory to archive. Everything below this path is archived. * @param visitor The {@link IArchiveEntryVisitor} to use. Can be null. */ public IHDF5Archiver archiveFromFilesystem(File path, IArchiveEntryVisitor visitor); /** * Archive the path from the filesystem. * * @param path The file or directory to archive. Everything below this path is archived. The * name part of path may be kept, depending on the value of * keepNameFromPath. * @param strategy The archiving strategy to use. This strategy object determines which files to * include and to exclude and which files to compress. * @param keepNameFromPath If true, the name part of path is kept in the * archive. Otherwise, path will represent "/" in the archive. * @param visitor The {@link IArchiveEntryVisitor} to use. Can be null. */ public IHDF5Archiver archiveFromFilesystem(File path, ArchivingStrategy strategy, boolean keepNameFromPath, IArchiveEntryVisitor visitor); /** * Archive the path from the filesystem. * * @param parentDirToStrip The parent directory of path on the filesystem which * should be stripped in the archive. It is an error, if parentDirToStrip * is not a parent directory of path. Example: If * path=/home/joe/work/a/b/c and * parentDirToStrip=/home/joe/work, then c will end up in * the archive at the path a/b. * @param path The file or directory to archive. */ public IHDF5Archiver archiveFromFilesystem(File parentDirToStrip, File path); /** * Archive the path from the filesystem. * * @param parentDirToStrip The parent directory of path on the filesystem which * should be stripped in the archive. It is an error, if parentDirToStrip * is not a parent directory of path. Example: If * path=/home/joe/work/a/b/c and * parentDirToStrip=/home/joe/work, then c will end up in * the archive at the path a/b. * @param path The file or directory to archive. * @param strategy The archiving strategy to use. This strategy object determines which files to * include and to exclude and which files to compress. */ public IHDF5Archiver archiveFromFilesystem(File parentDirToStrip, File path, ArchivingStrategy strategy); /** * Archive the path from the filesystem. * * @param parentDirToStrip The parent directory of path on the filesystem which * should be stripped in the archive. It is an error, if parentDirToStrip * is not a parent directory of path. Example: If * path=/home/joe/work/a/b/c and * parentDirToStrip=/home/joe/work, then c will end up in * the archive at the path /a/b/c. * @param path The file or directory to archive. * @param strategy The archiving strategy to use. This strategy object determines which files to * include and to exclude and which files to compress. * @param visitor The {@link IArchiveEntryVisitor} to use. Can be null. */ public IHDF5Archiver archiveFromFilesystem(File parentDirToStrip, File path, ArchivingStrategy strategy, IArchiveEntryVisitor visitor); /** * Archive the path from the filesystem. * * @param rootInArchive The root directory of path in the archive. Example: If * path=/home/joe/work/a/b/c and rootInArchive=/t, then * c will end up in the archive at the path /t/c. If * rootInArchive is the last part of the parent directory of * path on the filesystem, then its metadata will be taken from the * filesystem. * @param path The file or directory to archive. */ public IHDF5Archiver archiveFromFilesystem(String rootInArchive, File path); /** * Archive the path from the filesystem. * * @param rootInArchive The root directory of path in the archive. Example: If * path=/home/joe/work/a/b/c and rootInArchive=/t, then * c will end up in the archive at the path /t/c. If * rootInArchive is the last part of the parent directory of * path on the filesystem, then its metadata will be taken from the * filesystem. * @param path The file or directory to archive. * @param strategy The archiving strategy to use. This strategy object determines which files to * include and to exclude and which files to compress. */ public IHDF5Archiver archiveFromFilesystem(String rootInArchive, File path, ArchivingStrategy strategy); /** * Archive the path from the filesystem. * * @param rootInArchive The root directory of path in the archive. Example: If * path=/home/joe/work/a/b/c and rootInArchive=/t, then * c will end up in the archive at the path /t/c. If * rootInArchive is the last part of the parent directory of * path on the filesystem, then its metadata will be taken from the * filesystem. * @param path The file or directory to archive. * @param strategy The archiving strategy to use. This strategy object determines which files to * include and to exclude and which files to compress. * @param visitor The {@link IArchiveEntryVisitor} to use. Can be null. */ public IHDF5Archiver archiveFromFilesystem(String rootInArchive, File path, ArchivingStrategy strategy, IArchiveEntryVisitor visitor); /** * Archive the content below directory from the filesystem. * * @param rootInArchive The root directory of path in the archive. Example: If * directory=/home/joe/work/a/b, directory b has two files * c and d, and rootInArchive=/t, then the * archive will have c at path /t/c and d at * path /t/d. * @param directory The directory to archive the content of. It is an error if this is not a * directory on the filesystem. */ public IHDF5Archiver archiveFromFilesystemBelowDirectory(String rootInArchive, File directory); /** * Archive the content below directory from the filesystem. * * @param rootInArchive The root directory of path in the archive. Example: If * path=/home/joe/work/a/b/c and rootInArchive=/t, then * c will end up in the archive at the path /t/c. If * rootInArchive is the last part of the parent directory of * path on the filesystem, then its metadata will be taken from the * filesystem. * @param directory The directory to archive the content of. It is an error if this is not an * existing directory. * @param strategy The archiving strategy to use. This strategy object determines which files to * include and to exclude and which files to compress. */ public IHDF5Archiver archiveFromFilesystemBelowDirectory(String rootInArchive, File directory, ArchivingStrategy strategy); /** * Archive the content below directory from the filesystem. * * @param rootInArchive The root directory of path in the archive. Example: If * path=/home/joe/work/a/b/c and rootInArchive=/t, then * c will end up in the archive at the path /t/c. If * rootInArchive is the last part of the parent directory of * path on the filesystem, then its metadata will be taken from the * filesystem. * @param directory The directory to archive the content of. It is an error if this is not an * existing directory. * @param visitor The {@link IArchiveEntryVisitor} to use. Can be null. */ public IHDF5Archiver archiveFromFilesystemBelowDirectory(String rootInArchive, File directory, IArchiveEntryVisitor visitor); /** * Archive the content below directory from the filesystem. * * @param rootInArchive The root directory of path in the archive. Example: If * path=/home/joe/work/a/b/c and rootInArchive=/t, then * c will end up in the archive at the path /t/c. If * rootInArchive is the last part of the parent directory of * path on the filesystem, then its metadata will be taken from the * filesystem. * @param directory The directory to archive the content of. It is an error if this is not an * existing directory. * @param strategy The archiving strategy to use. This strategy object determines which files to * include and to exclude and which files to compress. * @param visitor The {@link IArchiveEntryVisitor} to use. Can be null. */ public IHDF5Archiver archiveFromFilesystemBelowDirectory(String rootInArchive, File directory, ArchivingStrategy strategy, IArchiveEntryVisitor visitor); /** * Archive the data as file in the archive. * * @param path The path to archive the data at. * @param data The bytes to archive as file content. */ public IHDF5Archiver archiveFile(String path, byte[] data); /** * Archive the input as file in the archive. * * @param path The path to archive the data at. * @param input The input stream to get the file content from. */ public IHDF5Archiver archiveFile(String path, InputStream input); /** * Archive the input as file in the archive. * * @param entry The archive entry (defining the path) to archive the data at. * @param input The input stream to get the file content from. */ public IHDF5Archiver archiveFile(NewFileArchiveEntry entry, InputStream input); /** * Archive the data as file in the archive. * * @param entry The archive entry (defining the path) to archive the data at. * @param data The bytes to archive as file content. */ public IHDF5Archiver archiveFile(NewFileArchiveEntry entry, byte[] data); /** * Return an {@link IOutputStream} that can be used to write the content of a file into the * archive. * * @param entry The archive entry (defining the path) to archive the data at. * @return The output stream that the file content is written to. */ public IOutputStream archiveFileAsIOutputStream(NewFileArchiveEntry entry); /** * Return an {@link OutputStream} that can be used to write the content of a file into the * archive. * * @param entry The archive entry (defining the path) to archive the data at. * @return The output stream that the file content is written to. */ public OutputStream archiveFileAsOutputStream(NewFileArchiveEntry entry); /** * Add a new symbolic link to the archive. * * @param path The path where the symbolic link resides. * @param linkTarget The target where the symbolic link points to. */ public IHDF5Archiver archiveSymlink(String path, String linkTarget); /** * Add a new symbolic link to the archive. * * @param entry The archive entry describing the symbolic link. */ public IHDF5Archiver archiveSymlink(NewSymLinkArchiveEntry entry); /** * Add a new directory to the archive. * * @param path The path in the archive where the directory resides. */ public IHDF5Archiver archiveDirectory(String path); /** * Add a new directory to the archive. * * @param entry The archive entry describing the directory. */ public IHDF5Archiver archiveDirectory(NewDirectoryArchiveEntry entry); /** * Deletes a path from the archive. * * @param path The path to delete. */ public IHDF5Archiver delete(String path); /** * Deletes a list of paths from the archive. * * @param paths The paths to delete. */ public IHDF5Archiver delete(List paths); /** * Deletes a list of paths from the archive. * * @param paths The paths to delete. * @param entryVisitorOrNull The visitor for each archive entry which is actually deleted. If no * errors occur, the visitor will be called once for each path in the list of * paths. */ public IHDF5Archiver delete(List paths, IArchiveEntryVisitor entryVisitorOrNull); // Method overridden from IHDF5ArchiveReader, see there for javadoc. @Override public IHDF5Archiver list(String fileOrDir, IArchiveEntryVisitor visitor); @Override public IHDF5Archiver list(String fileOrDir, IArchiveEntryVisitor visitor, ListParameters params); @Override public IHDF5Archiver verifyAgainstFilesystem(String fileOrDir, File rootDirectoryOnFS, String rootDirectoryInArchive, IArchiveEntryVisitor visitor, IArchiveEntryVisitor missingArchiveEntryVisitor, VerifyParameters params); @Override public IHDF5Archiver verifyAgainstFilesystem(String fileOrDir, File rootDirectoryOnFS, String rootDirectoryInArchive, IArchiveEntryVisitor visitor, VerifyParameters params); @Override public IHDF5Archiver verifyAgainstFilesystem(String fileOrDir, File rootDirectoryOnFS, IArchiveEntryVisitor visitor, IArchiveEntryVisitor missingArchiveEntryVisitor, VerifyParameters params); @Override public IHDF5Archiver verifyAgainstFilesystem(String fileOrDir, File rootDirectoryOnFS, IArchiveEntryVisitor visitor, VerifyParameters params); @Override public IHDF5Archiver verifyAgainstFilesystem(String fileOrDir, File rootDirectoryOnFS, IArchiveEntryVisitor visitor, IArchiveEntryVisitor missingArchiveEntryVisitor); @Override public IHDF5Archiver verifyAgainstFilesystem(String fileOrDir, File rootDirectoryOnFS, IArchiveEntryVisitor visitor); @Override public List verifyAgainstFilesystem(String fileOrDir, File rootDirectoryOnFS, String rootDirectoryInArchive, VerifyParameters params); @Override public List verifyAgainstFilesystem(String fileOrDir, File rootDirectoryOnFS, String rootDirectoryInArchive); @Override public IHDF5Archiver extractFile(String path, OutputStream out) throws IOExceptionUnchecked; @Override public IHDF5Archiver extractToFilesystem(File rootDirectory); @Override public IHDF5Archiver extractToFilesystem(File rootDirectory, String path) throws IllegalStateException; @Override public IHDF5Archiver extractToFilesystem(File rootDirectory, String path, IArchiveEntryVisitor visitor) throws IllegalStateException; @Override public IHDF5Archiver extractToFilesystem(File rootDirectory, String path, ArchivingStrategy strategy, IArchiveEntryVisitor visitor) throws IllegalStateException; @Override public IHDF5Archiver extractToFilesystemBelowDirectory(File rootDirectory, String rootPathInArchive); @Override public IHDF5Archiver extractToFilesystemBelowDirectory(File rootDirectory, String rootPathInArchive, IArchiveEntryVisitor visitorOrNull); @Override public IHDF5Archiver extractToFilesystemBelowDirectory(File rootDirectory, String rootPathInArchive, ArchivingStrategy strategy, IArchiveEntryVisitor visitorOrNull); @Override public IHDF5Archiver extractToFilesystemBelowDirectory(File rootDirectory, String rootPathInArchive, String path, ArchivingStrategy strategy, IArchiveEntryVisitor visitorOrNull) throws IllegalStateException; }libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/IdCache.java000066400000000000000000000060021256564762100263420ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import java.util.Collections; import java.util.HashMap; import java.util.Map; import ch.systemsx.cisd.base.unix.Unix; import ch.systemsx.cisd.base.unix.Unix.Stat; /** * Cache for ID -> Name mapping. * * @author Bernd Rinn */ final class IdCache { /** Gid -> Group Name */ private final Map gidMap = Collections .synchronizedMap(new HashMap()); /** Uid -> User Name */ private final Map uidMap = Collections .synchronizedMap(new HashMap()); /** * Returns the name for the given uid. */ String getUser(LinkRecord link, boolean numeric) { return getUser(link.getUid(), numeric); } /** * Returns the name for the given uid. */ String getUser(Stat link, boolean numeric) { return getUser(link.getUid(), numeric); } String getUser(int uid, boolean numeric) { String userNameOrNull = uidMap.get(uidMap); if (userNameOrNull == null) { userNameOrNull = (numeric == false && Unix.isOperational()) ? Unix.tryGetUserNameForUid(uid) : null; if (userNameOrNull == null) { userNameOrNull = Integer.toString(uid); } uidMap.put(uid, userNameOrNull); } return userNameOrNull; } /** * Returns the name for the given gid. */ String getGroup(LinkRecord link, boolean numeric) { return getGroup(link.getGid(), numeric); } /** * Returns the name for the given gid. */ String getGroup(Stat link, boolean numeric) { return getGroup(link.getGid(), numeric); } /** * Returns the name for the given gid. */ String getGroup(int gid, boolean numeric) { String groupNameOrNull = gidMap.get(uidMap); if (groupNameOrNull == null) { groupNameOrNull = (numeric == false && Unix.isOperational()) ? Unix.tryGetGroupNameForGid(gid) : null; if (groupNameOrNull == null) { groupNameOrNull = Integer.toString(gid); } gidMap.put(gid, groupNameOrNull); } return groupNameOrNull; } }libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/LinkRecord.java000066400000000000000000000331411256564762100271220ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import java.io.File; import ch.systemsx.cisd.base.exceptions.IErrorStrategy; import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked; import ch.systemsx.cisd.base.unix.FileLinkType; import ch.systemsx.cisd.base.unix.Unix; import ch.systemsx.cisd.base.unix.Unix.Stat; import ch.systemsx.cisd.hdf5.CompoundElement; import ch.systemsx.cisd.hdf5.CompoundType; import ch.systemsx.cisd.hdf5.HDF5LinkInformation; import ch.systemsx.cisd.hdf5.IHDF5Reader; /** * A class containing all information we need to have about a link either in the file system or in * an HDF5 container. * * @author Bernd Rinn */ @CompoundType(name = "Link", mapAllFields = false) final class LinkRecord implements Comparable { @CompoundElement(memberName = "linkNameLength") private int linkNameLength; @CompoundElement(memberName = "linkType", typeName = "linkType") private FileLinkType linkType; @CompoundElement(memberName = "size") private long size; @CompoundElement(memberName = "lastModified") private long lastModified; @CompoundElement(memberName = "uid") private int uid; @CompoundElement(memberName = "gid") private int gid; @CompoundElement(memberName = "permissions") private short permissions; @CompoundElement(memberName = "checksum") private int crc32; private boolean hasCrc32Checksum = false; private String linkName; private String linkTargetOrNull; private FileLinkType verifiedType; private long verifiedSize = Utils.UNKNOWN; private int verifiedCrc32 = 0; private long verifiedLastModified = Utils.UNKNOWN; /** * Returns a {@link LinkRecord} object for the given link {@link File}, or * null if a system call fails and continueOnError is true. */ public static LinkRecord tryCreate(File file, IErrorStrategy errorStrategy) { try { return new LinkRecord(file); } catch (IOExceptionUnchecked ex) { errorStrategy.dealWithError(new ArchivingException(file, ex.getCause())); return null; } } /** * Returns the link target of symbolicLink, or null, if * symbolicLink is not a symbolic link or the link target could not be read. */ public static String tryReadLinkTarget(File symbolicLink) { if (Unix.isOperational()) { return Unix.tryReadSymbolicLink(symbolicLink.getPath()); } else { return null; } } /** * Returns a link record for normalizedPath in the HDF5 archive represented by * hdf5Reader, or null, if this path does not exist in the archive. */ public static LinkRecord tryReadFromArchive(IHDF5Reader hdf5Reader, String normalizedPath) { final HDF5LinkInformation linfo = hdf5Reader.object().getLinkInformation(normalizedPath); if (linfo.exists() == false) { return null; } final long size = linfo.isDataSet() ? hdf5Reader.object().getSize(linfo.getPath()) : Utils.UNKNOWN; return new LinkRecord(linfo, size); } /** * Used by the HDF5 library during reading. */ LinkRecord() { } /** * A link for user-created {@Link NewArchiveEntry}. */ LinkRecord(NewArchiveEntry entry) { this(entry.getName(), entry.getLinkTarget(), entry.getLinkType(), Utils.UNKNOWN, entry .getLastModified(), entry.getUid(), entry.getGid(), entry.getPermissions(), Utils.UNKNOWN); } /** * Creates a link record for a new directory entry. */ LinkRecord(String hdf5DirectoryPath) { this(hdf5DirectoryPath, System.currentTimeMillis() / Utils.MILLIS_PER_SECOND, Utils .getCurrentUid(), Utils.getCurrentGid(), (short) 0755); } /** * Creates the root directory entry from the File of the HDF5 archive. */ static LinkRecord getLinkRecordForArchiveRoot(File hdf5Archive) { if (Unix.isOperational()) { final Stat stat = Unix.getFileInfo(hdf5Archive.getPath()); return new LinkRecord("", stat.getLastModified(), stat.getUid(), stat.getGid(), stat.getPermissions()); } else { return new LinkRecord("", hdf5Archive.lastModified() / Utils.MILLIS_PER_SECOND, Utils.getCurrentUid(), Utils.getCurrentGid(), Utils.UNKNOWN_S); } } /** * Creates the link record for a file in the file system. */ static LinkRecord getLinkRecordForLink(File file) { if (Unix.isOperational()) { final Stat stat = Unix.getLinkInfo(file.getPath()); return new LinkRecord(file.getName(), stat.tryGetSymbolicLink(), stat.getLinkType(), stat.getSize(), stat.getLastModified(), stat.getUid(), stat.getGid(), stat.getPermissions(), (short) 0); } else { return new LinkRecord(file.getName(), null, file.isDirectory() ? FileLinkType.DIRECTORY : FileLinkType.REGULAR_FILE, file.length(), file.lastModified() / Utils.MILLIS_PER_SECOND, Utils.getCurrentUid(), Utils.getCurrentGid(), Utils.UNKNOWN_S, (short) 0); } } /** * Creates a directory entry. */ LinkRecord(String hdf5DirectoryPath, long lastModified, int uid, int gid, short permissions) { this.linkName = hdf5DirectoryPath; this.linkTargetOrNull = null; this.linkType = FileLinkType.DIRECTORY; this.lastModified = lastModified; this.uid = uid; this.gid = gid; this.permissions = permissions; } /** * Used by {@link DirectoryIndex}. */ LinkRecord(HDF5LinkInformation info, long size) { this.linkName = info.getName(); this.linkTargetOrNull = info.tryGetSymbolicLinkTarget(); this.linkType = Utils.translateType(info.getType()); this.size = size; this.lastModified = Utils.UNKNOWN; this.uid = Utils.UNKNOWN; this.gid = Utils.UNKNOWN; this.permissions = Utils.UNKNOWN_S; } /** * Returns a {@link LinkRecord} object for the given link {@link File}. */ private LinkRecord(File file) { this.linkName = file.getName(); if (Unix.isOperational()) { final Stat info = Unix.getLinkInfo(file.getPath(), false); this.linkType = info.getLinkType(); this.size = (linkType == FileLinkType.REGULAR_FILE) ? info.getSize() : 0; this.lastModified = info.getLastModified(); this.uid = info.getUid(); this.gid = info.getGid(); this.permissions = info.getPermissions(); } else { this.linkType = (file.isDirectory()) ? FileLinkType.DIRECTORY : (file.isFile() ? FileLinkType.REGULAR_FILE : FileLinkType.OTHER); this.size = (linkType == FileLinkType.REGULAR_FILE) ? file.length() : 0; this.lastModified = file.lastModified() / Utils.MILLIS_PER_SECOND; this.uid = Utils.UNKNOWN; this.gid = Utils.UNKNOWN; this.permissions = Utils.UNKNOWN_S; } if (linkType == FileLinkType.SYMLINK) { this.linkTargetOrNull = tryReadLinkTarget(file); } } LinkRecord(String linkName, String linkTargetOrNull, FileLinkType linkType, long size, long lastModified, int uid, int gid, short permissions, int crc32) { this.linkName = linkName; this.linkTargetOrNull = linkTargetOrNull; this.linkType = linkType; this.size = size; this.lastModified = lastModified; this.uid = uid; this.gid = gid; this.permissions = permissions; this.crc32 = crc32; } /** * Call this method after reading the link from the archive and before using it. */ int initAfterReading(String concatenatedNames, int startPos, IHDF5Reader reader, String groupPath, boolean readLinkTarget) { this.hasCrc32Checksum = true; final int endPos = startPos + linkNameLength; this.linkName = concatenatedNames.substring(startPos, endPos); if (readLinkTarget && linkType == FileLinkType.SYMLINK) { this.linkTargetOrNull = reader.object().getLinkInformation(groupPath + "/" + linkName) .tryGetSymbolicLinkTarget(); } return endPos; } /** * Call this method to read additionally the link target of a symlink. */ void addLinkTarget(IHDF5Reader reader, String groupPath) { if (linkType == FileLinkType.SYMLINK && linkTargetOrNull == null) { this.linkTargetOrNull = reader.object().getLinkInformation(groupPath + "/" + linkName) .tryGetSymbolicLinkTarget(); } } /** * Call this method before writing the link to the archive. */ void prepareForWriting(StringBuilder concatenatedNames) { this.linkNameLength = this.linkName.length(); concatenatedNames.append(linkName); } public String getLinkName() { return linkName; } public String tryGetLinkTarget() { return linkTargetOrNull; } public boolean isDirectory() { return linkType == FileLinkType.DIRECTORY; } public boolean isSymLink() { return linkType == FileLinkType.SYMLINK; } public boolean isRegularFile() { return linkType == FileLinkType.REGULAR_FILE; } public FileLinkType getLinkType() { return linkType; } public void setSize(long size) { this.size = size; } public long getSize() { return size; } public boolean hasLastModified() { return lastModified >= 0; } public long getLastModified() { return lastModified; } public boolean hasUnixPermissions() { return uid >= 0 && gid >= 0 && permissions >= 0; } public int getUid() { return uid; } public int getGid() { return gid; } public short getPermissions() { return permissions; } public ArchiveEntryCompleteness getCompleteness() { if (hasUnixPermissions()) { return ArchiveEntryCompleteness.FULL; } else if (hasLastModified()) { return ArchiveEntryCompleteness.LAST_MODIFIED; } else { return ArchiveEntryCompleteness.BASE; } } public int getCrc32() { return crc32; } public void setCrc32(int crc32) { this.crc32 = crc32; this.hasCrc32Checksum = true; } boolean hasCRC32Checksum() { return hasCrc32Checksum; } public FileLinkType getVerifiedType() { return verifiedType; } public void setVerifiedType(FileLinkType verifiedType) { this.verifiedType = verifiedType; } public int getVerifiedCrc32() { return verifiedCrc32; } public long getVerifiedSize() { return verifiedSize; } public long getVerifiedLastModified() { return verifiedLastModified; } public void setFileVerification(long size, int crc32, long lastModified) { this.verifiedSize = size; this.verifiedCrc32 = crc32; this.verifiedLastModified = lastModified; } public void resetVerification() { verifiedType = null; verifiedSize = Utils.UNKNOWN; verifiedCrc32 = 0; verifiedLastModified = Utils.UNKNOWN; } // // Comparable // @Override public int compareTo(LinkRecord o) { // We put all directories before all files. if (isDirectory() && o.isDirectory() == false) { return -1; } else if (isDirectory() == false && o.isDirectory()) { return 1; } else { return getLinkName().compareTo(o.getLinkName()); } } // // Object // @Override public boolean equals(Object obj) { if (obj == null || obj instanceof LinkRecord == false) { return false; } final LinkRecord that = (LinkRecord) obj; return this.linkName.equals(that.linkName); } @Override public int hashCode() { return linkName.hashCode(); } @Override public String toString() { return "LinkRecord [linkName=" + linkName + ", linkType=" + linkType + ", size=" + size + ", lastModified=" + lastModified + ", uid=" + uid + ", gid=" + gid + ", permissions=" + permissions + ", crc32=" + crc32 + ", linkTargetOrNull=" + linkTargetOrNull + "]"; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/LinkStore.java000066400000000000000000000117621256564762100270050ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import java.util.ArrayList; import java.util.Arrays; import java.util.Collection; import java.util.HashMap; import java.util.Iterator; import java.util.Map; import ch.systemsx.cisd.hdf5.IHDF5Reader; /** * A store for {@link LinkRecord}s. * * @author Bernd Rinn */ final class LinkStore implements Iterable { private Map linkMap; private LinkRecord[] sortedArrayOrNull; private boolean linkMapPopulated = false; /** * Creates a new empty link list. */ LinkStore() { this(new LinkRecord[0]); } /** * Creates a new link store and populates it with entries. * * @param sortedEntries The links to populate the store with initially. The links are expected to be * sorted. */ LinkStore(LinkRecord[] sortedEntries) { this.sortedArrayOrNull = sortedEntries; } private Map getLinkMap() { if (linkMapPopulated == false && sortedArrayOrNull != null) { linkMap = new HashMap(sortedArrayOrNull.length); // Build the map lazily. for (LinkRecord entry : sortedArrayOrNull) { linkMap.put(entry.getLinkName(), entry); } linkMapPopulated = true; } return linkMap; } /** * Returns an array of the links in this store, in the order defined by * {@link LinkRecord#compareTo(LinkRecord)}. */ public synchronized LinkRecord[] getLinkArray() { if (sortedArrayOrNull == null) { sortedArrayOrNull = getLinkMap().values().toArray(new LinkRecord[getLinkMap().size()]); Arrays.sort(sortedArrayOrNull); } return sortedArrayOrNull; } public synchronized void amendLinkTargets(IHDF5Reader reader, String groupPath) { for (LinkRecord link : getLinkMap().values()) { link.addLinkTarget(reader, groupPath); } } /** * Returns the link with {@link LinkRecord#getLinkName()} equal to name, or * null, if there is no such link in the directory index. */ public synchronized LinkRecord tryGetLink(String name) { return getLinkMap().get(name); } public boolean exists(String name) { return tryGetLink(name) != null; } /** * Returns true if this list is empty. */ public synchronized boolean isEmpty() { return getLinkMap().isEmpty(); } // // Iterable // /** * Returns an iterator over all links in the list, in the order defined by * {@link LinkRecord#compareTo(LinkRecord)}. */ @Override public synchronized Iterator iterator() { final LinkRecord[] list = getLinkArray(); for (LinkRecord link : list) { link.resetVerification(); } return new ArrayList(Arrays.asList(list)).iterator(); } /** * Updates the entries in the store. */ public synchronized void update(LinkRecord entry) { getLinkMap().put(entry.getLinkName(), entry); sortedArrayOrNull = null; } /** * Updates the entries in the store. */ public synchronized void update(LinkRecord[] entries) { for (LinkRecord entry : entries) { getLinkMap().put(entry.getLinkName(), entry); } if (entries.length > 0) { sortedArrayOrNull = null; } } /** * Updates the entries in the store. */ public synchronized void update(Collection entries) { for (LinkRecord entry : entries) { getLinkMap().put(entry.getLinkName(), entry); } if (entries.size() > 0) { sortedArrayOrNull = null; } } /** * Removes linkName from the store. * * @return true, if it was removed, false, if it couldn't be found. */ public synchronized boolean remove(String linkName) { final boolean storeChanged = (getLinkMap().remove(linkName) != null); if (storeChanged) { sortedArrayOrNull = null; } return storeChanged; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/ListArchiveException.java000066400000000000000000000030731256564762100311630ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import java.io.File; import java.io.IOException; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; /** * Exception thrown when listing a file / directory in an archive fails. * * @author Bernd Rinn */ public class ListArchiveException extends ArchiverException { private static final long serialVersionUID = 1L; private static final String OPERATION_NAME = "listing"; public ListArchiveException(String objectPath, String detailedMsg) { super(objectPath, OPERATION_NAME, detailedMsg); } public ListArchiveException(String objectPath, HDF5Exception cause) { super(objectPath, OPERATION_NAME, cause); } public ListArchiveException(String objectPath, RuntimeException cause) { super(objectPath, OPERATION_NAME, cause); } public ListArchiveException(File file, IOException cause) { super(file, OPERATION_NAME, cause); } } ListArchiveTooManySymbolicLinksException.java000066400000000000000000000022271256564762100351160ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; /** * This exception is thrown when HDF5 detects too many symbolic links in a path. This error * indicates that there is an infinite loop of symbolic links. * * @author Bernd Rinn */ public class ListArchiveTooManySymbolicLinksException extends ListArchiveException { private static final long serialVersionUID = 1L; public ListArchiveTooManySymbolicLinksException(String objectPath, HDF5Exception cause) { super(objectPath, cause); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/ListParameters.java000066400000000000000000000275561256564762100300420ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; /** * A class that represents parameters for {@link HDF5Archiver#list(String, ListParameters)}. * * @author Bernd Rinn */ public final class ListParameters { private final boolean recursive; private final boolean readLinkTargets; private final boolean testArchive; private final boolean suppressDirectoryEntries; private final boolean includeTopLevelDirectoryEntry; private final boolean resolveSymbolicLinks; private final boolean followSymbolicLinks; /** * The default list parameters: *

    *
  • recursive
    • *
  • does not test the integrity of the archive
    • *
  • does not suppress directory entries
    • *
  • exclude the top-level directory
    • *
  • reads symbolic link targets
    • *
  • does not resolve symbolic links
    • *
  • does not follow symbolic links
    • *
*/ public static final ListParameters DEFAULT = new ListParameters(true, true, false, false, false, false, false); /** * The list parameters for testing the archive integrity: *
    *
  • recursive
    • *
  • tests the integrity of the archive
    • *
  • does not suppress directory entries
    • *
  • includes the top-level directory
    • *
  • reads symbolic link targets
    • *
  • does not resolve symbolic links
    • *
  • does not follow symbolic links
    • *
*/ public static final ListParameters TEST = new ListParameters(true, true, true, false, true, false, false); /** * A class for constructing a new list parameters object. */ public static final class ListParametersBuilder { private boolean recursive = true; private boolean readLinkTargets = true; private boolean testArchive = false; private boolean suppressDirectoryEntries = false; private boolean includeTopLevelDirectoryEntry = false; private boolean resolveSymbolicLinks = false; private boolean followSymbolicLinks = false; private ListParametersBuilder() { } /** * Perform a non-recursive listing, i.e. do not traverse sub-directories. */ public ListParametersBuilder nonRecursive() { this.recursive = false; return this; } /** * If recursive is true, perform a recursive listing, if it is * false, perform a non-recursive listing, i.e. do not traverse * sub-directories. */ public ListParametersBuilder recursive(@SuppressWarnings("hiding") boolean recursive) { this.recursive = recursive; return this; } /** * Do not read the link target of symbolic links. */ public ListParametersBuilder noReadLinkTarget() { this.readLinkTargets = false; return this; } /** * If readLinkTargets is true, then read the link targets of * symbolic links, if it is false, do not read the link targets. */ public ListParametersBuilder readLinkTargets(@SuppressWarnings("hiding") boolean readLinkTargets) { this.readLinkTargets = readLinkTargets; return this; } /** * Perform an integrity test of the archive, i.e. see whether the index and the content of * the archive match with respect to types, sizes and checksums. */ public ListParametersBuilder testArchive() { this.testArchive = true; return this; } /** * If testArchive is true, perform an integrity test of the archive, * i.e. see whether the index and the content of the archive match with respect to types, * sizes and checksums, if it is false, do not perform an integrity check. */ public ListParametersBuilder testArchive(@SuppressWarnings("hiding") boolean testArchive) { this.testArchive = testArchive; return this; } /** * Suppress directory entries from being listed. Only files and links will be listed. */ public ListParametersBuilder suppressDirectoryEntries() { this.suppressDirectoryEntries = true; return this; } /** * If suppressDirectoryEntries is true, suppress directory entries * from being listed. Only files and links will be listed, if it is false, list * also directories. */ public ListParametersBuilder suppressDirectoryEntries(@SuppressWarnings("hiding") boolean suppressDirectoryEntries) { this.suppressDirectoryEntries = suppressDirectoryEntries; return this; } /** * Includes the top-level (or starting) directory into the listing. *

* Note that the root directory "/" will never be listed, so this parameter is only * effective when the top-level directory of the listing is not the root directory. */ public ListParametersBuilder includeTopLevelDirectoryEntry() { this.includeTopLevelDirectoryEntry = true; return this; } /** * If includeTopLevelDirectoryEntry is true, includes the top-level * directory into the listing, if it is false, exclude the top-level directory * from the listing. *

* Note that the root directory "/" will never be listed, so this parameter is only * effective when the top-level directory of the listing is not the root directory. */ public ListParametersBuilder includeTopLevelDirectoryEntry(@SuppressWarnings("hiding") boolean includeTopLevelDirectoryEntry) { this.includeTopLevelDirectoryEntry = includeTopLevelDirectoryEntry; return this; } /** * Resolve symbolic links to their link targets. *

* This makes symbolic links kind of appear like hard links in the listing. Note, however, * that symbolic links to directories being resolved do not lead to the directory being * traversed expect if also {@link #followSymbolicLinks()} is given. */ public ListParametersBuilder resolveSymbolicLinks() { this.resolveSymbolicLinks = true; return this; } /** * If resolveSymbolicLinks is true, resolve symbolic links to their * link targets, if it is false, do not resolve symbolic links to their link * targets. *

* If set to true, this makes symbolic links kind of appear like hard links in * the listing. Note, however, that symbolic links to directories being resolved do not lead * to the directory being traversed expect if also {@link #followSymbolicLinks()} is given. */ public ListParametersBuilder resolveSymbolicLinks(@SuppressWarnings("hiding") boolean resolveSymbolicLinks) { this.resolveSymbolicLinks = resolveSymbolicLinks; return this; } /** * Traverse a directory that was resolved from a symbolic link. *

* Only effective if recursive listing is enabled. */ public ListParametersBuilder followSymbolicLinks() { this.followSymbolicLinks = true; return this; } /** * If followSymbolicLinks is set to true, traverse a directory that * was resolved from a symbolic link, if it is false, do not traverse a * directory when it was resolved from a symbolic link. *

* Only effective if recursive listing is enabled. */ public ListParametersBuilder followSymbolicLinks(@SuppressWarnings("hiding") boolean followSymbolicLinks) { this.followSymbolicLinks = followSymbolicLinks; return this; } /** * Returns the {@link ListParameters} object constructed. */ public ListParameters get() { return new ListParameters(recursive, readLinkTargets, testArchive, suppressDirectoryEntries, includeTopLevelDirectoryEntry, resolveSymbolicLinks, followSymbolicLinks); } } /** * Starts building new list parameters. * * @return A new {@link ListParametersBuilder}. */ public static ListParametersBuilder build() { return new ListParametersBuilder(); } private ListParameters(boolean recursive, boolean readLinkTargets, boolean testArchive, boolean suppressDirectoryEntries, boolean includeTopLevelDirectoryEntry, boolean resolveSymbolicLinks, boolean followSymbolicLinks) { this.recursive = recursive; this.readLinkTargets = readLinkTargets || resolveSymbolicLinks; this.testArchive = testArchive; this.suppressDirectoryEntries = suppressDirectoryEntries; this.includeTopLevelDirectoryEntry = includeTopLevelDirectoryEntry; this.resolveSymbolicLinks = resolveSymbolicLinks; this.followSymbolicLinks = followSymbolicLinks; } /** * Returns if recursive listing is enabled, i.e. if the listing will traverse into * sub-directories. * * @see ListParametersBuilder#recursive(boolean) */ public boolean isRecursive() { return recursive; } /** * Returns if symbolic link targets should be read. * * @see ListParametersBuilder#readLinkTargets(boolean) */ public boolean isReadLinkTargets() { return readLinkTargets; } /** * Returns if the archive should be tested for integrity. * * @see ListParametersBuilder#testArchive(boolean) */ public boolean isTestArchive() { return testArchive; } /** * Returns if directory entries should be suppressed from being listed. * * @see ListParametersBuilder#suppressDirectoryEntries(boolean) */ public boolean isSuppressDirectoryEntries() { return suppressDirectoryEntries; } /** * Returns if the top-level directory entry should be listed as well. * * @see ListParametersBuilder#includeTopLevelDirectoryEntry(boolean) */ public boolean isIncludeTopLevelDirectoryEntry() { return includeTopLevelDirectoryEntry; } /** * Returns if symbolic links should be resolved. * * @see ListParametersBuilder#resolveSymbolicLinks(boolean) */ public boolean isResolveSymbolicLinks() { return resolveSymbolicLinks; } /** * Returns if directories resolved from symbolic links should be traversed. * * @see ListParametersBuilder#followSymbolicLinks(boolean) */ public boolean isFollowSymbolicLinks() { return followSymbolicLinks; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/NewArchiveEntry.java000066400000000000000000000215441256564762100301470ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import ch.systemsx.cisd.base.unix.FileLinkType; /** * A class to describe a new (yet to be created) archive entry. * * @author Bernd Rinn */ public abstract class NewArchiveEntry { private final String parentPath; private final String name; private final FileLinkType linkType; private final String linkTarget; private long lastModified; private int uid; private int gid; private short permissions; private long size; private int crc32; /** * A class to describe a new regular file archive entry. */ public static final class NewFileArchiveEntry extends NewArchiveEntry { private boolean compress; private int chunkSize; private NewFileArchiveEntry(String parentPath, String name) { super(parentPath, name, FileLinkType.REGULAR_FILE, null); } @Override public NewFileArchiveEntry lastModified(long lastModified) { super.lastModified(lastModified); return this; } @Override public NewFileArchiveEntry uid(int uid) { super.uid(uid); return this; } @Override public NewFileArchiveEntry gid(int gid) { super.gid(gid); return this; } @Override public NewFileArchiveEntry permissions(short permissions) { super.permissions(permissions); return this; } public NewFileArchiveEntry compress() { this.compress = true; return this; } public NewFileArchiveEntry compress(@SuppressWarnings("hiding") boolean compress) { this.compress = compress; return this; } public boolean isCompress() { return compress; } /** * @param chunkSize The chunk size of the file in the archive. Will be capped to 10MB. */ public NewFileArchiveEntry chunkSize(@SuppressWarnings("hiding") int chunkSize) { this.chunkSize = chunkSize; return this; } public int getChunkSize() { return chunkSize; } } /** * A class to describe a new symlink archive entry. */ public static final class NewSymLinkArchiveEntry extends NewArchiveEntry { private NewSymLinkArchiveEntry(String parentPath, String name, String linkTarget) { super(parentPath, name, FileLinkType.SYMLINK, linkTarget); } @Override public NewSymLinkArchiveEntry lastModified(long lastModified) { super.lastModified(lastModified); return this; } @Override public NewSymLinkArchiveEntry uid(int uid) { super.uid(uid); return this; } @Override public NewSymLinkArchiveEntry gid(int gid) { super.gid(gid); return this; } @Override public NewSymLinkArchiveEntry permissions(short permissions) { super.permissions(permissions); return this; } } /** * A class to describe a new directory archive entry. */ public static final class NewDirectoryArchiveEntry extends NewArchiveEntry { private NewDirectoryArchiveEntry(String parentPath, String name) { super(parentPath, name, FileLinkType.DIRECTORY, null); } @Override public NewDirectoryArchiveEntry lastModified(long lastModified) { super.lastModified(lastModified); return this; } @Override public NewDirectoryArchiveEntry uid(int uid) { super.uid(uid); return this; } @Override public NewDirectoryArchiveEntry gid(int gid) { super.gid(gid); return this; } @Override public NewDirectoryArchiveEntry permissions(short permissions) { super.permissions(permissions); return this; } } /** * @param path The path of the file in the archive. */ public static NewFileArchiveEntry file(String path) { final String normalizedPath = Utils.normalizePath(path); final String parentPath = Utils.getParentPath(normalizedPath); final String name = Utils.getName(normalizedPath); if (name.length() == 0) { throw new ArchivingException(path, "Path does not contain a name."); } return new NewFileArchiveEntry(parentPath, name); } /** * @param parentPath The parent path of the file in the archive. * @param name The name of the file in the archive. */ public static NewFileArchiveEntry file(String parentPath, String name) { return new NewFileArchiveEntry(parentPath, name); } /** * @param path The path of the symlink in the archive. * @param linkTarget the link target of the symlink. */ public static NewSymLinkArchiveEntry symlink(String path, String linkTarget) { final String normalizedPath = Utils.normalizePath(path); final String parentPath = Utils.getParentPath(normalizedPath); final String name = Utils.getName(normalizedPath); if (name.length() == 0) { throw new ArchivingException(path, "Path does not contain a name."); } return new NewSymLinkArchiveEntry(parentPath, name, linkTarget); } public static NewSymLinkArchiveEntry symlink(String parentPath, String name, String linkTarget) { return new NewSymLinkArchiveEntry(parentPath, name, linkTarget); } public static NewDirectoryArchiveEntry directory(String path) { final String normalizedPath = Utils.normalizePath(path); final String parentPath = Utils.getParentPath(normalizedPath); final String name = Utils.getName(normalizedPath); if (name.length() == 0) { throw new ArchivingException(path, "Path does not contain a name."); } return new NewDirectoryArchiveEntry(parentPath, name); } public static NewDirectoryArchiveEntry directory(String parentPath, String name) { return new NewDirectoryArchiveEntry(parentPath, name); } private NewArchiveEntry(String parentPath, String name, FileLinkType linkType, String linkTarget) { this.parentPath = Utils.normalizePath(parentPath); this.name = name; this.linkType = linkType; this.linkTarget = linkTarget; this.size = Utils.UNKNOWN; this.lastModified = System.currentTimeMillis() / 1000; this.uid = Utils.getCurrentUid(); this.gid = Utils.getCurrentGid(); this.permissions = 0755; } public String getParentPath() { return parentPath; } public long getLastModified() { return lastModified; } public NewArchiveEntry lastModified(@SuppressWarnings("hiding") long lastModified) { this.lastModified = lastModified; return this; } public int getUid() { return uid; } public NewArchiveEntry uid(@SuppressWarnings("hiding") int uid) { this.uid = uid; return this; } public int getGid() { return gid; } public NewArchiveEntry gid(@SuppressWarnings("hiding") int gid) { this.gid = gid; return this; } public short getPermissions() { return permissions; } public NewArchiveEntry permissions(@SuppressWarnings("hiding") short permissions) { this.permissions = permissions; return this; } public int getCrc32() { return crc32; } void setCrc32(int crc32) { this.crc32 = crc32; } public String getName() { return name; } public FileLinkType getLinkType() { return linkType; } public String getLinkTarget() { return linkTarget; } public long getSize() { return size; } void setSize(long size) { this.size = size; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/UnarchivingException.java000066400000000000000000000035371256564762100312300ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import java.io.File; import java.io.IOException; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked; /** * Exception thrown when unarchiving a file / directory fails. * * @author Bernd Rinn */ public class UnarchivingException extends ArchiverException { private static final long serialVersionUID = 1L; private static final String OPERATION_NAME = "unarchiving"; public UnarchivingException(String msg) { super("GENERAL", OPERATION_NAME, msg); } public UnarchivingException(String objectPath, String detailedMsg) { super(objectPath, OPERATION_NAME, detailedMsg); } public UnarchivingException(String objectPath, HDF5Exception cause) { super(objectPath, OPERATION_NAME, cause); } public UnarchivingException(String objectPath, RuntimeException cause) { super(objectPath, OPERATION_NAME, cause); } public UnarchivingException(File file, IOException cause) { super(file, OPERATION_NAME, cause); } public UnarchivingException(File file, IOExceptionUnchecked cause) { super(file, OPERATION_NAME, cause); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/Utils.java000066400000000000000000000156651256564762100262010ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import java.io.File; import org.apache.commons.io.FilenameUtils; import ch.systemsx.cisd.base.unix.FileLinkType; import ch.systemsx.cisd.base.unix.Unix; import ch.systemsx.cisd.base.utilities.OSUtilities; import ch.systemsx.cisd.hdf5.HDF5ObjectType; /** * Utility methods for h5ar. * * @author Bernd Rinn */ final class Utils { static final long MILLIS_PER_SECOND = 1000L; final static int UNKNOWN = -1; final static short UNKNOWN_S = -1; private static final char[] HEX_CHARACTERS = { '0', '1', '2', '3', '4', '5', '6', '7', '8', '9', 'a', 'b', 'c', 'd', 'e', 'f', }; private Utils() { // Not to be instantiated. } /** * Converts a CRC32 checksum to a string representation. */ static String crc32ToString(final int checksum) { final char buf[] = new char[8]; int w = checksum; for (int i = 0, x = 7; i < 4; i++) { buf[x--] = HEX_CHARACTERS[w & 0xf]; buf[x--] = HEX_CHARACTERS[(w >>> 4) & 0xf]; w >>= 8; } return new String(buf); } /** * Creates a string representation for the given permissions. */ static String permissionsToString(int permissions, boolean directory, boolean numeric) { if (numeric) { return Integer.toString(permissions, 8); } else { final short perms = (short) permissions; final StringBuilder b = new StringBuilder(); b.append(directory ? 'd' : '-'); b.append((perms & Unix.S_IRUSR) != 0 ? 'r' : '-'); b.append((perms & Unix.S_IWUSR) != 0 ? 'w' : '-'); b.append((perms & Unix.S_IXUSR) != 0 ? ((perms & Unix.S_ISUID) != 0 ? 's' : 'x') : ((perms & Unix.S_ISUID) != 0 ? 'S' : '-')); b.append((perms & Unix.S_IRGRP) != 0 ? 'r' : '-'); b.append((perms & Unix.S_IWGRP) != 0 ? 'w' : '-'); b.append((perms & Unix.S_IXGRP) != 0 ? ((perms & Unix.S_ISGID) != 0 ? 's' : 'x') : ((perms & Unix.S_ISGID) != 0 ? 'S' : '-')); b.append((perms & Unix.S_IROTH) != 0 ? 'r' : '-'); b.append((perms & Unix.S_IWOTH) != 0 ? 'w' : '-'); b.append((perms & Unix.S_IXOTH) != 0 ? ((perms & Unix.S_ISVTX) != 0 ? 't' : 'x') : ((perms & Unix.S_ISVTX) != 0 ? 'T' : '-')); return b.toString(); } } /** * Returns the parent of normalizedPath, or "" if normalizedPath is the * root "/". */ static String getParentPath(String normalizedPath) { final int lastSlashIdx = normalizedPath.lastIndexOf('/'); if (lastSlashIdx <= 0) { return normalizedPath.length() <= 1 ? "" : "/"; } else { return normalizedPath.substring(0, lastSlashIdx); } } /** * Returns the name part of path. */ static String getName(String path) { return path.substring(path.lastIndexOf('/') + 1); } private static String normalizeToUnix(String unixOrWindowsPath) { final String pathToNormalize = OSUtilities.isWindows() ? unixOrWindowsPath.replace('/', '\\') : unixOrWindowsPath; final String normalized = FilenameUtils.normalize(pathToNormalize); return OSUtilities.isWindows() ? normalized.replace('\\', '/') : normalized; } /** * Returns a normalized path: it starts with "/" and doesn't have "/" at the end, except if it * is the root path "/". This method internally calls {@link FilenameUtils#normalize(String)} * and thus removes any '.' and '..' elements. */ static String normalizePath(String hdf5ObjectPath) { String prenormalizedPath = normalizeToUnix(hdf5ObjectPath); if (prenormalizedPath == null) { prenormalizedPath = normalizeToUnix(hdf5ObjectPath.replace("//", "/")); if (prenormalizedPath == null) { prenormalizedPath = hdf5ObjectPath.replace("//", "/"); } } final String pathStartingWithSlash = (prenormalizedPath.startsWith("/") ? prenormalizedPath : "/" + prenormalizedPath); return (pathStartingWithSlash.length() > 1 && pathStartingWithSlash.endsWith("/")) ? pathStartingWithSlash .substring(0, pathStartingWithSlash.length() - 1) : pathStartingWithSlash; } /** * Returns the absolute normalized {@link File} for path. */ static File normalizePath(File path) { return new File(FilenameUtils.normalizeNoEndSeparator(path.getAbsolutePath())); } /** * Concatenates parentDirectory and name to a new path and return it. */ static String concatLink(String parentDirectory, String name) { return parentDirectory.endsWith("/") ? parentDirectory + name : parentDirectory + "/" + name; } /** * /** Returns an {@link ArchiveEntry} from a {@link LinkRecord}. Can handle null * {@link LinkRecord}s. */ static ArchiveEntry tryToArchiveEntry(String dir, String path, LinkRecord linkOrNull, IdCache idCache) { return linkOrNull != null ? new ArchiveEntry(dir, path, linkOrNull, idCache) : null; } /** * Returns the UID of the current user or {@link Utils#UNKNOWN}, if that cannot be determined. */ static int getCurrentUid() { if (Unix.isOperational()) { return Unix.getUid(); } else { return Utils.UNKNOWN; } } /** * Returns the GID of the current user or {@link Utils#UNKNOWN}, if that cannot be determined. */ static int getCurrentGid() { if (Unix.isOperational()) { return Unix.getGid(); } else { return Utils.UNKNOWN; } } static FileLinkType translateType(final HDF5ObjectType hdf5Type) { switch (hdf5Type) { case DATASET: return FileLinkType.REGULAR_FILE; case GROUP: return FileLinkType.DIRECTORY; case SOFT_LINK: return FileLinkType.SYMLINK; default: return FileLinkType.OTHER; } } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/VerifyArchiveException.java000066400000000000000000000031331256564762100315110ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import java.io.File; import java.io.IOException; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; /** * Exception thrown when verifying a file / directory in an archive against the file system. * * @author Bernd Rinn */ public class VerifyArchiveException extends ArchiverException { private static final long serialVersionUID = 1L; private static final String OPERATION_NAME = "verifying"; public VerifyArchiveException(String objectPath, String detailedMsg) { super(objectPath, OPERATION_NAME, detailedMsg); } public VerifyArchiveException(String objectPath, HDF5Exception cause) { super(objectPath, OPERATION_NAME, cause); } public VerifyArchiveException(String objectPath, RuntimeException cause) { super(objectPath, OPERATION_NAME, cause); } public VerifyArchiveException(File file, IOException cause) { super(file, OPERATION_NAME, cause); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/VerifyParameters.java000066400000000000000000000122521256564762100303560ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; /** * A class that represents parameters for * {@link HDF5Archiver#verifyAgainstFilesystem(String, java.io.File, IArchiveEntryVisitor, VerifyParameters) * )} . * * @author Bernd Rinn */ public final class VerifyParameters { private final boolean recursive; private final boolean numeric; private final boolean verifyAttributes; public static final VerifyParameters DEFAULT = new VerifyParameters(true, false, false); /** * A class for constructing a new verify parameters object. */ public static final class VerifyParametersBuilder { private boolean recursive = true; private boolean numeric = false; private boolean verifyAttributes = false; private VerifyParametersBuilder() { } /** * Perform a non-recursive verification, i.e. do not traverse sub-directories. */ public VerifyParametersBuilder nonRecursive() { this.recursive = false; return this; } /** * If recursive is true, perform a recursive verification, if it is * false, perform a non-recursive listing, i.e. do not traverse * sub-directories. */ public VerifyParametersBuilder recursive(@SuppressWarnings("hiding") boolean recursive) { this.recursive = recursive; return this; } /** * Reports user ids and permissions as numerical values. *

* This is a pure display parameter that is only relevant if {@link #verifyAttributes()} has * been set. */ public VerifyParametersBuilder numeric() { this.numeric = true; return this; } /** * If numeric is true, reports user ids and permissions as numerical * values, if it is false, it reports user ids and permissions resolved to * strings. This is a pure display parameter. *

* This is a pure display parameter that is only relevant if {@link #verifyAttributes()} has * been set. */ public VerifyParametersBuilder numeric(@SuppressWarnings("hiding") boolean numeric) { this.numeric = numeric; return this; } /** * Verifies also last modification time, file ownership and access permissions. */ public VerifyParametersBuilder verifyAttributes() { this.verifyAttributes = true; return this; } /** * If verifyAttributes is true, verifies also last modification * time, file ownership and access permissions, if it is false, check only the * types and content of entries. */ public VerifyParametersBuilder verifyAttributes(@SuppressWarnings("hiding") boolean verifyAttributes) { this.verifyAttributes = verifyAttributes; return this; } /** * Returns the {@link VerifyParameters} object constructed. */ public VerifyParameters get() { return new VerifyParameters(recursive, numeric, verifyAttributes); } } /** * Starts building new verify parameters. * * @return A new {@link VerifyParametersBuilder}. */ public static VerifyParametersBuilder build() { return new VerifyParametersBuilder(); } private VerifyParameters(boolean recursive, boolean numeric, boolean verifyAttributes) { this.recursive = recursive; this.numeric = numeric; this.verifyAttributes = verifyAttributes; } /** * Returns if recursive verification is enabled, i.e. if the verify process will traverse into * sub-directories. * * @see VerifyParametersBuilder#recursive(boolean) */ public boolean isRecursive() { return recursive; } /** * Returns if user id and permissions failures should be reported numerically. * * @see VerifyParametersBuilder#numeric(boolean) */ public boolean isNumeric() { return numeric; } /** * Returns if file attributes (last modification time, file ownerships and access permissions) * are checked, too. * * @see VerifyParametersBuilder#verifyAttributes(boolean) */ public boolean isVerifyAttributes() { return verifyAttributes; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/h5ar/package.html000066400000000000000000000004431256564762100265030ustar00rootroot00000000000000 Tools Package

This package contains the JHDF5 archiver.

libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/hdf5lib/000077500000000000000000000000001256564762100246775ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/hdf5lib/H5.java000066400000000000000000005346261256564762100260360ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ package ch.systemsx.cisd.hdf5.hdf5lib; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import ch.systemsx.cisd.base.utilities.NativeLibraryUtilities; /** * The low-level C function wrappers. These functions are not thread-safe and need to be used * through thread-safe wrappers. *

* This is an internal API that should not be expected to be stable between releases! */ class H5 { /** Expected major number of the library. */ private final static int expectedMajnum = 1; /** Expected minor number of the library. */ private final static int expectedMinnum = 8; /** Expected minimal release number of the library. */ private final static int expectedRelnum = 13; static { if (NativeLibraryUtilities.loadNativeLibrary("jhdf5") == false) { throw new UnsupportedOperationException("No suitable HDF5 native library found for this platform."); } // Important! Exit quietly try { synchronized (ncsa.hdf.hdf5lib.H5.class) { H5dont_atexit(); } } catch (final HDF5LibraryException e) { System.exit(1); } // Important! Disable error output to C stdout synchronized (ncsa.hdf.hdf5lib.H5.class) { H5error_off(); } // Ensure we have the expected version of the library (with at least the expected release // number) final int[] libversion = new int[3]; synchronized (ncsa.hdf.hdf5lib.H5.class) { H5get_libversion(libversion); } if (libversion[0] != expectedMajnum || libversion[1] != expectedMinnum || libversion[2] < expectedRelnum) { throw new UnsupportedOperationException("The HDF5 native library is outdated! It is version " + libversion[0] + "." + libversion[1] + "." + libversion[2] + ", but we require " + expectedMajnum + "." + expectedMinnum + ".x with x >= " + expectedRelnum + "."); } } /** Call to ensure that the native library is loaded. */ public static void ensureNativeLibIsLoaded() { } // //////////////////////////////////////////////////////////////// /** * J2C converts a Java constant to an HDF5 constant determined at runtime * * @param java_constant The value of Java constant * @return the value of an HDF5 constant determined at runtime */ public static native int J2C(int java_constant); /** * Turn off error handling By default, the C library prints the error stack of the HDF-5 C * library on stdout. This behavior may be disabled by calling H5error_off(). */ public static native int H5error_off(); // //////////////////////////////////////////////////////////// // // // Functions related to variable-length string copying // // // // //////////////////////////////////////////////////////////// /** * Returns the size of a pointer on this platform. */ public static native int getPointerSize(); /** * Creates a C copy of str (using calloc) and put the reference of it into buf at bufOfs. */ public static native int compoundCpyVLStr(String str, byte[] buf, int bufOfs); /** * Creates a Java copy from a C char* pointer in the buf at bufOfs. */ public static native String createVLStrFromCompound(byte[] buf, int bufOfs); /** * Frees the variable-length strings in compound buf, where one compound has size recordSize and the * variable-length members can be found at byte-offsets vlIndices. */ public static native int freeCompoundVLStr(byte[] buf, int recordSize, int[] vlIndices); // //////////////////////////////////////////////////////////// // // // H5: General Library Functions // // // // //////////////////////////////////////////////////////////// /** * H5open initialize the library. * * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5open() throws HDF5LibraryException; /** * H5close flushes all data to disk, closes all file identifiers, and cleans up all memory used * by the library. * * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5close() throws HDF5LibraryException; /** * H5dont_atexit indicates to the library that an atexit() cleanup routine should not be * installed. In order to be effective, this routine must be called before any other HDF * function calls, and must be called each time the library is loaded/linked into the * application (the first time and after it's been un-loaded). *

* This is called by the static initializer, so this should never need to be explicitly called * by a Java program. * * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ private static native int H5dont_atexit() throws HDF5LibraryException; /** * H5get_libversion retrieves the major, minor, and release numbers of the version of the HDF * library which is linked to the application. * * @param libversion The version information of the HDF library. * * 

     * 
     *            libversion[0] = The major version of the library. libversion[1] = The minor
     *            version of the library. libversion[2] = The release number of the library.
     * 
     *
* @return a non-negative value if successful, along with the version information. * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5get_libversion(int[] libversion) throws HDF5LibraryException; /** * H5check_version verifies that the arguments match the version numbers compiled into the * library. * * @param majnum The major version of the library. * @param minnum The minor version of the library. * @param relnum The release number of the library. * @return a non-negative value if successful. Upon failure (when the versions do not match), * this function causes the application to abort (i.e., crash) See C API function: * herr_t H5check_version() */ public static native int H5check_version(int majnum, int minnum, int relnum); /** * H5garbage_collect collects on all free-lists of all types. *

* Note: this is new with HDF5.1.2.2. If using an earlier version, use 'configure * --enable-hdf5_1_2_1' so this routine will fail safely. * * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5garbage_collect() throws HDF5LibraryException; // //////////////////////////////////////////////////////////// // // // H5E: Error Stack // // // // //////////////////////////////////////////////////////////// /** * H5Eclear clears the error stack for the current thread. H5Eclear can fail if there are * problems initializing the library. *

* This may be used by exception handlers to assure that the error condition in the HDF-5 * library has been reset. * * @return Returns a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Eclear() throws HDF5LibraryException; // //////////////////////////////////////////////////////////// // // // H5A: Attribute Interface Functions // // // // //////////////////////////////////////////////////////////// /** * H5Lexists returns true if an attribute with name exists for the * object defined by obj_id and false otherwise. */ public static native boolean H5Aexists(int obj_id, String name) throws HDF5LibraryException, NullPointerException; /** * H5Acreate creates an attribute which is attached to the object specified with loc_id. * * @param loc_id IN: Object (dataset, group, or named datatype) to be attached to. * @param name IN: Name of attribute to create. * @param type_id IN: Identifier of datatype for attribute. * @param space_id IN: Identifier of dataspace for attribute. * @param create_plist_id IN: Identifier of creation property list (currently not used). * @param access_plist_id IN: Attribute access property list identifier (currently not used). * @return an attribute identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static native int H5Acreate(int loc_id, String name, int type_id, int space_id, int create_plist_id, int access_plist_id) throws HDF5LibraryException, NullPointerException; /** * H5Aopen_name opens an attribute specified by its name, name, which is attached to the object * specified with loc_id. * * @param loc_id IN: Identifier of a group, dataset, or named datatype atttribute * @param name IN: Attribute name. * @return attribute identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static native int H5Aopen_name(int loc_id, String name) throws HDF5LibraryException, NullPointerException; /** * H5Aopen_idx opens an attribute which is attached to the object specified with loc_id. The * location object may be either a group, dataset, or named datatype, all of which may have any * sort of attribute. * * @param loc_id IN: Identifier of the group, dataset, or named datatype attribute * @param idx IN: Index of the attribute to open. * @return attribute identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Aopen_idx(int loc_id, int idx) throws HDF5LibraryException; /** * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is * specified with mem_type_id. The entire attribute is written from buf to the file. * * @param attr_id IN: Identifier of an attribute to write. * @param mem_type_id IN: Identifier of the attribute datatype (in memory). * @param buf IN: Data to be written. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - data is null. */ public static native int H5Awrite(int attr_id, int mem_type_id, byte[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is * specified with mem_type_id. The entire attribute is written from buf to the file. * * @param attr_id IN: Identifier of an attribute to write. * @param mem_type_id IN: Identifier of the attribute datatype (in memory). * @param buf IN: Data to be written. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - data is null. */ public static native int H5Awrite(int attr_id, int mem_type_id, short[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is * specified with mem_type_id. The entire attribute is written from buf to the file. * * @param attr_id IN: Identifier of an attribute to write. * @param mem_type_id IN: Identifier of the attribute datatype (in memory). * @param buf IN: Data to be written. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - data is null. */ public static native int H5Awrite(int attr_id, int mem_type_id, int[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is * specified with mem_type_id. The entire attribute is written from buf to the file. * * @param attr_id IN: Identifier of an attribute to write. * @param mem_type_id IN: Identifier of the attribute datatype (in memory). * @param buf IN: Data to be written. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - data is null. */ public static native int H5Awrite(int attr_id, int mem_type_id, long[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is * specified with mem_type_id. The entire attribute is written from buf to the file. * * @param attr_id IN: Identifier of an attribute to write. * @param mem_type_id IN: Identifier of the attribute datatype (in memory). * @param buf IN: Data to be written. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - data is null. */ public static native int H5Awrite(int attr_id, int mem_type_id, float[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is * specified with mem_type_id. The entire attribute is written from buf to the file. * * @param attr_id IN: Identifier of an attribute to write. * @param mem_type_id IN: Identifier of the attribute datatype (in memory). * @param buf IN: Data to be written. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - data is null. */ public static native int H5Awrite(int attr_id, int mem_type_id, double[] buf) throws HDF5LibraryException, NullPointerException; /** * H5AwriteString writes a (partial) variable length String attribute, specified by its * identifier attr_id, from the application memory buffer buf into the file. * * @param attr_id Identifier of the dataset read from. * @param mem_type_id Identifier of the memory datatype. * @param buf Buffer with data to be written to the file. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static native int H5AwriteString(int attr_id, int mem_type_id, String[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Acopy copies the content of one attribute to another. * * @param src_aid the identifier of the source attribute * @param dst_aid the identifier of the destinaiton attribute */ public static native int H5Acopy(int src_aid, int dst_aid) throws HDF5LibraryException; /** * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is * specified with mem_type_id. The entire attribute is read into buf from the file. * * @param attr_id IN: Identifier of an attribute to read. * @param mem_type_id IN: Identifier of the attribute datatype (in memory). * @param buf IN: Buffer for data to be read. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - data buffer is null. */ public static native int H5Aread(int attr_id, int mem_type_id, byte[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is * specified with mem_type_id. The entire attribute is read into buf from the file. * * @param attr_id IN: Identifier of an attribute to read. * @param mem_type_id IN: Identifier of the attribute datatype (in memory). * @param buf IN: Buffer for data to be read. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - data buffer is null. */ public static native int H5Aread(int attr_id, int mem_type_id, short[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is * specified with mem_type_id. The entire attribute is read into buf from the file. * * @param attr_id IN: Identifier of an attribute to read. * @param mem_type_id IN: Identifier of the attribute datatype (in memory). * @param buf IN: Buffer for data to be read. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - data buffer is null. */ public static native int H5Aread(int attr_id, int mem_type_id, int[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is * specified with mem_type_id. The entire attribute is read into buf from the file. * * @param attr_id IN: Identifier of an attribute to read. * @param mem_type_id IN: Identifier of the attribute datatype (in memory). * @param buf IN: Buffer for data to be read. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - data buffer is null. */ public static native int H5Aread(int attr_id, int mem_type_id, long[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is * specified with mem_type_id. The entire attribute is read into buf from the file. * * @param attr_id IN: Identifier of an attribute to read. * @param mem_type_id IN: Identifier of the attribute datatype (in memory). * @param buf IN: Buffer for data to be read. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - data buffer is null. */ public static native int H5Aread(int attr_id, int mem_type_id, float[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is * specified with mem_type_id. The entire attribute is read into buf from the file. * * @param attr_id IN: Identifier of an attribute to read. * @param mem_type_id IN: Identifier of the attribute datatype (in memory). * @param buf IN: Buffer for data to be read. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - data buffer is null. */ public static native int H5Aread(int attr_id, int mem_type_id, double[] buf) throws HDF5LibraryException, NullPointerException; public static native int H5AreadVL(int attr_id, int mem_type_id, String[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Aget_space retrieves a copy of the dataspace for an attribute. * * @param attr_id IN: Identifier of an attribute. * @return attribute dataspace identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Aget_space(int attr_id) throws HDF5LibraryException; /** * H5Aget_type retrieves a copy of the datatype for an attribute. * * @param attr_id IN: Identifier of an attribute. * @return a datatype identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Aget_type(int attr_id) throws HDF5LibraryException; /** * H5Aget_name retrieves the name of an attribute specified by the identifier, attr_id. * * @param attr_id IN: Identifier of the attribute. * @param buf_size IN: The size of the buffer to store the name in. * @param name OUT: Buffer to store name in. * @exception ArrayIndexOutOfBoundsException JNI error writing back array * @exception ArrayStoreException JNI error writing back array * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. * @exception IllegalArgumentException - bub_size <= 0. * @return the length of the attribute's name if successful. */ public static native long H5Aget_name(int attr_id, long buf_size, String[] name) throws ArrayIndexOutOfBoundsException, ArrayStoreException, HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Aget_num_attrs returns the number of attributes attached to the object specified by its * identifier, loc_id. * * @param loc_id IN: Identifier of a group, dataset, or named datatype. * @return the number of attributes if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Aget_num_attrs(int loc_id) throws HDF5LibraryException; /** * H5Adelete removes the attribute specified by its name, name, from a dataset, group, or named * datatype. * * @param loc_id IN: Identifier of the dataset, group, or named datatype. * @param name IN: Name of the attribute to delete. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static native int H5Adelete(int loc_id, String name) throws HDF5LibraryException, NullPointerException; /** * H5Aclose terminates access to the attribute specified by its identifier, attr_id. * * @param attr_id IN: Attribute to release access to. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Aclose(int attr_id) throws HDF5LibraryException; // //////////////////////////////////////////////////////////// // // // H5D: Datasets Interface Functions // // // // //////////////////////////////////////////////////////////// /** * H5Dcreate creates a data set with a name, name, in the file or in the group specified by the * identifier loc_id. * * @param loc_id Identifier of the file or group to create the dataset within. * @param name The name of the dataset to create. * @param type_id Identifier of the datatype to use when creating the dataset. * @param space_id Identifier of the dataspace to use when creating the dataset. * @param link_create_plist_id Identifier of the link creation property list. * @param dset_create_plist_id Identifier of the dataset creation property list. * @param dset_access_plist_id Identifier of the dataset access property list. * @return a dataset identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static native int H5Dcreate(int loc_id, String name, int type_id, int space_id, int link_create_plist_id, int dset_create_plist_id, int dset_access_plist_id) throws HDF5LibraryException, NullPointerException; /** * H5Dopen opens an existing dataset for access in the file or group specified in loc_id. * * @param loc_id Identifier of the dataset to open or the file or group * @param name The name of the dataset to access. * @param access_plist_id Dataset access property list. * @return a dataset identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static native int H5Dopen(int loc_id, String name, int access_plist_id) throws HDF5LibraryException, NullPointerException; public static native int H5Dchdir_ext(String dir_name) throws HDF5LibraryException, NullPointerException; public static native int H5Dgetdir_ext(String[] dir_name, int size) throws HDF5LibraryException, NullPointerException; /** * H5Dget_space returns an identifier for a copy of the dataspace for a dataset. * * @param dataset_id Identifier of the dataset to query. * @return a dataspace identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Dget_space(int dataset_id) throws HDF5LibraryException; /** * H5Dget_type returns an identifier for a copy of the datatype for a dataset. * * @param dataset_id Identifier of the dataset to query. * @return a datatype identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Dget_type(int dataset_id) throws HDF5LibraryException; /** * H5Dget_create_plist returns an identifier for a copy of the dataset creation property list * for a dataset. * * @param dataset_id Identifier of the dataset to query. * @return a dataset creation property list identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Dget_create_plist(int dataset_id) throws HDF5LibraryException; /** * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into * the application memory buffer buf. * * @param dataset_id Identifier of the dataset read from. * @param mem_type_id Identifier of the memory datatype. * @param mem_space_id Identifier of the memory dataspace. * @param file_space_id Identifier of the dataset's dataspace in the file. * @param xfer_plist_id Identifier of a transfer property list for this I/O operation. * @param buf Buffer to store data read from the file. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - data buffer is null. */ public static native int H5Dread(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException; public static native int H5DreadVL(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, Object[] buf) throws HDF5LibraryException, NullPointerException; /** * H5DwriteString writes a (partial) variable length String dataset, specified by its identifier * dataset_id, from the application memory buffer buf into the file. *

* contributed by Rosetta Biosoftware. * * @param dataset_id Identifier of the dataset read from. * @param mem_type_id Identifier of the memory datatype. * @param mem_space_id Identifier of the memory dataspace. * @param file_space_id Identifier of the dataset's dataspace in the file. * @param xfer_plist_id Identifier of a transfer property list for this I/O operation. * @param buf Buffer with data to be written to the file. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static native int H5DwriteString(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the * application memory buffer buf into the file. * * @param dataset_id Identifier of the dataset read from. * @param mem_type_id Identifier of the memory datatype. * @param mem_space_id Identifier of the memory dataspace. * @param file_space_id Identifier of the dataset's dataspace in the file. * @param xfer_plist_id Identifier of a transfer property list for this I/O operation. * @param buf Buffer with data to be written to the file. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static native int H5Dwrite(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Dextend verifies that the dataset is at least of size size. * * @param dataset_id Identifier of the dataset. * @param size Array containing the new magnitude of each dimension. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - size array is null. */ public static native int H5Dextend(int dataset_id, byte[] size) throws HDF5LibraryException, NullPointerException; public static int H5Dextend(final int dataset_id, final long[] size) throws HDF5Exception, NullPointerException { final byte[] buf = HDFNativeData.longToByte(size); return H5Dextend(dataset_id, buf); } /** * H5Dset_extent sets the size of the dataset to size. Make sure that no important * are lost since this method will not check that the data dimensions are not larger than * size. * * @param dataset_id Identifier of the dataset. * @param size Array containing the new magnitude of each dimension. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - size array is null. */ public static native int H5Dset_extent(int dataset_id, byte[] size) throws HDF5LibraryException, NullPointerException; public static int H5Dset_extent(final int dataset_id, final long[] size) throws HDF5Exception, NullPointerException { final byte[] buf = HDFNativeData.longToByte(size); return H5Dset_extent(dataset_id, buf); } /** * H5Dclose ends access to a dataset specified by dataset_id and releases resources used by it. * * @param dataset_id Identifier of the dataset to finish access to. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Dclose(int dataset_id) throws HDF5LibraryException; // following static native functions are missing from HDF5 RM version 1.0.1 /** * H5Dget_storage_size returns the amount of storage that is required for the dataset. * * @param dataset_id Identifier of the dataset in question * @return he amount of storage space allocated for the dataset. * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native long H5Dget_storage_size(int dataset_id) throws HDF5LibraryException; /** * H5Dcopy copies the content of one dataset to another dataset. * * @param src_did the identifier of the source dataset * @param dst_did the identifier of the destinaiton dataset */ public static native int H5Dcopy(int src_did, int dst_did) throws HDF5LibraryException; /* * */ public static native int H5Dvlen_get_buf_size(int dataset_id, int type_id, int space_id, int[] size) throws HDF5LibraryException; /** * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - buf is null. */ public static native int H5Dvlen_reclaim(int type_id, int space_id, int xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException; // //////////////////////////////////////////////////////////// // // // H5F: File Interface Functions // // // // //////////////////////////////////////////////////////////// /** * H5Fopen opens an existing file and is the primary function for accessing existing HDF5 files. * * @param name Name of the file to access. * @param flags File access flags. * @param access_id Identifier for the file access properties list. * @return a file identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static native int H5Fopen(String name, int flags, int access_id) throws HDF5LibraryException, NullPointerException; /** * H5Fcreate is the primary function for creating HDF5 files. * * @param name Name of the file to access. * @param flags File access flags. Possible values include: *

    *
  • H5F_ACC_RDWR Allow read and write access to file.
    • *
  • H5F_ACC_RDONLY Allow read-only access to file.
    • *
  • H5F_ACC_TRUNC Truncate file, if it already exists, erasing all data previously * stored in the file.
    • *
  • H5F_ACC_EXCL Fail if file already exists.
    • *
  • H5F_ACC_DEBUG Print debug information.
    • *
  • H5P_DEFAULT Apply default file access and creation properties.
    • *
* @param create_id File creation property list identifier, used when modifying default file * meta-data. Use H5P_DEFAULT for default access properties. * @param access_id File access property list identifier. If parallel file access is desired, * this is a collective call according to the communicator stored in the access_id * (not supported in Java). Use H5P_DEFAULT for default access properties. * @return a file identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static native int H5Fcreate(String name, int flags, int create_id, int access_id) throws HDF5LibraryException, NullPointerException; /** * H5Fflush causes all buffers associated with a file or object to be immediately flushed * (written) to disk without removing the data from the (memory) cache. *

* After this call completes, the file (or object) is in a consistent state and all data written * to date is assured to be permanent. * * @param object_id Identifier of object used to identify the file. object_id can be any * object associated with the file, including the file itself, a dataset, a group, an * attribute, or a named data type. * @param scope specifies the scope of the flushing action, in the case that the HDF-5 file is * not a single physical file. *

* Valid values are: *

    *
  • H5F_SCOPE_GLOBAL Flushes the entire virtual file.
    • *
  • H5F_SCOPE_LOCAL Flushes only the specified file.
    • *
* @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Fflush(int object_id, int scope) throws HDF5LibraryException; /** * H5Fis_hdf5 determines whether a file is in the HDF5 format. * * @param name File name to check format. * @return true if is HDF-5, false if not. * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static native boolean H5Fis_hdf5(String name) throws HDF5LibraryException, NullPointerException; /** * H5Fget_create_plist returns a file creation property list identifier identifying the creation * properties used to create this file. * * @param file_id Identifier of the file to get creation property list * @return a file creation property list identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Fget_create_plist(int file_id) throws HDF5LibraryException; /** * H5Fget_access_plist returns the file access property list identifier of the specified file. * * @param file_id Identifier of file to get access property list of * @return a file access property list identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Fget_access_plist(int file_id) throws HDF5LibraryException; /** * H5Fclose terminates access to an HDF5 file. * * @param file_id Identifier of a file to terminate access to. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Fclose(int file_id) throws HDF5LibraryException; /** * H5Fmount mounts the file specified by child_id onto the group specified by loc_id and name * using the mount properties plist_id. * * @param loc_id The identifier for the group onto which the file specified by child_id is to be * mounted. * @param name The name of the group onto which the file specified by child_id is to be mounted. * @param child_id The identifier of the file to be mounted. * @param plist_id The identifier of the property list to be used. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static native int H5Fmount(int loc_id, String name, int child_id, int plist_id) throws HDF5LibraryException, NullPointerException; /** * Given a mount point, H5Funmount dissassociates the mount point's file from the file mounted * there. * * @param loc_id The identifier for the location at which the specified file is to be unmounted. * @param name The name of the file to be unmounted. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static native int H5Funmount(int loc_id, String name) throws HDF5LibraryException, NullPointerException; /** * H5Freopen reopens an HDF5 file. * * @param file_id Identifier of a file to terminate and reopen access to. * @exception HDF5LibraryException - Error from the HDF-5 Library. * @return a new file identifier if successful */ public static native int H5Freopen(int file_id) throws HDF5LibraryException; // //////////////////////////////////////////////////////////// // // // H5G: Group Interface Functions // // // // //////////////////////////////////////////////////////////// /** * H5Gcreate creates a new group with the specified name at the specified location, loc_id. * * @param loc_id The file or group identifier. * @param name The absolute or relative name of the new group. * @param link_create_plist_id Property list for link creation. * @param group_create_plist_id Property list for group creation. * @param group_access_plist_id Property list for group access. * @return a valid group identifier for the open group if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static native int H5Gcreate(int loc_id, String name, int link_create_plist_id, int group_create_plist_id, int group_access_plist_id) throws HDF5LibraryException, NullPointerException; /** * H5Gopen opens an existing group with the specified name at the specified location, loc_id. * * @param loc_id File or group identifier within which group is to be open. * @param name Name of group to open. * @param access_plist_id Group access property list identifier (H5P_DEFAULT for the default * property list). * @return a valid group identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static native int H5Gopen(int loc_id, String name, int access_plist_id) throws HDF5LibraryException, NullPointerException; /** * H5Gclose releases resources used by a group which was opened by a call to H5Gcreate() or * H5Gopen(). * * @param group_id Group identifier to release. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Gclose(int group_id) throws HDF5LibraryException; /** * H5Glink creates a new name for an already existing object. * * @param loc_id File, group, dataset, or datatype identifier. * @param link_type Link type. Possible values are: *
    *
  • H5G_LINK_HARD
    • *
  • H5G_LINK_SOFT.
    • *
* @param current_name A name of the existing object if link is a hard link. Can be anything for * the soft link. * @param new_name New name for the object. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - current_name or name is null. */ @Deprecated public static native int H5Glink(int loc_id, int link_type, String current_name, String new_name) throws HDF5LibraryException, NullPointerException; @Deprecated public static native int H5Glink2(int curr_loc_id, String current_name, int link_type, int new_loc_id, String new_name) throws HDF5LibraryException, NullPointerException; /** * H5Gunlink removes an association between a name and an object. * * @param loc_id Identifier of the file containing the object. * @param name Name of the object to unlink. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static native int H5Gunlink(int loc_id, String name) throws HDF5LibraryException, NullPointerException; /** * H5Gmove renames an object within an HDF5 file. The original name, src, is unlinked from the * group graph and the new name, dst, is inserted as an atomic operation. Both names are * interpreted relative to loc_id, which is either a file or a group identifier. * * @param loc_id File or group identifier. * @param src Object's original name. * @param dst Object's new name. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - src or dst is null. */ public static native int H5Gmove(int loc_id, String src, String dst) throws HDF5LibraryException, NullPointerException; /** * H5Gget_linkval returns size characters of the link value through the value argument if loc_id * (a file or group identifier) and name specify a symbolic link. * * @param loc_id IN: Identifier of the file, group, dataset, or datatype. * @param name IN: Name of the object whose link value is to be checked. * @param size IN: Maximum number of characters of value to be returned. * @param value OUT: Link value. * @return a non-negative value, with the link value in value, if successful. * @exception ArrayIndexOutOfBoundsException Copy back failed * @exception ArrayStoreException Copy back failed * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. * @exception IllegalArgumentException - size is invalid */ public static native int H5Gget_linkval(int loc_id, String name, int size, String[] value) throws ArrayIndexOutOfBoundsException, ArrayStoreException, HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Gset_comment sets the comment for the the object name to comment. Any previously existing * comment is overwritten. * * @param loc_id IN: Identifier of the file, group, dataset, or datatype. * @param name IN: Name of the object whose comment is to be set or reset. * @param comment IN: The new comment. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name or comment is null. */ public static native int H5Gset_comment(int loc_id, String name, String comment) throws HDF5LibraryException, NullPointerException; /** * H5Gget_comment retrieves the comment for the the object name. The comment is returned in the * buffer comment. * * @param loc_id IN: Identifier of the file, group, dataset, or datatype. * @param name IN: Name of the object whose comment is to be set or reset. * @param bufsize IN: Anticipated size of the buffer required to hold comment. * @param comment OUT: The comment. * @return the number of characters in the comment, counting the null terminator, if successful * @exception ArrayIndexOutOfBoundsException - JNI error writing back data * @exception ArrayStoreException - JNI error writing back data * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. * @exception IllegalArgumentException - size < 1, comment is invalid. */ public static native int H5Gget_comment(int loc_id, String name, int bufsize, String[] comment) throws ArrayIndexOutOfBoundsException, ArrayStoreException, HDF5LibraryException, NullPointerException, IllegalArgumentException; // //////////////////////////////////////////////////////////// // // // H5I: Identifier Interface Functions // // // // //////////////////////////////////////////////////////////// /** * H5Iget_type retrieves the type of the object identified by obj_id. * * @param obj_id IN: Object identifier whose type is to be determined. * @return the object type if successful; otherwise H5I_BADID. * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Iget_type(int obj_id) throws HDF5LibraryException; // //////////////////////////////////////////////////////////// // // // H5P: Property List Interface Functions // // // // //////////////////////////////////////////////////////////// /** * H5Pcreate creates a new property as an instance of some property list class. * * @param type IN: The type of property list to create. * @return a property list identifier (plist) if successful; otherwise Fail (-1). * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Pcreate(int type) throws HDF5LibraryException; /** * H5Pclose terminates access to a property list. * * @param plist IN: Identifier of the property list to terminate access to. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Pclose(int plist) throws HDF5LibraryException; /** * H5Pget_class returns the property list class for the property list identified by the plist * parameter. * * @param plist IN: Identifier of property list to query. * @return a property list class if successful. Otherwise returns H5P_NO_CLASS (-1). * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Pget_class(int plist) throws HDF5LibraryException; /** * H5Pcopy copies an existing property list to create a new property list. * * @param plist IN: Identifier of property list to duplicate. * @return a property list identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Pcopy(int plist) throws HDF5LibraryException; /** * H5Pget_version retrieves the version information of various objects for a file creation * property list. * * @param plist IN: Identifier of the file creation property list. * @param version_info OUT: version information. * * 
     * 
     *            version_info[0] = boot // boot block version number version_info[1] = freelist //
     *            global freelist version version_info[2] = stab // symbol tabl version number
     *            version_info[3] = shhdr // hared object header version
     * 
     *
* @return a non-negative value, with the values of version_info initialized, if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - version_info is null. * @exception IllegalArgumentException - version_info is illegal. */ public static native int H5Pget_version(int plist, int[] version_info) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Pset_userblock sets the user block size of a file creation property list. * * @param plist IN: Identifier of property list to modify. * @param size IN: Size of the user-block in bytes. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Pset_userblock(int plist, long size) throws HDF5LibraryException; /** * H5Pget_userblock retrieves the size of a user block in a file creation property list. * * @param plist IN: Identifier for property list to query. * @param size OUT: Pointer to location to return user-block size. * @return a non-negative value and the size of the user block; if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - size is null. */ public static native int H5Pget_userblock(int plist, long[] size) throws HDF5LibraryException, NullPointerException; /** * H5Pset_small_data_block_size reserves blocks of size bytes for the contiguous storage of the * raw data portion of small datasets. * * @param plist IN: Identifier of property list to modify. * @param size IN: Size of the blocks in bytes. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Pset_small_data_block_size(int plist, long size) throws HDF5LibraryException; /** * H5Pget_small_data_block_size retrieves the size of a block of small data in a file creation * property list. * * @param plist IN: Identifier for property list to query. * @param size OUT: Pointer to location to return block size. * @return a non-negative value and the size of the user block; if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - size is null. */ public static native int H5Pget_small_data_block_size(int plist, long[] size) throws HDF5LibraryException, NullPointerException; /** * H5Pset_sizes sets the byte size of the offsets and lengths used to address objects in an HDF5 * file. * * @param plist IN: Identifier of property list to modify. * @param sizeof_addr IN: Size of an object offset in bytes. * @param sizeof_size IN: Size of an object length in bytes. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Pset_sizes(int plist, int sizeof_addr, int sizeof_size) throws HDF5LibraryException; /** * H5Pget_sizes retrieves the size of the offsets and lengths used in an HDF5 file. This * function is only valid for file creation property lists. * * @param plist IN: Identifier of property list to query. * @param size OUT: the size of the offsets and length. * * 
     * 
     *            size[0] = sizeof_addr // offset size in bytes size[1] = sizeof_size // length size
     *            in bytes
     * 
     *
* @return a non-negative value with the sizes initialized; if successful; * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - size is null. * @exception IllegalArgumentException - size is invalid. */ public static native int H5Pget_sizes(int plist, int[] size) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Pset_sym_k sets the size of parameters used to control the symbol table nodes. * * @param plist IN: Identifier for property list to query. * @param ik IN: Symbol table tree rank. * @param lk IN: Symbol table node size. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Pset_sym_k(int plist, int ik, int lk) throws HDF5LibraryException; /** * H5Pget_sym_k retrieves the size of the symbol table B-tree 1/2 rank and the symbol table leaf * node 1/2 size. * * @param plist IN: Property list to query. * @param size OUT: the symbol table's B-tree 1/2 rank and leaf node 1/2 size. * * 
     * 
     *            size[0] = ik // the symbol table's B-tree 1/2 rank size[1] = lk // leaf node 1/2
     *            size
     * 
     *
* @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - size is null. * @exception IllegalArgumentException - size is invalid. */ public static native int H5Pget_sym_k(int plist, int[] size) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Pset_istore_k sets the size of the parameter used to control the B-trees for indexing * chunked datasets. * * @param plist IN: Identifier of property list to query. * @param ik IN: 1/2 rank of chunked storage B-tree. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Pset_istore_k(int plist, int ik) throws HDF5LibraryException; /** * H5Pget_istore_k queries the 1/2 rank of an indexed storage B-tree. * * @param plist IN: Identifier of property list to query. * @param ik OUT: Pointer to location to return the chunked storage B-tree 1/2 rank. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - ik array is null. */ public static native int H5Pget_istore_k(int plist, int[] ik) throws HDF5LibraryException, NullPointerException; /** * H5Pset_layout sets the type of storage used store the raw data for a dataset. * * @param plist IN: Identifier of property list to query. * @param layout IN: Type of storage layout for raw data. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Pset_layout(int plist, int layout) throws HDF5LibraryException; /** * H5Pget_layout returns the layout of the raw data for a dataset. * * @param plist IN: Identifier for property list to query. * @return the layout type of a dataset creation property list if successful. Otherwise returns * H5D_LAYOUT_ERROR (-1). * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Pget_layout(int plist) throws HDF5LibraryException; /** * H5Pset_chunk sets the size of the chunks used to store a chunked layout dataset. * * @param plist IN: Identifier for property list to query. * @param ndims IN: The number of dimensions of each chunk. * @param dim IN: An array containing the size of each chunk. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - dims array is null. * @exception IllegalArgumentException - dims <=0 */ public static native int H5Pset_chunk(int plist, int ndims, byte[] dim) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; public static int H5Pset_chunk(final int plist, final int ndims, final long[] dim) throws HDF5Exception, NullPointerException, IllegalArgumentException { if (dim == null) { return -1; } final byte[] thedims = HDFNativeData.longToByte(dim); return H5Pset_chunk(plist, ndims, thedims); } /** * H5Pget_chunk retrieves the size of chunks for the raw data of a chunked layout dataset. * * @param plist IN: Identifier of property list to query. * @param max_ndims IN: Size of the dims array. * @param dims OUT: Array to store the chunk dimensions. * @return chunk dimensionality successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - dims array is null. * @exception IllegalArgumentException - max_ndims <=0 */ public static native int H5Pget_chunk(int plist, int max_ndims, long[] dims) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Pset_alignment sets the alignment properties of a file access property list so that any * file object >= THRESHOLD bytes will be aligned on an address which is a multiple of * ALIGNMENT. * * @param plist IN: Identifier for a file access property list. * @param threshold IN: Threshold value. * @param alignment IN: Alignment value. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Pset_alignment(int plist, long threshold, long alignment) throws HDF5LibraryException; /** * H5Pget_alignment retrieves the current settings for alignment properties from a file access * property list. * * @param plist IN: Identifier of a file access property list. * @param alignment OUT: threshold value and alignment value. * * 
     * 
     *            alignment[0] = threshold // threshold value alignment[1] = alignment // alignment
     *            value
     * 
     *
* @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - aligment array is null. * @exception IllegalArgumentException - aligment array is invalid. */ public static native int H5Pget_alignment(int plist, long[] alignment) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Pset_external adds an external file to the list of external files. * * @param plist IN: Identifier of a dataset creation property list. * @param name IN: Name of an external file. * @param offset IN: Offset, in bytes, from the beginning of the file to the location in the * file where the data starts. * @param size IN: Number of bytes reserved in the file for the data. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static native int H5Pset_external(int plist, String name, long offset, long size) throws HDF5LibraryException, NullPointerException; /** * H5Pget_external_count returns the number of external files for the specified dataset. * * @param plist IN: Identifier of a dataset creation property list. * @return the number of external files if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Pget_external_count(int plist) throws HDF5LibraryException; /** * H5Pget_external returns information about an external file. * * @param plist IN: Identifier of a dataset creation property list. * @param idx IN: External file index. * @param name_size IN: Maximum length of name array. * @param name OUT: Name of the external file. * @param size OUT: the offset value and the size of the external file data. * * 
     * 
     *            size[0] = offset // a location to return an offset value size[1] = size // a
     *            location to return the size of // the external file data.
     * 
     *
* @return a non-negative value if successful * @exception ArrayIndexOutOfBoundsException Fatal error on Copyback * @exception ArrayStoreException Fatal error on Copyback * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name or size is null. * @exception IllegalArgumentException - name_size <= 0 . */ public static native int H5Pget_external(int plist, int idx, int name_size, String[] name, long[] size) throws ArrayIndexOutOfBoundsException, ArrayStoreException, HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Pset_fill_value sets the fill value for a dataset creation property list. * * @param plist_id IN: Property list identifier. * @param type_id IN: The datatype identifier of value. * @param value IN: The fill value. * @return a non-negative value if successful * @exception HDF5Exception - Error converting data array */ public static native int H5Pset_fill_value(int plist_id, int type_id, byte[] value) throws HDF5Exception; /** * H5Pget_fill_value queries the fill value property of a dataset creation property list. NOT * IMPLEMENTED YET * * @param plist_id IN: Property list identifier. * @param type_id IN: The datatype identifier of value. * @param value IN: The fill value. * @return a non-negative value if successful */ public static native int H5Pget_fill_value(int plist_id, int type_id, byte[] value) throws HDF5Exception; /** * H5Pset_filter adds the specified filter and corresponding properties to the end of an output * filter pipeline. * * @param plist IN: Property list identifier. * @param filter IN: Filter to be added to the pipeline. * @param flags IN: Bit vector specifying certain general properties of the filter. * @param cd_nelmts IN: Number of elements in cd_values * @param cd_values IN: Auxiliary data for the filter. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Pset_filter(int plist, int filter, int flags, int cd_nelmts, int[] cd_values) throws HDF5LibraryException; /** * H5Pget_nfilters returns the number of filters defined in the filter pipeline associated with * the property list plist. * * @param plist IN: Property list identifier. * @return the number of filters in the pipeline if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Pget_nfilters(int plist) throws HDF5LibraryException; /** * H5Pget_filter returns information about a filter, specified by its filter number, in a filter * pipeline, specified by the property list with which it is associated. * * @param plist IN: Property list identifier. * @param filter_number IN: Sequence number within the filter pipeline of the filter for which * information is sought. * @param flags OUT: Bit vector specifying certain general properties of the filter. * @param cd_nelmts IN/OUT: Number of elements in cd_values * @param cd_values OUT: Auxiliary data for the filter. * @param namelen IN: Anticipated number of characters in name. * @param name OUT: Name of the filter. * @return the filter identification number if successful. Otherwise returns H5Z_FILTER_ERROR * (-1). * @exception ArrayIndexOutOfBoundsException Fatal error on Copyback * @exception ArrayStoreException Fatal error on Copyback * @exception NullPointerException - name or an array is null. */ public static native int H5Pget_filter(int plist, int filter_number, int[] flags, int[] cd_nelmts, int[] cd_values, int namelen, String[] name) throws ArrayIndexOutOfBoundsException, ArrayStoreException, HDF5LibraryException, NullPointerException; // REMOVED in HDF5.1.4 // // /** // * H5Pget_driver returns the identifier of the low-level // * file driver. // *

// * Valid identifiers are: // *

    // *
  • // * H5F_LOW_STDIO (0) // *
    • // *
  • // * H5F_LOW_SEC2 (1) // *
    • // *
  • // * H5F_LOW_MPIO (2) // *
    • // *
  • // * H5F_LOW_CORE (3) // *
    • // *
  • // * H5F_LOW_SPLIT (4) // *
    • // *
  • // * H5F_LOW_FAMILY (5) // *
    • // *
// * // * @param plist IN: Identifier of a file access property list. // * // * @return a low-level driver identifier if successful. Otherwise returns // * H5F_LOW_ERROR (-1). // * // * @exception HDF5LibraryException - Error from the HDF-5 Library. // **/ // public static native int H5Pget_driver(int plist) // throws HDF5LibraryException; // // /** // * H5Pset_stdio sets the low level file driver to use the // * functions declared in the stdio.h file: fopen(), fseek() // * or fseek64(), fread(), fwrite(), and fclose(). // * // * @param plist IN: Identifier of a file access property list. // * // * @return a non-negative value if successful // * // **/ // public static native int H5Pset_stdio(int plist) // throws HDF5LibraryException; // // /** // * H5Pget_stdio checks to determine whether the file access // * property list is set to the stdio driver. // * // * @param plist IN: Identifier of a file access property list. // * @return true if the file access property list is set to // * the stdio driver. Otherwise returns a negative value. // * // **/ // public static native boolean H5Pget_stdio(int plist); // // /** // * H5Pset_sec2 sets the low-level file driver to use the // * functions declared in the unistd.h file: open(), lseek() // * or lseek64(), read(), write(), and close(). // * // * @param plist IN: Identifier of a file access property list. // * @return a non-negative value if successful // * // * @exception HDF5LibraryException - Error from the HDF-5 Library. // **/ // public static native int H5Pset_sec2(int plist) // throws HDF5LibraryException; // // // /** // * H5Pget_sec2 checks to determine whether the file access // * property list is set to the sec2 driver. // * // * @param plist IN: Identifier of a file access property list. // * @return true if the file access property list is set to // * the sec2 driver. Otherwise returns a negative value. // * // * @exception HDF5LibraryException - Error from the HDF-5 Library. // **/ // public static native boolean H5Pget_sec2(int plist) // throws HDF5LibraryException; // // /** // * H5Pset_core sets the low-level file driver to use malloc() and // * free(). // * // * @param plist IN: Identifier of a file access property list. // * @param increment IN: File block size in bytes. // * // * @return a non-negative value if successful // * // * @exception HDF5LibraryException - Error from the HDF-5 Library. // **/ // public static native int H5Pset_core(int plist, int increment) // throws HDF5LibraryException; // // // /** // * H5Pget_core checks to determine whether the file access // * property list is set to the core driver. // * // * @param plist IN: Identifier of the file access property list. // * @param increment OUT: A location to return the file block size // * @return true if the file access property list is set to // * the core driver. // * // * @exception HDF5LibraryException - Error from the HDF-5 Library. // **/ // public static native boolean H5Pget_core(int plist, // int[] increment) // throws HDF5LibraryException; // // // /** // * H5Pset_split sets the low-level driver to split meta data // * from raw data, storing meta data in one file and raw data // * in another file. // * // * @param plist IN: Identifier of the file access property list. // * @param meta_ext IN: Name of the extension for the metafile // * filename. Recommended default value: .meta. // * @param meta_plist IN: Identifier of the meta file access // * property list. // * @param raw_ext IN: Name extension for the raw file filename. // * Recommended default value: .raw. // * @param raw_plist IN: Identifier of the raw file access // * property list. // * @return a non-negative value if successful // * // * @exception HDF5LibraryException - Error from the HDF-5 Library. // * @exception NullPointerException - a string is null. // **/ // public static native int H5Pset_split(int plist, String meta_ext, // int meta_plist, String raw_ext, int raw_plist) // throws HDF5LibraryException, // NullPointerException; // // // /** // * H5Pget_split checks to determine whether the file access // * property list is set to the split driver. // * // * @param plist IN: Identifier of the file access property list. // * @param meta_ext_size IN: Number of characters of the // * meta file extension to be copied to the meta_ext buffer. // * @param meta_ext IN: Meta file extension. // * @param *meta_properties OUT: A copy of the meta file // * access property list. // * @param raw_ext_size IN: Number of characters of the // * raw file extension to be copied to the raw_ext buffer. // * @param raw_ext OUT: Raw file extension. // * @param *raw_properties OUT: A copy of the raw file // * access property list. // * // * @return true if the file access property list is set to // * the split driver. // * // * @exception ArrayIndexOutOfBoundsException JNI error // * writing back array // * @exception ArrayStoreException JNI error writing back array // * @exception HDF5LibraryException - Error from the HDF-5 Library. // * @exception NullPointerException - a string or array is null. // **/ // public static native boolean H5Pget_split(int plist, // int meta_ext_size, String[] meta_ext, // int[] meta_properties, int raw_ext_size, // String[] raw_ext, int[] raw_properties) // throws ArrayIndexOutOfBoundsException, // ArrayStoreException, // HDF5LibraryException, // NullPointerException; // // /** // * H5Pset_family sets the file access properties to use the // * family driver; any previously defined driver properties // * are erased from the property list. // * // * @param plist IN: Identifier of the file access property list. // * @param memb_size IN: Logical size, in bytes, of each // * family member. // * @param memb_plist IN: Identifier of the file access // * property list for each member of the family. // * @return a non-negative value if successful // * // * @exception HDF5LibraryException - Error from the HDF-5 Library. // **/ // public static native int H5Pset_family(int plist, long memb_size, // int memb_plist) // throws HDF5LibraryException; // // // /** // * H5Pget_family checks to determine whether the file access // * property list is set to the family driver. // * // * @param plist IN: Identifier of the file access property list. // * @param memb_size OUT: Logical size, in bytes, of each // * family member. // * @param *memb_plist OUT: Identifier of the file access // * property list for each member of the family. // * // * @return a non-negative value if the file access property // * list is set to the family driver. // * // * @exception HDF5LibraryException - Error from the HDF-5 Library. // * @exception NullPointerException - an array is null. // **/ // public static native int H5Pget_family(int tid, long[] memb_size, // int[] memb_plist) // throws HDF5LibraryException, NullPointerException; /** * H5Pset_cache sets the number of elements (objects) in the meta data cache and the total * number of bytes in the raw data chunk cache. * * @param plist IN: Identifier of the file access property list. * @param mdc_nelmts IN: Number of elements (objects) in the meta data cache. * @param rdcc_nbytes IN: Total size of the raw data chunk cache, in bytes. * @param rdcc_w0 IN: Preemption policy. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Pset_cache(int plist, int mdc_nelmts, int rdcc_nelmts, int rdcc_nbytes, double rdcc_w0) throws HDF5LibraryException; /** * Retrieves the maximum possible number of elements in the meta data cache and the maximum * possible number of bytes and the RDCC_W0 value in the raw data chunk cache. * * @param plist IN: Identifier of the file access property list. * @param mdc_nelmts IN/OUT: Number of elements (objects) in the meta data cache. * @param rdcc_nbytes IN/OUT: Total size of the raw data chunk cache, in bytes. * @param rdcc_w0 IN/OUT: Preemption policy. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - an array is null. */ public static native int H5Pget_cache(int plist, int[] mdc_nelmts, int[] rdcc_nelmts, int[] rdcc_nbytes, double[] rdcc_w0) throws HDF5LibraryException, NullPointerException; /** * H5Pset_buffer sets type conversion and background buffers. status to TRUE or FALSE. Given a * dataset transfer property list, H5Pset_buffer sets the maximum size for the type conversion * buffer and background buffer and optionally supplies pointers to application-allocated * buffers. If the buffer size is smaller than the entire amount of data being transferred * between the application and the file, and a type conversion buffer or background buffer is * required, then strip mining will be used. Note that there are minimum size requirements for * the buffer. Strip mining can only break the data up along the first dimension, so the buffer * must be large enough to accommodate a complete slice that encompasses all of the remaining * dimensions. For example, when strip mining a 100x200x300 hyperslab of a simple data space, * the buffer must be large enough to hold 1x200x300 data elements. When strip mining a * 100x200x300x150 hyperslab of a simple data space, the buffer must be large enough to hold * 1x200x300x150 data elements. If tconv and/or bkg are null pointers, then buffers will be * allocated and freed during the data transfer. * * @param plist Identifier for the dataset transfer property list. * @param size Size, in bytes, of the type conversion and background buffers. * @param tconv byte array of application-allocated type conversion buffer. * @param bkg byte array of application-allocated background buffer. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception IllegalArgumentException - plist is invalid. */ public static native int H5Pset_buffer(int plist, int size, byte[] tconv, byte[] bkg) throws HDF5LibraryException, IllegalArgumentException; /** * HH5Pget_buffer gets type conversion and background buffers. Returns buffer size, in bytes, if * successful; otherwise 0 on failure. * * @param plist Identifier for the dataset transfer property list. * @param tconv byte array of application-allocated type conversion buffer. * @param bkg byte array of application-allocated background buffer. * @return buffer size, in bytes, if successful; otherwise 0 on failure * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception IllegalArgumentException - plist is invalid. */ public static native int H5Pget_buffer(int plist, byte[] tconv, byte[] bkg) throws HDF5LibraryException, IllegalArgumentException; /** * H5Pset_preserve sets the dataset transfer property list status to TRUE or FALSE. * * @param plist IN: Identifier for the dataset transfer property list. * @param status IN: Status of for the dataset transfer property list. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception IllegalArgumentException - plist is invalid. */ public static native int H5Pset_preserve(int plist, boolean status) throws HDF5LibraryException, IllegalArgumentException; /** * H5Pget_preserve checks the status of the dataset transfer property list. * * @param plist IN: Identifier for the dataset transfer property list. * @return TRUE or FALSE if successful; otherwise returns a negative value * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Pget_preserve(int plist) throws HDF5LibraryException; /** * H5Pset_deflate sets the compression method for a dataset. * * @param plist IN: Identifier for the dataset creation property list. * @param level IN: Compression level. * @return non-negative if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Pset_deflate(int plist, int level) throws HDF5LibraryException; /** * H5Pset_nbit sets the compression method for a dataset to n-bits. *

* Keeps only n-bits from an integer or float value. * * @param plist IN: Identifier for the dataset creation property list. * @return non-negative if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Pset_nbit(int plist) throws HDF5LibraryException; /** * H5Pset_scaleoffset sets the compression method for a dataset to scale_offset. *

* Generally speaking, Scale-Offset compression performs a scale and/or offset operation on each * data value and truncates the resulting value to a minimum number of bits (MinBits) before * storing it. The current Scale-Offset filter supports integer and floating-point datatype. * * @param plist IN: Identifier for the dataset creation property list. * @param scale_type IN: One of {@link HDF5Constants#H5Z_SO_INT}, * {@link HDF5Constants#H5Z_SO_FLOAT_DSCALE} or * {@link HDF5Constants#H5Z_SO_FLOAT_ESCALE}. Note that * {@link HDF5Constants#H5Z_SO_FLOAT_ESCALE} is not implemented as of HDF5 1.8.2. * @return non-negative if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Pset_scaleoffset(int plist, int scale_type, int scale_factor) throws HDF5LibraryException; /** * H5Pset_gc_references Sets the flag for garbage collecting references for the file. Default * value for garbage collecting references is off. * * @param fapl_id IN File access property list * @param gc_ref IN set GC on (true) or off (false) * @return non-negative if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Pset_gc_references(int fapl_id, boolean gc_ref) throws HDF5LibraryException; /** * H5Pget_gc_references Returns the current setting for the garbage collection refernces * property from a file access property list. *

* Note: this routine changed name with HDF5.1.2.2. If using an earlier version, use 'configure * --enable-hdf5_1_2_1' so this routine will link to the old name. * * @param fapl_id IN File access property list * @param gc_ref OUT GC is on (true) or off (false) * @return non-negative if succeed * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - array is null. */ public static native int H5Pget_gc_references(int fapl_id, boolean[] gc_ref) throws HDF5LibraryException, NullPointerException; /* * Earlier versions of the HDF5 library had a different name. This is included as an alias. */ public static int H5Pget_gc_reference(final int fapl_id, final boolean[] gc_ref) throws HDF5LibraryException, NullPointerException { return H5Pget_gc_references(fapl_id, gc_ref); } /** * H5Pset_btree_ratio Sets B-tree split ratios for a dataset transfer property list. The split * ratios determine what percent of children go in the first node when a node splits. * * @param plist_id IN Dataset transfer property list * @param left IN split ratio for leftmost nodes * @param right IN split ratio for righttmost nodes * @param middle IN split ratio for all other nodes * @return non-negative if succeed * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Pset_btree_ratios(int plist_id, double left, double middle, double right) throws HDF5LibraryException; /** * H5Pget_btree_ratio Get the B-tree split ratios for a dataset transfer property list. * * @param plist_id IN Dataset transfer property list * @param left OUT split ratio for leftmost nodes * @param right OUT split ratio for righttmost nodes * @param middle OUT split ratio for all other nodes * @return non-negative if succeed * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - an input array is null. */ public static native int H5Pget_btree_ratios(int plist_id, double[] left, double[] middle, double[] right) throws HDF5LibraryException, NullPointerException; /** * H5Pset_create_intermediate_group pecifies in property list whether to create missing * intermediate groups. *

* H5Pset_create_intermediate_group specifies whether to set the link creation property list * lcpl_id so that calls to functions that create objects in groups different from the current * working group will create intermediate groups that may be missing in the path of a new or * moved object. *

* Functions that create objects in or move objects to a group other than the current working * group make use of this property. H5Gcreate_anon and H5Lmove are examles of such functions. *

* If crt_intermed_group is true, the H5G_CRT_INTMD_GROUP will be added to lcpl_id * (if it is not already there). Missing intermediate groups will be created upon calls to * functions such as those listed above that use lcpl_id. *

* If crt_intermed_group is false, the H5G_CRT_INTMD_GROUP, if present, will be * removed from lcpl_id. Missing intermediate groups will not be created upon calls to functions * such as those listed above that use lcpl_id. * * @param lcpl_id Link creation property list identifier * @param crt_intermed_group Flag specifying whether to create intermediate groups upon the * creation of an object * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native void H5Pset_create_intermediate_group(int lcpl_id, boolean crt_intermed_group) throws HDF5LibraryException; /** * Determines whether property is set to enable creating missing intermediate groups. * * @return true if intermediate groups are created, false otherwise. * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native boolean H5Pget_create_intermediate_group(int lcpl_id) throws HDF5LibraryException; /** * Returns a dataset transfer property list (H5P_DATASET_XFER) that has a * conversion exception handler set which abort conversions that triggers overflows. */ public static native int H5Pcreate_xfer_abort_overflow(); /** * Returns a dataset transfer property list (H5P_DATASET_XFER) that has a * conversion exception handler set which aborts all conversions. */ public static native int H5Pcreate_xfer_abort(); // //////////////////////////////////////////////////////////// // // // H5R: Reference Interface Functions // // // // //////////////////////////////////////////////////////////// private static native int H5Rcreate(byte[] ref, int loc_id, String name, int ref_type, int space_id) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Rcreate creates the reference, ref, of the type specified in ref_type, pointing to the * object name located at loc_id. * * @param loc_id IN: Location identifier used to locate the object being pointed to. * @param name IN: Name of object at location loc_id. * @param ref_type IN: Type of reference. * @param space_id IN: Dataspace identifier with selection. * @return the reference (byte[]) if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - an input array is null. * @exception IllegalArgumentException - an input array is invalid. */ public static byte[] H5Rcreate(final int loc_id, final String name, final int ref_type, final int space_id) throws HDF5LibraryException, NullPointerException, IllegalArgumentException { /* These sizes are correct for HDF5.1.2 */ int ref_size = 8; if (ref_type == HDF5Constants.H5R_DATASET_REGION) { ref_size = 12; } final byte rbuf[] = new byte[ref_size]; /* will raise an exception if fails */ H5Rcreate(rbuf, loc_id, name, ref_type, space_id); return rbuf; } /** * H5Rcreate creates the object references, pointing to the object names located at loc_id. * * @param loc_id IN: Location identifier used to locate the object being pointed to. * @param name IN: Names of objects at location loc_id. * @return the reference (long[]) if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - an input array is null. * @exception IllegalArgumentException - an input array is invalid. */ public static native long[] H5Rcreate(final int loc_id, final String[] name) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * Given a reference to some object, H5Rdereference opens that object and return an identifier. * * @param loc_id IN: Location identifier used to locate the object being pointed to. * @param ref_type IN: The reference type of ref. * @param ref IN: reference to an object * @return valid identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - output array is null. * @exception IllegalArgumentException - output array is invalid. */ public static native int H5Rdereference(int loc_id, int ref_type, byte[] ref) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * Given a reference to some object, H5Rdereference opens that object and return an identifier. * * @param loc_id IN: Location identifier used to locate the object being pointed to. * @param ref IN: reference to an object * @return valid identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - output array is null. * @exception IllegalArgumentException - output array is invalid. */ public static native int H5Rdereference(int loc_id, long ref) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * Given a reference to an object ref, H5Rget_region creates a copy of the dataspace of the * dataset pointed to and defines a selection in the copy which is the region pointed to. * * @param loc_id IN: loc_id of the reference object. * @param ref_type IN: The reference type of ref. * @param ref OUT: the reference to the object and region * @return a valid identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - output array is null. * @exception IllegalArgumentException - output array is invalid. */ public static native int H5Rget_region(int loc_id, int ref_type, byte[] ref) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * Given a reference to an object, H5Rget_obj_type returns the type of the object pointed to. * * @param loc_id Identifier of the reference object. * @param ref_type Type of reference to query. * @param ref The reference. * @return a valid identifier if successful; otherwise a negative value is returned to signal * failure. * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - array is null. * @exception IllegalArgumentException - array is invalid. */ public static native int H5Rget_obj_type(int loc_id, int ref_type, byte[] ref) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * Given a reference to an object, H5Rget_name returns the name (path) of the object pointed to. * * @param loc_id Identifier of the reference object. * @param ref_type Type of reference to query. * @param ref The reference. * @return The path of the object being pointed to, or an empty string, if the object being * pointed to has no name. * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - array is null. * @exception IllegalArgumentException - array is invalid. */ public static native String H5Rget_name(int loc_id, int ref_type, byte[] ref); /** * Given a reference to an object, H5Rget_name returns the name (path) of the object pointed to. * * @param loc_id Identifier of the reference object. * @param ref The reference. * @return The path of the object being pointed to, or an empty string, if the object being * pointed to has no name. * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - array is null. * @exception IllegalArgumentException - array is invalid. */ public static native String H5Rget_name(int loc_id, long ref); /** * Given an array of object references (ref), H5Rget_name returns the names (paths) of the * objects pointed to. * * @param loc_id Identifier of the reference object. * @param ref The references. * @return The paths of the objects being pointed to, or an empty string, if an object being * pointed to has no name. * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - array is null. * @exception IllegalArgumentException - array is invalid. */ public static native String[] H5Rget_name(int loc_id, long[] ref); // //////////////////////////////////////////////////////////// // // // H5S: Dataspace Interface Functions // // // // //////////////////////////////////////////////////////////// /** * H5Screate creates a new dataspace of a particular type. * * @param type The type of dataspace to be created. * @return a dataspace identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Screate(int type) throws HDF5LibraryException; /** * H5Screate_simple creates a new simple data space and opens it for access. * * @param rank Number of dimensions of dataspace. * @param dims An array of the size of each dimension. * @param maxdims An array of the maximum size of each dimension. * @return a dataspace identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - dims or maxdims is null. */ public static native int H5Screate_simple(int rank, byte[] dims, byte[] maxdims) throws HDF5LibraryException, NullPointerException; public static int H5Screate_simple(final int rank, final long[] dims, final long[] maxdims) throws HDF5Exception, NullPointerException { if (dims == null) { return -1; } final byte[] dimsAsByteArray = HDFNativeData.longToByte(dims); final byte[] maxDimsAsByteArray = (maxdims != null) ? HDFNativeData.longToByte(maxdims) : null; return H5Screate_simple(rank, dimsAsByteArray, maxDimsAsByteArray); } /** * H5Scopy creates a new dataspace which is an exact copy of the dataspace identified by * space_id. * * @param space_id Identifier of dataspace to copy. * @return a dataspace identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Scopy(int space_id) throws HDF5LibraryException; /** * H5Sselect_elements selects array elements to be included in the selection for the space_id * dataspace. * * @param space_id Identifier of the dataspace. * @param op operator specifying how the new selection is combined. * @param num_elements Number of elements to be selected. * @param coord A 2-dimensional array specifying the coordinates of the elements. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Sselect_elements(int space_id, int op, int num_elements, byte[] coord) throws HDF5LibraryException, NullPointerException; /** * H5Sselect_all selects the entire extent of the dataspace space_id. * * @param space_id IN: The identifier of the dataspace to be selected. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Sselect_all(int space_id) throws HDF5LibraryException; /** * H5Sselect_none resets the selection region for the dataspace space_id to include no elements. * * @param space_id IN: The identifier of the dataspace to be reset. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Sselect_none(int space_id) throws HDF5LibraryException; /** * H5Sselect_valid verifies that the selection for the dataspace. * * @param space_id The identifier for the dataspace in which the selection is being reset. * @return true if the selection is contained within the extent and FALSE if it is not or is an * error. * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native boolean H5Sselect_valid(int space_id) throws HDF5LibraryException; /** * H5Sget_simple_extent_npoints determines the number of elements in a dataspace. * * @param space_id ID of the dataspace object to query * @return the number of elements in the dataspace if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native long H5Sget_simple_extent_npoints(int space_id) throws HDF5LibraryException; /** * H5Sget_select_npoints determines the number of elements in the current selection of a * dataspace. * * @param space_id Dataspace identifier. * @return the number of elements in the selection if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native long H5Sget_select_npoints(int space_id) throws HDF5LibraryException; /** * H5Sget_simple_extent_ndims determines the dimensionality (or rank) of a dataspace. * * @param space_id Identifier of the dataspace * @return the number of dimensions in the dataspace if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Sget_simple_extent_ndims(int space_id) throws HDF5LibraryException; /** * H5Sget_simple_extent_dims returns the size and maximum sizes of each dimension of a dataspace * through the dims and maxdims parameters. * * @param space_id IN: Identifier of the dataspace object to query * @param dims OUT: Pointer to array to store the size of each dimension. * @param maxdims OUT: Pointer to array to store the maximum size of each dimension. * @return the number of dimensions in the dataspace if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - dims or maxdims is null. */ public static native int H5Sget_simple_extent_dims(int space_id, long[] dims, long[] maxdims) throws HDF5LibraryException, NullPointerException; /** * H5Sget_simple_extent_type queries a dataspace to determine the current class of a dataspace. * * @param space_id Dataspace identifier. * @return a dataspace class name if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Sget_simple_extent_type(int space_id) throws HDF5LibraryException; /** * H5Sset_extent_simple sets or resets the size of an existing dataspace. * * @param space_id Dataspace identifier. * @param rank Rank, or dimensionality, of the dataspace. * @param current_size Array containing current size of dataspace. * @param maximum_size Array containing maximum size of dataspace. * @return a dataspace identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Sset_extent_simple(int space_id, int rank, byte[] current_size, byte[] maximum_size) throws HDF5LibraryException, NullPointerException; public static int H5Sset_extent_simple(final int space_id, final int rank, final long[] currentSize, final long[] maxSize) throws HDF5Exception, NullPointerException { if (currentSize == null) { return -1; } final byte[] currentSizeAsByteArray = HDFNativeData.longToByte(currentSize); final byte[] maxSizeAsByteArray = (maxSize != null) ? HDFNativeData.longToByte(maxSize) : null; return H5Screate_simple(rank, currentSizeAsByteArray, maxSizeAsByteArray); } /** * H5Sis_simple determines whether a dataspace is a simple dataspace. * * @param space_id Identifier of the dataspace to query * @return true if is a simple dataspace * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native boolean H5Sis_simple(int space_id) throws HDF5LibraryException; /** * H5Soffset_simple sets the offset of a simple dataspace space_id. * * @param space_id IN: The identifier for the dataspace object to reset. * @param offset IN: The offset at which to position the selection. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - offset array is null. */ public static native int H5Soffset_simple(int space_id, byte[] offset) throws HDF5LibraryException, NullPointerException; public static int H5Soffset_simple(final int space_id, final long[] offset) throws HDF5Exception, NullPointerException { if (offset == null) { return -1; } final byte[] offsetAsByteArray = HDFNativeData.longToByte(offset); return H5Soffset_simple(space_id, offsetAsByteArray); } /** * H5Sextent_copy copies the extent from source_space_id to dest_space_id. This action may * change the type of the dataspace. * * @param dest_space_id IN: The identifier for the dataspace from which the extent is copied. * @param source_space_id IN: The identifier for the dataspace to which the extent is copied. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Sextent_copy(int dest_space_id, int source_space_id) throws HDF5LibraryException; /** * H5Sset_extent_none removes the extent from a dataspace and sets the type to H5S_NONE. * * @param space_id The identifier for the dataspace from which the extent is to be removed. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Sset_extent_none(int space_id) throws HDF5LibraryException; /** * H5Sselect_hyperslab selects a hyperslab region to add to the current selected region for the * dataspace specified by space_id. The start, stride, count, and block arrays must be the same * size as the rank of the dataspace. * * @param space_id IN: Identifier of dataspace selection to modify * @param op IN: Operation to perform on current selection. * @param start IN: Offset of start of hyperslab * @param count IN: Number of blocks included in hyperslab. * @param stride IN: Hyperslab stride. * @param block IN: Size of block in hyperslab. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - an input array is null. * @exception NullPointerException - an input array is invalid. */ public static native int H5Sselect_hyperslab(int space_id, int op, byte[] start, byte[] stride, byte[] count, byte[] block) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; public static int H5Sselect_hyperslab(final int space_id, final int op, final long[] start, final long[] stride, final long[] count, final long[] block) throws HDF5Exception, NullPointerException, IllegalArgumentException { final byte[] startAsByteArray = (start != null) ? HDFNativeData.longToByte(start) : null; final byte[] countAsByteArray = (count != null) ? HDFNativeData.longToByte(count) : null; final byte[] strideAsByteArray = (stride != null) ? HDFNativeData.longToByte(stride) : null; final byte[] blockAsByteArray = (block != null) ? HDFNativeData.longToByte(block) : null; return H5Sselect_hyperslab(space_id, op, startAsByteArray, strideAsByteArray, countAsByteArray, blockAsByteArray); } /** * H5Sclose releases a dataspace. * * @param space_id Identifier of dataspace to release. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Sclose(int space_id) throws HDF5LibraryException; // --// // following static native functions are missing from HDF5 (version 1.0.1) RM /** * H5Sget_select_hyper_nblocks returns the number of hyperslab blocks in the current dataspace * selection. * * @param spaceid Identifier of dataspace to release. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native long H5Sget_select_hyper_nblocks(int spaceid) throws HDF5LibraryException; /** * H5Sget_select_elem_npoints returns the number of element points in the current dataspace * selection. * * @param spaceid Identifier of dataspace to release. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native long H5Sget_select_elem_npoints(int spaceid) throws HDF5LibraryException; /** * H5Sget_select_hyper_blocklist returns an array of hyperslab blocks. The block coordinates * have the same dimensionality (rank) as the dataspace they are located within. The list of * blocks is formatted as follows: * * 

     * 
     * <"start" coordinate>, immediately followed by <"opposite" corner
     * coordinate>, followed by the next "start" and "opposite" coordinates,
     * etc. until all of the selected blocks have been listed.
     * 
     *
* * @param spaceid Identifier of dataspace to release. * @param startblock first block to retrieve * @param numblocks number of blocks to retrieve * @param buf returns blocks startblock to startblock+num-1, each block is rank * 2 * (corners) longs. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - buf is null. */ public static native int H5Sget_select_hyper_blocklist(int spaceid, long startblock, long numblocks, long[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Sget_select_elem_pointlist returns an array of of element points in the current dataspace * selection. The point coordinates have the same dimensionality (rank) as the dataspace they * are located within, one coordinate per point. * * @param spaceid Identifier of dataspace to release. * @param startpoint first point to retrieve * @param numpoints number of points to retrieve * @param buf returns points startblock to startblock+num-1, each points is rank longs. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - buf is null. */ public static native int H5Sget_select_elem_pointlist(int spaceid, long startpoint, long numpoints, long[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Sget_select_bounds retrieves the coordinates of the bounding box containing the current * selection and places them into user-supplied buffers. *

* The start and end buffers must be large enough to hold the dataspace rank number of * coordinates. * * @param spaceid Identifier of dataspace to release. * @param start coordinates of lowest corner of bounding box. * @param end coordinates of highest corner of bounding box. * @return a non-negative value if successful,with start and end initialized. * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - start or end is null. */ public static native int H5Sget_select_bounds(int spaceid, long[] start, long[] end) throws HDF5LibraryException, NullPointerException; // //////////////////////////////////////////////////////////// // // // H5T: Datatype Interface Functions // // // // //////////////////////////////////////////////////////////// /** * H5Topen opens a named datatype at the location specified by loc_id and return an identifier * for the datatype. * * @param loc_id A file, group, or datatype identifier. * @param name A datatype name. * @param access_plist_id Datatype access property list identifier. * @return a named datatype identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static native int H5Topen(int loc_id, String name, int access_plist_id) throws HDF5LibraryException, NullPointerException; /** * H5Tcommit commits a transient datatype (not immutable) to a file, turned it into a named * datatype. * * @param loc_id A file or group identifier. * @param name A datatype name. * @param type_id A datatype identifier. * @param link_create_plist_id Link creation property list. * @param dtype_create_plist_id Datatype creation property list. * @param dtype_access_plist_id Datatype access property list. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static native int H5Tcommit(int loc_id, String name, int type_id, int link_create_plist_id, int dtype_create_plist_id, int dtype_access_plist_id) throws HDF5LibraryException, NullPointerException; /** * H5Tcommitted queries a type to determine whether the type specified by the type identifier is * a named type or a transient type. * * @param type Datatype identifier. * @return true if successfully committed * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native boolean H5Tcommitted(int type) throws HDF5LibraryException; /** * H5Tcreate creates a new dataype of the specified class with the specified number of bytes. * * @param dclass Class of datatype to create. * @param size The number of bytes in the datatype to create. * @return datatype identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tcreate(int dclass, int size) throws HDF5LibraryException; /** * H5Tcopy copies an existing datatype. The returned type is always transient and unlocked. * * @param type_id Identifier of datatype to copy. Can be a datatype identifier, a predefined * datatype (defined in H5Tpublic.h), or a dataset Identifier. * @return a datatype identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tcopy(int type_id) throws HDF5LibraryException; /** * H5Tequal determines whether two datatype identifiers refer to the same datatype. * * @param type_id1 Identifier of datatype to compare. * @param type_id2 Identifier of datatype to compare. * @return true if the datatype identifiers refer to the same datatype, else FALSE. * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native boolean H5Tequal(int type_id1, int type_id2) throws HDF5LibraryException; /** * H5Tlock locks the datatype specified by the type_id identifier, making it read-only and * non-destrucible. * * @param type_id Identifier of datatype to lock. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tlock(int type_id) throws HDF5LibraryException; /** * H5Tget_class returns the datatype class identifier. * * @param type_id Identifier of datatype to query. * @return datatype class identifier if successful; otherwise H5T_NO_CLASS (-1). * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tget_class(int type_id) throws HDF5LibraryException; /** * H5Tget_size returns the size of a datatype in bytes as an int value. * * @param type_id Identifier of datatype to query. * @return the size of the datatype in bytes if successful * @exception HDF5LibraryException - Error from the HDF-5 Library, or if the size of the data * type exceeds an int */ public static native int H5Tget_size(int type_id) throws HDF5LibraryException; /** * H5Tget_size returns the size of a datatype in bytes as a long value. * * @param type_id Identifier of datatype to query. * @return the size of the datatype in bytes if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native long H5Tget_size_long(int type_id) throws HDF5LibraryException; /** * H5Tset_size sets the total size in bytes, size, for an atomic datatype (this operation is not * permitted on compound datatypes). * * @param type_id Identifier of datatype to change size. * @param size Size in bytes to modify datatype. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tset_size(int type_id, int size) throws HDF5LibraryException; /** * H5Tget_order returns the byte order of an atomic datatype. * * @param type_id Identifier of datatype to query. * @return a byte order constant if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tget_order(int type_id) throws HDF5LibraryException; /** * H5Tset_order sets the byte ordering of an atomic datatype. * * @param type_id Identifier of datatype to set. * @param order Byte ordering constant. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tset_order(int type_id, int order) throws HDF5LibraryException; /** * H5Tget_precision returns the precision of an atomic datatype. * * @param type_id Identifier of datatype to query. * @return the number of significant bits if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tget_precision(int type_id) throws HDF5LibraryException; /** * H5Tset_precision sets the precision of an atomic datatype. * * @param type_id Identifier of datatype to set. * @param precision Number of bits of precision for datatype. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tset_precision(int type_id, int precision) throws HDF5LibraryException; /** * H5Tget_offset retrieves the bit offset of the first significant bit. * * @param type_id Identifier of datatype to query. * @return a positive offset value if successful; otherwise 0. * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tget_offset(int type_id) throws HDF5LibraryException; /** * H5Tset_offset sets the bit offset of the first significant bit. * * @param type_id Identifier of datatype to set. * @param offset Offset of first significant bit. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tset_offset(int type_id, int offset) throws HDF5LibraryException; /** * H5Tget_pad retrieves the padding type of the least and most-significant bit padding. * * @param type_id IN: Identifier of datatype to query. * @param pad OUT: locations to return least-significant and most-significant bit padding type. * * 

     * 
     *            pad[0] = lsb // least-significant bit padding type pad[1] = msb //
     *            most-significant bit padding type
     * 
     *
* @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - pad is null. */ public static native int H5Tget_pad(int type_id, int[] pad) throws HDF5LibraryException, NullPointerException; /** * H5Tset_pad sets the least and most-significant bits padding types. * * @param type_id Identifier of datatype to set. * @param lsb Padding type for least-significant bits. * @param msb Padding type for most-significant bits. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tset_pad(int type_id, int lsb, int msb) throws HDF5LibraryException; /** * H5Tget_sign retrieves the sign type for an integer type. * * @param type_id Identifier of datatype to query. * @return a valid sign type if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tget_sign(int type_id) throws HDF5LibraryException; /** * H5Tset_sign sets the sign proprety for an integer type. * * @param type_id Identifier of datatype to set. * @param sign Sign type. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tset_sign(int type_id, int sign) throws HDF5LibraryException; /** * H5Tget_fields retrieves information about the locations of the various bit fields of a * floating point datatype. * * @param type_id IN: Identifier of datatype to query. * @param fields OUT: location of size and bit-position. * * 
     * 
     *            fields[0] = spos OUT: location to return size of in bits. fields[1] = epos OUT:
     *            location to return exponent bit-position. fields[2] = esize OUT: location to
     *            return size of exponent in bits. fields[3] = mpos OUT: location to return mantissa
     *            bit-position. fields[4] = msize OUT: location to return size of mantissa in bits.
     * 
     *
* @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - fileds is null. * @exception IllegalArgumentException - fileds array is invalid. */ public static native int H5Tget_fields(int type_id, int[] fields) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Tset_fields sets the locations and sizes of the various floating point bit fields. * * @param type_id Identifier of datatype to set. * @param spos Size position. * @param epos Exponent bit position. * @param esize Size of exponent in bits. * @param mpos Mantissa bit position. * @param msize Size of mantissa in bits. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tset_fields(int type_id, int spos, int epos, int esize, int mpos, int msize) throws HDF5LibraryException; /** * H5Tget_ebias retrieves the exponent bias of a floating-point type. * * @param type_id Identifier of datatype to query. * @return the bias if successful; otherwise 0. * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tget_ebias(int type_id) throws HDF5LibraryException; /** * H5Tset_ebias sets the exponent bias of a floating-point type. * * @param type_id Identifier of datatype to set. * @param ebias Exponent bias value. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tset_ebias(int type_id, int ebias) throws HDF5LibraryException; /** * H5Tget_norm retrieves the mantissa normalization of a floating-point datatype. * * @param type_id Identifier of datatype to query. * @return a valid normalization type if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tget_norm(int type_id) throws HDF5LibraryException; /** * H5Tset_norm sets the mantissa normalization of a floating-point datatype. * * @param type_id Identifier of datatype to set. * @param norm Mantissa normalization type. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tset_norm(int type_id, int norm) throws HDF5LibraryException; /** * H5Tget_inpad retrieves the internal padding type for unused bits in floating-point datatypes. * * @param type_id Identifier of datatype to query. * @return a valid padding type if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tget_inpad(int type_id) throws HDF5LibraryException; /** * If any internal bits of a floating point type are unused (that is, those significant bits * which are not part of the sign, exponent, or mantissa), then H5Tset_inpad will be filled * according to the value of the padding value property inpad. * * @param type_id Identifier of datatype to modify. * @param inpad Padding type. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tset_inpad(int type_id, int inpad) throws HDF5LibraryException; /** * H5Tget_cset retrieves the character set type of a string datatype. * * @param type_id Identifier of datatype to query. * @return a valid character set type if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tget_cset(int type_id) throws HDF5LibraryException; /** * H5Tset_cset the character set to be used. * * @param type_id Identifier of datatype to modify. * @param cset Character set type. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tset_cset(int type_id, int cset) throws HDF5LibraryException; /** * H5Tget_strpad retrieves the string padding method for a string datatype. * * @param type_id Identifier of datatype to query. * @return a valid string padding type if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tget_strpad(int type_id) throws HDF5LibraryException; /** * H5Tset_strpad defines the storage mechanism for the string. * * @param type_id Identifier of datatype to modify. * @param strpad String padding type. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tset_strpad(int type_id, int strpad) throws HDF5LibraryException; /** * H5Tget_nmembers retrieves the number of fields a compound datatype has. * * @param type_id Identifier of datatype to query. * @return number of members datatype has if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tget_nmembers(int type_id) throws HDF5LibraryException; /** * H5Tget_member_name retrieves the name of a field of a compound datatype. * * @param type_id Identifier of datatype to query. * @param field_idx Field index (0-based) of the field name to retrieve. * @return a valid pointer if successful; otherwise null. */ public static native String H5Tget_member_name(int type_id, int field_idx); /** * H5Tget_member_index retrieves the index of a field of a compound datatype. * * @param type_id Identifier of datatype to query. * @param field_name Field name of the field index to retrieve. * @return if field is defined, the index; else negative. */ public static native int H5Tget_member_index(int type_id, String field_name); /** * H5Tget_member_class returns the datatype of the specified member. * * @param type_id Identifier of datatype to query. * @param field_idx Field index (0-based) of the field type to retrieve. * @return the identifier of a copy of the datatype of the field if successful; * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tget_member_class(int type_id, int field_idx) throws HDF5LibraryException; /** * H5Tget_member_type returns the datatype of the specified member. * * @param type_id Identifier of datatype to query. * @param field_idx Field index (0-based) of the field type to retrieve. * @return the identifier of a copy of the datatype of the field if successful; * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tget_member_type(int type_id, int field_idx) throws HDF5LibraryException; /** * H5Tget_member_offset returns the byte offset of the specified member of the compound * datatype. This is the byte offset in the HDF-5 file/library, NOT the offset of any Java * object which might be mapped to this data item. * * @param type_id Identifier of datatype to query. * @param membno Field index (0-based) of the field type to retrieve. * @return the offset of the member. * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native long H5Tget_member_offset(int type_id, int membno) throws HDF5LibraryException; /** * H5Tinsert adds another member to the compound datatype type_id. * * @param type_id Identifier of compound datatype to modify. * @param name Name of the field to insert. * @param offset Offset in memory structure of the field to insert. * @param field_id Datatype identifier of the field to insert. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static native int H5Tinsert(int type_id, String name, long offset, int field_id) throws HDF5LibraryException, NullPointerException; /** * H5Tpack recursively removes padding from within a compound datatype to make it more efficient * (space-wise) to store that data. *

* WARNING: This call only affects the C-data, even if it succeeds, there may be no * visible effect on Java objects. * * @param type_id Identifier of datatype to modify. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tpack(int type_id) throws HDF5LibraryException; /** * H5Tclose releases a datatype. * * @param type_id Identifier of datatype to release. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tclose(int type_id) throws HDF5LibraryException; /** * H5Tenum_create creates a new enumeration datatype based on the specified base datatype, * parent_id, which must be an integer type. * * @param base_id Identifier of the parent datatype to release. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tenum_create(int base_id) throws HDF5LibraryException; /** * H5Tenum_insert inserts a new enumeration datatype member into an 8bit enumeration datatype. * * @param type Identifier of datatype. * @param name The name of the member * @param value The value of the member, data of the correct type * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static native int H5Tenum_insert(int type, String name, byte value) throws HDF5LibraryException, NullPointerException; /** * H5Tenum_insert inserts a new enumeration datatype member into a 16bit enumeration datatype. * * @param type Identifier of datatype. * @param name The name of the member * @param value The value of the member, data of the correct type * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static native int H5Tenum_insert(int type, String name, short value) throws HDF5LibraryException, NullPointerException; /** * H5Tenum_insert inserts a new enumeration datatype member into a 32bit enumeration datatype. * * @param type Identifier of datatype. * @param name The name of the member * @param value The value of the member, data of the correct type * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static native int H5Tenum_insert(int type, String name, int value) throws HDF5LibraryException, NullPointerException; /** * Converts the value (in place) to little endian. * * @return a non-negative value if successful */ public static native int H5Tconvert_to_little_endian(short[] value); /** * Converts the value (in place) to little endian. * * @return a non-negative value if successful */ public static native int H5Tconvert_to_little_endian(int[] value); /** * H5Tenum_nameof finds the symbol name that corresponds to the specified value of the * enumeration datatype type. * * @param type IN: Identifier of datatype. * @param value IN: The value of the member, data of the correct * @param name OUT: The name of the member * @param size IN: The max length of the name * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static native int H5Tenum_nameof(int type, int[] value, String[] name, int size) throws HDF5LibraryException, NullPointerException; /** * H5Tenum_valueof finds the value that corresponds to the specified name of the enumeration * datatype type. * * @param type IN: Identifier of datatype. * @param name IN: The name of the member * @param value OUT: The value of the member * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static native int H5Tenum_valueof(int type, String name, int[] value) throws HDF5LibraryException, NullPointerException; /** * H5Tvlen_create creates a new variable-length (VL) dataype. * * @param base_id IN: Identifier of parent datatype. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tvlen_create(int base_id) throws HDF5LibraryException; /** * H5Tset_tag tags an opaque datatype type_id with a unique ASCII identifier tag. * * @param type IN: Identifier of parent datatype. * @param tag IN: Name of the tag (will be stored as ASCII) * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tset_tag(int type, String tag) throws HDF5LibraryException; /** * H5Tget_tag returns the tag associated with datatype type_id. * * @param type IN: Identifier of datatype. * @return the tag * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native String H5Tget_tag(int type) throws HDF5LibraryException; /** * H5Tget_super returns the type from which TYPE is derived. * * @param type IN: Identifier of datatype. * @return the parent type * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Tget_super(int type) throws HDF5LibraryException; /** * H5Tget_member_value returns the value of the enumeration datatype member memb_no. * * @param type_id IN: Identifier of datatype. * @param membno IN: The name of the member * @param value OUT: The value of the member * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static native int H5Tget_member_value(int type_id, int membno, int[] value) throws HDF5LibraryException, NullPointerException; /** * * Array data types, new in HDF5.1.4. */ /** * Creates an array datatype object. * * @param base_type_id Datatype identifier for the array base datatype. * @param rank Rank of the array. * @param dims Size of each array dimension. * @return a valid datatype identifier if successful; otherwise returns a negative value. * @exception HDF5LibraryException Error from the HDF5 Library. * @exception NullPointerException rank is < 1 or dims is null. */ public static native int H5Tarray_create(int base_type_id, int rank, int[] dims) throws HDF5LibraryException, NullPointerException; /** * Returns the rank of an array datatype. * * @param adtype_id Datatype identifier of array object. * @return the rank of the array if successful; otherwise returns a negative value. * @exception HDF5LibraryException Error from the HDF5 Library. */ public static native int H5Tget_array_ndims(int adtype_id) throws HDF5LibraryException; /** * Returns sizes of array dimensions. * * @param adtype_id IN: Datatype identifier of array object. * @param dims OUT: Sizes of array dimensions. * @return the non-negative number of dimensions of the array type if successful; otherwise * returns a negative value. * @exception HDF5LibraryException Error from the HDF5 Library. * @exception NullPointerException dims is null. */ public static native int H5Tget_array_dims(int adtype_id, int[] dims) throws HDF5LibraryException, NullPointerException; // //////////////////////////////////////////////////////////// // // // New APIs for HDF5.1.6 // // removed APIs: H5Pset_hyper_cache, H5Pget_hyper_cache // // // // //////////////////////////////////////////////////////////// /** * Returns number of objects in the group specified by its identifier * * @param loc_id Identifier of the group or the file * @param num_obj Number of objects in the group * @return positive value if successful; otherwise returns a negative value. * @throws HDF5LibraryException * @throws NullPointerException */ public static native int H5Gget_num_objs(int loc_id, long[] num_obj) throws HDF5LibraryException, NullPointerException; /** * Returns a name of an object specified by an index. * * @param group_id Group or file identifier * @param idx Transient index identifying object * @param name the object name * @param size Name length * @return the size of the object name if successful, or 0 if no name is associated with the * group identifier. Otherwise returns a negative value * @throws HDF5LibraryException * @throws NullPointerException */ public static native long H5Gget_objname_by_idx(int group_id, long idx, String[] name, long size) throws HDF5LibraryException, NullPointerException; /** * Returns the type of an object specified by an index. * * @param group_id Group or file identifier. * @param idx Transient index identifying object. * @return Returns the type of the object if successful. Otherwise returns a negative value * @throws HDF5LibraryException * @throws NullPointerException */ public static native int H5Gget_objtype_by_idx(int group_id, long idx) throws HDF5LibraryException; public static native long H5Gget_nlinks(int group_id) throws HDF5LibraryException; public static native int H5Tget_native_type(int tid, int alloc_time) throws HDF5LibraryException, NullPointerException; // // Backward compatibility: // These functions have been replaced by new HDF5 library calls. // The interface is preserved as a convenience to existing code. // /** * H5Gn_members report the number of objects in a Group. The 'objects' include everything that * will be visited by H5Giterate. Each link is returned, so objects with multiple links will be * counted once for each link. * * @param loc_id file or group ID. * @param name name of the group to iterate, relative to the loc_id * @return the number of members in the group or -1 if error. * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static int H5Gn_members(final int loc_id, final String name) throws HDF5LibraryException, NullPointerException { final int grp_id = H5Gopen(loc_id, name, HDF5Constants.H5P_DEFAULT); final long[] nobj = new long[1]; nobj[0] = -1; H5Gget_num_objs(grp_id, nobj); final int r = (new Long(nobj[0])).intValue(); return (r); } /** * H5Gget_obj_info_idx report the name and type of object with index 'idx' in a Group. The 'idx' * corresponds to the index maintained by H5Giterate. Each link is returned, so objects with * multiple links will be counted once for each link. * * @param loc_id IN: file or group ID. * @param name IN: name of the group to iterate, relative to the loc_id * @param idx IN: the index of the object to iterate. * @param oname the name of the object [OUT] * @param type the type of the object [OUT] * @return non-negative if successful, -1 if not. * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static int H5Gget_obj_info_idx(final int loc_id, final String name, final int idx, final String[] oname, final int[] type) throws HDF5LibraryException, NullPointerException { final long default_buf_size = 4096; final String n[] = new String[1]; n[0] = new String(""); final int grp_id = H5Gopen(loc_id, name, HDF5Constants.H5P_DEFAULT); final long val = H5Gget_objname_by_idx(grp_id, idx, n, default_buf_size); final int type_code = H5Gget_objtype_by_idx(grp_id, idx); oname[0] = new String(n[0]); type[0] = type_code; final int ret = (new Long(val)).intValue(); return ret; } public static int H5Gget_obj_info_all(final int loc_id, final String name, final String[] oname, final int[] type) throws HDF5LibraryException, NullPointerException { if (oname == null) { throw new NullPointerException("H5Gget_obj_info_all(): name array is null"); } if (type == null) { throw new NullPointerException("H5Gget_obj_info_all(): type array is null"); } if (oname.length == 0) { throw new HDF5JavaException("H5Gget_obj_info_all(): array size is zero"); } if (oname.length != type.length) { throw new HDF5JavaException( "H5Gget_obj_info_all(): name and type array sizes are different"); } return H5Gget_obj_info_all(loc_id, name, oname, type, oname.length); } public static native int H5Gget_obj_info_all(int loc_id, String name, String[] oname, int[] type, int n) throws HDF5LibraryException, NullPointerException; // // This function is deprecated. It is recommended that the new // library calls should be used, // H5Gget_objname_by_idx // H5Gget_objtype_by_idx // /** * H5Gget_objinfo returns information about the specified object. * * @param loc_id IN: File, group, dataset, or datatype identifier. * @param name IN: Name of the object for which status is being sought. * @param follow_link IN: Link flag. * @param fileno OUT: file id numbers. * @param objno OUT: object id numbers. * @param link_info OUT: link information. * * 

     * 
     *            link_info[0] = nlink link_info[1] = type link_info[2] = linklen
     * 
     *
* @param mtime OUT: modification time * @return a non-negative value if successful, with the fields of link_info and mtime (if * non-null) initialized. * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name or array is null. * @exception IllegalArgumentException - bad argument. */ public static native int H5Gget_objinfo(int loc_id, String name, boolean follow_link, long[] fileno, long[] objno, int[] link_info, long[] mtime) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Gget_objinfo returns information about the specified object in an HDF5GroupInfo object. * * @param loc_id IN: File, group, dataset, or datatype identifier. * @param name IN: Name of the object for which status is being sought. * @param follow_link IN: Link flag. * @param info OUT: the HDF5GroupInfo object to store the object infomation * @return a non-negative value if successful, with the fields of HDF5GroupInfo object (if * non-null) initialized. * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. * @see ch.systemsx.cisd.hdf5.hdf5lib.HDF5GroupInfo See public static native int * H5Gget_objinfo(); */ public static int H5Gget_objinfo(final int loc_id, final String name, final boolean follow_link, final HDF5GroupInfo info) throws HDF5LibraryException, NullPointerException { int status = -1; final long[] fileno = new long[2]; final long[] objno = new long[2]; final int[] link_info = new int[3]; final long[] mtime = new long[1]; status = H5Gget_objinfo(loc_id, name, follow_link, fileno, objno, link_info, mtime); if (status >= 0) { info.setGroupInfo(fileno, objno, link_info[0], link_info[1], mtime[0], link_info[2]); } return status; } public static int H5Tget_native_type(final int tid) throws HDF5LibraryException, NullPointerException { return H5Tget_native_type(tid, HDF5Constants.H5T_DIR_ASCEND); } public static native int H5Pset_alloc_time(int plist_id, int alloc_time) throws HDF5LibraryException, NullPointerException; public static native int H5Pget_alloc_time(int plist_id, int[] alloc_time) throws HDF5LibraryException, NullPointerException; public static native int H5Pset_fill_time(int plist_id, int fill_time) throws HDF5LibraryException, NullPointerException; public static native int H5Pget_fill_time(int plist_id, int[] fill_time) throws HDF5LibraryException, NullPointerException; public static native int H5Pfill_value_defined(int plist_id, int[] status) throws HDF5LibraryException, NullPointerException; public static native int H5Pset_fletcher32(int plist) throws HDF5LibraryException, NullPointerException; public static native int H5Pset_edc_check(int plist, int check) throws HDF5LibraryException, NullPointerException; public static native int H5Pget_edc_check(int plist) throws HDF5LibraryException, NullPointerException; public static native int H5Pset_shuffle(int plist_id) throws HDF5LibraryException, NullPointerException; public static native int H5Pset_szip(int plist, int options_mask, int pixels_per_block) throws HDF5LibraryException, NullPointerException; public static native int H5Dget_space_status(int dset_id, int[] status) throws HDF5LibraryException, NullPointerException; public static native long H5Iget_name(int obj_id, String[] name, long size) throws HDF5LibraryException, NullPointerException; public static native int H5set_free_list_limits(int reg_global_lim, int reg_list_lim, int arr_global_lim, int arr_list_lim, int blk_global_lim, int blk_list_lim) throws HDF5LibraryException, NullPointerException; public static native int H5Fget_obj_ids(int file_id, int types, int max, int[] obj_id_list) throws HDF5LibraryException, NullPointerException; public static native int H5Fget_obj_count(int file_id, int types) throws HDF5LibraryException, NullPointerException; public static native boolean H5Tis_variable_str(int dtype_id) throws HDF5LibraryException, NullPointerException; public static native int H5Zfilter_avail(int filter) throws HDF5LibraryException, NullPointerException; public static native int H5Zunregister(int filter) throws HDF5LibraryException, NullPointerException; public static native int H5Pmodify_filter(int plist, int filter, int flags, long cd_nelmts, int[] cd_values) throws HDF5LibraryException, NullPointerException; public static native int H5Pget_filter_by_id(int plist_id, int filter, int[] flags, long[] cd_nelmts, int[] cd_values, long namelen, String[] name) throws HDF5LibraryException, NullPointerException; public static native boolean H5Pall_filters_avail(int dcpl_id) throws HDF5LibraryException, NullPointerException; public static native int H5Pset_hyper_vector_size(int dxpl_id, long vector_size) throws HDF5LibraryException, NullPointerException; public static native int H5Pget_hyper_vector_size(int dxpl_id, long[] vector_size) throws HDF5LibraryException, NullPointerException; public static native boolean H5Tdetect_class(int dtype_id, int dtype_class) throws HDF5LibraryException, NullPointerException; // ////////////////////////////////////////////////////////////////// // // // New APIs for read data from library // // Using H5Dread(..., Object buf) requires function calls // // theArray.emptyBytes() and theArray.arrayify( buf), which // // triples the actual memory needed by the data set. // // Using the following APIs solves the problem. // // // // ////////////////////////////////////////////////////////////////// public static native int H5Dread(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, short[] buf) throws HDF5LibraryException, NullPointerException; public static native int H5Dread(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, int[] buf) throws HDF5LibraryException, NullPointerException; public static native int H5Dread(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, long[] buf) throws HDF5LibraryException, NullPointerException; public static native int H5Dread(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, float[] buf) throws HDF5LibraryException, NullPointerException; public static native int H5Dread(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, double[] buf) throws HDF5LibraryException, NullPointerException; public static native int H5Dread_string(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException; public static native int H5Dread_reg_ref(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException; public static native int H5Dwrite(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, short[] buf) throws HDF5LibraryException, NullPointerException; public static native int H5Dwrite(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, int[] buf) throws HDF5LibraryException, NullPointerException; public static native int H5Dwrite(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, long[] buf) throws HDF5LibraryException, NullPointerException; public static native int H5Dwrite(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, float[] buf) throws HDF5LibraryException, NullPointerException; public static native int H5Dwrite(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, double[] buf) throws HDF5LibraryException, NullPointerException; public static native int H5Pset_fclose_degree(int plist, int degree) throws HDF5LibraryException, NullPointerException; public static native int H5Pget_fclose_degree(int plist_id) throws HDF5LibraryException, NullPointerException; // ////////////////////////////////////////////////////////////////// // // // New APIs from release 1.6.2 // // August 20, 2004 // // ////////////////////////////////////////////////////////////////// public static native int H5Iget_ref(int obj_id) throws HDF5LibraryException, NullPointerException; public static native int H5Iinc_ref(int obj_id) throws HDF5LibraryException, NullPointerException; public static native int H5Idec_ref(int obj_id) throws HDF5LibraryException, NullPointerException; public static native int H5Pset_fapl_family(int fapl_id, long memb_size, int memb_fapl_id) throws HDF5LibraryException, NullPointerException; public static native int H5Pget_fapl_family(int fapl_id, long[] memb_size, int[] memb_fapl_id) throws HDF5LibraryException, NullPointerException; public static native int H5Pset_fapl_core(int fapl_id, int increment, boolean backing_store) throws HDF5LibraryException, NullPointerException; public static native int H5Pget_fapl_core(int fapl_id, int[] increment, boolean[] backing_store) throws HDF5LibraryException, NullPointerException; public static native int H5Pset_family_offset(int fapl_id, long offset) throws HDF5LibraryException, NullPointerException; public static native long H5Pget_family_offset(int fapl_id) throws HDF5LibraryException, NullPointerException; public static native int H5Pset_fapl_log(int fapl_id, String logfile, int flags, int buf_size) throws HDF5LibraryException, NullPointerException; // ////////////////////////////////////////////////////////////////// // // // New APIs from release 1.6.3 // // August 25, 2004 // // ////////////////////////////////////////////////////////////////// public static native long H5Fget_name(int obj_id, String name, int size) throws HDF5LibraryException; public static native long H5Fget_filesize(int file_id) throws HDF5LibraryException; public static native int H5Iget_file_id(int obj_id) throws HDF5LibraryException; public static native int H5Premove_filter(int obj_id, int filter) throws HDF5LibraryException; public static native int H5Zget_filter_info(int filter) throws HDF5LibraryException; // //////////////////////////////////////////////////////////////////////// // Modified by Peter Cao on July 26, 2006: // // Some of the Generic Property APIs have callback function // // pointers, which Java does not support. Only the Generic // // Property APIs without function pointers are implemented // // //////////////////////////////////////////////////////////////////////// /** * Creates a new property list class of a given class * * @param cls IN: Class of property list to create * @return a valid property list identifier if successful; a negative value if failed * @throws HDF5LibraryException */ public static native int H5Pcreate_list(int cls) throws HDF5LibraryException; /** * Sets a property list value (support integer only) * * @param plid IN: Property list identifier to modify * @param name IN: Name of property to modify * @param value IN: value to set the property to * @return a non-negative value if successful; a negative value if failed * @throws HDF5LibraryException */ public static native int H5Pset(int plid, String name, int value) throws HDF5LibraryException; /** * H5Pexist determines whether a property exists within a property list or class * * @param plid IN: Identifier for the property to query * @param name IN: Name of property to check for * @return a positive value if the property exists in the property object; zero if the property * does not exist; a negative value if failed * @throws HDF5LibraryException */ public static native int H5Pexist(int plid, String name) throws HDF5LibraryException; /** * H5Pget_size retrieves the size of a property's value in bytes * * @param plid IN: Identifier of property object to query * @param name IN: Name of property to query * @return size of a property's value if successful; a negative value if failed * @throws HDF5LibraryException */ public static native long H5Pget_size(int plid, String name) throws HDF5LibraryException; /** * H5Pget_nprops retrieves the number of properties in a property list or class * * @param plid IN: Identifier of property object to query * @return number of properties if successful; a negative value if failed * @throws HDF5LibraryException */ public static native long H5Pget_nprops(int plid) throws HDF5LibraryException; /** * H5Pget_class_name retrieves the name of a generic property list class * * @param plid IN: Identifier of property object to query * @return name of a property list if successful; null if failed * @throws HDF5LibraryException */ public static native String H5Pget_class_name(int plid) throws HDF5LibraryException; /** * H5Pget_class_parent retrieves an identifier for the parent class of a property class * * @param plid IN: Identifier of the property class to query * @return a valid parent class object identifier if successful; a negative value if failed * @throws HDF5LibraryException */ public static native int H5Pget_class_parent(int plid) throws HDF5LibraryException; /** * H5Pisa_class checks to determine whether a property list is a member of the specified class * * @param plist IN: Identifier of the property list * @param pclass IN: Identifier of the property class * @return a positive value if equal; zero if unequal; a negative value if failed * @throws HDF5LibraryException */ public static native int H5Pisa_class(int plist, int pclass) throws HDF5LibraryException; /** * H5Pget retrieves a copy of the value for a property in a property list (support integer only) * * @param plid IN: Identifier of property object to query * @param name IN: Name of property to query * @return value for a property if successful; a negative value if failed * @throws HDF5LibraryException */ public static native int H5Pget(int plid, String name) throws HDF5LibraryException; /** * H5Pequal determines if two property lists or classes are equal * * @param plid1 IN: First property object to be compared * @param plid2 IN: Second property object to be compared * @return positive value if equal; zero if unequal, a negative value if failed * @throws HDF5LibraryException */ public static native int H5Pequal(int plid1, int plid2) throws HDF5LibraryException; /** * H5Pcopy_prop copies a property from one property list or class to another * * @param dst_id IN: Identifier of the destination property list or class * @param src_id IN: Identifier of the source property list or class * @param name IN: Name of the property to copy * @return a non-negative value if successful; a negative value if failed * @throws HDF5LibraryException */ public static native int H5Pcopy_prop(int dst_id, int src_id, String name) throws HDF5LibraryException; /** * H5Premove removes a property from a property list * * @param plid IN: Identifier of the property list to modify * @param name IN: Name of property to remove * @return a non-negative value if successful; a negative value if failed * @throws HDF5LibraryException */ public static native int H5Premove(int plid, String name) throws HDF5LibraryException; /** * H5Punregister removes a property from a property list class * * @param plid IN: Property list class from which to remove permanent property * @param name IN: Name of property to remove * @return a non-negative value if successful; a negative value if failed * @throws HDF5LibraryException */ public static native int H5Punregister(int plid, String name) throws HDF5LibraryException; /** * Closes an existing property list class * * @param plid IN: Property list class to close * @return a non-negative value if successful; a negative value if failed * @throws HDF5LibraryException */ public static native int H5Pclose_class(int plid) throws HDF5LibraryException; // ////////////////////////////////////////////////////////////////// // // // New APIs from release 1.8.0 // // January 21, 2008 // // ////////////////////////////////////////////////////////////////// /** * Sets the permissible bounds of the library's file format versions. *

* Can be set on the file access property list. *

* As of 1.8.0, only the combinations low=H5F_LIBVER_EARLIEST / * high=H5F_LIBVER_LATEST (which is the default and means that 1.6 compatible files are * created if no features are used that require a 1.8 format) and low=H5F_LIBVER_LATEST * / high=H5F_LIBVER_LATEST (which means that always 1.8 files are created * which cannot be read by an earlier library) are allowed. * * @param plist_id Property list identifier. * @param low The lower permissible bound. One of H5F_LIBVER_LATEST or * H5F_LIBVER_LATEST . * @param high The higher permissible bound. Must be H5F_LIBVER_LATEST. * @return a non-negative value if successful */ public static native int H5Pset_libver_bounds(int plist_id, int low, int high) throws HDF5LibraryException; /** * Returns the permissible bounds of the library's file format versions. * * @param plist_id Property list identifier. * @return an array containing [low, high] on success */ public static native int[] H5Pget_libver_bounds(int plist_id) throws HDF5LibraryException; /** * Sets the local heap size hint for an old-style group. This is the chunk size allocated on the * heap for a group. * * @param gcpl_id The group creation property list to change the heap size hint for * @param size_hint The size hint to set. * @return a non-negative value if successful */ public static native int H5Pset_local_heap_size_hint(int gcpl_id, int size_hint); /** * Returns the local heap size hint for an old-style group. This is the chunk size allocated on * the heap for a group. * * @param gcpl_id The group creation property list to change the heap size hint for * @return The size hint of the group if successful */ public static native int H5Pget_local_heap_size_hint(int gcpl_id); /** * Sets the phase change parameters for a new-style group. * * @param gcpl_id The group creation property list to set the link phase changes for * @param max_compact The maximum number of links in a group to store as header messages * @param min_dense The minimum number of links in a group to in the dense format * @return a non-negative value if successful */ public static native int H5Pset_link_phase_change(int gcpl_id, int max_compact, int min_dense); /** * Returns the phase change parameters for a new-style group. * * @param gcpl_id The group creation property list to set the link phase changes for * @return the phase change parameters as array [max_compact, min_dense] if successful */ public static native int[] H5Pget_link_phase_change(int gcpl_id); /** * Sets the character encoding for the given creation property list to the given encoding. * * @param cpl_id The creation property list to set the character encoding for. * @param encoding The encoding (one of {@link HDF5Constants#H5T_CSET_ASCII} or * {@link HDF5Constants#H5T_CSET_UTF8}) to use. * @return a non-negative value if successful */ public static native int H5Pset_char_encoding(int cpl_id, int encoding); /** * Returns the character encoding currently set for a creation property list. * * @param cpl_id The creation property list to get the character encoding for. * @return The encoding, one of {@link HDF5Constants#H5T_CSET_ASCII} or * {@link HDF5Constants#H5T_CSET_UTF8}. */ public static native int H5Pget_char_encoding(int cpl_id); /** * H5Oopen opens an existing object with the specified name at the specified location, loc_id. * * @param loc_id File or group identifier within which object is to be open. * @param name Name of object to open. * @param access_plist_id Object access property list identifier (H5P_DEFAULT for the default * property list). * @return a valid object identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static native int H5Oopen(int loc_id, String name, int access_plist_id) throws HDF5LibraryException, NullPointerException; /** * H5Oclose releases resources used by an object which was opened by a call to H5Oopen(). * * @param loc_id Object identifier to release. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Oclose(int loc_id) throws HDF5LibraryException; /** * H5Ocopy copies an existing object with the specified src_name at the specified location, * src_loc_id, to the specified dst_name at the specified destination location, dst_loc_id. * * @param src_loc_id Source File or group identifier within which object is to be open. * @param src_name Name of source object to open. * @param dst_loc_id Destination File or group identifier within which object is to be open. * @param dst_name Name of destination object to open. * @param object_copy_plist Object copy property list identifier (H5P_DEFAULT for the default * property list). * @param link_creation_plist Link creation property list identifier for the new hard link * (H5P_DEFAULT for the default property list). * @return a valid object identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static native int H5Ocopy(int src_loc_id, String src_name, int dst_loc_id, String dst_name, int object_copy_plist, int link_creation_plist) throws HDF5LibraryException, NullPointerException; /** * H5Oget_info_by_name returns information about the object. This method follows soft links and * returns information about the link target, rather than the link. *

* If not null, info needs to be an array of length 5 and will return * the following information in each index: *

    *
  • 0: filenumber that the object is in
    • *
  • 1: address of the object in the file
    • *
  • 2: reference count of the object (will be {@code > 1} if more than one hard link exists * to the object)
    • *
  • 3: creation time of the object (in seconds since start of the epoch)
    • *
  • 4: number of attributes that this object has
    • *
* * @param loc_id File or group identifier within which object is to be open. * @param object_name Name of object to get info for. * @param infoOrNull If not null, it will return additional information about this * object. Needs to be either null or an array of length 5. * @param exception_when_non_existent If true, -1 will be returned when the object * does not exist, otherwise a HDF5LibraryException will be thrown. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static native int H5Oget_info_by_name(int loc_id, String object_name, long[] infoOrNull, boolean exception_when_non_existent) throws HDF5LibraryException; /** * H5Lcreate_hard creates a hard link for an already existing object. * * @param obj_loc_id File, group, dataset, or datatype identifier of the existing object * @param obj_name A name of the existing object * @param link_loc_id Location identifier of the link to create * @param link_name Name of the link to create * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - current_name or name is null. */ public static native int H5Lcreate_hard(int obj_loc_id, String obj_name, int link_loc_id, String link_name, int lcpl_id, int lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Lcreate_soft creates a soft link to some target path. * * @param target_path The path of the link target * @param link_loc_id Location identifier of the link to create * @param link_name Name of the link to create * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - current_name or name is null. */ public static native int H5Lcreate_soft(String target_path, int link_loc_id, String link_name, int lcpl_id, int lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Lcreate_external creates an external link to some object in another file. * * @param file_name File name of the link target * @param obj_name Object name of the link target * @param link_loc_id Location identifier of the link to create * @param link_name Name of the link to create * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - current_name or name is null. */ public static native int H5Lcreate_external(String file_name, String obj_name, int link_loc_id, String link_name, int lcpl_id, int lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Lmove moves a link atomically to a new group or renames it. * * @param src_loc_id The old location identifier of the object to be renamed * @param src_name The old name of the object to be renamed * @param dst_loc_id The new location identifier of the link * @param dst_name The new name the object * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - current_name or name is null. */ public static native int H5Lmove(int src_loc_id, String src_name, int dst_loc_id, String dst_name, int lcpl_id, int lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Lexists returns true if a link with name exists and false * otherwise. *

* Note: The Java wrapper differs from the low-level C routine in that it will return * false if name is a path that contains groups which don't exist (the C * routine will give you an H5E_NOTFOUND in this case). */ public static native boolean H5Lexists(int loc_id, String name) throws HDF5LibraryException, NullPointerException; /** * H5Lget_link_info returns the type of the link. If lname != null and * name is a symbolic link, lname[0] will contain the target of the * link. If exception_when_non_existent is true, the method will throw * an exception when the link does not exist, otherwise -1 will be returned. */ public static native int H5Lget_link_info(int loc_id, String name, String[] lname, boolean exception_when_non_existent) throws HDF5LibraryException, NullPointerException; /** * H5Lget_link_info_all returns the names, types and link targets of all links in group * name. */ public static int H5Lget_link_info_all(final int loc_id, final String name, final String[] oname, final int[] type, final String[] lname) throws HDF5LibraryException, NullPointerException { if (oname == null) { throw new NullPointerException("H5Lget_obj_info_all(): name array is null"); } if (type == null) { throw new NullPointerException("H5Lget_obj_info_all(): type array is null"); } if (oname.length != type.length) { throw new HDF5JavaException( "H5Lget_obj_info_all(): oname and type array sizes are different"); } if (lname != null && oname.length != lname.length) { throw new HDF5JavaException( "H5Lget_obj_info_all(): oname and lname array sizes are different"); } return H5Lget_link_info_all(loc_id, name, oname, type, lname, oname.length); } public static native int H5Lget_link_info_all(int loc_id, String name, String[] oname, int[] type, String[] lname, int n) throws HDF5LibraryException, NullPointerException; /** * H5Lget_link_names_all returns the names of all links in group name. */ public static int H5Lget_link_names_all(final int loc_id, final String name, final String[] oname) throws HDF5LibraryException, NullPointerException { if (oname == null) { throw new NullPointerException("H5Lget_obj_info_all(): name array is null"); } return H5Lget_link_names_all(loc_id, name, oname, oname.length); } public static native int H5Lget_link_names_all(int loc_id, String name, String[] oname, int n) throws HDF5LibraryException, NullPointerException; } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/hdf5lib/H5A.java000066400000000000000000000461031256564762100261230ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.hdf5lib; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; /** * Low-level interface for HDF5 attribute functions. *

* This is an internal API that should not be expected to be stable between releases! * * @author Bernd Rinn */ public class H5A { static { H5.ensureNativeLibIsLoaded(); } /** * H5Lexists returns true if an attribute with name exists for the * object defined by obj_id and false otherwise. */ public static boolean H5Aexists(int obj_id, String name) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Aexists(obj_id, name); } } /** * H5Acreate creates an attribute which is attached to the object specified with loc_id. * * @param loc_id IN: Object (dataset, group, or named datatype) to be attached to. * @param name IN: Name of attribute to create. * @param type_id IN: Identifier of datatype for attribute. * @param space_id IN: Identifier of dataspace for attribute. * @param create_plist_id IN: Identifier of creation property list (currently not used). * @param access_plist_id IN: Attribute access property list identifier (currently not used). * @return an attribute identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static int H5Acreate(int loc_id, String name, int type_id, int space_id, int create_plist_id, int access_plist_id) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Acreate(loc_id, name, type_id, space_id, create_plist_id, access_plist_id); } } /** * H5Aopen_name opens an attribute specified by its name, name, which is attached to the object * specified with loc_id. * * @param loc_id IN: Identifier of a group, dataset, or named datatype atttribute * @param name IN: Attribute name. * @return attribute identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static int H5Aopen_name(int loc_id, String name) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Aopen_name(loc_id, name); } } /** * H5Aopen_idx opens an attribute which is attached to the object specified with loc_id. The * location object may be either a group, dataset, or named datatype, all of which may have any * sort of attribute. * * @param loc_id IN: Identifier of the group, dataset, or named datatype attribute * @param idx IN: Index of the attribute to open. * @return attribute identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Aopen_idx(int loc_id, int idx) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Aopen_idx(loc_id, idx); } } /** * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is * specified with mem_type_id. The entire attribute is written from buf to the file. * * @param attr_id IN: Identifier of an attribute to write. * @param mem_type_id IN: Identifier of the attribute datatype (in memory). * @param buf IN: Data to be written. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - data is null. */ public static int H5Awrite(int attr_id, int mem_type_id, byte[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Awrite(attr_id, mem_type_id, buf); } } /** * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is * specified with mem_type_id. The entire attribute is written from buf to the file. * * @param attr_id IN: Identifier of an attribute to write. * @param mem_type_id IN: Identifier of the attribute datatype (in memory). * @param buf IN: Data to be written. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - data is null. */ public static int H5Awrite(int attr_id, int mem_type_id, short[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Awrite(attr_id, mem_type_id, buf); } } /** * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is * specified with mem_type_id. The entire attribute is written from buf to the file. * * @param attr_id IN: Identifier of an attribute to write. * @param mem_type_id IN: Identifier of the attribute datatype (in memory). * @param buf IN: Data to be written. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - data is null. */ public static int H5Awrite(int attr_id, int mem_type_id, int[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Awrite(attr_id, mem_type_id, buf); } } /** * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is * specified with mem_type_id. The entire attribute is written from buf to the file. * * @param attr_id IN: Identifier of an attribute to write. * @param mem_type_id IN: Identifier of the attribute datatype (in memory). * @param buf IN: Data to be written. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - data is null. */ public static int H5Awrite(int attr_id, int mem_type_id, long[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Awrite(attr_id, mem_type_id, buf); } } /** * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is * specified with mem_type_id. The entire attribute is written from buf to the file. * * @param attr_id IN: Identifier of an attribute to write. * @param mem_type_id IN: Identifier of the attribute datatype (in memory). * @param buf IN: Data to be written. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - data is null. */ public static int H5Awrite(int attr_id, int mem_type_id, float[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Awrite(attr_id, mem_type_id, buf); } } /** * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is * specified with mem_type_id. The entire attribute is written from buf to the file. * * @param attr_id IN: Identifier of an attribute to write. * @param mem_type_id IN: Identifier of the attribute datatype (in memory). * @param buf IN: Data to be written. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - data is null. */ public static int H5Awrite(int attr_id, int mem_type_id, double[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Awrite(attr_id, mem_type_id, buf); } } /** * H5AwriteString writes a (partial) variable length String attribute, specified by its * identifier attr_id, from the application memory buffer buf into the file. * * @param attr_id Identifier of the dataset read from. * @param mem_type_id Identifier of the memory datatype. * @param buf Buffer with data to be written to the file. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static int H5AwriteString(int attr_id, int mem_type_id, String[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5AwriteString(attr_id, mem_type_id, buf); } } /** * H5Acopy copies the content of one attribute to another. * * @param src_aid the identifier of the source attribute * @param dst_aid the identifier of the destinaiton attribute */ public static int H5Acopy(int src_aid, int dst_aid) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Acopy(src_aid, dst_aid); } } /** * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is * specified with mem_type_id. The entire attribute is read into buf from the file. * * @param attr_id IN: Identifier of an attribute to read. * @param mem_type_id IN: Identifier of the attribute datatype (in memory). * @param buf IN: Buffer for data to be read. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - data buffer is null. */ public static int H5Aread(int attr_id, int mem_type_id, byte[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Aread(attr_id, mem_type_id, buf); } } /** * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is * specified with mem_type_id. The entire attribute is read into buf from the file. * * @param attr_id IN: Identifier of an attribute to read. * @param mem_type_id IN: Identifier of the attribute datatype (in memory). * @param buf IN: Buffer for data to be read. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - data buffer is null. */ public static int H5Aread(int attr_id, int mem_type_id, short[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Aread(attr_id, mem_type_id, buf); } } /** * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is * specified with mem_type_id. The entire attribute is read into buf from the file. * * @param attr_id IN: Identifier of an attribute to read. * @param mem_type_id IN: Identifier of the attribute datatype (in memory). * @param buf IN: Buffer for data to be read. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - data buffer is null. */ public static int H5Aread(int attr_id, int mem_type_id, int[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Aread(attr_id, mem_type_id, buf); } } /** * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is * specified with mem_type_id. The entire attribute is read into buf from the file. * * @param attr_id IN: Identifier of an attribute to read. * @param mem_type_id IN: Identifier of the attribute datatype (in memory). * @param buf IN: Buffer for data to be read. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - data buffer is null. */ public static int H5Aread(int attr_id, int mem_type_id, long[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Aread(attr_id, mem_type_id, buf); } } /** * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is * specified with mem_type_id. The entire attribute is read into buf from the file. * * @param attr_id IN: Identifier of an attribute to read. * @param mem_type_id IN: Identifier of the attribute datatype (in memory). * @param buf IN: Buffer for data to be read. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - data buffer is null. */ public static int H5Aread(int attr_id, int mem_type_id, float[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Aread(attr_id, mem_type_id, buf); } } /** * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is * specified with mem_type_id. The entire attribute is read into buf from the file. * * @param attr_id IN: Identifier of an attribute to read. * @param mem_type_id IN: Identifier of the attribute datatype (in memory). * @param buf IN: Buffer for data to be read. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - data buffer is null. */ public static int H5Aread(int attr_id, int mem_type_id, double[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Aread(attr_id, mem_type_id, buf); } } public static int H5AreadVL(int attr_id, int mem_type_id, String[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5AreadVL(attr_id, mem_type_id, buf); } } /** * H5Aget_space retrieves a copy of the dataspace for an attribute. * * @param attr_id IN: Identifier of an attribute. * @return attribute dataspace identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Aget_space(int attr_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Aget_space(attr_id); } } /** * H5Aget_type retrieves a copy of the datatype for an attribute. * * @param attr_id IN: Identifier of an attribute. * @return a datatype identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Aget_type(int attr_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Aget_type(attr_id); } } /** * H5Aget_name retrieves the name of an attribute specified by the identifier, attr_id. * * @param attr_id IN: Identifier of the attribute. * @param buf_size IN: The size of the buffer to store the name in. * @param name OUT: Buffer to store name in. * @exception ArrayIndexOutOfBoundsException JNI error writing back array * @exception ArrayStoreException JNI error writing back array * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. * @exception IllegalArgumentException - bub_size <= 0. * @return the length of the attribute's name if successful. */ public static long H5Aget_name(int attr_id, long buf_size, String[] name) throws ArrayIndexOutOfBoundsException, ArrayStoreException, HDF5LibraryException, NullPointerException, IllegalArgumentException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Aget_name(attr_id, buf_size, name); } } /** * H5Aget_num_attrs returns the number of attributes attached to the object specified by its * identifier, loc_id. * * @param loc_id IN: Identifier of a group, dataset, or named datatype. * @return the number of attributes if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Aget_num_attrs(int loc_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Aget_num_attrs(loc_id); } } /** * H5Adelete removes the attribute specified by its name, name, from a dataset, group, or named * datatype. * * @param loc_id IN: Identifier of the dataset, group, or named datatype. * @param name IN: Name of the attribute to delete. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static int H5Adelete(int loc_id, String name) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Adelete(loc_id, name); } } /** * H5Aclose terminates access to the attribute specified by its identifier, attr_id. * * @param attr_id IN: Attribute to release access to. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Aclose(int attr_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Aclose(attr_id); } } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/hdf5lib/H5D.java000066400000000000000000000454301256564762100261300ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.hdf5lib; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; /** * Low-level interface for HDF5 dataset functions. *

* This is an internal API that should not be expected to be stable between releases! * * @author Bernd Rinn */ public class H5D { static { H5.ensureNativeLibIsLoaded(); } /** * H5Dcreate creates a data set with a name, name, in the file or in the group specified by the * identifier loc_id. * * @param loc_id Identifier of the file or group to create the dataset within. * @param name The name of the dataset to create. * @param type_id Identifier of the datatype to use when creating the dataset. * @param space_id Identifier of the dataspace to use when creating the dataset. * @param link_create_plist_id Identifier of the link creation property list. * @param dset_create_plist_id Identifier of the dataset creation property list. * @param dset_access_plist_id Identifier of the dataset access property list. * @return a dataset identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static int H5Dcreate(int loc_id, String name, int type_id, int space_id, int link_create_plist_id, int dset_create_plist_id, int dset_access_plist_id) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Dcreate(loc_id, name, type_id, space_id, link_create_plist_id, dset_create_plist_id, dset_access_plist_id); } } /** * H5Dopen opens an existing dataset for access in the file or group specified in loc_id. * * @param loc_id Identifier of the dataset to open or the file or group * @param name The name of the dataset to access. * @param access_plist_id Dataset access property list. * @return a dataset identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static int H5Dopen(int loc_id, String name, int access_plist_id) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Dopen(loc_id, name, access_plist_id); } } public static int H5Dchdir_ext(String dir_name) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Dchdir_ext(dir_name); } } public static int H5Dgetdir_ext(String[] dir_name, int size) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Dgetdir_ext(dir_name, size); } } /** * H5Dget_space returns an identifier for a copy of the dataspace for a dataset. * * @param dataset_id Identifier of the dataset to query. * @return a dataspace identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Dget_space(int dataset_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Dget_space(dataset_id); } } /** * H5Dget_type returns an identifier for a copy of the datatype for a dataset. * * @param dataset_id Identifier of the dataset to query. * @return a datatype identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Dget_type(int dataset_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Dget_type(dataset_id); } } /** * H5Dget_create_plist returns an identifier for a copy of the dataset creation property list * for a dataset. * * @param dataset_id Identifier of the dataset to query. * @return a dataset creation property list identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Dget_create_plist(int dataset_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Dget_create_plist(dataset_id); } } /** * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into * the application memory buffer buf. * * @param dataset_id Identifier of the dataset read from. * @param mem_type_id Identifier of the memory datatype. * @param mem_space_id Identifier of the memory dataspace. * @param file_space_id Identifier of the dataset's dataspace in the file. * @param xfer_plist_id Identifier of a transfer property list for this I/O operation. * @param buf Buffer to store data read from the file. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - data buffer is null. */ public static int H5Dread(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf); } } public static int H5DreadVL(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, Object[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5DreadVL(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf); } } /** * H5DwriteString writes a (partial) variable length String dataset, specified by its identifier * dataset_id, from the application memory buffer buf into the file. *

* contributed by Rosetta Biosoftware. * * @param dataset_id Identifier of the dataset read from. * @param mem_type_id Identifier of the memory datatype. * @param mem_space_id Identifier of the memory dataspace. * @param file_space_id Identifier of the dataset's dataspace in the file. * @param xfer_plist_id Identifier of a transfer property list for this I/O operation. * @param buf Buffer with data to be written to the file. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static int H5DwriteString(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5DwriteString(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf); } } /** * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the * application memory buffer buf into the file. * * @param dataset_id Identifier of the dataset read from. * @param mem_type_id Identifier of the memory datatype. * @param mem_space_id Identifier of the memory dataspace. * @param file_space_id Identifier of the dataset's dataspace in the file. * @param xfer_plist_id Identifier of a transfer property list for this I/O operation. * @param buf Buffer with data to be written to the file. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static int H5Dwrite(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf); } } /** * H5Dextend verifies that the dataset is at least of size size. * * @param dataset_id Identifier of the dataset. * @param size Array containing the new magnitude of each dimension. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - size array is null. */ public static int H5Dextend(int dataset_id, byte[] size) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Dextend(dataset_id, size); } } public static int H5Dextend(final int dataset_id, final long[] size) throws HDF5Exception, NullPointerException { final byte[] buf = HDFNativeData.longToByte(size); return H5Dextend(dataset_id, buf); } /** * H5Dset_extent sets the size of the dataset to size. Make sure that no important * are lost since this method will not check that the data dimensions are not larger than * size. * * @param dataset_id Identifier of the dataset. * @param size Array containing the new magnitude of each dimension. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - size array is null. */ public static int H5Dset_extent(int dataset_id, byte[] size) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Dset_extent(dataset_id, size); } } public static int H5Dset_extent(final int dataset_id, final long[] size) throws HDF5Exception, NullPointerException { final byte[] buf = HDFNativeData.longToByte(size); return H5Dset_extent(dataset_id, buf); } /** * H5Dclose ends access to a dataset specified by dataset_id and releases resources used by it. * * @param dataset_id Identifier of the dataset to finish access to. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Dclose(int dataset_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Dclose(dataset_id); } } /** * H5Dget_storage_size returns the amount of storage that is required for the dataset. * * @param dataset_id Identifier of the dataset in question * @return he amount of storage space allocated for the dataset. * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static long H5Dget_storage_size(int dataset_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Dget_storage_size(dataset_id); } } /** * H5Dcopy copies the content of one dataset to another dataset. * * @param src_did the identifier of the source dataset * @param dst_did the identifier of the destinaiton dataset */ public static int H5Dcopy(int src_did, int dst_did) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Dcopy(src_did, dst_did); } } /* * */ public static int H5Dvlen_get_buf_size(int dataset_id, int type_id, int space_id, int[] size) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Dvlen_get_buf_size(dataset_id, type_id, space_id, size); } } /** * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - buf is null. */ public static int H5Dvlen_reclaim(int type_id, int space_id, int xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Dvlen_reclaim(type_id, space_id, xfer_plist_id, buf); } } public static int H5Dget_space_status(int dset_id, int[] status) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Dget_space_status(dset_id, status); } } // ////////////////////////////////////////////////////////////////// // // // New APIs for read data from library // // Using H5Dread(..., Object buf) requires function calls // // theArray.emptyBytes() and theArray.arrayify( buf), which // // triples the actual memory needed by the data set. // // Using the following APIs solves the problem. // // // // ////////////////////////////////////////////////////////////////// public static int H5Dread(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, short[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf); } } public static int H5Dread(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, int[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf); } } public static int H5Dread(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, long[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf); } } public static int H5Dread(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, float[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf); } } public static int H5Dread(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, double[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf); } } public static int H5Dread_string(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Dread_string(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf); } } public static int H5Dread_reg_ref(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Dread_reg_ref(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf); } } public static int H5Dwrite(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, short[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf); } } public static int H5Dwrite(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, int[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf); } } public static int H5Dwrite(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, long[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf); } } public static int H5Dwrite(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, float[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf); } } public static int H5Dwrite(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, double[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf); } } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/hdf5lib/H5F.java000066400000000000000000000235431256564762100261330ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.hdf5lib; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; /** * Low-level interface for HDF5 file functions. *

* This is an internal API that should not be expected to be stable between releases! * * @author Bernd Rinn */ public class H5F { static { H5.ensureNativeLibIsLoaded(); } /** * H5Fopen opens an existing file and is the primary function for accessing existing HDF5 files. * * @param name Name of the file to access. * @param flags File access flags. * @param access_id Identifier for the file access properties list. * @return a file identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static int H5Fopen(String name, int flags, int access_id) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Fopen(name, flags, access_id); } } /** * H5Fcreate is the primary function for creating HDF5 files. * * @param name Name of the file to access. * @param flags File access flags. Possible values include: *

    *
  • H5F_ACC_RDWR Allow read and write access to file.
    • *
  • H5F_ACC_RDONLY Allow read-only access to file.
    • *
  • H5F_ACC_TRUNC Truncate file, if it already exists, erasing all data previously * stored in the file.
    • *
  • H5F_ACC_EXCL Fail if file already exists.
    • *
  • H5F_ACC_DEBUG Print debug information.
    • *
  • H5P_DEFAULT Apply default file access and creation properties.
    • *
* @param create_id File creation property list identifier, used when modifying default file * meta-data. Use H5P_DEFAULT for default access properties. * @param access_id File access property list identifier. If parallel file access is desired, * this is a collective call according to the communicator stored in the access_id * (not supported in Java). Use H5P_DEFAULT for default access properties. * @return a file identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static int H5Fcreate(String name, int flags, int create_id, int access_id) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Fcreate(name, flags, create_id, access_id); } } /** * H5Fflush causes all buffers associated with a file or object to be immediately flushed * (written) to disk without removing the data from the (memory) cache. *

* After this call completes, the file (or object) is in a consistent state and all data written * to date is assured to be permanent. * * @param object_id Identifier of object used to identify the file. object_id can be any * object associated with the file, including the file itself, a dataset, a group, an * attribute, or a named data type. * @param scope specifies the scope of the flushing action, in the case that the HDF-5 file is * not a single physical file. *

* Valid values are: *

    *
  • H5F_SCOPE_GLOBAL Flushes the entire virtual file.
    • *
  • H5F_SCOPE_LOCAL Flushes only the specified file.
    • *
* @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Fflush(int object_id, int scope) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Fflush(object_id, scope); } } /** * H5Fis_hdf5 determines whether a file is in the HDF5 format. * * @param name File name to check format. * @return true if is HDF-5, false if not. * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static boolean H5Fis_hdf5(String name) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Fis_hdf5(name); } } /** * H5Fget_create_plist returns a file creation property list identifier identifying the creation * properties used to create this file. * * @param file_id Identifier of the file to get creation property list * @return a file creation property list identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Fget_create_plist(int file_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Fget_create_plist(file_id); } } /** * H5Fget_access_plist returns the file access property list identifier of the specified file. * * @param file_id Identifier of file to get access property list of * @return a file access property list identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Fget_access_plist(int file_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Fget_access_plist(file_id); } } /** * H5Fclose terminates access to an HDF5 file. * * @param file_id Identifier of a file to terminate access to. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Fclose(int file_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Fclose(file_id); } } /** * H5Fmount mounts the file specified by child_id onto the group specified by loc_id and name * using the mount properties plist_id. * * @param loc_id The identifier for the group onto which the file specified by child_id is to be * mounted. * @param name The name of the group onto which the file specified by child_id is to be mounted. * @param child_id The identifier of the file to be mounted. * @param plist_id The identifier of the property list to be used. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static int H5Fmount(int loc_id, String name, int child_id, int plist_id) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Fmount(loc_id, name, child_id, plist_id); } } /** * Given a mount point, H5Funmount dissassociates the mount point's file from the file mounted * there. * * @param loc_id The identifier for the location at which the specified file is to be unmounted. * @param name The name of the file to be unmounted. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static int H5Funmount(int loc_id, String name) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Funmount(loc_id, name); } } /** * H5Freopen reopens an HDF5 file. * * @param file_id Identifier of a file to terminate and reopen access to. * @exception HDF5LibraryException - Error from the HDF-5 Library. * @return a new file identifier if successful */ public static int H5Freopen(int file_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Freopen(file_id); } } public static int H5Fget_obj_ids(int file_id, int types, int max, int[] obj_id_list) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Fget_obj_ids(file_id, types, max, obj_id_list); } } public static int H5Fget_obj_count(int file_id, int types) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Fget_obj_count(file_id, types); } } public static long H5Fget_name(int obj_id, String name, int size) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Fget_name(obj_id, name, size); } } public static long H5Fget_filesize(int file_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Fget_filesize(file_id); } } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/hdf5lib/H5GLO.java000066400000000000000000000436041256564762100263670ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.hdf5lib; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; /** * Low-level interface for HDF5 group, link and object functions. *

* This is an internal API that should not be expected to be stable between releases! * * @author Bernd Rinn */ public class H5GLO { static { H5.ensureNativeLibIsLoaded(); } // //////////////////////////////////////////////////////////// // // // H5G: Group Interface Functions // // // // //////////////////////////////////////////////////////////// /** * H5Gcreate creates a new group with the specified name at the specified location, loc_id. * * @param loc_id The file or group identifier. * @param name The absolute or relative name of the new group. * @param link_create_plist_id Property list for link creation. * @param group_create_plist_id Property list for group creation. * @param group_access_plist_id Property list for group access. * @return a valid group identifier for the open group if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static int H5Gcreate(int loc_id, String name, int link_create_plist_id, int group_create_plist_id, int group_access_plist_id) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Gcreate(loc_id, name, link_create_plist_id, group_create_plist_id, group_access_plist_id); } } /** * H5Gopen opens an existing group with the specified name at the specified location, loc_id. * * @param loc_id File or group identifier within which group is to be open. * @param name Name of group to open. * @param access_plist_id Group access property list identifier (H5P_DEFAULT for the default * property list). * @return a valid group identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static int H5Gopen(int loc_id, String name, int access_plist_id) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Gopen(loc_id, name, access_plist_id); } } /** * H5Gclose releases resources used by a group which was opened by a call to H5Gcreate() or * H5Gopen(). * * @param group_id Group identifier to release. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Gclose(int group_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Gclose(group_id); } } /** * H5Gunlink removes an association between a name and an object. * * @param loc_id Identifier of the file containing the object. * @param name Name of the object to unlink. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static int H5Gunlink(int loc_id, String name) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Gunlink(loc_id, name); } } /** * H5Gset_comment sets the comment for the the object name to comment. Any previously existing * comment is overwritten. * * @param loc_id IN: Identifier of the file, group, dataset, or datatype. * @param name IN: Name of the object whose comment is to be set or reset. * @param comment IN: The new comment. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name or comment is null. */ public static int H5Gset_comment(int loc_id, String name, String comment) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Gset_comment(loc_id, name, comment); } } /** * H5Gget_comment retrieves the comment for the the object name. The comment is returned in the * buffer comment. * * @param loc_id IN: Identifier of the file, group, dataset, or datatype. * @param name IN: Name of the object whose comment is to be set or reset. * @param bufsize IN: Anticipated size of the buffer required to hold comment. * @param comment OUT: The comment. * @return the number of characters in the comment, counting the null terminator, if successful * @exception ArrayIndexOutOfBoundsException - JNI error writing back data * @exception ArrayStoreException - JNI error writing back data * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. * @exception IllegalArgumentException - size < 1, comment is invalid. */ public static int H5Gget_comment(int loc_id, String name, int bufsize, String[] comment) throws ArrayIndexOutOfBoundsException, ArrayStoreException, HDF5LibraryException, NullPointerException, IllegalArgumentException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Gget_comment(loc_id, name, bufsize, comment); } } /** * Returns the number of links in the group specified by group_id. * * @param group_id Group identifier. * @return Return the number of link in the group if successful. */ public static long H5Gget_nlinks(int group_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Gget_nlinks(group_id); } } // //////////////////////////////////////////////////////////// // // // H5G: Object Interface Functions // // // // //////////////////////////////////////////////////////////// /** * H5Oopen opens an existing object with the specified name at the specified location, loc_id. * * @param loc_id File or group identifier within which object is to be open. * @param name Name of object to open. * @param access_plist_id Object access property list identifier (H5P_DEFAULT for the default * property list). * @return a valid object identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static int H5Oopen(int loc_id, String name, int access_plist_id) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Oopen(loc_id, name, access_plist_id); } } /** * H5Oclose releases resources used by an object which was opened by a call to H5Oopen(). * * @param loc_id Object identifier to release. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Oclose(int loc_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Oclose(loc_id); } } /** * H5Ocopy copies an existing object with the specified src_name at the specified location, * src_loc_id, to the specified dst_name at the specified destination location, dst_loc_id. * * @param src_loc_id Source File or group identifier within which object is to be open. * @param src_name Name of source object to open. * @param dst_loc_id Destination File or group identifier within which object is to be open. * @param dst_name Name of destination object to open. * @param object_copy_plist Object copy property list identifier (H5P_DEFAULT for the default * property list). * @param link_creation_plist Link creation property list identifier for the new hard link * (H5P_DEFAULT for the default property list). * @return a valid object identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static int H5Ocopy(int src_loc_id, String src_name, int dst_loc_id, String dst_name, int object_copy_plist, int link_creation_plist) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Ocopy(src_loc_id, src_name, dst_loc_id, dst_name, object_copy_plist, link_creation_plist); } } /** * H5Oget_info_by_name returns information about the object. This method follows soft links and * returns information about the link target, rather than the link. *

* If not null, info needs to be an array of length 5 and will return * the following information in each index: *

    *
  • 0: filenumber that the object is in
    • *
  • 1: address of the object in the file
    • *
  • 2: reference count of the object (will be {@code > 1} if more than one hard link exists * to the object)
    • *
  • 3: creation time of the object (in seconds since start of the epoch)
    • *
  • 4: number of attributes that this object has
    • *
* * @param loc_id File or group identifier within which object is to be open. * @param object_name Name of object to get info for. * @param infoOrNull If not null, it will return additional information about this * object. Needs to be either null or an array of length 5. * @param exception_when_non_existent If true, -1 will be returned when the object * does not exist, otherwise a HDF5LibraryException will be thrown. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Oget_info_by_name(int loc_id, String object_name, long[] infoOrNull, boolean exception_when_non_existent) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Oget_info_by_name(loc_id, object_name, infoOrNull, exception_when_non_existent); } } // //////////////////////////////////////////////////////////// // // // H5G: Link Interface Functions // // // // //////////////////////////////////////////////////////////// /** * H5Lcreate_hard creates a hard link for an already existing object. * * @param obj_loc_id File, group, dataset, or datatype identifier of the existing object * @param obj_name A name of the existing object * @param link_loc_id Location identifier of the link to create * @param link_name Name of the link to create * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - current_name or name is null. */ public static int H5Lcreate_hard(int obj_loc_id, String obj_name, int link_loc_id, String link_name, int lcpl_id, int lapl_id) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5 .H5Lcreate_hard(obj_loc_id, obj_name, link_loc_id, link_name, lcpl_id, lapl_id); } } /** * H5Lcreate_soft creates a soft link to some target path. * * @param target_path The path of the link target * @param link_loc_id Location identifier of the link to create * @param link_name Name of the link to create * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - current_name or name is null. */ public static int H5Lcreate_soft(String target_path, int link_loc_id, String link_name, int lcpl_id, int lapl_id) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Lcreate_soft(target_path, link_loc_id, link_name, lcpl_id, lapl_id); } } /** * H5Lcreate_external creates an external link to some object in another file. * * @param file_name File name of the link target * @param obj_name Object name of the link target * @param link_loc_id Location identifier of the link to create * @param link_name Name of the link to create * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - current_name or name is null. */ public static int H5Lcreate_external(String file_name, String obj_name, int link_loc_id, String link_name, int lcpl_id, int lapl_id) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Lcreate_external(file_name, obj_name, link_loc_id, link_name, lcpl_id, lapl_id); } } /** * H5Lmove moves a link atomically to a new group or renames it. * * @param src_loc_id The old location identifier of the object to be renamed * @param src_name The old name of the object to be renamed * @param dst_loc_id The new location identifier of the link * @param dst_name The new name the object * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - current_name or name is null. */ public static int H5Lmove(int src_loc_id, String src_name, int dst_loc_id, String dst_name, int lcpl_id, int lapl_id) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Lmove(src_loc_id, src_name, dst_loc_id, dst_name, lcpl_id, lapl_id); } } /** * H5Lexists returns true if a link with name exists and false * otherwise. *

* Note: The Java wrapper differs from the low-level C routine in that it will return * false if name is a path that contains groups which don't exist (the C * routine will give you an H5E_NOTFOUND in this case). */ public static boolean H5Lexists(int loc_id, String name) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Lexists(loc_id, name); } } /** * H5Lget_link_info returns the type of the link. If lname != null and * name is a symbolic link, lname[0] will contain the target of the * link. If exception_when_non_existent is true, the method will throw * an exception when the link does not exist, otherwise -1 will be returned. */ public static int H5Lget_link_info(int loc_id, String name, String[] lname, boolean exception_when_non_existent) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Lget_link_info(loc_id, name, lname, exception_when_non_existent); } } /** * H5Lget_link_info_all returns the names, types and link targets of all links in group * name. */ public static int H5Lget_link_info_all(final int loc_id, final String name, final String[] oname, final int[] type, final String[] lname) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Lget_link_info_all(loc_id, name, oname, type, lname); } } public static int H5Lget_link_info_all(int loc_id, String name, String[] oname, int[] type, String[] lname, int n) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Lget_link_info_all(loc_id, name, oname, type, lname, n); } } /** * H5Lget_link_names_all returns the names of all links in group name. */ public static int H5Lget_link_names_all(final int loc_id, final String name, final String[] oname) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Lget_link_names_all(loc_id, name, oname); } } public static int H5Lget_link_names_all(int loc_id, String name, String[] oname, int n) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Lget_link_names_all(loc_id, name, oname, n); } } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/hdf5lib/H5General.java000066400000000000000000000071771256564762100273300ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.hdf5lib; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; /** * Low-level interface for HDF5 general functions. *

* This is an internal API that should not be expected to be stable between releases! * * @author Bernd Rinn */ public class H5General { static { H5.ensureNativeLibIsLoaded(); } /** Call to ensure that the native library is loaded. */ public static void ensureNativeLibIsLoaded() { H5.ensureNativeLibIsLoaded(); } // //////////////////////////////////////////////////////////// // // // H5: General Library Functions // // // // //////////////////////////////////////////////////////////// /** * H5open initialize the library. * * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5open() throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5open(); } } /** * H5get_libversion retrieves the major, minor, and release numbers of the version of the HDF * library which is linked to the application. * * @param libversion The version information of the HDF library. * * 

     * 
     *            libversion[0] = The major version of the library. libversion[1] = The minor
     *            version of the library. libversion[2] = The release number of the library.
     * 
     *
* @return a non-negative value if successful, along with the version information. * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5get_libversion(int[] libversion) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5get_libversion(libversion); } } public static int H5set_free_list_limits(int reg_global_lim, int reg_list_lim, int arr_global_lim, int arr_list_lim, int blk_global_lim, int blk_list_lim) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5set_free_list_limits(reg_global_lim, reg_list_lim, arr_global_lim, arr_list_lim, blk_global_lim, blk_list_lim); } } public static int H5Zfilter_avail(int filter) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Zfilter_avail(filter); } } public static int H5Zunregister(int filter) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Zunregister(filter); } } public static int H5Zget_filter_info(int filter) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Zget_filter_info(filter); } } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/hdf5lib/H5P.java000066400000000000000000001521201256564762100261370ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.hdf5lib; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; /** * Low-level interface for HDF5 property list functions. *

* This is an internal API that should not be expected to be stable between releases! * * @author Bernd Rinn */ public class H5P { static { H5.ensureNativeLibIsLoaded(); } /** * H5Pcreate creates a new property as an instance of some property list class. * * @param type IN: The type of property list to create. * @return a property list identifier (plist) if successful; otherwise Fail (-1). * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Pcreate(int type) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pcreate(type); } } /** * H5Pclose terminates access to a property list. * * @param plist IN: Identifier of the property list to terminate access to. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Pclose(int plist) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pclose(plist); } } /** * H5Pget_class returns the property list class for the property list identified by the plist * parameter. * * @param plist IN: Identifier of property list to query. * @return a property list class if successful. Otherwise returns H5P_NO_CLASS (-1). * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Pget_class(int plist) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_class(plist); } } /** * H5Pcopy copies an existing property list to create a new property list. * * @param plist IN: Identifier of property list to duplicate. * @return a property list identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Pcopy(int plist) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pcopy(plist); } } /** * H5Pget_version retrieves the version information of various objects for a file creation * property list. * * @param plist IN: Identifier of the file creation property list. * @param version_info OUT: version information. * * 

     * 
     *            version_info[0] = boot // boot block version number version_info[1] = freelist //
     *            global freelist version version_info[2] = stab // symbol tabl version number
     *            version_info[3] = shhdr // hared object header version
     * 
     *
* @return a non-negative value, with the values of version_info initialized, if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - version_info is null. * @exception IllegalArgumentException - version_info is illegal. */ public static int H5Pget_version(int plist, int[] version_info) throws HDF5LibraryException, NullPointerException, IllegalArgumentException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_version(plist, version_info); } } /** * H5Pset_userblock sets the user block size of a file creation property list. * * @param plist IN: Identifier of property list to modify. * @param size IN: Size of the user-block in bytes. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Pset_userblock(int plist, long size) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset_userblock(plist, size); } } /** * H5Pget_userblock retrieves the size of a user block in a file creation property list. * * @param plist IN: Identifier for property list to query. * @param size OUT: Pointer to location to return user-block size. * @return a non-negative value and the size of the user block; if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - size is null. */ public static int H5Pget_userblock(int plist, long[] size) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_userblock(plist, size); } } /** * H5Pset_small_data_block_size reserves blocks of size bytes for the contiguous storage of the * raw data portion of small datasets. * * @param plist IN: Identifier of property list to modify. * @param size IN: Size of the blocks in bytes. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Pset_small_data_block_size(int plist, long size) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset_small_data_block_size(plist, size); } } /** * H5Pget_small_data_block_size retrieves the size of a block of small data in a file creation * property list. * * @param plist IN: Identifier for property list to query. * @param size OUT: Pointer to location to return block size. * @return a non-negative value and the size of the user block; if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - size is null. */ public static int H5Pget_small_data_block_size(int plist, long[] size) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_small_data_block_size(plist, size); } } /** * H5Pset_sizes sets the byte size of the offsets and lengths used to address objects in an HDF5 * file. * * @param plist IN: Identifier of property list to modify. * @param sizeof_addr IN: Size of an object offset in bytes. * @param sizeof_size IN: Size of an object length in bytes. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Pset_sizes(int plist, int sizeof_addr, int sizeof_size) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset_sizes(plist, sizeof_addr, sizeof_size); } } /** * H5Pget_sizes retrieves the size of the offsets and lengths used in an HDF5 file. This * function is only valid for file creation property lists. * * @param plist IN: Identifier of property list to query. * @param size OUT: the size of the offsets and length. * * 
     * 
     *            size[0] = sizeof_addr // offset size in bytes size[1] = sizeof_size // length size
     *            in bytes
     * 
     *
* @return a non-negative value with the sizes initialized; if successful; * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - size is null. * @exception IllegalArgumentException - size is invalid. */ public static int H5Pget_sizes(int plist, int[] size) throws HDF5LibraryException, NullPointerException, IllegalArgumentException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_sizes(plist, size); } } /** * H5Pset_sym_k sets the size of parameters used to control the symbol table nodes. * * @param plist IN: Identifier for property list to query. * @param ik IN: Symbol table tree rank. * @param lk IN: Symbol table node size. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Pset_sym_k(int plist, int ik, int lk) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset_sym_k(plist, ik, lk); } } /** * H5Pget_sym_k retrieves the size of the symbol table B-tree 1/2 rank and the symbol table leaf * node 1/2 size. * * @param plist IN: Property list to query. * @param size OUT: the symbol table's B-tree 1/2 rank and leaf node 1/2 size. * * 
     * 
     *            size[0] = ik // the symbol table's B-tree 1/2 rank size[1] = lk // leaf node 1/2
     *            size
     * 
     *
* @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - size is null. * @exception IllegalArgumentException - size is invalid. */ public static int H5Pget_sym_k(int plist, int[] size) throws HDF5LibraryException, NullPointerException, IllegalArgumentException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_sym_k(plist, size); } } /** * H5Pset_istore_k sets the size of the parameter used to control the B-trees for indexing * chunked datasets. * * @param plist IN: Identifier of property list to query. * @param ik IN: 1/2 rank of chunked storage B-tree. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Pset_istore_k(int plist, int ik) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset_istore_k(plist, ik); } } /** * H5Pget_istore_k queries the 1/2 rank of an indexed storage B-tree. * * @param plist IN: Identifier of property list to query. * @param ik OUT: Pointer to location to return the chunked storage B-tree 1/2 rank. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - ik array is null. */ public static int H5Pget_istore_k(int plist, int[] ik) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_istore_k(plist, ik); } } /** * H5Pset_layout sets the type of storage used store the raw data for a dataset. * * @param plist IN: Identifier of property list to query. * @param layout IN: Type of storage layout for raw data. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Pset_layout(int plist, int layout) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset_layout(plist, layout); } } /** * H5Pget_layout returns the layout of the raw data for a dataset. * * @param plist IN: Identifier for property list to query. * @return the layout type of a dataset creation property list if successful. Otherwise returns * H5D_LAYOUT_ERROR (-1). * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Pget_layout(int plist) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_layout(plist); } } /** * H5Pset_chunk sets the size of the chunks used to store a chunked layout dataset. * * @param plist IN: Identifier for property list to query. * @param ndims IN: The number of dimensions of each chunk. * @param dim IN: An array containing the size of each chunk. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - dims array is null. * @exception IllegalArgumentException - dims <=0 */ public static int H5Pset_chunk(int plist, int ndims, byte[] dim) throws HDF5LibraryException, NullPointerException, IllegalArgumentException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset_chunk(plist, ndims, dim); } } public static int H5Pset_chunk(final int plist, final int ndims, final long[] dim) throws HDF5Exception, NullPointerException, IllegalArgumentException { if (dim == null) { return -1; } final byte[] thedims = HDFNativeData.longToByte(dim); return H5Pset_chunk(plist, ndims, thedims); } /** * H5Pget_chunk retrieves the size of chunks for the raw data of a chunked layout dataset. * * @param plist IN: Identifier of property list to query. * @param max_ndims IN: Size of the dims array. * @param dims OUT: Array to store the chunk dimensions. * @return chunk dimensionality successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - dims array is null. * @exception IllegalArgumentException - max_ndims <=0 */ public static int H5Pget_chunk(int plist, int max_ndims, long[] dims) throws HDF5LibraryException, NullPointerException, IllegalArgumentException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_chunk(plist, max_ndims, dims); } } /** * H5Pset_alignment sets the alignment properties of a file access property list so that any * file object >= THRESHOLD bytes will be aligned on an address which is a multiple of * ALIGNMENT. * * @param plist IN: Identifier for a file access property list. * @param threshold IN: Threshold value. * @param alignment IN: Alignment value. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Pset_alignment(int plist, long threshold, long alignment) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset_alignment(plist, threshold, alignment); } } /** * H5Pget_alignment retrieves the current settings for alignment properties from a file access * property list. * * @param plist IN: Identifier of a file access property list. * @param alignment OUT: threshold value and alignment value. * * 
     * 
     *            alignment[0] = threshold // threshold value alignment[1] = alignment // alignment
     *            value
     * 
     *
* @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - aligment array is null. * @exception IllegalArgumentException - aligment array is invalid. */ public static int H5Pget_alignment(int plist, long[] alignment) throws HDF5LibraryException, NullPointerException, IllegalArgumentException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_alignment(plist, alignment); } } /** * H5Pset_external adds an external file to the list of external files. * * @param plist IN: Identifier of a dataset creation property list. * @param name IN: Name of an external file. * @param offset IN: Offset, in bytes, from the beginning of the file to the location in the * file where the data starts. * @param size IN: Number of bytes reserved in the file for the data. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static int H5Pset_external(int plist, String name, long offset, long size) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset_external(plist, name, offset, size); } } /** * H5Pget_external_count returns the number of external files for the specified dataset. * * @param plist IN: Identifier of a dataset creation property list. * @return the number of external files if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Pget_external_count(int plist) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_external_count(plist); } } /** * H5Pget_external returns information about an external file. * * @param plist IN: Identifier of a dataset creation property list. * @param idx IN: External file index. * @param name_size IN: Maximum length of name array. * @param name OUT: Name of the external file. * @param size OUT: the offset value and the size of the external file data. * * 
     * 
     *            size[0] = offset // a location to return an offset value size[1] = size // a
     *            location to return the size of // the external file data.
     * 
     *
* @return a non-negative value if successful * @exception ArrayIndexOutOfBoundsException Fatal error on Copyback * @exception ArrayStoreException Fatal error on Copyback * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name or size is null. * @exception IllegalArgumentException - name_size <= 0 . */ public static int H5Pget_external(int plist, int idx, int name_size, String[] name, long[] size) throws ArrayIndexOutOfBoundsException, ArrayStoreException, HDF5LibraryException, NullPointerException, IllegalArgumentException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_external(plist, idx, name_size, name, size); } } /** * H5Pset_fill_value sets the fill value for a dataset creation property list. * * @param plist_id IN: Property list identifier. * @param type_id IN: The datatype identifier of value. * @param value IN: The fill value. * @return a non-negative value if successful * @exception HDF5Exception - Error converting data array */ public static int H5Pset_fill_value(int plist_id, int type_id, byte[] value) throws HDF5Exception { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset_fill_value(plist_id, type_id, value); } } /** * H5Pget_fill_value queries the fill value property of a dataset creation property list. NOT * IMPLEMENTED YET * * @param plist_id IN: Property list identifier. * @param type_id IN: The datatype identifier of value. * @param value IN: The fill value. * @return a non-negative value if successful */ public static int H5Pget_fill_value(int plist_id, int type_id, byte[] value) throws HDF5Exception { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_fill_value(plist_id, type_id, value); } } /** * H5Pset_filter adds the specified filter and corresponding properties to the end of an output * filter pipeline. * * @param plist IN: Property list identifier. * @param filter IN: Filter to be added to the pipeline. * @param flags IN: Bit vector specifying certain general properties of the filter. * @param cd_nelmts IN: Number of elements in cd_values * @param cd_values IN: Auxiliary data for the filter. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Pset_filter(int plist, int filter, int flags, int cd_nelmts, int[] cd_values) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset_filter(plist, filter, flags, cd_nelmts, cd_values); } } /** * H5Pget_nfilters returns the number of filters defined in the filter pipeline associated with * the property list plist. * * @param plist IN: Property list identifier. * @return the number of filters in the pipeline if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Pget_nfilters(int plist) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_nfilters(plist); } } /** * H5Pget_filter returns information about a filter, specified by its filter number, in a filter * pipeline, specified by the property list with which it is associated. * * @param plist IN: Property list identifier. * @param filter_number IN: Sequence number within the filter pipeline of the filter for which * information is sought. * @param flags OUT: Bit vector specifying certain general properties of the filter. * @param cd_nelmts IN/OUT: Number of elements in cd_values * @param cd_values OUT: Auxiliary data for the filter. * @param namelen IN: Anticipated number of characters in name. * @param name OUT: Name of the filter. * @return the filter identification number if successful. Otherwise returns H5Z_FILTER_ERROR * (-1). * @exception ArrayIndexOutOfBoundsException Fatal error on Copyback * @exception ArrayStoreException Fatal error on Copyback * @exception NullPointerException - name or an array is null. */ public static int H5Pget_filter(int plist, int filter_number, int[] flags, int[] cd_nelmts, int[] cd_values, int namelen, String[] name) throws ArrayIndexOutOfBoundsException, ArrayStoreException, HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_filter(plist, filter_number, flags, cd_nelmts, cd_values, namelen, name); } } /** * H5Pset_cache sets the number of elements (objects) in the meta data cache and the total * number of bytes in the raw data chunk cache. * * @param plist IN: Identifier of the file access property list. * @param mdc_nelmts IN: Number of elements (objects) in the meta data cache. * @param rdcc_nbytes IN: Total size of the raw data chunk cache, in bytes. * @param rdcc_w0 IN: Preemption policy. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Pset_cache(int plist, int mdc_nelmts, int rdcc_nelmts, int rdcc_nbytes, double rdcc_w0) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset_cache(plist, mdc_nelmts, rdcc_nelmts, rdcc_nbytes, rdcc_w0); } } /** * Retrieves the maximum possible number of elements in the meta data cache and the maximum * possible number of bytes and the RDCC_W0 value in the raw data chunk cache. * * @param plist IN: Identifier of the file access property list. * @param mdc_nelmts IN/OUT: Number of elements (objects) in the meta data cache. * @param rdcc_nbytes IN/OUT: Total size of the raw data chunk cache, in bytes. * @param rdcc_w0 IN/OUT: Preemption policy. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - an array is null. */ public static int H5Pget_cache(int plist, int[] mdc_nelmts, int[] rdcc_nelmts, int[] rdcc_nbytes, double[] rdcc_w0) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_cache(plist, mdc_nelmts, rdcc_nelmts, rdcc_nbytes, rdcc_w0); } } /** * H5Pset_buffer sets type conversion and background buffers. status to TRUE or FALSE. Given a * dataset transfer property list, H5Pset_buffer sets the maximum size for the type conversion * buffer and background buffer and optionally supplies pointers to application-allocated * buffers. If the buffer size is smaller than the entire amount of data being transferred * between the application and the file, and a type conversion buffer or background buffer is * required, then strip mining will be used. Note that there are minimum size requirements for * the buffer. Strip mining can only break the data up along the first dimension, so the buffer * must be large enough to accommodate a complete slice that encompasses all of the remaining * dimensions. For example, when strip mining a 100x200x300 hyperslab of a simple data space, * the buffer must be large enough to hold 1x200x300 data elements. When strip mining a * 100x200x300x150 hyperslab of a simple data space, the buffer must be large enough to hold * 1x200x300x150 data elements. If tconv and/or bkg are null pointers, then buffers will be * allocated and freed during the data transfer. * * @param plist Identifier for the dataset transfer property list. * @param size Size, in bytes, of the type conversion and background buffers. * @param tconv byte array of application-allocated type conversion buffer. * @param bkg byte array of application-allocated background buffer. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception IllegalArgumentException - plist is invalid. */ public static int H5Pset_buffer(int plist, int size, byte[] tconv, byte[] bkg) throws HDF5LibraryException, IllegalArgumentException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset_buffer(plist, size, tconv, bkg); } } /** * HH5Pget_buffer gets type conversion and background buffers. Returns buffer size, in bytes, if * successful; otherwise 0 on failure. * * @param plist Identifier for the dataset transfer property list. * @param tconv byte array of application-allocated type conversion buffer. * @param bkg byte array of application-allocated background buffer. * @return buffer size, in bytes, if successful; otherwise 0 on failure * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception IllegalArgumentException - plist is invalid. */ public static int H5Pget_buffer(int plist, byte[] tconv, byte[] bkg) throws HDF5LibraryException, IllegalArgumentException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_buffer(plist, tconv, bkg); } } /** * H5Pset_preserve sets the dataset transfer property list status to TRUE or FALSE. * * @param plist IN: Identifier for the dataset transfer property list. * @param status IN: Status of for the dataset transfer property list. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception IllegalArgumentException - plist is invalid. */ public static int H5Pset_preserve(int plist, boolean status) throws HDF5LibraryException, IllegalArgumentException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset_preserve(plist, status); } } /** * H5Pget_preserve checks the status of the dataset transfer property list. * * @param plist IN: Identifier for the dataset transfer property list. * @return TRUE or FALSE if successful; otherwise returns a negative value * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Pget_preserve(int plist) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_preserve(plist); } } /** * H5Pset_deflate sets the compression method for a dataset. * * @param plist IN: Identifier for the dataset creation property list. * @param level IN: Compression level. * @return non-negative if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Pset_deflate(int plist, int level) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset_deflate(plist, level); } } /** * H5Pset_nbit sets the compression method for a dataset to n-bits. *

* Keeps only n-bits from an integer or float value. * * @param plist IN: Identifier for the dataset creation property list. * @return non-negative if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Pset_nbit(int plist) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset_nbit(plist); } } /** * H5Pset_scaleoffset sets the compression method for a dataset to scale_offset. *

* Generally speaking, Scale-Offset compression performs a scale and/or offset operation on each * data value and truncates the resulting value to a minimum number of bits (MinBits) before * storing it. The current Scale-Offset filter supports integer and floating-point datatype. * * @param plist IN: Identifier for the dataset creation property list. * @param scale_type IN: One of {@link HDF5Constants#H5Z_SO_INT}, * {@link HDF5Constants#H5Z_SO_FLOAT_DSCALE} or * {@link HDF5Constants#H5Z_SO_FLOAT_ESCALE}. Note that * {@link HDF5Constants#H5Z_SO_FLOAT_ESCALE} is not implemented as of HDF5 1.8.2. * @return non-negative if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Pset_scaleoffset(int plist, int scale_type, int scale_factor) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset_scaleoffset(plist, scale_type, scale_factor); } } /** * H5Pset_create_intermediate_group pecifies in property list whether to create missing * intermediate groups. *

* H5Pset_create_intermediate_group specifies whether to set the link creation property list * lcpl_id so that calls to functions that create objects in groups different from the current * working group will create intermediate groups that may be missing in the path of a new or * moved object. *

* Functions that create objects in or move objects to a group other than the current working * group make use of this property. H5Gcreate_anon and H5Lmove are examles of such functions. *

* If crt_intermed_group is true, the H5G_CRT_INTMD_GROUP will be added to lcpl_id * (if it is not already there). Missing intermediate groups will be created upon calls to * functions such as those listed above that use lcpl_id. *

* If crt_intermed_group is false, the H5G_CRT_INTMD_GROUP, if present, will be * removed from lcpl_id. Missing intermediate groups will not be created upon calls to functions * such as those listed above that use lcpl_id. * * @param lcpl_id Link creation property list identifier * @param crt_intermed_group Flag specifying whether to create intermediate groups upon the * creation of an object * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static void H5Pset_create_intermediate_group(int lcpl_id, boolean crt_intermed_group) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { H5.H5Pset_create_intermediate_group(lcpl_id, crt_intermed_group); } } /** * Determines whether property is set to enable creating missing intermediate groups. * * @return true if intermediate groups are created, false otherwise. * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static boolean H5Pget_create_intermediate_group(int lcpl_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_create_intermediate_group(lcpl_id); } } /** * Returns a dataset transfer property list (H5P_DATASET_XFER) that has a * conversion exception handler set which abort conversions that triggers overflows. */ public static int H5Pcreate_xfer_abort_overflow() { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pcreate_xfer_abort_overflow(); } } /** * Returns a dataset transfer property list (H5P_DATASET_XFER) that has a * conversion exception handler set which aborts all conversions. */ public static int H5Pcreate_xfer_abort() { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pcreate_xfer_abort(); } } public static int H5Pset_alloc_time(int plist_id, int alloc_time) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset_alloc_time(plist_id, alloc_time); } } public static int H5Pget_alloc_time(int plist_id, int[] alloc_time) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_alloc_time(plist_id, alloc_time); } } public static int H5Pset_fill_time(int plist_id, int fill_time) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset_fill_time(plist_id, fill_time); } } public static int H5Pget_fill_time(int plist_id, int[] fill_time) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_fill_time(plist_id, fill_time); } } public static int H5Pfill_value_defined(int plist_id, int[] status) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pfill_value_defined(plist_id, status); } } public static int H5Pset_fletcher32(int plist) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset_fletcher32(plist); } } public static int H5Pset_edc_check(int plist, int check) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset_edc_check(plist, check); } } public static int H5Pget_edc_check(int plist) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_edc_check(plist); } } public static int H5Pset_shuffle(int plist_id) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset_shuffle(plist_id); } } public static int H5Pmodify_filter(int plist, int filter, int flags, long cd_nelmts, int[] cd_values) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pmodify_filter(plist, filter, flags, cd_nelmts, cd_values); } } public static int H5Pget_filter_by_id(int plist_id, int filter, int[] flags, long[] cd_nelmts, int[] cd_values, long namelen, String[] name) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_filter_by_id(plist_id, filter, flags, cd_nelmts, cd_values, namelen, name); } } public static boolean H5Pall_filters_avail(int dcpl_id) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pall_filters_avail(dcpl_id); } } public static int H5Pset_hyper_vector_size(int dxpl_id, long vector_size) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset_hyper_vector_size(dxpl_id, vector_size); } } public static int H5Pget_hyper_vector_size(int dxpl_id, long[] vector_size) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_hyper_vector_size(dxpl_id, vector_size); } } public static int H5Pset_fclose_degree(int plist, int degree) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset_fclose_degree(plist, degree); } } public static int H5Pget_fclose_degree(int plist_id) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_fclose_degree(plist_id); } } public static int H5Pset_fapl_family(int fapl_id, long memb_size, int memb_fapl_id) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset_fapl_family(fapl_id, memb_size, memb_fapl_id); } } public static int H5Pget_fapl_family(int fapl_id, long[] memb_size, int[] memb_fapl_id) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_fapl_family(fapl_id, memb_size, memb_fapl_id); } } public static int H5Pset_fapl_core(int fapl_id, int increment, boolean backing_store) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset_fapl_core(fapl_id, increment, backing_store); } } public static int H5Pget_fapl_core(int fapl_id, int[] increment, boolean[] backing_store) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_fapl_core(fapl_id, increment, backing_store); } } public static int H5Pset_family_offset(int fapl_id, long offset) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset_family_offset(fapl_id, offset); } } public static long H5Pget_family_offset(int fapl_id) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_family_offset(fapl_id); } } public static int H5Pset_fapl_log(int fapl_id, String logfile, int flags, int buf_size) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset_fapl_log(fapl_id, logfile, flags, buf_size); } } public static int H5Premove_filter(int obj_id, int filter) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Premove_filter(obj_id, filter); } } /** * Creates a new property list class of a given class * * @param cls IN: Class of property list to create * @return a valid property list identifier if successful; a negative value if failed * @throws HDF5LibraryException */ public static int H5Pcreate_list(int cls) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pcreate_list(cls); } } /** * Sets a property list value (support integer only) * * @param plid IN: Property list identifier to modify * @param name IN: Name of property to modify * @param value IN: value to set the property to * @return a non-negative value if successful; a negative value if failed * @throws HDF5LibraryException */ public static int H5Pset(int plid, String name, int value) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset(plid, name, value); } } /** * H5Pexist determines whether a property exists within a property list or class * * @param plid IN: Identifier for the property to query * @param name IN: Name of property to check for * @return a positive value if the property exists in the property object; zero if the property * does not exist; a negative value if failed * @throws HDF5LibraryException */ public static int H5Pexist(int plid, String name) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pexist(plid, name); } } /** * H5Pget_size retrieves the size of a property's value in bytes * * @param plid IN: Identifier of property object to query * @param name IN: Name of property to query * @return size of a property's value if successful; a negative value if failed * @throws HDF5LibraryException */ public static long H5Pget_size(int plid, String name) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_size(plid, name); } } /** * H5Pget_nprops retrieves the number of properties in a property list or class * * @param plid IN: Identifier of property object to query * @return number of properties if successful; a negative value if failed * @throws HDF5LibraryException */ public static long H5Pget_nprops(int plid) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_nprops(plid); } } /** * H5Pget_class_name retrieves the name of a generic property list class * * @param plid IN: Identifier of property object to query * @return name of a property list if successful; null if failed * @throws HDF5LibraryException */ public static String H5Pget_class_name(int plid) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_class_name(plid); } } /** * H5Pget_class_parent retrieves an identifier for the parent class of a property class * * @param plid IN: Identifier of the property class to query * @return a valid parent class object identifier if successful; a negative value if failed * @throws HDF5LibraryException */ public static int H5Pget_class_parent(int plid) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_class_parent(plid); } } /** * H5Pisa_class checks to determine whether a property list is a member of the specified class * * @param plist IN: Identifier of the property list * @param pclass IN: Identifier of the property class * @return a positive value if equal; zero if unequal; a negative value if failed * @throws HDF5LibraryException */ public static int H5Pisa_class(int plist, int pclass) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pisa_class(plist, pclass); } } /** * H5Pget retrieves a copy of the value for a property in a property list (support integer only) * * @param plid IN: Identifier of property object to query * @param name IN: Name of property to query * @return value for a property if successful; a negative value if failed * @throws HDF5LibraryException */ public static int H5Pget(int plid, String name) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget(plid, name); } } /** * H5Pequal determines if two property lists or classes are equal * * @param plid1 IN: First property object to be compared * @param plid2 IN: Second property object to be compared * @return positive value if equal; zero if unequal, a negative value if failed * @throws HDF5LibraryException */ public static int H5Pequal(int plid1, int plid2) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pequal(plid1, plid2); } } /** * H5Pcopy_prop copies a property from one property list or class to another * * @param dst_id IN: Identifier of the destination property list or class * @param src_id IN: Identifier of the source property list or class * @param name IN: Name of the property to copy * @return a non-negative value if successful; a negative value if failed * @throws HDF5LibraryException */ public static int H5Pcopy_prop(int dst_id, int src_id, String name) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pcopy_prop(dst_id, src_id, name); } } /** * H5Premove removes a property from a property list * * @param plid IN: Identifier of the property list to modify * @param name IN: Name of property to remove * @return a non-negative value if successful; a negative value if failed * @throws HDF5LibraryException */ public static int H5Premove(int plid, String name) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Premove(plid, name); } } /** * H5Punregister removes a property from a property list class * * @param plid IN: Property list class from which to remove permanent property * @param name IN: Name of property to remove * @return a non-negative value if successful; a negative value if failed * @throws HDF5LibraryException */ public static int H5Punregister(int plid, String name) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Punregister(plid, name); } } /** * Closes an existing property list class * * @param plid IN: Property list class to close * @return a non-negative value if successful; a negative value if failed * @throws HDF5LibraryException */ public static int H5Pclose_class(int plid) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pclose_class(plid); } } /** * Sets the permissible bounds of the library's file format versions. *

* Can be set on the file access property list. *

* As of 1.8.0, only the combinations low=H5F_LIBVER_EARLIEST / * high=H5F_LIBVER_LATEST (which is the default and means that 1.6 compatible files are * created if no features are used that require a 1.8 format) and low=H5F_LIBVER_LATEST * / high=H5F_LIBVER_LATEST (which means that always 1.8 files are created * which cannot be read by an earlier library) are allowed. * * @param plist_id Property list identifier. * @param low The lower permissible bound. One of H5F_LIBVER_LATEST or * H5F_LIBVER_LATEST . * @param high The higher permissible bound. Must be H5F_LIBVER_LATEST. * @return a non-negative value if successful */ public static int H5Pset_libver_bounds(int plist_id, int low, int high) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset_libver_bounds(plist_id, low, high); } } /** * Returns the permissible bounds of the library's file format versions. * * @param plist_id Property list identifier. * @return an array containing [low, high] on success */ public static int[] H5Pget_libver_bounds(int plist_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_libver_bounds(plist_id); } } /** * Sets the local heap size hint for an old-style group. This is the chunk size allocated on the * heap for a group. * * @param gcpl_id The group creation property list to change the heap size hint for * @param size_hint The size hint to set. * @return a non-negative value if successful */ public static int H5Pset_local_heap_size_hint(int gcpl_id, int size_hint) { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset_local_heap_size_hint(gcpl_id, size_hint); } } /** * Returns the local heap size hint for an old-style group. This is the chunk size allocated on * the heap for a group. * * @param gcpl_id The group creation property list to change the heap size hint for * @return The size hint of the group if successful */ public static int H5Pget_local_heap_size_hint(int gcpl_id) { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_local_heap_size_hint(gcpl_id); } } /** * Sets the phase change parameters for a new-style group. * * @param gcpl_id The group creation property list to set the link phase changes for * @param max_compact The maximum number of links in a group to store as header messages * @param min_dense The minimum number of links in a group to in the dense format * @return a non-negative value if successful */ public static int H5Pset_link_phase_change(int gcpl_id, int max_compact, int min_dense) { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset_link_phase_change(gcpl_id, max_compact, min_dense); } } /** * Returns the phase change parameters for a new-style group. * * @param gcpl_id The group creation property list to set the link phase changes for * @return the phase change parameters as array [max_compact, min_dense] if successful */ public static int[] H5Pget_link_phase_change(int gcpl_id) { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_link_phase_change(gcpl_id); } } /** * Sets the character encoding for the given creation property list to the given encoding. * * @param cpl_id The creation property list to set the character encoding for. * @param encoding The encoding (one of {@link HDF5Constants#H5T_CSET_ASCII} or * {@link HDF5Constants#H5T_CSET_UTF8}) to use. * @return a non-negative value if successful */ public static int H5Pset_char_encoding(int cpl_id, int encoding) { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pset_char_encoding(cpl_id, encoding); } } /** * Returns the character encoding currently set for a creation property list. * * @param cpl_id The creation property list to get the character encoding for. * @return The encoding, one of {@link HDF5Constants#H5T_CSET_ASCII} or * {@link HDF5Constants#H5T_CSET_UTF8}. */ public static int H5Pget_char_encoding(int cpl_id) { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Pget_char_encoding(cpl_id); } } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/hdf5lib/H5RI.java000066400000000000000000000250211256564762100262510ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.hdf5lib; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; /** * Low-level interface for HDF5 reference and identifier functions. *

* This is an internal API that should not be expected to be stable between releases! * * @author Bernd Rinn */ public class H5RI { static { H5.ensureNativeLibIsLoaded(); } // //////////////////////////////////////////////////////////// // // // H5R: Reference Interface Functions // // // // //////////////////////////////////////////////////////////// /** * H5Rcreate creates the reference, ref, of the type specified in ref_type, pointing to the * object name located at loc_id. * * @param loc_id IN: Location identifier used to locate the object being pointed to. * @param name IN: Name of object at location loc_id. * @param ref_type IN: Type of reference. * @param space_id IN: Dataspace identifier with selection. * @return the reference (byte[]) if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - an input array is null. * @exception IllegalArgumentException - an input array is invalid. */ public static byte[] H5Rcreate(final int loc_id, final String name, final int ref_type, final int space_id) throws HDF5LibraryException, NullPointerException, IllegalArgumentException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Rcreate(loc_id, name, ref_type, space_id); } } /** * H5Rcreate creates the object references, pointing to the object names located at loc_id. * * @param loc_id IN: Location identifier used to locate the object being pointed to. * @param name IN: Names of objects at location loc_id. * @return the reference (long[]) if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - an input array is null. * @exception IllegalArgumentException - an input array is invalid. */ public static long[] H5Rcreate(final int loc_id, final String[] name) throws HDF5LibraryException, NullPointerException, IllegalArgumentException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Rcreate(loc_id, name); } } /** * Given a reference to some object, H5Rdereference opens that object and return an identifier. * * @param loc_id IN: Location identifier used to locate the object being pointed to. * @param ref IN: reference to an object * @return valid identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - output array is null. * @exception IllegalArgumentException - output array is invalid. */ public static int H5Rdereference(int loc_id, long ref) throws HDF5LibraryException, NullPointerException, IllegalArgumentException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Rdereference(loc_id, ref); } } /** * Given a reference to some object, H5Rdereference opens that object and return an identifier. * * @param loc_id IN: Location identifier used to locate the object being pointed to. * @param ref_type IN: The reference type of ref. * @param ref IN: reference to an object * @return valid identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - output array is null. * @exception IllegalArgumentException - output array is invalid. */ public static int H5Rdereference(int loc_id, int ref_type, byte[] ref) throws HDF5LibraryException, NullPointerException, IllegalArgumentException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Rdereference(loc_id, ref_type, ref); } } /** * Given a reference to an object ref, H5Rget_region creates a copy of the dataspace of the * dataset pointed to and defines a selection in the copy which is the region pointed to. * * @param loc_id IN: loc_id of the reference object. * @param ref_type IN: The reference type of ref. * @param ref OUT: the reference to the object and region * @return a valid identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - output array is null. * @exception IllegalArgumentException - output array is invalid. */ public static int H5Rget_region(int loc_id, int ref_type, byte[] ref) throws HDF5LibraryException, NullPointerException, IllegalArgumentException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Rget_region(loc_id, ref_type, ref); } } /** * Given a reference to an object, H5Rget_obj_type returns the type of the object pointed to. * * @param loc_id Identifier of the reference object. * @param ref_type Type of reference to query. * @param ref The reference. * @return a valid identifier if successful; otherwise a negative value is returned to signal * failure. * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - array is null. * @exception IllegalArgumentException - array is invalid. */ public static int H5Rget_obj_type(int loc_id, int ref_type, byte[] ref) throws HDF5LibraryException, NullPointerException, IllegalArgumentException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Rget_obj_type(loc_id, ref_type, ref); } } /** * Given a reference to an object, H5Rget_name returns the name (path) of the object pointed to. * * @param loc_id Identifier of the reference object. * @param ref_type Type of reference to query. * @param ref The reference. * @return The path of the object being pointed to, or an empty string, if the object being * pointed to has no name. * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - array is null. * @exception IllegalArgumentException - array is invalid. */ public static String H5Rget_name(int loc_id, int ref_type, byte[] ref) { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Rget_name(loc_id, ref_type, ref); } } /** * Given a reference to an object, H5Rget_name returns the name (path) of the object pointed to. * * @param loc_id Identifier of the reference object. * @param ref The reference. * @return The path of the object being pointed to, or an empty string, if the object being * pointed to has no name. * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - array is null. * @exception IllegalArgumentException - array is invalid. */ public static String H5Rget_name(int loc_id, long ref) throws HDF5LibraryException, NullPointerException, IllegalArgumentException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Rget_name(loc_id, ref); } } /** * Given an array of object references (ref), H5Rget_name returns the names (paths) of the * objects pointed to. * * @param loc_id Identifier of the reference object. * @param ref The references. * @return The paths of the objects being pointed to, or an empty string, if an object being * pointed to has no name. * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - array is null. * @exception IllegalArgumentException - array is invalid. */ public static String[] H5Rget_name(int loc_id, long[] ref) { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Rget_name(loc_id, ref); } } // //////////////////////////////////////////////////////////// // // // H5I: Identifier Interface Functions // // // // //////////////////////////////////////////////////////////// /** * H5Iget_type retrieves the type of the object identified by obj_id. * * @param obj_id IN: Object identifier whose type is to be determined. * @return the object type if successful; otherwise H5I_BADID. * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Iget_type(int obj_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Iget_type(obj_id); } } public static long H5Iget_name(int obj_id, String[] name, long size) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Iget_name(obj_id, name, size); } } public static int H5Iget_ref(int obj_id) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Iget_ref(obj_id); } } public static int H5Iinc_ref(int obj_id) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Iinc_ref(obj_id); } } public static int H5Idec_ref(int obj_id) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Idec_ref(obj_id); } } public static int H5Iget_file_id(int obj_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Iget_file_id(obj_id); } } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/hdf5lib/H5S.java000066400000000000000000000453611256564762100261520ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.hdf5lib; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; /** * Low-level interface for HDF5 dataspace functions. *

* This is an internal API that should not be expected to be stable between releases! * * @author Bernd Rinn */ public class H5S { static { H5.ensureNativeLibIsLoaded(); } /** * H5Screate creates a new dataspace of a particular type. * * @param type The type of dataspace to be created. * @return a dataspace identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Screate(int type) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Screate(type); } } /** * H5Screate_simple creates a new simple data space and opens it for access. * * @param rank Number of dimensions of dataspace. * @param dims An array of the size of each dimension. * @param maxdims An array of the maximum size of each dimension. * @return a dataspace identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - dims or maxdims is null. */ public static int H5Screate_simple(int rank, byte[] dims, byte[] maxdims) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Screate_simple(rank, dims, maxdims); } } public static int H5Screate_simple(final int rank, final long[] dims, final long[] maxdims) throws HDF5Exception, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Screate_simple(rank, dims, maxdims); } } /** * H5Scopy creates a new dataspace which is an exact copy of the dataspace identified by * space_id. * * @param space_id Identifier of dataspace to copy. * @return a dataspace identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Scopy(int space_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Scopy(space_id); } } /** * H5Sselect_elements selects array elements to be included in the selection for the space_id * dataspace. * * @param space_id Identifier of the dataspace. * @param op operator specifying how the new selection is combined. * @param num_elements Number of elements to be selected. * @param coord A 2-dimensional array specifying the coordinates of the elements. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Sselect_elements(int space_id, int op, int num_elements, byte[] coord) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Sselect_elements(space_id, op, num_elements, coord); } } /** * H5Sselect_all selects the entire extent of the dataspace space_id. * * @param space_id IN: The identifier of the dataspace to be selected. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Sselect_all(int space_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Sselect_all(space_id); } } /** * H5Sselect_none resets the selection region for the dataspace space_id to include no elements. * * @param space_id IN: The identifier of the dataspace to be reset. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Sselect_none(int space_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Sselect_none(space_id); } } /** * H5Sselect_valid verifies that the selection for the dataspace. * * @param space_id The identifier for the dataspace in which the selection is being reset. * @return true if the selection is contained within the extent and FALSE if it is not or is an * error. * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static boolean H5Sselect_valid(int space_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Sselect_valid(space_id); } } /** * H5Sget_simple_extent_npoints determines the number of elements in a dataspace. * * @param space_id ID of the dataspace object to query * @return the number of elements in the dataspace if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static long H5Sget_simple_extent_npoints(int space_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Sget_simple_extent_npoints(space_id); } } /** * H5Sget_select_npoints determines the number of elements in the current selection of a * dataspace. * * @param space_id Dataspace identifier. * @return the number of elements in the selection if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static long H5Sget_select_npoints(int space_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Sget_select_npoints(space_id); } } /** * H5Sget_simple_extent_ndims determines the dimensionality (or rank) of a dataspace. * * @param space_id Identifier of the dataspace * @return the number of dimensions in the dataspace if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Sget_simple_extent_ndims(int space_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Sget_simple_extent_ndims(space_id); } } /** * H5Sget_simple_extent_dims returns the size and maximum sizes of each dimension of a dataspace * through the dims and maxdims parameters. * * @param space_id IN: Identifier of the dataspace object to query * @param dims OUT: Pointer to array to store the size of each dimension. * @param maxdims OUT: Pointer to array to store the maximum size of each dimension. * @return the number of dimensions in the dataspace if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - dims or maxdims is null. */ public static int H5Sget_simple_extent_dims(int space_id, long[] dims, long[] maxdims) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Sget_simple_extent_dims(space_id, dims, maxdims); } } /** * H5Sget_simple_extent_type queries a dataspace to determine the current class of a dataspace. * * @param space_id Dataspace identifier. * @return a dataspace class name if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Sget_simple_extent_type(int space_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Sget_simple_extent_type(space_id); } } /** * H5Sset_extent_simple sets or resets the size of an existing dataspace. * * @param space_id Dataspace identifier. * @param rank Rank, or dimensionality, of the dataspace. * @param current_size Array containing current size of dataspace. * @param maximum_size Array containing maximum size of dataspace. * @return a dataspace identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Sset_extent_simple(int space_id, int rank, byte[] current_size, byte[] maximum_size) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Sset_extent_simple(space_id, rank, current_size, maximum_size); } } public static int H5Sset_extent_simple(final int space_id, final int rank, final long[] currentSize, final long[] maxSize) throws HDF5Exception, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Sset_extent_simple(space_id, rank, currentSize, maxSize); } } /** * H5Sis_simple determines whether a dataspace is a simple dataspace. * * @param space_id Identifier of the dataspace to query * @return true if is a simple dataspace * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static boolean H5Sis_simple(int space_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Sis_simple(space_id); } } /** * H5Soffset_simple sets the offset of a simple dataspace space_id. * * @param space_id IN: The identifier for the dataspace object to reset. * @param offset IN: The offset at which to position the selection. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - offset array is null. */ public static int H5Soffset_simple(int space_id, byte[] offset) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Soffset_simple(space_id, offset); } } public static int H5Soffset_simple(final int space_id, final long[] offset) throws HDF5Exception, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Soffset_simple(space_id, offset); } } /** * H5Sextent_copy copies the extent from source_space_id to dest_space_id. This action may * change the type of the dataspace. * * @param dest_space_id IN: The identifier for the dataspace from which the extent is copied. * @param source_space_id IN: The identifier for the dataspace to which the extent is copied. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Sextent_copy(int dest_space_id, int source_space_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Sextent_copy(dest_space_id, source_space_id); } } /** * H5Sset_extent_none removes the extent from a dataspace and sets the type to H5S_NONE. * * @param space_id The identifier for the dataspace from which the extent is to be removed. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Sset_extent_none(int space_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Sset_extent_none(space_id); } } /** * H5Sselect_hyperslab selects a hyperslab region to add to the current selected region for the * dataspace specified by space_id. The start, stride, count, and block arrays must be the same * size as the rank of the dataspace. * * @param space_id IN: Identifier of dataspace selection to modify * @param op IN: Operation to perform on current selection. * @param start IN: Offset of start of hyperslab * @param count IN: Number of blocks included in hyperslab. * @param stride IN: Hyperslab stride. * @param block IN: Size of block in hyperslab. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - an input array is null. * @exception NullPointerException - an input array is invalid. */ public static int H5Sselect_hyperslab(int space_id, int op, byte[] start, byte[] stride, byte[] count, byte[] block) throws HDF5LibraryException, NullPointerException, IllegalArgumentException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Sselect_hyperslab(space_id, op, start, stride, count, block); } } public static int H5Sselect_hyperslab(final int space_id, final int op, final long[] start, final long[] stride, final long[] count, final long[] block) throws HDF5Exception, NullPointerException, IllegalArgumentException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Sselect_hyperslab(space_id, op, start, stride, count, block); } } /** * H5Sclose releases a dataspace. * * @param space_id Identifier of dataspace to release. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Sclose(int space_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Sclose(space_id); } } /** * H5Sget_select_hyper_nblocks returns the number of hyperslab blocks in the current dataspace * selection. * * @param spaceid Identifier of dataspace to release. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static long H5Sget_select_hyper_nblocks(int spaceid) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Sget_select_hyper_nblocks(spaceid); } } /** * H5Sget_select_elem_npoints returns the number of element points in the current dataspace * selection. * * @param spaceid Identifier of dataspace to release. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static long H5Sget_select_elem_npoints(int spaceid) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Sget_select_elem_npoints(spaceid); } } /** * H5Sget_select_hyper_blocklist returns an array of hyperslab blocks. The block coordinates * have the same dimensionality (rank) as the dataspace they are located within. The list of * blocks is formatted as follows: * * 

     * 
     * <"start" coordinate>, immediately followed by <"opposite" corner
     * coordinate>, followed by the next "start" and "opposite" coordinates,
     * etc. until all of the selected blocks have been listed.
     * 
     *
* * @param spaceid Identifier of dataspace to release. * @param startblock first block to retrieve * @param numblocks number of blocks to retrieve * @param buf returns blocks startblock to startblock+num-1, each block is rank * 2 * (corners) longs. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - buf is null. */ public static int H5Sget_select_hyper_blocklist(int spaceid, long startblock, long numblocks, long[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Sget_select_hyper_blocklist(spaceid, startblock, numblocks, buf); } } /** * H5Sget_select_elem_pointlist returns an array of of element points in the current dataspace * selection. The point coordinates have the same dimensionality (rank) as the dataspace they * are located within, one coordinate per point. * * @param spaceid Identifier of dataspace to release. * @param startpoint first point to retrieve * @param numpoints number of points to retrieve * @param buf returns points startblock to startblock+num-1, each points is rank longs. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - buf is null. */ public static int H5Sget_select_elem_pointlist(int spaceid, long startpoint, long numpoints, long[] buf) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Sget_select_elem_pointlist(spaceid, startpoint, numpoints, buf); } } /** * H5Sget_select_bounds retrieves the coordinates of the bounding box containing the current * selection and places them into user-supplied buffers. *

* The start and end buffers must be large enough to hold the dataspace rank number of * coordinates. * * @param spaceid Identifier of dataspace to release. * @param start coordinates of lowest corner of bounding box. * @param end coordinates of highest corner of bounding box. * @return a non-negative value if successful,with start and end initialized. * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - start or end is null. */ public static int H5Sget_select_bounds(int spaceid, long[] start, long[] end) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Sget_select_bounds(spaceid, start, end); } } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/hdf5lib/H5T.java000066400000000000000000001100211256564762100261350ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.hdf5lib; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; /** * Low-level interface for HDF5 datatype functions. *

* This is an internal API that should not be expected to be stable between releases! * * @author Bernd Rinn */ public class H5T { static { H5.ensureNativeLibIsLoaded(); } /** * H5Topen opens a named datatype at the location specified by loc_id and return an identifier * for the datatype. * * @param loc_id A file, group, or datatype identifier. * @param name A datatype name. * @param access_plist_id Datatype access property list identifier. * @return a named datatype identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static int H5Topen(int loc_id, String name, int access_plist_id) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Topen(loc_id, name, access_plist_id); } } /** * H5Tcommit commits a transient datatype (not immutable) to a file, turned it into a named * datatype. * * @param loc_id A file or group identifier. * @param name A datatype name. * @param type_id A datatype identifier. * @param link_create_plist_id Link creation property list. * @param dtype_create_plist_id Datatype creation property list. * @param dtype_access_plist_id Datatype access property list. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static int H5Tcommit(int loc_id, String name, int type_id, int link_create_plist_id, int dtype_create_plist_id, int dtype_access_plist_id) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tcommit(loc_id, name, type_id, link_create_plist_id, dtype_create_plist_id, dtype_access_plist_id); } } /** * H5Tcommitted queries a type to determine whether the type specified by the type identifier is * a named type or a transient type. * * @param type Datatype identifier. * @return true if successfully committed * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static boolean H5Tcommitted(int type) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tcommitted(type); } } /** * H5Tcreate creates a new dataype of the specified class with the specified number of bytes. * * @param dclass Class of datatype to create. * @param size The number of bytes in the datatype to create. * @return datatype identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tcreate(int dclass, int size) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tcreate(dclass, size); } } /** * H5Tcopy copies an existing datatype. The returned type is always transient and unlocked. * * @param type_id Identifier of datatype to copy. Can be a datatype identifier, a predefined * datatype (defined in H5Tpublic.h), or a dataset Identifier. * @return a datatype identifier if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tcopy(int type_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tcopy(type_id); } } /** * H5Tequal determines whether two datatype identifiers refer to the same datatype. * * @param type_id1 Identifier of datatype to compare. * @param type_id2 Identifier of datatype to compare. * @return true if the datatype identifiers refer to the same datatype, else FALSE. * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static boolean H5Tequal(int type_id1, int type_id2) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tequal(type_id1, type_id2); } } /** * H5Tlock locks the datatype specified by the type_id identifier, making it read-only and * non-destructible. * * @param type_id Identifier of datatype to lock. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tlock(int type_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tlock(type_id); } } /** * H5Tget_class returns the datatype class identifier. * * @param type_id Identifier of datatype to query. * @return datatype class identifier if successful; otherwise H5T_NO_CLASS (-1). * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tget_class(int type_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tget_class(type_id); } } /** * H5Tget_size returns the size of a datatype in bytes as an int value. * * @param type_id Identifier of datatype to query. * @return the size of the datatype in bytes if successful * @exception HDF5LibraryException - Error from the HDF-5 Library, or if the size of the data * type exceeds an int */ public static int H5Tget_size(int type_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tget_size(type_id); } } /** * H5Tget_size returns the size of a datatype in bytes as a long value. * * @param type_id Identifier of datatype to query. * @return the size of the datatype in bytes if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static long H5Tget_size_long(int type_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tget_size_long(type_id); } } /** * H5Tset_size sets the total size in bytes, size, for an atomic datatype (this operation is not * permitted on compound datatypes). * * @param type_id Identifier of datatype to change size. * @param size Size in bytes to modify datatype. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tset_size(int type_id, int size) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tset_size(type_id, size); } } /** * H5Tget_order returns the byte order of an atomic datatype. * * @param type_id Identifier of datatype to query. * @return a byte order constant if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tget_order(int type_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tget_order(type_id); } } /** * H5Tset_order sets the byte ordering of an atomic datatype. * * @param type_id Identifier of datatype to set. * @param order Byte ordering constant. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tset_order(int type_id, int order) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tset_order(type_id, order); } } /** * H5Tget_precision returns the precision of an atomic datatype. * * @param type_id Identifier of datatype to query. * @return the number of significant bits if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tget_precision(int type_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tget_precision(type_id); } } /** * H5Tset_precision sets the precision of an atomic datatype. * * @param type_id Identifier of datatype to set. * @param precision Number of bits of precision for datatype. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tset_precision(int type_id, int precision) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tset_precision(type_id, precision); } } /** * H5Tget_offset retrieves the bit offset of the first significant bit. * * @param type_id Identifier of datatype to query. * @return a positive offset value if successful; otherwise 0. * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tget_offset(int type_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tget_offset(type_id); } } /** * H5Tset_offset sets the bit offset of the first significant bit. * * @param type_id Identifier of datatype to set. * @param offset Offset of first significant bit. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tset_offset(int type_id, int offset) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tset_offset(type_id, offset); } } /** * H5Tget_pad retrieves the padding type of the least and most-significant bit padding. * * @param type_id IN: Identifier of datatype to query. * @param pad OUT: locations to return least-significant and most-significant bit padding type. * * 

     * 
     *            pad[0] = lsb // least-significant bit padding type pad[1] = msb //
     *            most-significant bit padding type
     * 
     *
* @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - pad is null. */ public static int H5Tget_pad(int type_id, int[] pad) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tget_pad(type_id, pad); } } /** * H5Tset_pad sets the least and most-significant bits padding types. * * @param type_id Identifier of datatype to set. * @param lsb Padding type for least-significant bits. * @param msb Padding type for most-significant bits. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tset_pad(int type_id, int lsb, int msb) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tset_pad(type_id, lsb, msb); } } /** * H5Tget_sign retrieves the sign type for an integer type. * * @param type_id Identifier of datatype to query. * @return a valid sign type if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tget_sign(int type_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tget_sign(type_id); } } /** * H5Tset_sign sets the sign proprety for an integer type. * * @param type_id Identifier of datatype to set. * @param sign Sign type. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tset_sign(int type_id, int sign) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tset_sign(type_id, sign); } } /** * H5Tget_fields retrieves information about the locations of the various bit fields of a * floating point datatype. * * @param type_id IN: Identifier of datatype to query. * @param fields OUT: location of size and bit-position. * * 
     * 
     *            fields[0] = spos OUT: location to return size of in bits. fields[1] = epos OUT:
     *            location to return exponent bit-position. fields[2] = esize OUT: location to
     *            return size of exponent in bits. fields[3] = mpos OUT: location to return mantissa
     *            bit-position. fields[4] = msize OUT: location to return size of mantissa in bits.
     * 
     *
* @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - fileds is null. * @exception IllegalArgumentException - fileds array is invalid. */ public static int H5Tget_fields(int type_id, int[] fields) throws HDF5LibraryException, NullPointerException, IllegalArgumentException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tget_fields(type_id, fields); } } /** * H5Tset_fields sets the locations and sizes of the various floating point bit fields. * * @param type_id Identifier of datatype to set. * @param spos Size position. * @param epos Exponent bit position. * @param esize Size of exponent in bits. * @param mpos Mantissa bit position. * @param msize Size of mantissa in bits. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tset_fields(int type_id, int spos, int epos, int esize, int mpos, int msize) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tset_fields(type_id, spos, epos, esize, mpos, msize); } } /** * H5Tget_ebias retrieves the exponent bias of a floating-point type. * * @param type_id Identifier of datatype to query. * @return the bias if successful; otherwise 0. * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tget_ebias(int type_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tget_ebias(type_id); } } /** * H5Tset_ebias sets the exponent bias of a floating-point type. * * @param type_id Identifier of datatype to set. * @param ebias Exponent bias value. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tset_ebias(int type_id, int ebias) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tset_ebias(type_id, ebias); } } /** * H5Tget_norm retrieves the mantissa normalization of a floating-point datatype. * * @param type_id Identifier of datatype to query. * @return a valid normalization type if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tget_norm(int type_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tget_norm(type_id); } } /** * H5Tset_norm sets the mantissa normalization of a floating-point datatype. * * @param type_id Identifier of datatype to set. * @param norm Mantissa normalization type. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tset_norm(int type_id, int norm) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tset_norm(type_id, norm); } } /** * H5Tget_inpad retrieves the internal padding type for unused bits in floating-point datatypes. * * @param type_id Identifier of datatype to query. * @return a valid padding type if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tget_inpad(int type_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tget_inpad(type_id); } } /** * If any internal bits of a floating point type are unused (that is, those significant bits * which are not part of the sign, exponent, or mantissa), then H5Tset_inpad will be filled * according to the value of the padding value property inpad. * * @param type_id Identifier of datatype to modify. * @param inpad Padding type. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tset_inpad(int type_id, int inpad) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tset_inpad(type_id, inpad); } } /** * H5Tget_cset retrieves the character set type of a string datatype. * * @param type_id Identifier of datatype to query. * @return a valid character set type if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tget_cset(int type_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tget_cset(type_id); } } /** * H5Tset_cset the character set to be used. * * @param type_id Identifier of datatype to modify. * @param cset Character set type. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tset_cset(int type_id, int cset) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tset_cset(type_id, cset); } } /** * H5Tget_strpad retrieves the string padding method for a string datatype. * * @param type_id Identifier of datatype to query. * @return a valid string padding type if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tget_strpad(int type_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tget_strpad(type_id); } } /** * H5Tset_strpad defines the storage mechanism for the string. * * @param type_id Identifier of datatype to modify. * @param strpad String padding type. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tset_strpad(int type_id, int strpad) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tset_strpad(type_id, strpad); } } /** * H5Tget_nmembers retrieves the number of fields a compound datatype has. * * @param type_id Identifier of datatype to query. * @return number of members datatype has if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tget_nmembers(int type_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tget_nmembers(type_id); } } /** * H5Tget_member_name retrieves the name of a field of a compound datatype. * * @param type_id Identifier of datatype to query. * @param field_idx Field index (0-based) of the field name to retrieve. * @return a valid pointer if successful; otherwise null. */ public static String H5Tget_member_name(int type_id, int field_idx) { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tget_member_name(type_id, field_idx); } } /** * H5Tget_member_index retrieves the index of a field of a compound datatype. * * @param type_id Identifier of datatype to query. * @param field_name Field name of the field index to retrieve. * @return if field is defined, the index; else negative. */ public static int H5Tget_member_index(int type_id, String field_name) { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tget_member_index(type_id, field_name); } } /** * H5Tget_member_class returns the datatype of the specified member. * * @param type_id Identifier of datatype to query. * @param field_idx Field index (0-based) of the field type to retrieve. * @return the identifier of a copy of the datatype of the field if successful; * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tget_member_class(int type_id, int field_idx) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tget_member_class(type_id, field_idx); } } /** * H5Tget_member_type returns the datatype of the specified member. * * @param type_id Identifier of datatype to query. * @param field_idx Field index (0-based) of the field type to retrieve. * @return the identifier of a copy of the datatype of the field if successful; * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tget_member_type(int type_id, int field_idx) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tget_member_type(type_id, field_idx); } } /** * H5Tget_member_offset returns the byte offset of the specified member of the compound * datatype. This is the byte offset in the HDF-5 file/library, NOT the offset of any Java * object which might be mapped to this data item. * * @param type_id Identifier of datatype to query. * @param membno Field index (0-based) of the field type to retrieve. * @return the offset of the member. * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static long H5Tget_member_offset(int type_id, int membno) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tget_member_offset(type_id, membno); } } /** * H5Tinsert adds another member to the compound datatype type_id. * * @param type_id Identifier of compound datatype to modify. * @param name Name of the field to insert. * @param offset Offset in memory structure of the field to insert. * @param field_id Datatype identifier of the field to insert. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static int H5Tinsert(int type_id, String name, long offset, int field_id) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tinsert(type_id, name, offset, field_id); } } /** * H5Tpack recursively removes padding from within a compound datatype to make it more efficient * (space-wise) to store that data. *

* WARNING: This call only affects the C-data, even if it succeeds, there may be no * visible effect on Java objects. * * @param type_id Identifier of datatype to modify. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tpack(int type_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tpack(type_id); } } /** * H5Tclose releases a datatype. * * @param type_id Identifier of datatype to release. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tclose(int type_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tclose(type_id); } } /** * H5Tenum_create creates a new enumeration datatype based on the specified base datatype, * parent_id, which must be an integer type. * * @param base_id Identifier of the parent datatype to release. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tenum_create(int base_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tenum_create(base_id); } } /** * H5Tenum_insert inserts a new enumeration datatype member into an 8bit enumeration datatype. * * @param type Identifier of datatype. * @param name The name of the member * @param value The value of the member, data of the correct type * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static int H5Tenum_insert(int type, String name, byte value) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tenum_insert(type, name, value); } } /** * H5Tenum_insert inserts a new enumeration datatype member into a 16bit enumeration datatype. * * @param type Identifier of datatype. * @param name The name of the member * @param value The value of the member, data of the correct type * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static int H5Tenum_insert(int type, String name, short value) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tenum_insert(type, name, value); } } /** * H5Tenum_insert inserts a new enumeration datatype member into a 32bit enumeration datatype. * * @param type Identifier of datatype. * @param name The name of the member * @param value The value of the member, data of the correct type * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static int H5Tenum_insert(int type, String name, int value) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tenum_insert(type, name, value); } } /** * Converts the value (in place) to little endian. * * @return a non-negative value if successful */ public static int H5Tconvert_to_little_endian(short[] value) { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tconvert_to_little_endian(value); } } /** * Converts the value (in place) to little endian. * * @return a non-negative value if successful */ public static int H5Tconvert_to_little_endian(int[] value) { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tconvert_to_little_endian(value); } } /** * H5Tenum_nameof finds the symbol name that corresponds to the specified value of the * enumeration datatype type. * * @param type IN: Identifier of datatype. * @param value IN: The value of the member, data of the correct * @param name OUT: The name of the member * @param size IN: The max length of the name * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static int H5Tenum_nameof(int type, int[] value, String[] name, int size) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tenum_nameof(type, value, name, size); } } /** * H5Tenum_valueof finds the value that corresponds to the specified name of the enumeration * datatype type. * * @param type IN: Identifier of datatype. * @param name IN: The name of the member * @param value OUT: The value of the member * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static int H5Tenum_valueof(int type, String name, int[] value) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tenum_valueof(type, name, value); } } /** * H5Tvlen_create creates a new variable-length (VL) dataype. * * @param base_id IN: Identifier of parent datatype. * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tvlen_create(int base_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tvlen_create(base_id); } } /** * H5Tset_tag tags an opaque datatype type_id with a unique ASCII identifier tag. * * @param type IN: Identifier of parent datatype. * @param tag IN: Name of the tag (will be stored as ASCII) * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tset_tag(int type, String tag) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tset_tag(type, tag); } } /** * H5Tget_tag returns the tag associated with datatype type_id. * * @param type IN: Identifier of datatype. * @return the tag * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static String H5Tget_tag(int type) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tget_tag(type); } } /** * H5Tget_super returns the type from which TYPE is derived. * * @param type IN: Identifier of datatype. * @return the parent type * @exception HDF5LibraryException - Error from the HDF-5 Library. */ public static int H5Tget_super(int type) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tget_super(type); } } /** * H5Tget_member_value returns the value of the enumeration datatype member memb_no. * * @param type_id IN: Identifier of datatype. * @param membno IN: The name of the member * @param value OUT: The value of the member * @return a non-negative value if successful * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. */ public static int H5Tget_member_value(int type_id, int membno, int[] value) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tget_member_value(type_id, membno, value); } } /** * Creates an array datatype object. * * @param base_type_id Datatype identifier for the array base datatype. * @param rank Rank of the array. * @param dims Size of each array dimension. * @return a valid datatype identifier if successful; otherwise returns a negative value. * @exception HDF5LibraryException Error from the HDF5 Library. * @exception NullPointerException rank is < 1 or dims is null. */ public static int H5Tarray_create(int base_type_id, int rank, int[] dims) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tarray_create(base_type_id, rank, dims); } } /** * Returns the rank of an array datatype. * * @param adtype_id Datatype identifier of array object. * @return the rank of the array if successful; otherwise returns a negative value. * @exception HDF5LibraryException Error from the HDF5 Library. */ public static int H5Tget_array_ndims(int adtype_id) throws HDF5LibraryException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tget_array_ndims(adtype_id); } } /** * Returns sizes of array dimensions. * * @param adtype_id IN: Datatype identifier of array object. * @param dims OUT: Sizes of array dimensions. * @return the non-negative number of dimensions of the array type if successful; otherwise * returns a negative value. * @exception HDF5LibraryException Error from the HDF5 Library. * @exception NullPointerException dims is null. */ public static int H5Tget_array_dims(int adtype_id, int[] dims) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tget_array_dims(adtype_id, dims); } } public static int H5Tget_native_type(int tid, int alloc_time) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tget_native_type(tid, alloc_time); } } public static int H5Tget_native_type(final int tid) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tget_native_type(tid); } } public static boolean H5Tis_variable_str(int dtype_id) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tis_variable_str(dtype_id); } } public static boolean H5Tdetect_class(int dtype_id, int dtype_class) throws HDF5LibraryException, NullPointerException { synchronized (ncsa.hdf.hdf5lib.H5.class) { return H5.H5Tdetect_class(dtype_id, dtype_class); } } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/hdf5lib/HDF5Constants.java000077500000000000000000001724651256564762100301470ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ package ch.systemsx.cisd.hdf5.hdf5lib; /** * /** This class contains C constants and enumerated types of HDF5 library. The values of these constants are obtained * from the library by calling J2C(int jconstant), where jconstant is any of the private constants which start their * name with "JH5" need to be converted. *

* Do not edit this file! See also: ncsa.hdf.hdf5lib.HDF5Library *

* This is an internal API that should not be expected to be stable between releases! */ public class HDF5Constants { // ///////////////////////////////////////////////////////////////////////// // This list must be identical to H5Constants.h // // DO NOT EDIT THE LIST !!! // // ///////////////////////////////////////////////////////////////////////// final private static int JH5_SZIP_MAX_PIXELS_PER_BLOCK = 1000; final private static int JH5_SZIP_NN_OPTION_MASK = 1010; final private static int JH5_SZIP_EC_OPTION_MASK = 1020; final private static int JH5_SZIP_ALLOW_K13_OPTION_MASK = 1021; final private static int JH5_SZIP_CHIP_OPTION_MASK = 1022; final private static int JH5D_ALLOC_TIME_DEFAULT = 1030; final private static int JH5D_ALLOC_TIME_EARLY = 1040; final private static int JH5D_ALLOC_TIME_ERROR = 1050; final private static int JH5D_ALLOC_TIME_INCR = 1060; final private static int JH5D_ALLOC_TIME_LATE = 1070; final private static int JH5D_CHUNKED = 1080; final private static int JH5D_COMPACT = 1090; final private static int JH5D_CONTIGUOUS = 1100; final private static int JH5D_FILL_TIME_ALLOC = 1110; final private static int JH5D_FILL_TIME_ERROR = 1120; final private static int JH5D_FILL_TIME_NEVER = 1130; final private static int JH5D_FILL_VALUE_DEFAULT = 1140; final private static int JH5D_FILL_VALUE_ERROR = 1150; final private static int JH5D_FILL_VALUE_UNDEFINED = 1160; final private static int JH5D_FILL_VALUE_USER_DEFINED = 1170; final private static int JH5D_LAYOUT_ERROR = 1180; final private static int JH5D_NLAYOUTS = 1190; final private static int JH5D_SPACE_STATUS_ALLOCATED = 1200; final private static int JH5D_SPACE_STATUS_ERROR = 1210; final private static int JH5D_SPACE_STATUS_NOT_ALLOCATED = 1220; final private static int JH5D_SPACE_STATUS_PART_ALLOCATED = 1230; final private static int JH5E_ALIGNMENT = 1240; final private static int JH5E_ALREADYEXISTS = 1250; final private static int JH5E_ALREADYINIT = 1260; final private static int JH5E_ARGS = 1270; final private static int JH5E_ATOM = 1280; final private static int JH5E_ATTR = 1290; final private static int JH5E_BADATOM = 1300; final private static int JH5E_BADFILE = 1310; final private static int JH5E_BADGROUP = 1320; final private static int JH5E_BADMESG = 1330; final private static int JH5E_BADRANGE = 1340; final private static int JH5E_BADSELECT = 1350; final private static int JH5E_BADSIZE = 1360; final private static int JH5E_BADTYPE = 1370; final private static int JH5E_BADVALUE = 1380; final private static int JH5E_BTREE = 1390; final private static int JH5E_CACHE = 1400; final private static int JH5E_CALLBACK = 1410; final private static int JH5E_CANAPPLY = 1420; final private static int JH5E_CANTCLIP = 1450; final private static int JH5E_CANTCLOSEFILE = 1460; final private static int JH5E_CANTCONVERT = 1470; final private static int JH5E_CANTCOPY = 1480; final private static int JH5E_CANTCOUNT = 1490; final private static int JH5E_CANTCREATE = 1500; final private static int JH5E_CANTDEC = 1510; final private static int JH5E_CANTDECODE = 1520; final private static int JH5E_CANTDELETE = 1530; final private static int JH5E_CANTENCODE = 1540; final private static int JH5E_CANTFLUSH = 1550; final private static int JH5E_CANTFREE = 1560; final private static int JH5E_CANTGET = 1570; final private static int JH5E_CANTINC = 1580; final private static int JH5E_CANTINIT = 1590; final private static int JH5E_CANTINSERT = 1600; final private static int JH5E_CANTLIST = 1610; final private static int JH5E_CANTLOAD = 1620; final private static int JH5E_CANTLOCK = 1630; final private static int JH5E_CANTNEXT = 1650; final private static int JH5E_CANTOPENFILE = 1660; final private static int JH5E_CANTOPENOBJ = 1670; final private static int JH5E_CANTREGISTER = 1690; final private static int JH5E_CANTRELEASE = 1700; final private static int JH5E_CANTSELECT = 1710; final private static int JH5E_CANTSET = 1730; final private static int JH5E_CANTSPLIT = 1740; final private static int JH5E_CANTUNLOCK = 1750; final private static int JH5E_CLOSEERROR = 1760; final private static int JH5E_COMPLEN = 1770; final private static int JH5E_DATASET = 1790; final private static int JH5E_DATASPACE = 1800; final private static int JH5E_DATATYPE = 1810; final private static int JH5E_DUPCLASS = 1820; final private static int JH5E_EFL = 1830; final private static int JH5E_EXISTS = 1840; final private static int JH5E_FCNTL = 1850; final private static int JH5E_FILE = 1860; final private static int JH5E_FILEEXISTS = 1870; final private static int JH5E_FILEOPEN = 1880; final private static int JH5E_FUNC = 1900; final private static int JH5E_HEAP = 1910; final private static int JH5E_INTERNAL = 1920; final private static int JH5E_IO = 1930; final private static int JH5E_LINK = 1940; final private static int JH5E_LINKCOUNT = 1950; final private static int JH5E_MOUNT = 1960; final private static int JH5E_MPI = 1970; final private static int JH5E_MPIERRSTR = 1980; final private static int JH5E_NOFILTER = 1990; final private static int JH5E_NOIDS = 2000; final private static int JH5E_NONE_MAJOR = 2010; final private static int JH5E_NONE_MINOR = 2020; final private static int JH5E_NOSPACE = 2030; final private static int JH5E_NOTCACHED = 2040; final private static int JH5E_NOTFOUND = 2050; final private static int JH5E_NOTHDF5 = 2060; final private static int JH5E_OHDR = 2070; final private static int JH5E_OVERFLOW = 2080; final private static int JH5E_PLINE = 2090; final private static int JH5E_PLIST = 2100; final private static int JH5E_PROTECT = 2110; final private static int JH5E_READERROR = 2120; final private static int JH5E_REFERENCE = 2130; final private static int JH5E_RESOURCE = 2140; final private static int JH5E_RS = 2150; final private static int JH5E_SEEKERROR = 2160; final private static int JH5E_SETLOCAL = 2170; final private static int JH5E_STORAGE = 2190; final private static int JH5E_SYM = 2200; final private static int JH5E_TRUNCATED = 2220; final private static int JH5E_TST = 2230; final private static int JH5E_UNINITIALIZED = 2240; final private static int JH5E_UNSUPPORTED = 2250; final private static int JH5E_VERSION = 2260; final private static int JH5E_VFL = 2270; final private static int JH5E_WALK_DOWNWARD = 2280; final private static int JH5E_WALK_UPWARD = 2290; final private static int JH5E_WRITEERROR = 2300; final private static int JH5F_ACC_CREAT = 2310; final private static int JH5F_ACC_DEBUG = 2320; final private static int JH5F_ACC_EXCL = 2330; final private static int JH5F_ACC_RDONLY = 2340; final private static int JH5F_ACC_RDWR = 2350; final private static int JH5F_ACC_TRUNC = 2360; final private static int JH5F_CLOSE_DEFAULT = 2370; final private static int JH5F_CLOSE_SEMI = 2380; final private static int JH5F_CLOSE_STRONG = 2390; final private static int JH5F_CLOSE_WEAK = 2400; final private static int JH5F_OBJ_ALL = 2410; final private static int JH5F_OBJ_ATTR = 2415; final private static int JH5F_OBJ_DATASET = 2420; final private static int JH5F_OBJ_DATATYPE = 2430; final private static int JH5F_OBJ_FILE = 2440; final private static int JH5F_OBJ_GROUP = 2450; final private static int JH5F_SCOPE_GLOBAL = 2470; final private static int JH5F_SCOPE_LOCAL = 2480; final private static int JH5F_UNLIMITED = 2490; final private static int JH5F_LIBVER_EARLIEST = 2494; final private static int JH5F_LIBVER_LATEST = 2495; final private static int JH5G_DATASET = 2500; final private static int JH5G_GROUP = 2510; final private static int JH5G_LINK = 2520; final private static int JH5G_LINK_ERROR = 2530; final private static int JH5G_LINK_HARD = 2540; final private static int JH5G_LINK_SOFT = 2550; final private static int JH5G_NLIBTYPES = 2560; final private static int JH5G_NTYPES = 2570; final private static int JH5G_NUSERTYPES = 2580; final private static int JH5G_RESERVED_5 = 2600; final private static int JH5G_RESERVED_6 = 2610; final private static int JH5G_RESERVED_7 = 2620; final private static int JH5G_SAME_LOC = 2630; final private static int JH5G_TYPE = 2640; final private static int JH5G_UNKNOWN = 2650; final private static int JH5I_ATTR = 2670; final private static int JH5I_BADID = 2680; final private static int JH5I_DATASET = 2690; final private static int JH5I_DATASPACE = 2700; final private static int JH5I_DATATYPE = 2710; final private static int JH5I_FILE = 2720; final private static int JH5I_GENPROP_CLS = 2740; final private static int JH5I_GENPROP_LST = 2750; final private static int JH5I_GROUP = 2760; final private static int JH5I_INVALID_HID = 2770; final private static int JH5I_REFERENCE = 2790; final private static int JH5I_VFL = 2810; final private static int JH5O_TYPE_UNKNOWN = 5510; final private static int JH5O_TYPE_GROUP = 5520; final private static int JH5O_TYPE_DATASET = 5530; final private static int JH5O_TYPE_NAMED_DATATYPE = 5540; final private static int JH5O_TYPE_NTYPES = 5550; final private static int JH5L_TYPE_ERROR = 5560; final private static int JH5L_TYPE_HARD = 5570; final private static int JH5L_TYPE_SOFT = 5580; final private static int JH5L_TYPE_EXTERNAL = 5590; final private static int JH5L_TYPE_MAX = 5600; final private static int JH5P_DATASET_CREATE = 2820; final private static int JH5P_DATASET_CREATE_DEFAULT = 2830; final private static int JH5P_DATASET_XFER = 2840; final private static int JH5P_DATASET_XFER_DEFAULT = 2850; final private static int JH5P_DEFAULT = 2860; final private static int JH5P_FILE_ACCESS = 2870; final private static int JH5P_FILE_ACCESS_DEFAULT = 2880; final private static int JH5P_FILE_CREATE = 2890; final private static int JH5P_FILE_CREATE_DEFAULT = 2900; final private static int JH5P_NO_CLASS = 2930; final private static int JH5P_ROOT = 6000; final private static int JH5P_OBJECT_CREATE = 6010; final private static int JH5P_DATASET_ACCESS = 6020; final private static int JH5P_DATASET_ACCESS_DEFAULT = 6030; final private static int JH5P_FILE_MOUNT = 6040; final private static int JH5P_FILE_MOUNT_DEFAULT = 6050; final private static int JH5P_GROUP_CREATE = 6060; final private static int JH5P_GROUP_CREATE_DEFAULT = 6070; final private static int JH5P_GROUP_ACCESS = 6080; final private static int JH5P_GROUP_ACCESS_DEFAULT = 6090; final private static int JH5P_DATATYPE_CREATE = 6100; final private static int JH5P_DATATYPE_CREATE_DEFAULT = 6110; final private static int JH5P_DATATYPE_ACCESS = 6120; final private static int JH5P_DATATYPE_ACCESS_DEFAULT = 6130; final private static int JH5P_STRING_CREATE = 6140; final private static int JH5P_ATTRIBUTE_CREATE = 6150; final private static int JH5P_ATTRIBUTE_CREATE_DEFAULT = 6160; final private static int JH5P_OBJECT_COPY = 6170; final private static int JH5P_OBJECT_COPY_DEFAULT = 6180; final private static int JH5P_LINK_CREATE = 6190; final private static int JH5P_LINK_CREATE_DEFAULT = 6200; final private static int JH5P_LINK_ACCESS = 6210; final private static int JH5P_LINK_ACCESS_DEFAULT = 6220; final private static int JH5R_BADTYPE = 2950; final private static int JH5R_DATASET_REGION = 2960; final private static int JH5R_MAXTYPE = 2980; final private static int JH5R_OBJ_REF_BUF_SIZE = 2990; final private static int JH5R_OBJECT = 3000; final private static int JH5S_ALL = 3010; final private static int JH5S_MAX_RANK = 3030; final private static int JH5S_NO_CLASS = 3040; final private static int JH5S_SCALAR = 3050; final private static int JH5S_SEL_ALL = 3060; final private static int JH5S_SEL_ERROR = 3070; final private static int JH5S_SEL_HYPERSLABS = 3080; final private static int JH5S_SEL_N = 3090; final private static int JH5S_SEL_NONE = 3100; final private static int JH5S_SEL_POINTS = 3110; final private static int JH5S_SELECT_AND = 3120; final private static int JH5S_SELECT_APPEND = 3130; final private static int JH5S_SELECT_INVALID = 3140; final private static int JH5S_SELECT_NOOP = 3150; final private static int JH5S_SELECT_NOTA = 3160; final private static int JH5S_SELECT_NOTB = 3170; final private static int JH5S_SELECT_OR = 3180; final private static int JH5S_SELECT_PREPEND = 3190; final private static int JH5S_SELECT_SET = 3200; final private static int JH5S_SELECT_XOR = 3210; final private static int JH5S_SIMPLE = 3220; final private static int JH5S_UNLIMITED = 3230; final private static int JH5T_ALPHA_B16 = 3240; final private static int JH5T_ALPHA_B32 = 3250; final private static int JH5T_ALPHA_B64 = 3260; final private static int JH5T_ALPHA_B8 = 3270; final private static int JH5T_ALPHA_F32 = 3280; final private static int JH5T_ALPHA_F64 = 3290; final private static int JH5T_ALPHA_I16 = 3300; final private static int JH5T_ALPHA_I32 = 3310; final private static int JH5T_ALPHA_I64 = 3320; final private static int JH5T_ALPHA_I8 = 3330; final private static int JH5T_ALPHA_U16 = 3340; final private static int JH5T_ALPHA_U32 = 3350; final private static int JH5T_ALPHA_U64 = 3360; final private static int JH5T_ALPHA_U8 = 3370; final private static int JH5T_ARRAY = 3380; final private static int JH5T_BITFIELD = 3390; final private static int JH5T_BKG_NO = 3400; final private static int JH5T_BKG_YES = 3410; final private static int JH5T_C_S1 = 3420; final private static int JH5T_COMPOUND = 3430; final private static int JH5T_CONV_CONV = 3440; final private static int JH5T_CONV_FREE = 3450; final private static int JH5T_CONV_INIT = 3460; final private static int JH5T_CSET_ASCII = 3470; final private static int JH5T_CSET_ERROR = 3480; final private static int JH5T_CSET_UTF8 = 3490; final private static int JH5T_CSET_RESERVED_10 = 3500; final private static int JH5T_CSET_RESERVED_11 = 3510; final private static int JH5T_CSET_RESERVED_12 = 3520; final private static int JH5T_CSET_RESERVED_13 = 3530; final private static int JH5T_CSET_RESERVED_14 = 3540; final private static int JH5T_CSET_RESERVED_15 = 3550; final private static int JH5T_CSET_RESERVED_2 = 3560; final private static int JH5T_CSET_RESERVED_3 = 3570; final private static int JH5T_CSET_RESERVED_4 = 3580; final private static int JH5T_CSET_RESERVED_5 = 3590; final private static int JH5T_CSET_RESERVED_6 = 3600; final private static int JH5T_CSET_RESERVED_7 = 3610; final private static int JH5T_CSET_RESERVED_8 = 3620; final private static int JH5T_CSET_RESERVED_9 = 3630; final private static int JH5T_DIR_ASCEND = 3640; final private static int JH5T_DIR_DEFAULT = 3650; final private static int JH5T_DIR_DESCEND = 3660; final private static int JH5T_ENUM = 3670; final private static int JH5T_FLOAT = 3680; final private static int JH5T_FORTRAN_S1 = 3690; final private static int JH5T_IEEE_F32BE = 3700; final private static int JH5T_IEEE_F32LE = 3710; final private static int JH5T_IEEE_F64BE = 3720; final private static int JH5T_IEEE_F64LE = 3730; final private static int JH5T_INTEGER = 3740; final private static int JH5T_INTEL_B16 = 3750; final private static int JH5T_INTEL_B32 = 3760; final private static int JH5T_INTEL_B64 = 3770; final private static int JH5T_INTEL_B8 = 3780; final private static int JH5T_INTEL_F32 = 3790; final private static int JH5T_INTEL_F64 = 3800; final private static int JH5T_INTEL_I16 = 3810; final private static int JH5T_INTEL_I32 = 3820; final private static int JH5T_INTEL_I64 = 3830; final private static int JH5T_INTEL_I8 = 3840; final private static int JH5T_INTEL_U16 = 3850; final private static int JH5T_INTEL_U32 = 3860; final private static int JH5T_INTEL_U64 = 3870; final private static int JH5T_INTEL_U8 = 3880; final private static int JH5T_MIPS_B16 = 3890; final private static int JH5T_MIPS_B32 = 3900; final private static int JH5T_MIPS_B64 = 3910; final private static int JH5T_MIPS_B8 = 3920; final private static int JH5T_MIPS_F32 = 3930; final private static int JH5T_MIPS_F64 = 3940; final private static int JH5T_MIPS_I16 = 3950; final private static int JH5T_MIPS_I32 = 3960; final private static int JH5T_MIPS_I64 = 3970; final private static int JH5T_MIPS_I8 = 3980; final private static int JH5T_MIPS_U16 = 3990; final private static int JH5T_MIPS_U32 = 4000; final private static int JH5T_MIPS_U64 = 4010; final private static int JH5T_MIPS_U8 = 4020; final private static int JH5T_NATIVE_B16 = 4030; final private static int JH5T_NATIVE_B32 = 4040; final private static int JH5T_NATIVE_B64 = 4050; final private static int JH5T_NATIVE_B8 = 4060; final private static int JH5T_NATIVE_CHAR = 4070; final private static int JH5T_NATIVE_DOUBLE = 4080; final private static int JH5T_NATIVE_FLOAT = 4090; final private static int JH5T_NATIVE_HADDR = 4100; final private static int JH5T_NATIVE_HBOOL = 4110; final private static int JH5T_NATIVE_HERR = 4120; final private static int JH5T_NATIVE_HSIZE = 4130; final private static int JH5T_NATIVE_HSSIZE = 4140; final private static int JH5T_NATIVE_INT = 4150; final private static int JH5T_NATIVE_INT_FAST16 = 4160; final private static int JH5T_NATIVE_INT_FAST32 = 4170; final private static int JH5T_NATIVE_INT_FAST64 = 4180; final private static int JH5T_NATIVE_INT_FAST8 = 4190; final private static int JH5T_NATIVE_INT_LEAST16 = 4200; final private static int JH5T_NATIVE_INT_LEAST32 = 4210; final private static int JH5T_NATIVE_INT_LEAST64 = 4220; final private static int JH5T_NATIVE_INT_LEAST8 = 4230; final private static int JH5T_NATIVE_INT16 = 4240; final private static int JH5T_NATIVE_INT32 = 4250; final private static int JH5T_NATIVE_INT64 = 4260; final private static int JH5T_NATIVE_INT8 = 4270; final private static int JH5T_NATIVE_LDOUBLE = 4280; final private static int JH5T_NATIVE_LLONG = 4290; final private static int JH5T_NATIVE_LONG = 4300; final private static int JH5T_NATIVE_OPAQUE = 4310; final private static int JH5T_NATIVE_SCHAR = 4320; final private static int JH5T_NATIVE_SHORT = 4330; final private static int JH5T_NATIVE_UCHAR = 4340; final private static int JH5T_NATIVE_UINT = 4350; final private static int JH5T_NATIVE_UINT_FAST16 = 4360; final private static int JH5T_NATIVE_UINT_FAST32 = 4370; final private static int JH5T_NATIVE_UINT_FAST64 = 4380; final private static int JH5T_NATIVE_UINT_FAST8 = 4390; final private static int JH5T_NATIVE_UINT_LEAST16 = 4400; final private static int JH5T_NATIVE_UINT_LEAST32 = 4410; final private static int JH5T_NATIVE_UINT_LEAST64 = 4420; final private static int JH5T_NATIVE_UINT_LEAST8 = 4430; final private static int JH5T_NATIVE_UINT16 = 4440; final private static int JH5T_NATIVE_UINT32 = 4450; final private static int JH5T_NATIVE_UINT64 = 4460; final private static int JH5T_NATIVE_UINT8 = 4470; final private static int JH5T_NATIVE_ULLONG = 4480; final private static int JH5T_NATIVE_ULONG = 4490; final private static int JH5T_NATIVE_USHORT = 4500; final private static int JH5T_NCLASSES = 4510; final private static int JH5T_NO_CLASS = 4520; final private static int JH5T_NORM_ERROR = 4530; final private static int JH5T_NORM_IMPLIED = 4540; final private static int JH5T_NORM_MSBSET = 4550; final private static int JH5T_NORM_NONE = 4560; final private static int JH5T_NPAD = 4570; final private static int JH5T_NSGN = 4580; final private static int JH5T_OPAQUE = 4590; final private static int JH5T_OPAQUE_TAG_MAX = 4595; /* 1.6.5 */ final private static int JH5T_ORDER_BE = 4600; final private static int JH5T_ORDER_ERROR = 4610; final private static int JH5T_ORDER_LE = 4620; final private static int JH5T_ORDER_NONE = 4630; final private static int JH5T_ORDER_VAX = 4640; final private static int JH5T_PAD_BACKGROUND = 4650; final private static int JH5T_PAD_ERROR = 4660; final private static int JH5T_PAD_ONE = 4670; final private static int JH5T_PAD_ZERO = 4680; final private static int JH5T_PERS_DONTCARE = 4690; final private static int JH5T_PERS_HARD = 4700; final private static int JH5T_PERS_SOFT = 4710; final private static int JH5T_REFERENCE = 4720; final private static int JH5T_SGN_2 = 4730; final private static int JH5T_SGN_ERROR = 4740; final private static int JH5T_SGN_NONE = 4750; final private static int JH5T_STD_B16BE = 4760; final private static int JH5T_STD_B16LE = 4770; final private static int JH5T_STD_B32BE = 4780; final private static int JH5T_STD_B32LE = 4790; final private static int JH5T_STD_B64BE = 4800; final private static int JH5T_STD_B64LE = 4810; final private static int JH5T_STD_B8BE = 4820; final private static int JH5T_STD_B8LE = 4830; final private static int JH5T_STD_I16BE = 4840; final private static int JH5T_STD_I16LE = 4850; final private static int JH5T_STD_I32BE = 4860; final private static int JH5T_STD_I32LE = 4870; final private static int JH5T_STD_I64BE = 4880; final private static int JH5T_STD_I64LE = 4890; final private static int JH5T_STD_I8BE = 4900; final private static int JH5T_STD_I8LE = 4910; final private static int JH5T_STD_REF_DSETREG = 4920; final private static int JH5T_STD_REF_OBJ = 4930; final private static int JH5T_STD_U16BE = 4940; final private static int JH5T_STD_U16LE = 4950; final private static int JH5T_STD_U32BE = 4960; final private static int JH5T_STD_U32LE = 4970; final private static int JH5T_STD_U64BE = 4980; final private static int JH5T_STD_U64LE = 4990; final private static int JH5T_STD_U8BE = 5000; final private static int JH5T_STD_U8LE = 5010; final private static int JH5T_STR_ERROR = 5020; final private static int JH5T_STR_NULLPAD = 5030; final private static int JH5T_STR_NULLTERM = 5040; final private static int JH5T_STR_RESERVED_10 = 5050; final private static int JH5T_STR_RESERVED_11 = 5060; final private static int JH5T_STR_RESERVED_12 = 5070; final private static int JH5T_STR_RESERVED_13 = 5080; final private static int JH5T_STR_RESERVED_14 = 5090; final private static int JH5T_STR_RESERVED_15 = 5100; final private static int JH5T_STR_RESERVED_3 = 5110; final private static int JH5T_STR_RESERVED_4 = 5120; final private static int JH5T_STR_RESERVED_5 = 5130; final private static int JH5T_STR_RESERVED_6 = 5140; final private static int JH5T_STR_RESERVED_7 = 5150; final private static int JH5T_STR_RESERVED_8 = 5160; final private static int JH5T_STR_RESERVED_9 = 5170; final private static int JH5T_STR_SPACEPAD = 5180; final private static int JH5T_STRING = 5190; final private static int JH5T_TIME = 5200; final private static int JH5T_UNIX_D32BE = 5210; final private static int JH5T_UNIX_D32LE = 5220; final private static int JH5T_UNIX_D64BE = 5230; final private static int JH5T_UNIX_D64LE = 5240; final private static int JH5T_VARIABLE = 5245; final private static int JH5T_VLEN = 5250; final private static int JH5Z_CB_CONT = 5260; final private static int JH5Z_CB_ERROR = 5270; final private static int JH5Z_CB_FAIL = 5280; final private static int JH5Z_CB_NO = 5290; final private static int JH5Z_DISABLE_EDC = 5300; final private static int JH5Z_ENABLE_EDC = 5310; final private static int JH5Z_ERROR_EDC = 5320; final private static int JH5Z_FILTER_DEFLATE = 5330; final private static int JH5Z_FILTER_ERROR = 5340; final private static int JH5Z_FILTER_FLETCHER32 = 5350; final private static int JH5Z_FILTER_MAX = 5360; final private static int JH5Z_FILTER_NONE = 5370; final private static int JH5Z_FILTER_RESERVED = 5380; final private static int JH5Z_FILTER_SHUFFLE = 5390; final private static int JH5Z_FILTER_SZIP = 5400; final private static int JH5Z_FLAG_DEFMASK = 5410; final private static int JH5Z_FLAG_INVMASK = 5420; final private static int JH5Z_FLAG_MANDATORY = 5430; final private static int JH5Z_FLAG_OPTIONAL = 5440; final private static int JH5Z_FLAG_REVERSE = 5450; final private static int JH5Z_FLAG_SKIP_EDC = 5460; final private static int JH5Z_MAX_NFILTERS = 5470; final private static int JH5Z_NO_EDC = 5480; final private static int JH5Z_SO_INT = 5481; final private static int JH5Z_SO_FLOAT_DSCALE = 5482; final private static int JH5Z_SO_FLOAT_ESCALE = 5483; final private static int JH5Z_FILTER_CONFIG_ENCODE_ENABLED = 5490; final private static int JH5Z_FILTER_CONFIG_DECODE_ENABLED = 5500; // ///////////////////////////////////////////////////////////////////////// // Get the HDF5 constants from the library // // ///////////////////////////////////////////////////////////////////////// final public static int H5_SZIP_MAX_PIXELS_PER_BLOCK = javaToC(JH5_SZIP_MAX_PIXELS_PER_BLOCK); final public static int H5_SZIP_NN_OPTION_MASK = javaToC(JH5_SZIP_NN_OPTION_MASK); final public static int H5_SZIP_EC_OPTION_MASK = javaToC(JH5_SZIP_EC_OPTION_MASK); final public static int H5_SZIP_ALLOW_K13_OPTION_MASK = javaToC(JH5_SZIP_ALLOW_K13_OPTION_MASK); final public static int H5_SZIP_CHIP_OPTION_MASK = javaToC(JH5_SZIP_CHIP_OPTION_MASK); final public static int H5D_ALLOC_TIME_DEFAULT = javaToC(JH5D_ALLOC_TIME_DEFAULT); final public static int H5D_ALLOC_TIME_EARLY = javaToC(JH5D_ALLOC_TIME_EARLY); final public static int H5D_ALLOC_TIME_ERROR = javaToC(JH5D_ALLOC_TIME_ERROR); final public static int H5D_ALLOC_TIME_INCR = javaToC(JH5D_ALLOC_TIME_INCR); final public static int H5D_ALLOC_TIME_LATE = javaToC(JH5D_ALLOC_TIME_LATE); final public static int H5D_CHUNKED = javaToC(JH5D_CHUNKED); final public static int H5D_COMPACT = javaToC(JH5D_COMPACT); final public static int H5D_CONTIGUOUS = javaToC(JH5D_CONTIGUOUS); final public static int H5D_FILL_TIME_ALLOC = javaToC(JH5D_FILL_TIME_ALLOC); final public static int H5D_FILL_TIME_ERROR = javaToC(JH5D_FILL_TIME_ERROR); final public static int H5D_FILL_TIME_NEVER = javaToC(JH5D_FILL_TIME_NEVER); final public static int H5D_FILL_VALUE_DEFAULT = javaToC(JH5D_FILL_VALUE_DEFAULT); final public static int H5D_FILL_VALUE_ERROR = javaToC(JH5D_FILL_VALUE_ERROR); final public static int H5D_FILL_VALUE_UNDEFINED = javaToC(JH5D_FILL_VALUE_UNDEFINED); final public static int H5D_FILL_VALUE_USER_DEFINED = javaToC(JH5D_FILL_VALUE_USER_DEFINED); final public static int H5D_LAYOUT_ERROR = javaToC(JH5D_LAYOUT_ERROR); final public static int H5D_NLAYOUTS = javaToC(JH5D_NLAYOUTS); final public static int H5D_SPACE_STATUS_ALLOCATED = javaToC(JH5D_SPACE_STATUS_ALLOCATED); final public static int H5D_SPACE_STATUS_ERROR = javaToC(JH5D_SPACE_STATUS_ERROR); final public static int H5D_SPACE_STATUS_NOT_ALLOCATED = javaToC(JH5D_SPACE_STATUS_NOT_ALLOCATED); final public static int H5D_SPACE_STATUS_PART_ALLOCATED = javaToC(JH5D_SPACE_STATUS_PART_ALLOCATED); final public static int H5E_ALIGNMENT = javaToC(JH5E_ALIGNMENT); final public static int H5E_ALREADYEXISTS = javaToC(JH5E_ALREADYEXISTS); final public static int H5E_ALREADYINIT = javaToC(JH5E_ALREADYINIT); final public static int H5E_ARGS = javaToC(JH5E_ARGS); final public static int H5E_ATOM = javaToC(JH5E_ATOM); final public static int H5E_ATTR = javaToC(JH5E_ATTR); final public static int H5E_BADATOM = javaToC(JH5E_BADATOM); final public static int H5E_BADFILE = javaToC(JH5E_BADFILE); final public static int H5E_BADGROUP = javaToC(JH5E_BADGROUP); final public static int H5E_BADMESG = javaToC(JH5E_BADMESG); final public static int H5E_BADRANGE = javaToC(JH5E_BADRANGE); final public static int H5E_BADSELECT = javaToC(JH5E_BADSELECT); final public static int H5E_BADSIZE = javaToC(JH5E_BADSIZE); final public static int H5E_BADTYPE = javaToC(JH5E_BADTYPE); final public static int H5E_BADVALUE = javaToC(JH5E_BADVALUE); final public static int H5E_BTREE = javaToC(JH5E_BTREE); final public static int H5E_CACHE = javaToC(JH5E_CACHE); final public static int H5E_CALLBACK = javaToC(JH5E_CALLBACK); final public static int H5E_CANAPPLY = javaToC(JH5E_CANAPPLY); final public static int H5E_CANTCLIP = javaToC(JH5E_CANTCLIP); final public static int H5E_CANTCLOSEFILE = javaToC(JH5E_CANTCLOSEFILE); final public static int H5E_CANTCONVERT = javaToC(JH5E_CANTCONVERT); final public static int H5E_CANTCOPY = javaToC(JH5E_CANTCOPY); final public static int H5E_CANTCOUNT = javaToC(JH5E_CANTCOUNT); final public static int H5E_CANTCREATE = javaToC(JH5E_CANTCREATE); final public static int H5E_CANTDEC = javaToC(JH5E_CANTDEC); final public static int H5E_CANTDECODE = javaToC(JH5E_CANTDECODE); final public static int H5E_CANTDELETE = javaToC(JH5E_CANTDELETE); final public static int H5E_CANTENCODE = javaToC(JH5E_CANTENCODE); final public static int H5E_CANTFLUSH = javaToC(JH5E_CANTFLUSH); final public static int H5E_CANTFREE = javaToC(JH5E_CANTFREE); final public static int H5E_CANTGET = javaToC(JH5E_CANTGET); final public static int H5E_CANTINC = javaToC(JH5E_CANTINC); final public static int H5E_CANTINIT = javaToC(JH5E_CANTINIT); final public static int H5E_CANTINSERT = javaToC(JH5E_CANTINSERT); final public static int H5E_CANTLIST = javaToC(JH5E_CANTLIST); final public static int H5E_CANTLOAD = javaToC(JH5E_CANTLOAD); final public static int H5E_CANTLOCK = javaToC(JH5E_CANTLOCK); final public static int H5E_CANTNEXT = javaToC(JH5E_CANTNEXT); final public static int H5E_CANTOPENFILE = javaToC(JH5E_CANTOPENFILE); final public static int H5E_CANTOPENOBJ = javaToC(JH5E_CANTOPENOBJ); final public static int H5E_CANTREGISTER = javaToC(JH5E_CANTREGISTER); final public static int H5E_CANTRELEASE = javaToC(JH5E_CANTRELEASE); final public static int H5E_CANTSELECT = javaToC(JH5E_CANTSELECT); final public static int H5E_CANTSET = javaToC(JH5E_CANTSET); final public static int H5E_CANTSPLIT = javaToC(JH5E_CANTSPLIT); final public static int H5E_CANTUNLOCK = javaToC(JH5E_CANTUNLOCK); final public static int H5E_CLOSEERROR = javaToC(JH5E_CLOSEERROR); final public static int H5E_COMPLEN = javaToC(JH5E_COMPLEN); final public static int H5E_DATASET = javaToC(JH5E_DATASET); final public static int H5E_DATASPACE = javaToC(JH5E_DATASPACE); final public static int H5E_DATATYPE = javaToC(JH5E_DATATYPE); final public static int H5E_DUPCLASS = javaToC(JH5E_DUPCLASS); final public static int H5E_EFL = javaToC(JH5E_EFL); final public static int H5E_EXISTS = javaToC(JH5E_EXISTS); final public static int H5E_FCNTL = javaToC(JH5E_FCNTL); final public static int H5E_FILE = javaToC(JH5E_FILE); final public static int H5E_FILEEXISTS = javaToC(JH5E_FILEEXISTS); final public static int H5E_FILEOPEN = javaToC(JH5E_FILEOPEN); final public static int H5E_FUNC = javaToC(JH5E_FUNC); final public static int H5E_HEAP = javaToC(JH5E_HEAP); final public static int H5E_INTERNAL = javaToC(JH5E_INTERNAL); final public static int H5E_IO = javaToC(JH5E_IO); final public static int H5E_LINK = javaToC(JH5E_LINK); final public static int H5E_LINKCOUNT = javaToC(JH5E_LINKCOUNT); final public static int H5E_MOUNT = javaToC(JH5E_MOUNT); final public static int H5E_MPI = javaToC(JH5E_MPI); final public static int H5E_MPIERRSTR = javaToC(JH5E_MPIERRSTR); final public static int H5E_NOFILTER = javaToC(JH5E_NOFILTER); final public static int H5E_NOIDS = javaToC(JH5E_NOIDS); final public static int H5E_NONE_MAJOR = javaToC(JH5E_NONE_MAJOR); final public static int H5E_NONE_MINOR = javaToC(JH5E_NONE_MINOR); final public static int H5E_NOSPACE = javaToC(JH5E_NOSPACE); final public static int H5E_NOTCACHED = javaToC(JH5E_NOTCACHED); final public static int H5E_NOTFOUND = javaToC(JH5E_NOTFOUND); final public static int H5E_NOTHDF5 = javaToC(JH5E_NOTHDF5); final public static int H5E_OHDR = javaToC(JH5E_OHDR); final public static int H5E_OVERFLOW = javaToC(JH5E_OVERFLOW); final public static int H5E_PLINE = javaToC(JH5E_PLINE); final public static int H5E_PLIST = javaToC(JH5E_PLIST); final public static int H5E_PROTECT = javaToC(JH5E_PROTECT); final public static int H5E_READERROR = javaToC(JH5E_READERROR); final public static int H5E_REFERENCE = javaToC(JH5E_REFERENCE); final public static int H5E_RESOURCE = javaToC(JH5E_RESOURCE); final public static int H5E_RS = javaToC(JH5E_RS); final public static int H5E_SEEKERROR = javaToC(JH5E_SEEKERROR); final public static int H5E_SETLOCAL = javaToC(JH5E_SETLOCAL); final public static int H5E_STORAGE = javaToC(JH5E_STORAGE); final public static int H5E_SYM = javaToC(JH5E_SYM); final public static int H5E_TRUNCATED = javaToC(JH5E_TRUNCATED); final public static int H5E_TST = javaToC(JH5E_TST); final public static int H5E_UNINITIALIZED = javaToC(JH5E_UNINITIALIZED); final public static int H5E_UNSUPPORTED = javaToC(JH5E_UNSUPPORTED); final public static int H5E_VERSION = javaToC(JH5E_VERSION); final public static int H5E_VFL = javaToC(JH5E_VFL); final public static int H5E_WALK_DOWNWARD = javaToC(JH5E_WALK_DOWNWARD); final public static int H5E_WALK_UPWARD = javaToC(JH5E_WALK_UPWARD); final public static int H5E_WRITEERROR = javaToC(JH5E_WRITEERROR); final public static int H5F_ACC_CREAT = javaToC(JH5F_ACC_CREAT); final public static int H5F_ACC_DEBUG = javaToC(JH5F_ACC_DEBUG); final public static int H5F_ACC_EXCL = javaToC(JH5F_ACC_EXCL); final public static int H5F_ACC_RDONLY = javaToC(JH5F_ACC_RDONLY); final public static int H5F_ACC_RDWR = javaToC(JH5F_ACC_RDWR); final public static int H5F_ACC_TRUNC = javaToC(JH5F_ACC_TRUNC); final public static int H5F_CLOSE_DEFAULT = javaToC(JH5F_CLOSE_DEFAULT); final public static int H5F_CLOSE_SEMI = javaToC(JH5F_CLOSE_SEMI); final public static int H5F_CLOSE_STRONG = javaToC(JH5F_CLOSE_STRONG); final public static int H5F_CLOSE_WEAK = javaToC(JH5F_CLOSE_WEAK); final public static int H5F_OBJ_ALL = javaToC(JH5F_OBJ_ALL); final public static int H5F_OBJ_ATTR = javaToC(JH5F_OBJ_ATTR); final public static int H5F_OBJ_DATASET = javaToC(JH5F_OBJ_DATASET); final public static int H5F_OBJ_DATATYPE = javaToC(JH5F_OBJ_DATATYPE); final public static int H5F_OBJ_FILE = javaToC(JH5F_OBJ_FILE); final public static int H5F_OBJ_GROUP = javaToC(JH5F_OBJ_GROUP); final public static int H5F_SCOPE_GLOBAL = javaToC(JH5F_SCOPE_GLOBAL); final public static int H5F_SCOPE_LOCAL = javaToC(JH5F_SCOPE_LOCAL); final public static int H5F_UNLIMITED = javaToC(JH5F_UNLIMITED); final public static int H5F_LIBVER_EARLIEST = javaToC(JH5F_LIBVER_EARLIEST); final public static int H5F_LIBVER_LATEST = javaToC(JH5F_LIBVER_LATEST); final public static int H5G_DATASET = javaToC(JH5G_DATASET); final public static int H5G_GROUP = javaToC(JH5G_GROUP); final public static int H5G_LINK = javaToC(JH5G_LINK); final public static int H5G_LINK_ERROR = javaToC(JH5G_LINK_ERROR); final public static int H5G_LINK_HARD = javaToC(JH5G_LINK_HARD); final public static int H5G_LINK_SOFT = javaToC(JH5G_LINK_SOFT); final public static int H5G_NLIBTYPES = javaToC(JH5G_NLIBTYPES); final public static int H5G_NTYPES = javaToC(JH5G_NTYPES); final public static int H5G_NUSERTYPES = javaToC(JH5G_NUSERTYPES); final public static int H5G_RESERVED_5 = javaToC(JH5G_RESERVED_5); final public static int H5G_RESERVED_6 = javaToC(JH5G_RESERVED_6); final public static int H5G_RESERVED_7 = javaToC(JH5G_RESERVED_7); final public static int H5G_SAME_LOC = javaToC(JH5G_SAME_LOC); final public static int H5G_TYPE = javaToC(JH5G_TYPE); final public static int H5G_UNKNOWN = javaToC(JH5G_UNKNOWN); final public static int H5I_ATTR = javaToC(JH5I_ATTR); final public static int H5I_BADID = javaToC(JH5I_BADID); final public static int H5I_DATASET = javaToC(JH5I_DATASET); final public static int H5I_DATASPACE = javaToC(JH5I_DATASPACE); final public static int H5I_DATATYPE = javaToC(JH5I_DATATYPE); final public static int H5I_FILE = javaToC(JH5I_FILE); final public static int H5I_GENPROP_CLS = javaToC(JH5I_GENPROP_CLS); final public static int H5I_GENPROP_LST = javaToC(JH5I_GENPROP_LST); final public static int H5I_GROUP = javaToC(JH5I_GROUP); final public static int H5I_INVALID_HID = javaToC(JH5I_INVALID_HID); final public static int H5I_REFERENCE = javaToC(JH5I_REFERENCE); final public static int H5I_VFL = javaToC(JH5I_VFL); final public static int H5O_TYPE_UNKNOWN = javaToC(JH5O_TYPE_UNKNOWN); final public static int H5O_TYPE_GROUP = javaToC(JH5O_TYPE_GROUP); final public static int H5O_TYPE_DATASET = javaToC(JH5O_TYPE_DATASET); final public static int H5O_TYPE_NAMED_DATATYPE = javaToC(JH5O_TYPE_NAMED_DATATYPE); final public static int H5O_TYPE_NTYPES = javaToC(JH5O_TYPE_NTYPES); final public static int H5L_TYPE_ERROR = javaToC(JH5L_TYPE_ERROR); final public static int H5L_TYPE_HARD = javaToC(JH5L_TYPE_HARD); final public static int H5L_TYPE_SOFT = javaToC(JH5L_TYPE_SOFT); final public static int H5L_TYPE_EXTERNAL = javaToC(JH5L_TYPE_EXTERNAL); final public static int H5L_TYPE_MAX = javaToC(JH5L_TYPE_MAX); final public static int H5P_DATASET_CREATE = javaToC(JH5P_DATASET_CREATE); final public static int H5P_DATASET_CREATE_DEFAULT = javaToC(JH5P_DATASET_CREATE_DEFAULT); final public static int H5P_DATASET_XFER = javaToC(JH5P_DATASET_XFER); final public static int H5P_DATASET_XFER_DEFAULT = javaToC(JH5P_DATASET_XFER_DEFAULT); final public static int H5P_DEFAULT = javaToC(JH5P_DEFAULT); final public static int H5P_FILE_ACCESS = javaToC(JH5P_FILE_ACCESS); final public static int H5P_FILE_ACCESS_DEFAULT = javaToC(JH5P_FILE_ACCESS_DEFAULT); final public static int H5P_FILE_CREATE = javaToC(JH5P_FILE_CREATE); final public static int H5P_FILE_CREATE_DEFAULT = javaToC(JH5P_FILE_CREATE_DEFAULT); final public static int H5P_NO_CLASS = javaToC(JH5P_NO_CLASS); final public static int H5P_ROOT = javaToC(JH5P_ROOT); final public static int H5P_OBJECT_CREATE = javaToC(JH5P_OBJECT_CREATE); final public static int H5P_DATASET_ACCESS = javaToC(JH5P_DATASET_ACCESS); final public static int H5P_DATASET_ACCESS_DEFAULT = javaToC(JH5P_DATASET_ACCESS_DEFAULT); final public static int H5P_FILE_MOUNT = javaToC(JH5P_FILE_MOUNT); final public static int H5P_FILE_MOUNT_DEFAULT = javaToC(JH5P_FILE_MOUNT_DEFAULT); final public static int H5P_GROUP_CREATE = javaToC(JH5P_GROUP_CREATE); final public static int H5P_GROUP_CREATE_DEFAULT = javaToC(JH5P_GROUP_CREATE_DEFAULT); final public static int H5P_GROUP_ACCESS = javaToC(JH5P_GROUP_ACCESS); final public static int H5P_GROUP_ACCESS_DEFAULT = javaToC(JH5P_GROUP_ACCESS_DEFAULT); final public static int H5P_DATATYPE_CREATE = javaToC(JH5P_DATATYPE_CREATE); final public static int H5P_DATATYPE_CREATE_DEFAULT = javaToC(JH5P_DATATYPE_CREATE_DEFAULT); final public static int H5P_DATATYPE_ACCESS = javaToC(JH5P_DATATYPE_ACCESS); final public static int H5P_DATATYPE_ACCESS_DEFAULT = javaToC(JH5P_DATATYPE_ACCESS_DEFAULT); final public static int H5P_STRING_CREATE = javaToC(JH5P_STRING_CREATE); final public static int H5P_ATTRIBUTE_CREATE = javaToC(JH5P_ATTRIBUTE_CREATE); final public static int H5P_ATTRIBUTE_CREATE_DEFAULT = javaToC(JH5P_ATTRIBUTE_CREATE_DEFAULT); final public static int H5P_OBJECT_COPY = javaToC(JH5P_OBJECT_COPY); final public static int H5P_OBJECT_COPY_DEFAULT = javaToC(JH5P_OBJECT_COPY_DEFAULT); final public static int H5P_LINK_CREATE = javaToC(JH5P_LINK_CREATE); final public static int H5P_LINK_CREATE_DEFAULT = javaToC(JH5P_LINK_CREATE_DEFAULT); final public static int H5P_LINK_ACCESS = javaToC(JH5P_LINK_ACCESS); final public static int H5P_LINK_ACCESS_DEFAULT = javaToC(JH5P_LINK_ACCESS_DEFAULT); final public static int H5R_BADTYPE = javaToC(JH5R_BADTYPE); final public static int H5R_DATASET_REGION = javaToC(JH5R_DATASET_REGION); final public static int H5R_MAXTYPE = javaToC(JH5R_MAXTYPE); final public static int H5R_OBJ_REF_BUF_SIZE = javaToC(JH5R_OBJ_REF_BUF_SIZE); final public static int H5R_OBJECT = javaToC(JH5R_OBJECT); final public static int H5S_ALL = javaToC(JH5S_ALL); final public static int H5S_MAX_RANK = javaToC(JH5S_MAX_RANK); final public static int H5S_NO_CLASS = javaToC(JH5S_NO_CLASS); final public static int H5S_SCALAR = javaToC(JH5S_SCALAR); final public static int H5S_SEL_ALL = javaToC(JH5S_SEL_ALL); final public static int H5S_SEL_ERROR = javaToC(JH5S_SEL_ERROR); final public static int H5S_SEL_HYPERSLABS = javaToC(JH5S_SEL_HYPERSLABS); final public static int H5S_SEL_N = javaToC(JH5S_SEL_N); final public static int H5S_SEL_NONE = javaToC(JH5S_SEL_NONE); final public static int H5S_SEL_POINTS = javaToC(JH5S_SEL_POINTS); final public static int H5S_SELECT_AND = javaToC(JH5S_SELECT_AND); final public static int H5S_SELECT_APPEND = javaToC(JH5S_SELECT_APPEND); final public static int H5S_SELECT_INVALID = javaToC(JH5S_SELECT_INVALID); final public static int H5S_SELECT_NOOP = javaToC(JH5S_SELECT_NOOP); final public static int H5S_SELECT_NOTA = javaToC(JH5S_SELECT_NOTA); final public static int H5S_SELECT_NOTB = javaToC(JH5S_SELECT_NOTB); final public static int H5S_SELECT_OR = javaToC(JH5S_SELECT_OR); final public static int H5S_SELECT_PREPEND = javaToC(JH5S_SELECT_PREPEND); final public static int H5S_SELECT_SET = javaToC(JH5S_SELECT_SET); final public static int H5S_SELECT_XOR = javaToC(JH5S_SELECT_XOR); final public static int H5S_SIMPLE = javaToC(JH5S_SIMPLE); final public static int H5S_UNLIMITED = javaToC(JH5S_UNLIMITED); final public static int H5T_ALPHA_B16 = javaToC(JH5T_ALPHA_B16); final public static int H5T_ALPHA_B32 = javaToC(JH5T_ALPHA_B32); final public static int H5T_ALPHA_B64 = javaToC(JH5T_ALPHA_B64); final public static int H5T_ALPHA_B8 = javaToC(JH5T_ALPHA_B8); final public static int H5T_ALPHA_F32 = javaToC(JH5T_ALPHA_F32); final public static int H5T_ALPHA_F64 = javaToC(JH5T_ALPHA_F64); final public static int H5T_ALPHA_I16 = javaToC(JH5T_ALPHA_I16); final public static int H5T_ALPHA_I32 = javaToC(JH5T_ALPHA_I32); final public static int H5T_ALPHA_I64 = javaToC(JH5T_ALPHA_I64); final public static int H5T_ALPHA_I8 = javaToC(JH5T_ALPHA_I8); final public static int H5T_ALPHA_U16 = javaToC(JH5T_ALPHA_U16); final public static int H5T_ALPHA_U32 = javaToC(JH5T_ALPHA_U32); final public static int H5T_ALPHA_U64 = javaToC(JH5T_ALPHA_U64); final public static int H5T_ALPHA_U8 = javaToC(JH5T_ALPHA_U8); final public static int H5T_ARRAY = javaToC(JH5T_ARRAY); final public static int H5T_BITFIELD = javaToC(JH5T_BITFIELD); final public static int H5T_BKG_NO = javaToC(JH5T_BKG_NO); final public static int H5T_BKG_YES = javaToC(JH5T_BKG_YES); final public static int H5T_C_S1 = javaToC(JH5T_C_S1); final public static int H5T_COMPOUND = javaToC(JH5T_COMPOUND); final public static int H5T_CONV_CONV = javaToC(JH5T_CONV_CONV); final public static int H5T_CONV_FREE = javaToC(JH5T_CONV_FREE); final public static int H5T_CONV_INIT = javaToC(JH5T_CONV_INIT); final public static int H5T_CSET_ASCII = javaToC(JH5T_CSET_ASCII); final public static int H5T_CSET_UTF8 = javaToC(JH5T_CSET_UTF8); final public static int H5T_CSET_ERROR = javaToC(JH5T_CSET_ERROR); final public static int H5T_CSET_RESERVED_10 = javaToC(JH5T_CSET_RESERVED_10); final public static int H5T_CSET_RESERVED_11 = javaToC(JH5T_CSET_RESERVED_11); final public static int H5T_CSET_RESERVED_12 = javaToC(JH5T_CSET_RESERVED_12); final public static int H5T_CSET_RESERVED_13 = javaToC(JH5T_CSET_RESERVED_13); final public static int H5T_CSET_RESERVED_14 = javaToC(JH5T_CSET_RESERVED_14); final public static int H5T_CSET_RESERVED_15 = javaToC(JH5T_CSET_RESERVED_15); final public static int H5T_CSET_RESERVED_2 = javaToC(JH5T_CSET_RESERVED_2); final public static int H5T_CSET_RESERVED_3 = javaToC(JH5T_CSET_RESERVED_3); final public static int H5T_CSET_RESERVED_4 = javaToC(JH5T_CSET_RESERVED_4); final public static int H5T_CSET_RESERVED_5 = javaToC(JH5T_CSET_RESERVED_5); final public static int H5T_CSET_RESERVED_6 = javaToC(JH5T_CSET_RESERVED_6); final public static int H5T_CSET_RESERVED_7 = javaToC(JH5T_CSET_RESERVED_7); final public static int H5T_CSET_RESERVED_8 = javaToC(JH5T_CSET_RESERVED_8); final public static int H5T_CSET_RESERVED_9 = javaToC(JH5T_CSET_RESERVED_9); final public static int H5T_DIR_ASCEND = javaToC(JH5T_DIR_ASCEND); final public static int H5T_DIR_DEFAULT = javaToC(JH5T_DIR_DEFAULT); final public static int H5T_DIR_DESCEND = javaToC(JH5T_DIR_DESCEND); final public static int H5T_ENUM = javaToC(JH5T_ENUM); final public static int H5T_FLOAT = javaToC(JH5T_FLOAT); final public static int H5T_FORTRAN_S1 = javaToC(JH5T_FORTRAN_S1); final public static int H5T_IEEE_F32BE = javaToC(JH5T_IEEE_F32BE); final public static int H5T_IEEE_F32LE = javaToC(JH5T_IEEE_F32LE); final public static int H5T_IEEE_F64BE = javaToC(JH5T_IEEE_F64BE); final public static int H5T_IEEE_F64LE = javaToC(JH5T_IEEE_F64LE); final public static int H5T_INTEGER = javaToC(JH5T_INTEGER); final public static int H5T_INTEL_B16 = javaToC(JH5T_INTEL_B16); final public static int H5T_INTEL_B32 = javaToC(JH5T_INTEL_B32); final public static int H5T_INTEL_B64 = javaToC(JH5T_INTEL_B64); final public static int H5T_INTEL_B8 = javaToC(JH5T_INTEL_B8); final public static int H5T_INTEL_F32 = javaToC(JH5T_INTEL_F32); final public static int H5T_INTEL_F64 = javaToC(JH5T_INTEL_F64); final public static int H5T_INTEL_I16 = javaToC(JH5T_INTEL_I16); final public static int H5T_INTEL_I32 = javaToC(JH5T_INTEL_I32); final public static int H5T_INTEL_I64 = javaToC(JH5T_INTEL_I64); final public static int H5T_INTEL_I8 = javaToC(JH5T_INTEL_I8); final public static int H5T_INTEL_U16 = javaToC(JH5T_INTEL_U16); final public static int H5T_INTEL_U32 = javaToC(JH5T_INTEL_U32); final public static int H5T_INTEL_U64 = javaToC(JH5T_INTEL_U64); final public static int H5T_INTEL_U8 = javaToC(JH5T_INTEL_U8); final public static int H5T_MIPS_B16 = javaToC(JH5T_MIPS_B16); final public static int H5T_MIPS_B32 = javaToC(JH5T_MIPS_B32); final public static int H5T_MIPS_B64 = javaToC(JH5T_MIPS_B64); final public static int H5T_MIPS_B8 = javaToC(JH5T_MIPS_B8); final public static int H5T_MIPS_F32 = javaToC(JH5T_MIPS_F32); final public static int H5T_MIPS_F64 = javaToC(JH5T_MIPS_F64); final public static int H5T_MIPS_I16 = javaToC(JH5T_MIPS_I16); final public static int H5T_MIPS_I32 = javaToC(JH5T_MIPS_I32); final public static int H5T_MIPS_I64 = javaToC(JH5T_MIPS_I64); final public static int H5T_MIPS_I8 = javaToC(JH5T_MIPS_I8); final public static int H5T_MIPS_U16 = javaToC(JH5T_MIPS_U16); final public static int H5T_MIPS_U32 = javaToC(JH5T_MIPS_U32); final public static int H5T_MIPS_U64 = javaToC(JH5T_MIPS_U64); final public static int H5T_MIPS_U8 = javaToC(JH5T_MIPS_U8); final public static int H5T_NATIVE_B16 = javaToC(JH5T_NATIVE_B16); final public static int H5T_NATIVE_B32 = javaToC(JH5T_NATIVE_B32); final public static int H5T_NATIVE_B64 = javaToC(JH5T_NATIVE_B64); final public static int H5T_NATIVE_B8 = javaToC(JH5T_NATIVE_B8); final public static int H5T_NATIVE_CHAR = javaToC(JH5T_NATIVE_CHAR); final public static int H5T_NATIVE_DOUBLE = javaToC(JH5T_NATIVE_DOUBLE); final public static int H5T_NATIVE_FLOAT = javaToC(JH5T_NATIVE_FLOAT); final public static int H5T_NATIVE_HADDR = javaToC(JH5T_NATIVE_HADDR); final public static int H5T_NATIVE_HBOOL = javaToC(JH5T_NATIVE_HBOOL); final public static int H5T_NATIVE_HERR = javaToC(JH5T_NATIVE_HERR); final public static int H5T_NATIVE_HSIZE = javaToC(JH5T_NATIVE_HSIZE); final public static int H5T_NATIVE_HSSIZE = javaToC(JH5T_NATIVE_HSSIZE); final public static int H5T_NATIVE_INT = javaToC(JH5T_NATIVE_INT); final public static int H5T_NATIVE_INT_FAST16 = javaToC(JH5T_NATIVE_INT_FAST16); final public static int H5T_NATIVE_INT_FAST32 = javaToC(JH5T_NATIVE_INT_FAST32); final public static int H5T_NATIVE_INT_FAST64 = javaToC(JH5T_NATIVE_INT_FAST64); final public static int H5T_NATIVE_INT_FAST8 = javaToC(JH5T_NATIVE_INT_FAST8); final public static int H5T_NATIVE_INT_LEAST16 = javaToC(JH5T_NATIVE_INT_LEAST16); final public static int H5T_NATIVE_INT_LEAST32 = javaToC(JH5T_NATIVE_INT_LEAST32); final public static int H5T_NATIVE_INT_LEAST64 = javaToC(JH5T_NATIVE_INT_LEAST64); final public static int H5T_NATIVE_INT_LEAST8 = javaToC(JH5T_NATIVE_INT_LEAST8); final public static int H5T_NATIVE_INT16 = javaToC(JH5T_NATIVE_INT16); final public static int H5T_NATIVE_INT32 = javaToC(JH5T_NATIVE_INT32); final public static int H5T_NATIVE_INT64 = javaToC(JH5T_NATIVE_INT64); final public static int H5T_NATIVE_INT8 = javaToC(JH5T_NATIVE_INT8); final public static int H5T_NATIVE_LDOUBLE = javaToC(JH5T_NATIVE_LDOUBLE); final public static int H5T_NATIVE_LLONG = javaToC(JH5T_NATIVE_LLONG); final public static int H5T_NATIVE_LONG = javaToC(JH5T_NATIVE_LONG); final public static int H5T_NATIVE_OPAQUE = javaToC(JH5T_NATIVE_OPAQUE); final public static int H5T_NATIVE_SCHAR = javaToC(JH5T_NATIVE_SCHAR); final public static int H5T_NATIVE_SHORT = javaToC(JH5T_NATIVE_SHORT); final public static int H5T_NATIVE_UCHAR = javaToC(JH5T_NATIVE_UCHAR); final public static int H5T_NATIVE_UINT = javaToC(JH5T_NATIVE_UINT); final public static int H5T_NATIVE_UINT_FAST16 = javaToC(JH5T_NATIVE_UINT_FAST16); final public static int H5T_NATIVE_UINT_FAST32 = javaToC(JH5T_NATIVE_UINT_FAST32); final public static int H5T_NATIVE_UINT_FAST64 = javaToC(JH5T_NATIVE_UINT_FAST64); final public static int H5T_NATIVE_UINT_FAST8 = javaToC(JH5T_NATIVE_UINT_FAST8); final public static int H5T_NATIVE_UINT_LEAST16 = javaToC(JH5T_NATIVE_UINT_LEAST16); final public static int H5T_NATIVE_UINT_LEAST32 = javaToC(JH5T_NATIVE_UINT_LEAST32); final public static int H5T_NATIVE_UINT_LEAST64 = javaToC(JH5T_NATIVE_UINT_LEAST64); final public static int H5T_NATIVE_UINT_LEAST8 = javaToC(JH5T_NATIVE_UINT_LEAST8); final public static int H5T_NATIVE_UINT16 = javaToC(JH5T_NATIVE_UINT16); final public static int H5T_NATIVE_UINT32 = javaToC(JH5T_NATIVE_UINT32); final public static int H5T_NATIVE_UINT64 = javaToC(JH5T_NATIVE_UINT64); final public static int H5T_NATIVE_UINT8 = javaToC(JH5T_NATIVE_UINT8); final public static int H5T_NATIVE_ULLONG = javaToC(JH5T_NATIVE_ULLONG); final public static int H5T_NATIVE_ULONG = javaToC(JH5T_NATIVE_ULONG); final public static int H5T_NATIVE_USHORT = javaToC(JH5T_NATIVE_USHORT); final public static int H5T_NCLASSES = javaToC(JH5T_NCLASSES); final public static int H5T_NO_CLASS = javaToC(JH5T_NO_CLASS); final public static int H5T_NORM_ERROR = javaToC(JH5T_NORM_ERROR); final public static int H5T_NORM_IMPLIED = javaToC(JH5T_NORM_IMPLIED); final public static int H5T_NORM_MSBSET = javaToC(JH5T_NORM_MSBSET); final public static int H5T_NORM_NONE = javaToC(JH5T_NORM_NONE); final public static int H5T_NPAD = javaToC(JH5T_NPAD); final public static int H5T_NSGN = javaToC(JH5T_NSGN); final public static int H5T_OPAQUE = javaToC(JH5T_OPAQUE); final public static int H5T_OPAQUE_TAG_MAX = javaToC(JH5T_OPAQUE_TAG_MAX); /* 1.6.5 */ final public static int H5T_ORDER_BE = javaToC(JH5T_ORDER_BE); final public static int H5T_ORDER_ERROR = javaToC(JH5T_ORDER_ERROR); final public static int H5T_ORDER_LE = javaToC(JH5T_ORDER_LE); final public static int H5T_ORDER_NONE = javaToC(JH5T_ORDER_NONE); final public static int H5T_ORDER_VAX = javaToC(JH5T_ORDER_VAX); final public static int H5T_PAD_BACKGROUND = javaToC(JH5T_PAD_BACKGROUND); final public static int H5T_PAD_ERROR = javaToC(JH5T_PAD_ERROR); final public static int H5T_PAD_ONE = javaToC(JH5T_PAD_ONE); final public static int H5T_PAD_ZERO = javaToC(JH5T_PAD_ZERO); final public static int H5T_PERS_DONTCARE = javaToC(JH5T_PERS_DONTCARE); final public static int H5T_PERS_HARD = javaToC(JH5T_PERS_HARD); final public static int H5T_PERS_SOFT = javaToC(JH5T_PERS_SOFT); final public static int H5T_REFERENCE = javaToC(JH5T_REFERENCE); final public static int H5T_SGN_2 = javaToC(JH5T_SGN_2); final public static int H5T_SGN_ERROR = javaToC(JH5T_SGN_ERROR); final public static int H5T_SGN_NONE = javaToC(JH5T_SGN_NONE); final public static int H5T_STD_B16BE = javaToC(JH5T_STD_B16BE); final public static int H5T_STD_B16LE = javaToC(JH5T_STD_B16LE); final public static int H5T_STD_B32BE = javaToC(JH5T_STD_B32BE); final public static int H5T_STD_B32LE = javaToC(JH5T_STD_B32LE); final public static int H5T_STD_B64BE = javaToC(JH5T_STD_B64BE); final public static int H5T_STD_B64LE = javaToC(JH5T_STD_B64LE); final public static int H5T_STD_B8BE = javaToC(JH5T_STD_B8BE); final public static int H5T_STD_B8LE = javaToC(JH5T_STD_B8LE); final public static int H5T_STD_I16BE = javaToC(JH5T_STD_I16BE); final public static int H5T_STD_I16LE = javaToC(JH5T_STD_I16LE); final public static int H5T_STD_I32BE = javaToC(JH5T_STD_I32BE); final public static int H5T_STD_I32LE = javaToC(JH5T_STD_I32LE); final public static int H5T_STD_I64BE = javaToC(JH5T_STD_I64BE); final public static int H5T_STD_I64LE = javaToC(JH5T_STD_I64LE); final public static int H5T_STD_I8BE = javaToC(JH5T_STD_I8BE); final public static int H5T_STD_I8LE = javaToC(JH5T_STD_I8LE); final public static int H5T_STD_REF_DSETREG = javaToC(JH5T_STD_REF_DSETREG); final public static int H5T_STD_REF_OBJ = javaToC(JH5T_STD_REF_OBJ); final public static int H5T_STD_U16BE = javaToC(JH5T_STD_U16BE); final public static int H5T_STD_U16LE = javaToC(JH5T_STD_U16LE); final public static int H5T_STD_U32BE = javaToC(JH5T_STD_U32BE); final public static int H5T_STD_U32LE = javaToC(JH5T_STD_U32LE); final public static int H5T_STD_U64BE = javaToC(JH5T_STD_U64BE); final public static int H5T_STD_U64LE = javaToC(JH5T_STD_U64LE); final public static int H5T_STD_U8BE = javaToC(JH5T_STD_U8BE); final public static int H5T_STD_U8LE = javaToC(JH5T_STD_U8LE); final public static int H5T_STR_ERROR = javaToC(JH5T_STR_ERROR); final public static int H5T_STR_NULLPAD = javaToC(JH5T_STR_NULLPAD); final public static int H5T_STR_NULLTERM = javaToC(JH5T_STR_NULLTERM); final public static int H5T_STR_RESERVED_10 = javaToC(JH5T_STR_RESERVED_10); final public static int H5T_STR_RESERVED_11 = javaToC(JH5T_STR_RESERVED_11); final public static int H5T_STR_RESERVED_12 = javaToC(JH5T_STR_RESERVED_12); final public static int H5T_STR_RESERVED_13 = javaToC(JH5T_STR_RESERVED_13); final public static int H5T_STR_RESERVED_14 = javaToC(JH5T_STR_RESERVED_14); final public static int H5T_STR_RESERVED_15 = javaToC(JH5T_STR_RESERVED_15); final public static int H5T_STR_RESERVED_3 = javaToC(JH5T_STR_RESERVED_3); final public static int H5T_STR_RESERVED_4 = javaToC(JH5T_STR_RESERVED_4); final public static int H5T_STR_RESERVED_5 = javaToC(JH5T_STR_RESERVED_5); final public static int H5T_STR_RESERVED_6 = javaToC(JH5T_STR_RESERVED_6); final public static int H5T_STR_RESERVED_7 = javaToC(JH5T_STR_RESERVED_7); final public static int H5T_STR_RESERVED_8 = javaToC(JH5T_STR_RESERVED_8); final public static int H5T_STR_RESERVED_9 = javaToC(JH5T_STR_RESERVED_9); final public static int H5T_STR_SPACEPAD = javaToC(JH5T_STR_SPACEPAD); final public static int H5T_STRING = javaToC(JH5T_STRING); final public static int H5T_TIME = javaToC(JH5T_TIME); final public static int H5T_UNIX_D32BE = javaToC(JH5T_UNIX_D32BE); final public static int H5T_UNIX_D32LE = javaToC(JH5T_UNIX_D32LE); final public static int H5T_UNIX_D64BE = javaToC(JH5T_UNIX_D64BE); final public static int H5T_UNIX_D64LE = javaToC(JH5T_UNIX_D64LE); final public static int H5T_VARIABLE = javaToC(JH5T_VARIABLE); // Rosetta Biosoftware final public static int H5T_VLEN = javaToC(JH5T_VLEN); final public static int H5Z_CB_CONT = javaToC(JH5Z_CB_CONT); final public static int H5Z_CB_ERROR = javaToC(JH5Z_CB_ERROR); final public static int H5Z_CB_FAIL = javaToC(JH5Z_CB_FAIL); final public static int H5Z_CB_NO = javaToC(JH5Z_CB_NO); final public static int H5Z_DISABLE_EDC = javaToC(JH5Z_DISABLE_EDC); final public static int H5Z_ENABLE_EDC = javaToC(JH5Z_ENABLE_EDC); final public static int H5Z_ERROR_EDC = javaToC(JH5Z_ERROR_EDC); final public static int H5Z_FILTER_DEFLATE = javaToC(JH5Z_FILTER_DEFLATE); final public static int H5Z_FILTER_ERROR = javaToC(JH5Z_FILTER_ERROR); final public static int H5Z_FILTER_FLETCHER32 = javaToC(JH5Z_FILTER_FLETCHER32); final public static int H5Z_FILTER_MAX = javaToC(JH5Z_FILTER_MAX); final public static int H5Z_FILTER_NONE = javaToC(JH5Z_FILTER_NONE); final public static int H5Z_FILTER_RESERVED = javaToC(JH5Z_FILTER_RESERVED); final public static int H5Z_FILTER_SHUFFLE = javaToC(JH5Z_FILTER_SHUFFLE); final public static int H5Z_FILTER_SZIP = javaToC(JH5Z_FILTER_SZIP); final public static int H5Z_FLAG_DEFMASK = javaToC(JH5Z_FLAG_DEFMASK); final public static int H5Z_FLAG_INVMASK = javaToC(JH5Z_FLAG_INVMASK); final public static int H5Z_FLAG_MANDATORY = javaToC(JH5Z_FLAG_MANDATORY); final public static int H5Z_FLAG_OPTIONAL = javaToC(JH5Z_FLAG_OPTIONAL); final public static int H5Z_FLAG_REVERSE = javaToC(JH5Z_FLAG_REVERSE); final public static int H5Z_FLAG_SKIP_EDC = javaToC(JH5Z_FLAG_SKIP_EDC); final public static int H5Z_MAX_NFILTERS = javaToC(JH5Z_MAX_NFILTERS); final public static int H5Z_NO_EDC = javaToC(JH5Z_NO_EDC); final public static int H5Z_SO_INT = javaToC(JH5Z_SO_INT); final public static int H5Z_SO_FLOAT_DSCALE = javaToC(JH5Z_SO_FLOAT_DSCALE); final public static int H5Z_SO_FLOAT_ESCALE = javaToC(JH5Z_SO_FLOAT_ESCALE); final public static int H5Z_FILTER_CONFIG_ENCODE_ENABLED = javaToC(JH5Z_FILTER_CONFIG_ENCODE_ENABLED); final public static int H5Z_FILTER_CONFIG_DECODE_ENABLED = javaToC(JH5Z_FILTER_CONFIG_DECODE_ENABLED); private static int javaToC(int javaConstant) { synchronized(ncsa.hdf.hdf5lib.H5.class) { return H5.J2C(javaConstant); } } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/hdf5lib/HDF5GroupInfo.java000066400000000000000000000123011256564762100300560ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ package ch.systemsx.cisd.hdf5.hdf5lib; import org.apache.commons.lang.builder.HashCodeBuilder; /** *

* This class is a container for the information reported about an HDF5 Object from the H5Gget_obj_info() method. *

* The fileno and objno fields contain four values which uniquely identify an object among those HDF5 files which are * open: if all four values are the same between two objects, then the two objects are the same (provided both files are * still open). The nlink field is the number of hard links to the object or zero when information is being returned * about a symbolic link (symbolic links do not have hard links but all other objects always have at least one). The * type field contains the type of the object, one of H5G_GROUP, H5G_DATASET, or H5G_LINK. The mtime field contains the * modification time. If information is being returned about a symbolic link then linklen will be the length of the link * value (the name of the pointed-to object with the null terminator); otherwise linklen will be zero. Other fields may * be added to this structure in the future. *

* For details of the HDF5 libraries, see the HDF5 Documentation at: http://hdf.ncsa.uiuc.edu/HDF5/doc/ *

* This is an internal API that should not be expected to be stable between releases! */ public class HDF5GroupInfo { long[] fileno; long[] objno; int nlink; int type; long mtime; int linklen; public HDF5GroupInfo() { fileno = new long[2]; objno = new long[2]; nlink = -1; type = -1; mtime = 0; linklen = 0; } /** * Sets the HDF5 group information. Used by the JHI5. * * @param fn File id number * @param on Object id number * @param nl Number of links * @param t Type of the object * @param mt Modification time * @param len Length of link */ public void setGroupInfo(final long[] fn, final long[] on, final int nl, final int t, final long mt, final int len) { fileno = fn; objno = on; nlink = nl; type = t; mtime = mt; linklen = len; } /** Resets all the group information to defaults. */ public void reset() { fileno[0] = 0; fileno[1] = 0; objno[0] = 0; objno[1] = 0; nlink = -1; type = -1; mtime = 0; linklen = 0; } /* accessors */ public long[] getFileno() { return fileno; } public long[] getObjno() { return objno; } public int getType() { return type; } public int getNlink() { return nlink; } public long getMtime() { return mtime; } public int getLinklen() { return linklen; } /** * The fileno and objno fields contain four values which uniquely identify an object among those HDF5 files. */ @Override public boolean equals(final Object obj) { if ((obj instanceof HDF5GroupInfo) == false) { return false; } final HDF5GroupInfo target = (HDF5GroupInfo) obj; if ((fileno[0] == target.fileno[0]) && (fileno[1] == target.fileno[1]) && (objno[0] == target.objno[0]) && (objno[1] == target.objno[1])) { return true; } else { return false; } } @Override public int hashCode() { final HashCodeBuilder builder = new HashCodeBuilder(); builder.append(fileno); builder.append(objno); return builder.toHashCode(); } /** * Returns the object id. */ public long getOID() { return objno[0]; } /** * /** Converts this object to a String representation. * * @return a string representation of this object */ @Override public String toString() { String fileStr = "fileno=null"; String objStr = "objno=null"; if (fileno != null) { fileStr = "fileno[0]=" + fileno[0] + ",fileno[1]=" + fileno[1]; } if (objno != null) { objStr = "objno[0]=" + objno[0] + ",objno[1]=" + objno[1]; } return getClass().getName() + "[" + fileStr + "," + objStr + ",type=" + type + ",nlink=" + nlink + ",mtime=" + mtime + ",linklen=" + linklen + "]"; } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/hdf5lib/HDFNativeData.java000066400000000000000000000253401256564762100301100ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ package ch.systemsx.cisd.hdf5.hdf5lib; import ch.systemsx.cisd.base.convert.NativeData; import ch.systemsx.cisd.base.convert.NativeData.ByteOrder; /** * This class provides a convenience interface to {@link NativeData}. *

* This is an internal API that should not be expected to be stable between releases! */ public class HDFNativeData { static final int pointerSize; static { NativeData.ensureNativeLibIsLoaded(); pointerSize = H5.getPointerSize(); } /** * Converts a byte value into a byte[]. * * @param data The value to convert. * @return The array containing the value. */ public static byte[] byteToByte(byte data) { return new byte[] { data }; } /** * Converts a short value into a byte[]. * * @param data The value to convert. * @return The array containing the value. */ public static byte[] shortToByte(short data) { return NativeData.shortToByte(new short[] { data }, ByteOrder.NATIVE); } /** * Converts an int value into a byte[]. * * @param data The value to convert. * @return The array containing the value. */ public static byte[] intToByte(int data) { return NativeData.intToByte(new int[] { data }, ByteOrder.NATIVE); } /** * Converts a long value into a byte[]. * * @param data The value to convert. * @return The array containing the value. */ public static byte[] longToByte(long data) { return NativeData.longToByte(new long[] { data }, ByteOrder.NATIVE); } /** * Converts a float value into a byte[]. * * @param data The value to convert. * @return The array containing the value. */ public static byte[] floatToByte(float data) { return NativeData.floatToByte(new float[] { data }, ByteOrder.NATIVE); } /** * Converts a double value into a byte[]. * * @param data The value to convert. * @return The array containing the value. */ public static byte[] doubleToByte(double data) { return NativeData.doubleToByte(new double[] { data }, ByteOrder.NATIVE); } /** * Converts a range of a byte[] to a short value. * * @param byteArr The value to convert. * @param start The position in the byteArr to start the conversion. * @return The short value. */ public static short byteToShort(byte[] byteArr, int start) { return NativeData.byteToShort(byteArr, ByteOrder.NATIVE, start, 1)[0]; } /** * Converts a byte[] array into a short[] array. * * @param byteArr The byte[] to convert. * @param start The position in the byteArr to start the conversion. * @param len The number of short values to convert. * @return The short[] array. */ public static short[] byteToShort(byte[] byteArr, int start, int len) { return NativeData.byteToShort(byteArr, ByteOrder.NATIVE, start, len); } /** * Converts a range of a byte[] to a int value. * * @param byteArr The value to convert. * @param start The position in the byteArr to start the conversion. * @return The int value. */ public static int byteToInt(byte[] byteArr, int start) { return NativeData.byteToInt(byteArr, ByteOrder.NATIVE, start, 1)[0]; } /** * Converts a byte[] array into an int[] array. * * @param byteArr The byte[] to convert. * @param start The position in the byteArr to start the conversion. * @param len The number of int values to convert. * @return The int[] array. */ public static int[] byteToInt(byte[] byteArr, int start, int len) { return NativeData.byteToInt(byteArr, ByteOrder.NATIVE, start, len); } /** * Converts a range of a byte[] to a long value. * * @param byteArr The value to convert. * @param start The position in the byteArr to start the conversion. * @return The long value. */ public static long byteToLong(byte[] byteArr, int start) { return NativeData.byteToLong(byteArr, ByteOrder.NATIVE, start, 1)[0]; } /** * Converts a byte[] array into a long[] array. * * @param byteArr The byte[] to convert. * @param start The position in the byteArr to start the conversion. * @param len The number of long values to convert. * @return The long[] array. */ public static long[] byteToLong(byte[] byteArr, int start, int len) { return NativeData.byteToLong(byteArr, ByteOrder.NATIVE, start, len); } /** * Converts a range of a byte[] to a float value. * * @param byteArr The value to convert. * @param start The position in the byteArr to start the conversion. * @return The float value. */ public static float byteToFloat(byte[] byteArr, int start) { return NativeData.byteToFloat(byteArr, ByteOrder.NATIVE, start, 1)[0]; } /** * Converts a byte[] array into a float[] array. * * @param byteArr The byte[] to convert. * @param start The position in the byteArr to start the conversion. * @param len The number of float values to convert. * @return The float[] array. */ public static float[] byteToFloat(byte[] byteArr, int start, int len) { return NativeData.byteToFloat(byteArr, ByteOrder.NATIVE, start, len); } /** * Converts a range of a byte[] to a double value. * * @param byteArr The value to convert. * @param start The position in the byteArr to start the conversion. * @return The double value. */ public static double byteToDouble(byte[] byteArr, int start) { return NativeData.byteToDouble(byteArr, ByteOrder.NATIVE, start, 1)[0]; } /** * Converts a byte[] array into a double[] array. * * @param byteArr The byte[] to convert. * @param start The position in the byteArr to start the conversion. * @param len The number of double values to convert. * @return The double[] array. */ public static double[] byteToDouble(byte[] byteArr, int start, int len) { return NativeData.byteToDouble(byteArr, ByteOrder.NATIVE, start, len); } /** * Converts a short[] array to a byte[] array. * * @param data The long[] array to convert. * @return The byte[] array that corresponding to the short[] array. */ public static byte[] shortToByte(short[] data) { return NativeData.shortToByte(data, ByteOrder.NATIVE); } /** * Converts an int[] array to a byte[] array. * * @param data The long[] array to convert. * @return The byte[] array that corresponding to the int[] array. */ public static byte[] intToByte(int[] data) { return NativeData.intToByte(data, ByteOrder.NATIVE); } /** * Converts a long[] array to a byte[] array. * * @param data The long[] array to convert. * @return The byte[] array that corresponding to the long[] array. */ public static byte[] longToByte(long[] data) { return NativeData.longToByte(data, ByteOrder.NATIVE); } /** * Converts a float[] array to a byte[] array. * * @param data The long[] array to convert. * @return The byte[] array that corresponding to the float[] array. */ public static byte[] floatToByte(float[] data) { return NativeData.floatToByte(data, ByteOrder.NATIVE); } /** * Converts a double[] array to a byte[] array. * * @param data The long[] array to convert. * @return The byte[] array that corresponding to the double[] array. */ public static byte[] doubleToByte(double[] data) { return NativeData.doubleToByte(data, ByteOrder.NATIVE); } // String copying methods /** * Returns the size of a machine word on this platform. */ public static int getMachineWordSize() { return pointerSize; } /** * Creates a C copy of str (using calloc) and put the reference of it into buf at bufOfs. */ public static int compoundCpyVLStr(String str, byte[] buf, int bufOfs) { return H5.compoundCpyVLStr(str, buf, bufOfs); } /** * Creates a Java copy from a C char* pointer in the buf at bufOfs. */ public static String createVLStrFromCompound(byte[] buf, int bufOfs) { return H5.createVLStrFromCompound(buf, bufOfs); } /** * Frees the variable-length strings in compound buf, where one compound has size recordSize and the * variable-length members can be found at byte-offsets vlIndices. */ public static int freeCompoundVLStr(byte[] buf, int recordSize, int[] vlIndices) { return H5.freeCompoundVLStr(buf, recordSize, vlIndices); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/hdf5lib/package.html000066400000000000000000000124731256564762100271670ustar00rootroot00000000000000 ch.systemsx.cisd.hdf5.hdf5lib

Introduction

This package is the low-level Java interface for the CISD HDF5 library. It is derived from the the low-level Java interface of the HDF Group's HDF-Java library.

It should be considered an internal interface and is likely to change in future versions.

This code is called by Java programs to access the entry points of the HDF5 library. Each routine wraps a single HDF5 entry point, generally with the arguments and return codes analogous to the C interface.

For details of the HDF5 library, see the HDF5 Documentation at: http://hdf.ncsa.uiuc.edu/HDF5/

Mapping of arguments for Java

In general, arguments to the HDF Java API are straightforward translations from the 'C' API described in the HDF Reference Manual.

HDF-5 C types to Java types
HDF-5 Java
H5T_NATIVE_INT int, Integer
H5T_NATIVE_SHORT short, Short
H5T_NATIVE_FLOAT float, Float
H5T_NATIVE_DOUBLE double, Double
H5T_NATIVE_CHAR byte, Byte
H5T_C_S1 java.lang.String
void *
(i.e., pointer to `Any')		 Special -- see HDFArray

General Rules for Passing Arguments and Results

In general, arguments passed IN to Java are the analogous basic types, as above. The exception is for arrays, which are discussed below.

The return value of Java methods is also the analogous type, as above. A major exception to that rule is that all HDF functions that return SUCCEED/FAIL are declared boolean in the Java version, rather than int as in the C. Functions that return a value or else FAIL are declared the equivalent to the C function. However, in most cases the Java method will raise an exception instead of returning an error code. See Errors and Exceptions below.

Java does not support pass by reference of arguments, so arguments that are returned through OUT parameters must be wrapped in an object or array. The Java API for HDF consistently wraps arguments in arrays.

For instance, a function that returns two integers is declared: 

       h_err_t HDF5dummy( int *a1, int *a2)
For the Java interface, this would be declared: 

 public static native int HDF5dummy(int args[]);
where a1 is args[0] and a2 is args[1], and would be invoked: 

 H5.HDF5dummy(a);

All the routines where this convention is used will have specific documentation of the details, given below.

HDF-5 Constants

The HDF-5 API defines a set of constants and enumerated values. Most of these values are available to Java programs via the class HDF55Constants. For example, the parameters for the h5open() call include two numeric values, HDF5Constants.H5F_ACC_RDWR and HDF5Constants.H5P_DEFAULT. As would be expected, these numbers correspond to the C constants H5F_ACC_RDWR and H5P_DEFAULT.

The HDF-5 API defines a set of values that describe number types and sizes, such as "H5T_NATIVE_INT" and "hsize_t". These values are determined at run time by the HDF-5 C library. To support these parameters, the Java class HDF55Constants looks up the values when initiated. The values can be accessed as public variables of the Java class, such as: 

 int data_type = HDF55Constants.JH5T_NATIVE_INT;
The Java application uses both types of constants the same way, the only difference is that the HDF55Constants may have different values on different platforms.

Error handling and Exceptions

The HDF5 error API (H5E) manages the behavior of the error stack in the HDF-5 library. This API is omitted from the JHI5. Errors are converted into Java exceptions. This is totally different from the C interface, but is very natural for Java programming.

The exceptions of the JHI5 are organized as sub-classes of the class HDF5Exception. There are two subclasses of HDF5Exception, HDF5LibraryException and HDF5JavaException. The sub-classes of the former represent errors from the HDF-5 C library, while sub-classes of the latter represent errors in the JHI5 wrapper and support code.

The super-class HDF5LibraryException implements the method 'printStackTrace()', which prints out the HDF-5 error stack, as described in the HDF-5 C API H5Eprint(). This may be used by Java exception handlers to print out the HDF-5 error stack.

libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/io/000077500000000000000000000000001256564762100237715ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/io/HDF5DataSetRandomAccessFile.java000066400000000000000000000577711256564762100316740ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.io; import java.io.EOFException; import java.io.File; import java.io.FileNotFoundException; import java.io.Flushable; import java.io.IOException; import java.io.UnsupportedEncodingException; import java.nio.ByteOrder; import java.util.Arrays; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ncsa.hdf.hdf5lib.exceptions.HDF5FileNotFoundException; import ch.systemsx.cisd.base.convert.NativeData; import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel; import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked; import ch.systemsx.cisd.base.io.IRandomAccessFile; import ch.systemsx.cisd.hdf5.HDF5DataClass; import ch.systemsx.cisd.hdf5.HDF5DataSetInformation; import ch.systemsx.cisd.hdf5.HDF5FactoryProvider; import ch.systemsx.cisd.hdf5.HDF5GenericStorageFeatures; import ch.systemsx.cisd.hdf5.HDF5IntStorageFeatures; import ch.systemsx.cisd.hdf5.HDF5OpaqueType; import ch.systemsx.cisd.hdf5.HDF5StorageLayout; import ch.systemsx.cisd.hdf5.IHDF5Reader; import ch.systemsx.cisd.hdf5.IHDF5Writer; /** * A {@link IRandomAccessFile} backed by an HDF5 dataset. The HDF5 dataset needs to be a byte array * (or opaque byte array) of rank 1. * * @author Bernd Rinn */ public class HDF5DataSetRandomAccessFile implements IRandomAccessFile, Flushable { private final IHDF5Reader reader; private final IHDF5Writer writerOrNull; private final String dataSetPath; private final HDF5DataSetInformation dataSetInfo; private final HDF5OpaqueType opaqueTypeOrNull; private final int blockSize; private final boolean extendable; private final boolean closeReaderOnCloseFile; private long length; private int realBlockSize; private byte[] block; private long blockOffset; private int positionInBlock; private boolean blockDirty; private long blockOffsetMark = -1; private int positionInBlockMark = -1; private boolean extensionPending; private ch.systemsx.cisd.base.convert.NativeData.ByteOrder byteOrder = ch.systemsx.cisd.base.convert.NativeData.ByteOrder.BIG_ENDIAN; /** * Creates a new HDF5DataSetRandomAccessFile for the given hdf5File and dataSetPath. */ HDF5DataSetRandomAccessFile(File hdf5File, String dataSetPath, HDF5GenericStorageFeatures creationStorageFeature, int size, String opaqueTagOrNull, boolean readOnly) { this(createHDF5ReaderOrWriter(hdf5File, readOnly), dataSetPath, creationStorageFeature, size, opaqueTagOrNull, true); } private static IHDF5Reader createHDF5ReaderOrWriter(File hdf5File, boolean readOnly) { try { if (readOnly) { return HDF5FactoryProvider.get().openForReading(hdf5File); } else { return HDF5FactoryProvider.get().open(hdf5File); } } catch (HDF5FileNotFoundException ex) { throw new IOExceptionUnchecked(new FileNotFoundException(ex.getMessage())); } catch (HDF5Exception ex) { throw new IOExceptionUnchecked(ex); } } /** * Creates a new HDF5DataSetRandomAccessFile for the given reader and dataSetPath. *

* If reader instanceof IHDF5Writer, the random access file will be in read-write * mode, else it will be in readonly mode. */ HDF5DataSetRandomAccessFile(IHDF5Reader reader, String dataSetPath, HDF5GenericStorageFeatures creationStorageFeature, int size, String opaqueTagOrNull, boolean closeReaderOnCloseFile) throws IOExceptionUnchecked { this.closeReaderOnCloseFile = closeReaderOnCloseFile; final boolean readOnly = (reader instanceof IHDF5Writer) == false; try { if (readOnly) { this.reader = reader; this.writerOrNull = null; } else { this.writerOrNull = (IHDF5Writer) reader; this.writerOrNull.file().addFlushable(this); this.reader = writerOrNull; if (writerOrNull.exists(dataSetPath) == false) { long maxSize = requiresFixedMaxSize(creationStorageFeature) ? size : 0; if (opaqueTagOrNull == null) { writerOrNull.int8().createArray(dataSetPath, maxSize, size, HDF5IntStorageFeatures.createFromGeneric(creationStorageFeature)); } else { writerOrNull.opaque().createArray(dataSetPath, opaqueTagOrNull, maxSize, size, creationStorageFeature); } } } } catch (HDF5Exception ex) { throw new IOExceptionUnchecked(ex); } this.dataSetPath = dataSetPath; this.dataSetInfo = reader.getDataSetInformation(dataSetPath); if (readOnly == false && dataSetInfo.getTypeInformation().getDataClass() == HDF5DataClass.OPAQUE) { this.opaqueTypeOrNull = reader.opaque().tryGetOpaqueType(dataSetPath); } else { this.opaqueTypeOrNull = null; } if (dataSetInfo.getRank() != 1) { throw new IOExceptionUnchecked("Dataset has wrong rank (r=" + dataSetInfo.getRank() + ")"); } if (dataSetInfo.getTypeInformation().getElementSize() != 1) { throw new IOExceptionUnchecked("Dataset has wrong element size (size=" + dataSetInfo.getTypeInformation().getElementSize() + " bytes)"); } this.length = dataSetInfo.getSize(); // Chunked data sets are read chunk by chunk, other layouts are read completely. if (dataSetInfo.getStorageLayout() == HDF5StorageLayout.CHUNKED) { this.blockSize = dataSetInfo.tryGetChunkSizes()[0]; } else { // Limitation: we do not yet handle the case of contiguous data sets larger than 2GB if ((int) length != length()) { throw new IOExceptionUnchecked("Dataset is too large (size=" + length + " bytes)"); } this.blockSize = (int) length; } this.extendable = (dataSetInfo.getStorageLayout() == HDF5StorageLayout.CHUNKED); this.blockOffset = 0; this.block = new byte[blockSize]; this.realBlockSize = -1; this.positionInBlock = 0; } private static boolean requiresFixedMaxSize(HDF5GenericStorageFeatures features) { return features.tryGetProposedLayout() != null && features.tryGetProposedLayout() != HDF5StorageLayout.CHUNKED; } private void ensureInitalizedForWriting(int lenCurrentOp) throws IOExceptionUnchecked { if (realBlockSize < 0) { realBlockSize = blockSize; long minLen = blockOffset + realBlockSize; final long oldLength = length(); if (minLen > oldLength) { realBlockSize = Math.min(realBlockSize, lenCurrentOp); minLen = blockOffset + realBlockSize; if (minLen > oldLength) { setLength(minLen); } } if ((oldLength - blockSize) > 0) { try { this.realBlockSize = reader.opaque().readArrayToBlockWithOffset(dataSetPath, block, realBlockSize, blockOffset, 0); } catch (HDF5Exception ex) { throw new IOExceptionUnchecked(ex); } } else { Arrays.fill(block, (byte) 0); } } } private void ensureInitalizedForReading() throws IOExceptionUnchecked { if (realBlockSize < 0) { try { this.realBlockSize = reader.opaque().readArrayToBlockWithOffset(dataSetPath, block, blockSize, blockOffset, 0); } catch (HDF5Exception ex) { throw new IOExceptionUnchecked(ex); } } } private void readBlock(long newBlockOffset) throws IOExceptionUnchecked { if (newBlockOffset != blockOffset) { flush(); try { this.realBlockSize = reader.opaque().readArrayToBlockWithOffset(dataSetPath, block, blockSize, newBlockOffset, 0); } catch (HDF5Exception ex) { throw new IOExceptionUnchecked(ex); } this.blockOffset = newBlockOffset; } } private void readNextBlockResetPosition() { readBlock(blockOffset + realBlockSize); this.positionInBlock = 0; } private boolean eof() { return (available() == 0); } private void checkEoFOnWrite() { if (extendable == false && eof()) { throw new IOExceptionUnchecked(new EOFException("Dataset is EOF and not extendable.")); } } public File getHdf5File() { return reader.file().getFile(); } public String getDataSetPath() { return dataSetPath; } /** * Returns true if the HDF5 file has been opened in read-only mode. */ public boolean isReadOnly() { return (writerOrNull == null); } private void extend(int numberOfBytesToExtend) throws IOExceptionUnchecked { final long len = length(); final long pos = getFilePointer(); final long newLen = pos + numberOfBytesToExtend; if (newLen > len) { if (extendable == false) { throw new IOExceptionUnchecked("Unable to extend dataset from " + len + " to " + newLen + ": dataset is not extenable."); } setLength(pos + numberOfBytesToExtend); } } private void checkWrite(int lenCurrentOp) throws IOExceptionUnchecked { ensureInitalizedForWriting(lenCurrentOp); checkWriteDoNotExtend(); if (extensionPending) { setLength(blockOffset + positionInBlock); } } private void checkWriteDoNotExtend() throws IOExceptionUnchecked { if (isReadOnly()) { throw new IOExceptionUnchecked("HDF5 dataset opened in read-only mode."); } } @Override public long getFilePointer() throws IOExceptionUnchecked { return blockOffset + positionInBlock; } @Override public int read() throws IOExceptionUnchecked { ensureInitalizedForReading(); if (positionInBlock == realBlockSize) { if (eof()) { return -1; } readNextBlockResetPosition(); if (eof()) { return -1; } } return block[positionInBlock++] & 0xff; } @Override public int read(byte[] b) throws IOExceptionUnchecked { return read(b, 0, b.length); } @Override public int read(byte[] b, int off, int len) throws IOExceptionUnchecked { ensureInitalizedForReading(); int realLen = getRealLen(len); if (realLen == 0) { return -1; } int bytesLeft = realLen; int currentOff = off; while (bytesLeft > 0) { final int lenInBlock = Math.min(bytesLeft, bytesLeftInBlock()); System.arraycopy(block, positionInBlock, b, currentOff, lenInBlock); positionInBlock += lenInBlock; currentOff += lenInBlock; bytesLeft -= lenInBlock; if (bytesLeft > 0) { readNextBlockResetPosition(); } } return realLen; } private int bytesLeftInBlock() { return (realBlockSize - positionInBlock); } private int getRealLen(int len) { return Math.min(len, available()); } private long getRealLen(long len) { return Math.min(len, available()); } @Override public long skip(long n) throws IOExceptionUnchecked { final long realN = getRealLen(n); seek(getFilePointer() + realN); return realN; } @Override public int available() { return (int) Math.min(availableLong(), Integer.MAX_VALUE); } private long availableLong() { return length() - getFilePointer(); } @Override public void close() throws IOExceptionUnchecked { flush(); if (closeReaderOnCloseFile) { try { reader.close(); } catch (HDF5Exception ex) { throw new IOExceptionUnchecked(ex); } } else if (writerOrNull != null) { writerOrNull.file().removeFlushable(this); } } @Override public void mark(int readlimit) { this.blockOffsetMark = blockOffset; this.positionInBlockMark = positionInBlock; } @Override public void reset() throws IOExceptionUnchecked { if (blockOffsetMark < 0) { throw new IOExceptionUnchecked(new IOException("Stream not marked.")); } readBlock(blockOffsetMark); this.positionInBlock = positionInBlockMark; } @Override public boolean markSupported() { return true; } @Override public void flush() throws IOExceptionUnchecked { if (isReadOnly() == false && blockDirty) { try { if (opaqueTypeOrNull != null) { writerOrNull.opaque().writeArrayBlockWithOffset(dataSetPath, opaqueTypeOrNull, block, realBlockSize, blockOffset); } else { writerOrNull.int8().writeArrayBlockWithOffset(dataSetPath, block, realBlockSize, blockOffset); } } catch (HDF5Exception ex) { throw new IOExceptionUnchecked(ex); } blockDirty = false; } } @Override public void synchronize() throws IOExceptionUnchecked { if (writerOrNull != null) { flush(); try { writerOrNull.file().flushSyncBlocking(); } catch (HDF5Exception ex) { throw new IOExceptionUnchecked(ex); } } } @Override public ByteOrder getByteOrder() { return byteOrder == ch.systemsx.cisd.base.convert.NativeData.ByteOrder.BIG_ENDIAN ? ByteOrder.BIG_ENDIAN : ByteOrder.LITTLE_ENDIAN; } @Override public void setByteOrder(ByteOrder byteOrder) { if (byteOrder == ByteOrder.BIG_ENDIAN) { this.byteOrder = ch.systemsx.cisd.base.convert.NativeData.ByteOrder.BIG_ENDIAN; } else { this.byteOrder = ch.systemsx.cisd.base.convert.NativeData.ByteOrder.LITTLE_ENDIAN; } } @Override public void seek(long pos) throws IOExceptionUnchecked { if (pos < 0) { throw new IOExceptionUnchecked("New position may not be negative."); } if (isReadOnly() && pos >= length()) { throw new IOExceptionUnchecked( "In read-only mode, new position may not be larger than file size."); } final long newBlockOffset = (pos / blockSize) * blockSize; this.positionInBlock = (int) (pos % blockSize); if (newBlockOffset < length()) { readBlock(newBlockOffset); } else { this.blockOffset = newBlockOffset; this.realBlockSize = positionInBlock + 1; } if (pos >= length()) { this.extensionPending = true; } } @Override public long length() throws IOExceptionUnchecked { return length; } @Override public void setLength(long newLength) throws IOExceptionUnchecked { checkWriteDoNotExtend(); if (extendable == false) { throw new IOExceptionUnchecked("setLength() called on non-extendable dataset."); } try { writerOrNull.object().setDataSetSize(dataSetPath, newLength); } catch (HDF5Exception ex) { throw new IOExceptionUnchecked(ex); } length = newLength; } @Override public void readFully(byte[] b) throws IOExceptionUnchecked { readFully(b, 0, b.length); } @Override public void readFully(byte[] b, int off, int len) throws IOExceptionUnchecked { final int bytesRead = read(b, off, len); if (bytesRead != len) { throw new IOExceptionUnchecked(new EOFException()); } } @Override public int skipBytes(int n) throws IOExceptionUnchecked { return (int) skip(n); } @Override public boolean readBoolean() throws IOExceptionUnchecked { return readUnsignedByte() != 0; } @Override public byte readByte() throws IOExceptionUnchecked { return (byte) readUnsignedByte(); } @Override public int readUnsignedByte() throws IOExceptionUnchecked { final int b = read(); if (b < 0) { throw new IOExceptionUnchecked(new EOFException()); } return b; } @Override public short readShort() throws IOExceptionUnchecked { final byte[] byteArr = new byte[NativeData.SHORT_SIZE]; readFully(byteArr); return NativeData.byteToShort(byteArr, byteOrder)[0]; } @Override public int readUnsignedShort() throws IOExceptionUnchecked { return readShort() & 0xffff; } @Override public char readChar() throws IOExceptionUnchecked { final byte[] byteArr = new byte[NativeData.CHAR_SIZE]; readFully(byteArr); return NativeData.byteToChar(byteArr, byteOrder)[0]; } @Override public int readInt() throws IOExceptionUnchecked { final byte[] byteArr = new byte[NativeData.INT_SIZE]; readFully(byteArr); return NativeData.byteToInt(byteArr, byteOrder)[0]; } @Override public long readLong() throws IOExceptionUnchecked { final byte[] byteArr = new byte[NativeData.LONG_SIZE]; readFully(byteArr); return NativeData.byteToLong(byteArr, byteOrder)[0]; } @Override public float readFloat() throws IOExceptionUnchecked { final byte[] byteArr = new byte[NativeData.FLOAT_SIZE]; readFully(byteArr); return NativeData.byteToFloat(byteArr, byteOrder)[0]; } @Override public double readDouble() throws IOExceptionUnchecked { final byte[] byteArr = new byte[NativeData.DOUBLE_SIZE]; readFully(byteArr); return NativeData.byteToDouble(byteArr, byteOrder)[0]; } @Override public String readLine() throws IOExceptionUnchecked { final StringBuilder builder = new StringBuilder(); int b; boolean byteRead = false; while ((b = read()) >= 0) { byteRead = true; final char c = (char) b; if (c == '\r') { continue; } if (c == '\n') { break; } builder.append(c); } if (byteRead == false) { return null; } else { return builder.toString(); } } @Override public String readUTF() throws IOExceptionUnchecked { try { final byte[] strBuf = new byte[readUnsignedShort()]; readFully(strBuf); return new String(strBuf, "UTF-8"); } catch (UnsupportedEncodingException ex) { throw CheckedExceptionTunnel.wrapIfNecessary(ex); } } @Override public void write(int b) throws IOExceptionUnchecked { checkWrite(1); extend(1); if (positionInBlock == realBlockSize) { checkEoFOnWrite(); readNextBlockResetPosition(); checkEoFOnWrite(); } block[positionInBlock++] = (byte) b; blockDirty = true; } @Override public void write(byte[] b) throws IOExceptionUnchecked { write(b, 0, b.length); } @Override public void write(byte[] b, int off, int len) throws IOExceptionUnchecked { checkWrite(len); extend(len); int bytesLeft = len; int currentOff = off; while (bytesLeft > 0) { final int lenInBlock = Math.min(bytesLeft, bytesLeftInBlock()); System.arraycopy(b, currentOff, block, positionInBlock, lenInBlock); blockDirty = true; positionInBlock += lenInBlock; currentOff += lenInBlock; bytesLeft -= lenInBlock; if (bytesLeft > 0) { readNextBlockResetPosition(); } } } @Override public void writeBoolean(boolean v) throws IOExceptionUnchecked { write(v ? 1 : 0); } @Override public void writeByte(int v) throws IOExceptionUnchecked { write(v); } @Override public void writeShort(int v) throws IOExceptionUnchecked { write(NativeData.shortToByte(new short[] { (short) v }, byteOrder)); } @Override public void writeChar(int v) throws IOExceptionUnchecked { write(NativeData.charToByte(new char[] { (char) v }, byteOrder)); } @Override public void writeInt(int v) throws IOExceptionUnchecked { write(NativeData.intToByte(new int[] { v }, byteOrder)); } @Override public void writeLong(long v) throws IOExceptionUnchecked { write(NativeData.longToByte(new long[] { v }, byteOrder)); } @Override public void writeFloat(float v) throws IOExceptionUnchecked { write(NativeData.floatToByte(new float[] { v }, byteOrder)); } @Override public void writeDouble(double v) throws IOExceptionUnchecked { write(NativeData.doubleToByte(new double[] { v }, byteOrder)); } @Override public void writeBytes(String s) throws IOExceptionUnchecked { for (int i = 0; i < s.length(); i++) { write((byte) s.charAt(i)); } } @Override public void writeChars(String s) throws IOExceptionUnchecked { for (int i = 0; i < s.length(); i++) { final char v = s.charAt(i); write((byte) ((v >>> 8) & 0xFF)); write((byte) ((v >>> 0) & 0xFF)); } } @Override public void writeUTF(String str) throws IOExceptionUnchecked { try { final byte[] strBuf = str.getBytes("UTF-8"); writeShort(strBuf.length); write(strBuf); } catch (UnsupportedEncodingException ex) { throw CheckedExceptionTunnel.wrapIfNecessary(ex); } } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/io/HDF5IOAdapterFactory.java000066400000000000000000000424331256564762100304110ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.io; import java.io.File; import java.io.InputStream; import java.io.OutputStream; import ch.systemsx.cisd.base.io.AdapterIInputStreamToInputStream; import ch.systemsx.cisd.base.io.AdapterIOutputStreamToOutputStream; import ch.systemsx.cisd.base.io.IInputStream; import ch.systemsx.cisd.base.io.IOutputStream; import ch.systemsx.cisd.hdf5.HDF5GenericStorageFeatures; import ch.systemsx.cisd.hdf5.IHDF5Reader; import ch.systemsx.cisd.hdf5.IHDF5Writer; /** * A factory of I/O adapter for HDF5 data sets. * * @author Bernd Rinn */ public class HDF5IOAdapterFactory { private static final String OPAQUE_TAG_FILE = "FILE"; private final static int BUFFER_SIZE = 1024 * 1024; // // File methods // /** * Creates an adapter of the hdf5File as an {@link IOutputStream}. *

* If the dataset does not yet exist, it will create a chunked opaque dataset with a chunk size * of 1MB and an opaque tag FILE. * * @param hdf5File The HDF5 file to create the adapter for. * @param dataSetPath The path of the HDF5 dataset in the HDF5 container to use as a file. * @return The {@link IOutputStream}. */ public static IOutputStream asIOutputStream(File hdf5File, String dataSetPath) { return new HDF5DataSetRandomAccessFile(hdf5File, dataSetPath, HDF5GenericStorageFeatures.GENERIC_CHUNKED, BUFFER_SIZE, OPAQUE_TAG_FILE, false); } /** * Creates an adapter of the hdf5File as an {@link IOutputStream}. * * @param hdf5File The HDF5 file to create the adapter for. * @param dataSetPath The path of the HDF5 dataset in the HDF5 container to use as a file. * @param creationStorageFeature If the dataset does not yet exist, use this value as the * storage features when creating it. * @param chunkSize If the dataset does not yet exist, use this value as the chunk size. * @param opaqueTagOrNull If the dataset does not yet exist and this value is not * null, then an opaque dataset will be created using this value will be * used as opaque tag. * @return The {@link IOutputStream}. */ public static IOutputStream asIOutputStream(File hdf5File, String dataSetPath, HDF5GenericStorageFeatures creationStorageFeature, int chunkSize, String opaqueTagOrNull) { return new HDF5DataSetRandomAccessFile(hdf5File, dataSetPath, creationStorageFeature, chunkSize, opaqueTagOrNull, false); } /** * Creates an adapter of the hdf5File as an {@link HDF5DataSetRandomAccessFile} in * read/write mode. * * @param hdf5File The HDF5 file to create the adapter for. * @param dataSetPath The path of the HDF5 dataset in the HDF5 container to use as a file. * @return The {@link HDF5DataSetRandomAccessFile}. */ public static HDF5DataSetRandomAccessFile asRandomAccessFileReadWrite(File hdf5File, String dataSetPath) { return new HDF5DataSetRandomAccessFile(hdf5File, dataSetPath, HDF5GenericStorageFeatures.GENERIC_CHUNKED, BUFFER_SIZE, OPAQUE_TAG_FILE, false); } /** * Creates an adapter of the hdf5File as an {@link OutputStream}. * * @param hdf5File The HDF5 file to create the adapter for. * @param dataSetPath The path of the HDF5 dataset in the HDF5 container to use as a file. * @param creationStorageFeature If the dataset does not yet exist, use this value as the * storage features when creating it. * @param chunkSize If the dataset does not yet exist, use this value as the chunk size. * @param opaqueTagOrNull If the dataset does not yet exist and this value is not * null, then an opaque dataset will be created using this value will be * used as opaque tag. * @return The {@link OutputStream}. */ public static OutputStream asOutputStream(File hdf5File, String dataSetPath, HDF5GenericStorageFeatures creationStorageFeature, int chunkSize, String opaqueTagOrNull) { return new AdapterIOutputStreamToOutputStream(asIOutputStream(hdf5File, dataSetPath, creationStorageFeature, chunkSize, opaqueTagOrNull)); } /** * Creates an adapter of the hdf5File as an {@link IOutputStream}. *

* If the dataset does not yet exist, it will create a chunked opaque dataset with a chunk size * of 1MB and an opaque tag FILE. * * @param hdf5File The HDF5 file to create the adapter for. * @param dataSetPath The path of the HDF5 dataset in the HDF5 container to use as a file. * @return The {@link OutputStream}. */ public static OutputStream asOutputStream(File hdf5File, String dataSetPath) { return new AdapterIOutputStreamToOutputStream(asIOutputStream(hdf5File, dataSetPath, HDF5GenericStorageFeatures.GENERIC_CHUNKED, BUFFER_SIZE, OPAQUE_TAG_FILE)); } /** * Creates an adapter of the hdf5File as an {@link HDF5DataSetRandomAccessFile} in * read/write mode. * * @param hdf5File The HDF5 file to create the adapter for. * @param dataSetPath The path of the HDF5 dataset in the HDF5 container to use as a file. * @param creationStorageFeature If the dataset does not yet exist, use this value as the * storage features when creating it. * @param chunkSize If the dataset does not yet exist, use this value as the chunk size. * @param opaqueTagOrNull If the dataset does not yet exist and this value is not * null, then an opaque dataset will be created using this value will be * used as opaque tag. * @return The {@link HDF5DataSetRandomAccessFile}. */ public static HDF5DataSetRandomAccessFile asRandomAccessFile(File hdf5File, String dataSetPath, HDF5GenericStorageFeatures creationStorageFeature, int chunkSize, String opaqueTagOrNull) { return new HDF5DataSetRandomAccessFile(hdf5File, dataSetPath, creationStorageFeature, chunkSize, opaqueTagOrNull, false); } /** * Creates an adapter of the hdf5File as an {@link IInputStream}. * * @param hdf5File The HDF5 file to create the adapter for. * @param dataSetPath The path of the HDF5 dataset in the HDF5 container to use as a file. * @return The {@link IInputStream}. */ public static IInputStream asIInputStream(File hdf5File, String dataSetPath) { return new HDF5DataSetRandomAccessFile(hdf5File, dataSetPath, null, 0, null, true); } /** * Creates an adapter of the hdf5File as an {@link InputStream}. * * @param hdf5File The HDF5 file to create the adapter for. * @param dataSetPath The path of the HDF5 dataset in the HDF5 container to use as a file. * @return The {@link InputStream}. */ public static InputStream asInputStream(File hdf5File, String dataSetPath) { return new AdapterIInputStreamToInputStream(asIInputStream(hdf5File, dataSetPath)); } /** * Creates an adapter of the hdf5File as an {@link HDF5DataSetRandomAccessFile} in * read-only mode. * * @param hdf5File The HDF5 file to create the adapter for. * @param dataSetPath The path of the HDF5 dataset in the HDF5 container to use as a file. * @return The {@link HDF5DataSetRandomAccessFile}. */ public static HDF5DataSetRandomAccessFile asRandomAccessFileReadOnly(File hdf5File, String dataSetPath) { return new HDF5DataSetRandomAccessFile(hdf5File, dataSetPath, null, 0, null, true); } // // Writer methods // /** * Creates an adapter of the writer as an {@link IOutputStream}. *

* If the dataset does not yet exist, it will create a chunked opaque dataset with a chunk size * of 1MB and an opaque tag FILE. *

* Note that returned object is buffered. Do not access dataSetPath by directly * accessing writer while this object is used or else the behavior is undefined! * * @param writer The HDF5 writer to create the adapter for. The writer will not be closed * when the returned object is closed. * @param dataSetPath The path of the HDF5 dataset in the HDF5 container to use as a file. * @return The {@link IOutputStream}. */ public static IOutputStream asIOutputStream(IHDF5Writer writer, String dataSetPath) { return new HDF5DataSetRandomAccessFile(writer, dataSetPath, HDF5GenericStorageFeatures.GENERIC_CHUNKED, BUFFER_SIZE, OPAQUE_TAG_FILE, false); } /** * Creates an adapter of the writer as an {@link IOutputStream}. *

* Note that returned object is buffered. Do not access dataSetPath by directly * accessing writer while this object is used or else the behavior is undefined! * * @param writer The HDF5 writer to create the adapter for. The writer will not be closed * when the returned object is closed. * @param dataSetPath The path of the HDF5 dataset in the HDF5 container to use as a file. * @param creationStorageFeature If the dataset does not yet exist, use this value as the * storage features when creating it. * @param chunkSize If the dataset does not yet exist, use this value as the chunk size. * @param opaqueTagOrNull If the dataset does not yet exist and this value is not * null, then an opaque dataset will be created using this value will be * used as opaque tag. * @return The {@link IOutputStream}. */ public static IOutputStream asIOutputStream(IHDF5Writer writer, String dataSetPath, HDF5GenericStorageFeatures creationStorageFeature, int chunkSize, String opaqueTagOrNull) { return new HDF5DataSetRandomAccessFile(writer, dataSetPath, creationStorageFeature, chunkSize, opaqueTagOrNull, false); } /** * Creates an adapter of the writer as an {@link IOutputStream}. *

* If the dataset does not yet exist, it will create a chunked opaque dataset with a chunk size * of 1MB and an opaque tag FILE. *

* Note that returned object is buffered. Do not access dataSetPath by directly * accessing writer while this object is used or else the behavior is undefined! * * @param writer The HDF5 writer to create the adapter for. The writer will not be closed * when the returned object is closed. * @param dataSetPath The path of the HDF5 dataset in the HDF5 container to use as a file. * @return The {@link OutputStream}. */ public static OutputStream asOutputStream(IHDF5Writer writer, String dataSetPath) { return new AdapterIOutputStreamToOutputStream(asIOutputStream(writer, dataSetPath, HDF5GenericStorageFeatures.GENERIC_CHUNKED, BUFFER_SIZE, OPAQUE_TAG_FILE)); } /** * Creates an adapter of the writer as an {@link OutputStream}. *

* Note that returned object is buffered. Do not access dataSetPath by directly * accessing writer while this object is used or else the behavior is undefined! * * @param writer The HDF5 writer to create the adapter for. The writer will not be closed * when the returned object is closed. * @param dataSetPath The path of the HDF5 dataset in the HDF5 container to use as a file. * @param creationStorageFeature If the dataset does not yet exist, use this value as the * storage features when creating it. * @param chunkSize If the dataset does not yet exist, use this value as the chunk size. * @param opaqueTagOrNull If the dataset does not yet exist and this value is not * null, then an opaque dataset will be created using this value will be * used as opaque tag. * @return The {@link OutputStream}. */ public static OutputStream asOutputStream(IHDF5Writer writer, String dataSetPath, HDF5GenericStorageFeatures creationStorageFeature, int chunkSize, String opaqueTagOrNull) { return new AdapterIOutputStreamToOutputStream(asIOutputStream(writer, dataSetPath, creationStorageFeature, chunkSize, opaqueTagOrNull)); } /** * Creates an adapter of the writer as an {@link HDF5DataSetRandomAccessFile}. *

* Note that returned object is buffered. Do not access dataSetPath by directly * accessing writer while this object is used or else the behavior is undefined! * * @param writer The HDF5 writer to create the adapter for. The writer will not be closed * when the returned object is closed. * @param dataSetPath The path of the HDF5 dataset in the HDF5 container to use as a file. * @param creationStorageFeature If the dataset does not yet exist, use this value as the * storage features when creating it. * @param chunkSize If the dataset does not yet exist, use this value as the chunk size. * @param opaqueTagOrNull If the dataset does not yet exist and this value is not * null, then an opaque dataset will be created using this value will be * used as opaque tag. * @return The {@link HDF5DataSetRandomAccessFile}. */ public static HDF5DataSetRandomAccessFile asRandomAccessFile(IHDF5Writer writer, String dataSetPath, HDF5GenericStorageFeatures creationStorageFeature, int chunkSize, String opaqueTagOrNull) { return new HDF5DataSetRandomAccessFile(writer, dataSetPath, creationStorageFeature, chunkSize, opaqueTagOrNull, false); } /** * Creates an adapter of the writer as an {@link HDF5DataSetRandomAccessFile}. *

* Note that returned object is buffered. Do not access dataSetPath by directly * accessing writer while this object is used or else the behavior is undefined! * * @param writer The HDF5 writer to create the adapter for. The writer will not be closed * when the returned object is closed. * @param dataSetPath The path of the HDF5 dataset in the HDF5 container to use as a file. * @return The {@link HDF5DataSetRandomAccessFile}. */ public static HDF5DataSetRandomAccessFile asRandomAccessFile(IHDF5Writer writer, String dataSetPath) { return new HDF5DataSetRandomAccessFile(writer, dataSetPath, HDF5GenericStorageFeatures.GENERIC_CHUNKED, BUFFER_SIZE, OPAQUE_TAG_FILE, false); } // // Reader methods // /** * Creates an adapter of the reader as an {@link IInputStream}. * * @param reader The HDF5 reader to create the adapter for. The reader will not be closed * when the returned object is closed. * @param dataSetPath The path of the HDF5 dataset in the HDF5 container to use as a file. * @return The {@link IInputStream}. */ public static IInputStream asIInputStream(IHDF5Reader reader, String dataSetPath) { return new HDF5DataSetRandomAccessFile(reader, dataSetPath, null, 0, null, false); } /** * Creates an adapter of the reader as an {@link InputStream}. * * @param reader The HDF5 reader to create the adapter for. The reader will not be closed * when the returned object is closed. * @param dataSetPath The path of the HDF5 dataset in the HDF5 container to use as a file. * @return The {@link InputStream}. */ public static InputStream asInputStream(IHDF5Reader reader, String dataSetPath) { return new AdapterIInputStreamToInputStream(asIInputStream(reader, dataSetPath)); } /** * Creates an adapter of the reader as an {@link HDF5DataSetRandomAccessFile}. * * @param reader The HDF5 reader to create the adapter for. The reader will not be closed * when the returned object is closed. * @param dataSetPath The path of the HDF5 dataset in the HDF5 container to use as a file. * @return The {@link HDF5DataSetRandomAccessFile}. */ public static HDF5DataSetRandomAccessFile asRandomAccessFile(IHDF5Reader reader, String dataSetPath) { return new HDF5DataSetRandomAccessFile(reader, dataSetPath, null, 0, null, false); } } libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/io/package.html000066400000000000000000000004521256564762100262530ustar00rootroot00000000000000 I/O Package

This package contains classes to access an HDF5 file like an Operating System file.

libsis-jhdf5-java-14.12.1/source/java/ch/systemsx/cisd/hdf5/package.html000066400000000000000000000005151256564762100256440ustar00rootroot00000000000000 Main Package

Main package that contains the JHDF5 reader and writer.

libsis-jhdf5-java-14.12.1/source/java/ncsa/000077500000000000000000000000001256564762100202455ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/000077500000000000000000000000001256564762100210065ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/000077500000000000000000000000001256564762100223235ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/H5.java000066400000000000000000012217501256564762100234520ustar00rootroot00000000000000/**************************************************************************** * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF Java Products. The full HDF Java copyright * * notice, including terms governing use, modification, and redistribution, * * is contained in the file, COPYING. COPYING can be found at the root of * * the source code distribution tree. You can also access it online at * * http://www.hdfgroup.org/products/licenses.html. If you do not have * * access to the file, you may request a copy from help@hdfgroup.org. * ****************************************************************************/ package ncsa.hdf.hdf5lib; import java.nio.ByteBuffer; import java.util.Vector; import ncsa.hdf.hdf5lib.callbacks.H5D_iterate_cb; import ncsa.hdf.hdf5lib.callbacks.H5D_iterate_t; import ncsa.hdf.hdf5lib.callbacks.H5L_iterate_cb; import ncsa.hdf.hdf5lib.callbacks.H5L_iterate_t; import ncsa.hdf.hdf5lib.callbacks.H5O_iterate_cb; import ncsa.hdf.hdf5lib.callbacks.H5O_iterate_t; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import ncsa.hdf.hdf5lib.structs.H5AC_cache_config_t; import ncsa.hdf.hdf5lib.structs.H5A_info_t; import ncsa.hdf.hdf5lib.structs.H5G_info_t; import ncsa.hdf.hdf5lib.structs.H5L_info_t; import ncsa.hdf.hdf5lib.structs.H5O_info_t; /** * This class is the Java interface for the HDF5 library. *

* This code is the called by Java programs to access the entry points of the * HDF5 library. Each routine wraps a single HDF5 entry point, generally * with the arguments and return codes analogous to the C interface. *

* For details of the HDF5 library, see the HDF5 Documentation at: http://hdfgroup.org/HDF5/ *

*

* Mapping of arguments for Java * *

* In general, arguments to the HDF Java API are straightforward translations * from the 'C' API described in the HDF Reference Manual. *

* *

* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
HDF-5 C types to Java types
HDF-5Java
H5T_NATIVE_INTint, Integer
H5T_NATIVE_SHORTshort, Short
H5T_NATIVE_FLOATfloat, Float
H5T_NATIVE_DOUBLEdouble, Double
H5T_NATIVE_CHARbyte, Byte
H5T_C_S1java.lang.String
void *
* (i.e., pointer to `Any')		Special -- see HDFArray
*
*

*

General Rules for Passing Arguments and Results
*

* In general, arguments passed IN to Java are the analogous basic types, * as above. The exception is for arrays, which are discussed below. *

* The return value of Java methods is also the analogous type, as above. * A major exception to that rule is that all HDF functions that return * SUCCEED/FAIL are declared boolean in the Java version, rather than * int as in the C. Functions that return a value or else FAIL are * declared the equivalent to the C function. However, in most cases the Java * method will raise an exception instead of returning an error code. See Errors and Exceptions below. *

* Java does not support pass by reference of arguments, so arguments that are * returned through OUT parameters must be wrapped in an object or array. * The Java API for HDF consistently wraps arguments in arrays. *

* For instance, a function that returns two integers is declared: *

* * 

 *       h_err_t HDF5dummy( int *a1, int *a2)
 *
* * For the Java interface, this would be declared: *

* * 

 * public synchronized static native int HDF5dummy(int args[]);
 *
* * where a1 is args[0] and a2 is args[1], and would * be invoked: *

* * 

 * H5.HDF5dummy(a);
 *
* *

* All the routines where this convention is used will have specific * documentation of the details, given below. *

* Arrays *

* HDF5 needs to read and write multi-dimensional arrays of any number type (and * records). The HDF5 API describes the layout of the source and destination, * and the data for the array passed as a block of bytes, for instance, *

* * 

 *      herr_t H5Dread(int fid, int filetype, int memtype, int memspace,
 *      void * data);
 *
* *

* where ``void *'' means that the data may be any valid numeric type, and is a * contiguous block of bytes that is the data for a multi-dimensional array. The * other parameters describe the dimensions, rank, and datatype of the array on * disk (source) and in memory (destination). *

* For Java, this ``ANY'' is a problem, as the type of data must always be * declared. Furthermore, multidimensional arrays are definitely not * layed out contiguously in memory. It would be infeasible to declare a * separate routine for every combination of number type and dimensionality. For * that reason, the HDFArray class is used to * discover the type, shape, and size of the data array at run time, and to * convert to and from a contiguous array of bytes in synchronized static native * C order. *

* The upshot is that any Java array of numbers (either primitive or sub-classes * of type Number) can be passed as an ``Object'', and the Java API will * translate to and from the appropriate packed array of bytes needed by the C * library. So the function above would be declared: *

* * 

 * public synchronized static native int H5Dread(int fid, int filetype,
 *         int memtype, int memspace, Object data);
 *
* * and the parameter data can be any multi-dimensional array of numbers, * such as float[][], or int[][][], or Double[][]. *

* HDF-5 Constants *

* The HDF-5 API defines a set of constants and enumerated values. Most of these * values are available to Java programs via the class HDF5Constants. For * example, the parameters for the h5open() call include two numeric values, * HDFConstants.H5F_ACC_RDWR and * HDF5Constants.H5P_DEFAULT. As would be expected, these numbers * correspond to the C constants H5F_ACC_RDWR and * H5P_DEFAULT. *

* The HDF-5 API defines a set of values that describe number types and sizes, * such as "H5T_NATIVE_INT" and "hsize_t". These values are determined at run * time by the HDF-5 C library. To support these parameters, the Java class HDF5CDataTypes * looks up the values when initiated. The values can be accessed as public * variables of the Java class, such as: * * 

 * int data_type = HDF5CDataTypes.JH5T_NATIVE_INT;
 *
* * The Java application uses both types of constants the same way, the only * difference is that the HDF5CDataTypes may have different values * on different platforms. *

* Error handling and Exceptions *

* The HDF5 error API (H5E) manages the behavior of the error stack in the HDF-5 * library. This API is omitted from the JHI5. Errors are converted into Java * exceptions. This is totally different from the C interface, but is very * natural for Java programming. *

* The exceptions of the JHI5 are organized as sub-classes of the class * HDF5Exception. There are two subclasses of HDF5Exception, * * HDF5LibraryException and * HDF5JavaException. The sub-classes of the former represent errors * from the HDF-5 C library, while sub-classes of the latter represent errors in * the JHI5 wrapper and support code. *

* The super-class HDF5LibraryException implements the method * 'printStackTrace()', which prints out the HDF-5 error stack, as * described in the HDF-5 C API H5Eprint(). This may be used by * Java exception handlers to print out the HDF-5 error stack. *

* * @version HDF5 1.2
* See also: * ncsa.hdf.hdf5lib.HDFArray
* * ncsa.hdf.hdf5lib.HDF5Constants
* * ncsa.hdf.hdf5lib.HDF5CDataTypes
* * ncsa.hdf.hdf5lib.HDF5Exception
* * http://hdfgroup.org/HDF5" **/ @SuppressWarnings("all") public class H5 implements java.io.Serializable { /** * */ private static final long serialVersionUID = 6129888282117053288L; /** * The version number of the HDF5 library:
* LIB_VERSION[0]: The major version of the library.
* LIB_VERSION[1]: The minor version of the library.
* LIB_VERSION[2]: The release number of the library.
* * Make sure to update the versions number when a different library is used. */ public final static int LIB_VERSION[] = { 1, 8, 13 }; public final static String H5PATH_PROPERTY_KEY = "ncsa.hdf.hdf5lib.H5.hdf5lib"; // add system property to load library by name from library path, via // System.loadLibrary() public final static String H5_LIBRARY_NAME_PROPERTY_KEY = "ncsa.hdf.hdf5lib.H5.loadLibraryName"; private static String s_libraryName; private static boolean isLibraryLoaded = false; private final static boolean IS_CRITICAL_PINNING = true; private final static Vector OPEN_IDS = new Vector(); static { loadH5Lib(); } public static void loadH5Lib() { ch.systemsx.cisd.hdf5.hdf5lib.H5General.ensureNativeLibIsLoaded(); } // //////////////////////////////////////////////////////////// // // // H5: General Library Functions // // // // //////////////////////////////////////////////////////////// /** * Get number of open IDs. */ public final static int getOpenIDCount() { return OPEN_IDS.size(); } /** * Get the open ID at the specified index. * * @param index -- an index of the open ID. * @return Returns the open ID at the specified index. */ public final static int getOpenID(int index) { int id = -1; if (index >= 0 && index < OPEN_IDS.size()) id = OPEN_IDS.elementAt(index); return id; } /** * H5check_version verifies that the arguments match the version numbers * compiled into the library. * * @param majnum * The major version of the library. * @param minnum * The minor version of the library. * @param relnum * The release number of the library. * @return a non-negative value if successful. Upon failure (when the * versions do not match), this function causes the application to * abort (i.e., crash) * * See C API function: herr_t H5check_version() **/ public synchronized static native int H5check_version(int majnum, int minnum, int relnum); /** * H5close flushes all data to disk, closes all file identifiers, and cleans * up all memory used by the library. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5close() throws HDF5LibraryException; /** * H5open initialize the library. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5open() throws HDF5LibraryException; /** * H5dont_atexit indicates to the library that an atexit() cleanup routine * should not be installed. In order to be effective, this routine must be * called before any other HDF function calls, and must be called each time * the library is loaded/linked into the application (the first time and * after it's been unloaded). *

* This is called by the static initializer, so this should never need to be * explicitly called by a Java program. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ private synchronized static native int H5dont_atexit() throws HDF5LibraryException; /** * Turn off error handling By default, the C library prints the error stack * of the HDF-5 C library on stdout. This behavior may be disabled by * calling H5error_off(). */ public synchronized static native int H5error_off(); /** * H5garbage_collect collects on all free-lists of all types. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5garbage_collect() throws HDF5LibraryException; /** * H5get_libversion retrieves the major, minor, and release numbers of the * version of the HDF library which is linked to the application. * * @param libversion * The version information of the HDF library. * * 

 *      libversion[0] = The major version of the library.
 *      libversion[1] = The minor version of the library.
 *      libversion[2] = The release number of the library.
 *
* @return a non-negative value if successful, along with the version * information. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5get_libversion(int[] libversion) throws HDF5LibraryException; public synchronized static native int H5set_free_list_limits( int reg_global_lim, int reg_list_lim, int arr_global_lim, int arr_list_lim, int blk_global_lim, int blk_list_lim) throws HDF5LibraryException; /** * H5export_dataset is a utility function to save data in a file. * * @param file_export_name * The file name to export data into. * @param file_name * The name of the HDF5 file containing the dataset. * @param object_path * The full path of the dataset to be exported. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5export_dataset(String file_export_name, String file_name, String object_path, int binary_order) throws HDF5LibraryException; ////////////////////////////////////////////////////////////// //// //H5A: HDF5 1.8 Attribute Interface API Functions // //// ////////////////////////////////////////////////////////////// /** * H5Aclose terminates access to the attribute specified by its identifier, * attr_id. * * @param attr_id * IN: Attribute to release access to. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Aclose(int attr_id) throws HDF5LibraryException { if (attr_id < 0) return 0; // throw new HDF5LibraryException("Negative ID");; OPEN_IDS.removeElement(attr_id); return _H5Aclose(attr_id); } private synchronized static native int _H5Aclose(int attr_id) throws HDF5LibraryException; /** * H5Acopy copies the content of one attribute to another. * * @param src_aid * the identifier of the source attribute * @param dst_aid * the identifier of the destination attribute */ public synchronized static native int H5Acopy(int src_aid, int dst_aid) throws HDF5LibraryException; /** * H5Acreate creates an attribute which is attached to the object specified * with loc_id. * * @deprecated As of HDF5 1.8, replaced by {@link #H5Acreate( int, String, int, int, int, int) } * * @param loc_id * IN: Object (dataset, group, or named datatype) to be attached * to. * @param name * IN: Name of attribute to create. * @param type_id * IN: Identifier of datatype for attribute. * @param space_id * IN: Identifier of dataspace for attribute. * @param create_plist * IN: Identifier of creation property list (currently not used). * * @return an attribute identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ @Deprecated public static int H5Acreate(int loc_id, String name, int type_id, int space_id, int create_plist) throws HDF5LibraryException, NullPointerException { int id = _H5Acreate(loc_id, name, type_id, space_id, create_plist); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Acreate(int loc_id, String name, int type_id, int space_id, int create_plist) throws HDF5LibraryException, NullPointerException; /** * H5Acreate creates an attribute, attr_name, which is attached to the object specified by the identifier loc_id. * * @param loc_id IN: Location or object identifier; may be dataset or group * @param attr_name IN: Attribute name * @param type_id IN: Attribute datatype identifier * @param space_id IN: Attribute dataspace identifier * @param acpl_id IN: Attribute creation property list identifier * @param aapl_id IN: Attribute access property list identifier * * @return An attribute identifier if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - Name is null. **/ public static int H5Acreate( int loc_id, String attr_name, int type_id, int space_id, int acpl_id, int aapl_id ) throws HDF5LibraryException, NullPointerException { int id = _H5Acreate2(loc_id, attr_name, type_id, space_id, acpl_id, aapl_id ); if (id > 0) OPEN_IDS.addElement(id); return id; } /** * H5Acreate2 an attribute, attr_name, which is attached to the object * specified by the identifier loc_id. * * @see public static int H5Acreate( int loc_id, String attr_name, int * type_id, int space_id, int acpl_id, int aapl_id ) **/ private synchronized static native int _H5Acreate2( int loc_id, String attr_name, int type_id, int space_id, int acpl_id, int aapl_id ) throws HDF5LibraryException, NullPointerException; /** * H5Acreate_by_name creates an attribute, attr_name, which is attached to the object specified by loc_id and obj_name. * * @param loc_id IN: Location or object identifier; may be dataset or group * @param obj_name IN: Name, relative to loc_id, of object that attribute is to be attached to * @param attr_name IN: Attribute name * @param type_id IN: Attribute datatype identifier * @param space_id IN: Attribute dataspace identifier * @param acpl_id IN: Attribute creation property list identifier (currently not used). * @param aapl_id IN: Attribute access property list identifier (currently not used). * @param lapl_id IN: Link access property list * * @return An attribute identifier if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. **/ public static int H5Acreate_by_name(int loc_id, String obj_name, String attr_name, int type_id, int space_id, int acpl_id, int aapl_id, int lapl_id) throws HDF5LibraryException, NullPointerException { int id = _H5Acreate_by_name(loc_id, obj_name, attr_name, type_id, space_id, acpl_id, aapl_id, lapl_id); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Acreate_by_name(int loc_id, String obj_name, String attr_name, int type_id, int space_id, int acpl_id, int aapl_id, int lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Adelete removes the attribute specified by its name, name, from a * dataset, group, or named datatype. * * @param loc_id * IN: Identifier of the dataset, group, or named datatype. * @param name * IN: Name of the attribute to delete. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native int H5Adelete(int loc_id, String name) throws HDF5LibraryException, NullPointerException; /** * H5Adelete_by_idx removes an attribute, specified by its location in an index, from an object. * * @param loc_id IN: Location or object identifier; may be dataset or group * @param obj_name IN: Name of object, relative to location, from which attribute is to be removed * @param idx_type IN: Type of index * @param order IN: Order in which to iterate over index * @param n IN: Offset within index * @param lapl_id IN: Link access property list identifier * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - obj_name is null. **/ public synchronized static native void H5Adelete_by_idx(int loc_id, String obj_name, int idx_type, int order, long n, int lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Adelete_by_name removes the attribute attr_name from an object specified by location and name, loc_id and obj_name, respectively. * * @param loc_id IN: Location or object identifier; may be dataset or group * @param obj_name IN: Name of object, relative to location, from which attribute is to be removed * @param attr_name IN: Name of attribute to delete * @param lapl_id IN: Link access property list identifier. * * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. **/ public synchronized static native int H5Adelete_by_name(int loc_id, String obj_name, String attr_name, int lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Aexists determines whether the attribute attr_name exists on the object specified by obj_id. * * @param obj_id IN: Object identifier. * @param attr_name IN: Name of the attribute. * * @return boolean true if an attribute with a given name exists. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - attr_name is null. **/ public synchronized static native boolean H5Aexists(int obj_id, String attr_name) throws HDF5LibraryException, NullPointerException; /** * H5Aexists_by_name determines whether the attribute attr_name exists on an object. That object is specified by its location and name, * loc_id and obj_name, respectively. * * @param loc_id IN: Location of object to which attribute is attached . * @param obj_name IN: Name, relative to loc_id, of object that attribute is attached to. * @param attr_name IN: Name of attribute. * @param lapl_id IN: Link access property list identifier. * * @return boolean true if an attribute with a given name exists, otherwise returns false. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. **/ public synchronized static native boolean H5Aexists_by_name(int loc_id, String obj_name, String attr_name, int lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Aget_info retrieves attribute information, by attribute identifier. * * @param attr_id IN: Attribute identifier * * @return A buffer(H5A_info_t) for Attribute information * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native H5A_info_t H5Aget_info(int attr_id) throws HDF5LibraryException; /** * H5Aget_info_by_idx Retrieves attribute information, by attribute index position. * * @param loc_id IN: Location of object to which attribute is attached * @param obj_name IN: Name of object to which attribute is attached, relative to location * @param idx_type IN: Type of index * @param order IN: Index traversal order * @param n IN: Attribute's position in index * @param lapl_id IN: Link access property list * * @return A buffer(H5A_info_t) for Attribute information * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - obj_name is null. **/ public synchronized static native H5A_info_t H5Aget_info_by_idx(int loc_id, String obj_name, int idx_type, int order, long n, int lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Aget_info_by_name Retrieves attribute information, by attribute name. * * @param loc_id IN: Location of object to which attribute is attached * @param obj_name IN: Name of object to which attribute is attached, relative to location * @param attr_name IN: Attribute name * @param lapl_id IN: Link access property list * * @return A buffer(H5A_info_t) for Attribute information * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - obj_name is null. **/ public synchronized static native H5A_info_t H5Aget_info_by_name(int loc_id, String obj_name, String attr_name, int lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Aget_name retrieves the name of an attribute specified by the * identifier, attr_id. * * @param attr_id * IN: Identifier of the attribute. * @param buf_size * IN: The size of the buffer to store the name in. * @param name * OUT: Buffer to store name in. * * @exception ArrayIndexOutOfBoundsException * JNI error writing back array * @exception ArrayStoreException * JNI error writing back array * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. * @exception IllegalArgumentException * - bub_size <= 0. * * @return the length of the attribute's name if successful. **/ public synchronized static native long H5Aget_name(int attr_id, long buf_size, String[] name) throws ArrayIndexOutOfBoundsException, ArrayStoreException, HDF5LibraryException, NullPointerException, IllegalArgumentException; public static long H5Aget_name(int attr_id, String[] name) throws ArrayIndexOutOfBoundsException, ArrayStoreException, HDF5LibraryException, NullPointerException, IllegalArgumentException { long len = H5Aget_name(attr_id, 0, null); return H5Aget_name(attr_id, len+1, name); } /** * H5Aget_name_by_idx retrieves the name of an attribute that is attached to an object, which is specified by its location and name, * loc_id and obj_name, respectively. * * @param attr_id IN: Attribute identifier * @param obj_name IN: Name of object to which attribute is attached, relative to location * @param idx_type IN: Type of index * @param order IN: Index traversal order * @param n IN: Attribute's position in index * @param lapl_id IN: Link access property list * * @return String for Attribute name. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - obj_name is null. **/ public synchronized static native String H5Aget_name_by_idx(int attr_id, String obj_name, int idx_type, int order, long n, int lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Aget_num_attrs returns the number of attributes attached to the object * specified by its identifier, loc_id. * * @deprecated As of HDF5 1.8, replaced by {@link #H5Oget_info( int )} * * @param loc_id * IN: Identifier of a group, dataset, or named datatype. * * @return the number of attributes if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ @Deprecated public synchronized static native int H5Aget_num_attrs(int loc_id) throws HDF5LibraryException; /** * H5Aget_space retrieves a copy of the dataspace for an attribute. * * @param attr_id * IN: Identifier of an attribute. * * @return attribute dataspace identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Aget_space(int attr_id) throws HDF5LibraryException { int id = _H5Aget_space(attr_id); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Aget_space(int attr_id) throws HDF5LibraryException; /** * H5Aget_storage_size returns the amount of storage that is required for the specified attribute, attr_id. * * @param attr_id IN: Identifier of the attribute to query. * * @return the amount of storage size allocated for the attribute; otherwise returns 0 (zero) * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native long H5Aget_storage_size(int attr_id) throws HDF5LibraryException; /** * H5Aget_type retrieves a copy of the datatype for an attribute. * * @param attr_id * IN: Identifier of an attribute. * * @return a datatype identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Aget_type(int attr_id) throws HDF5LibraryException { int id = _H5Aget_type(attr_id); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Aget_type(int attr_id) throws HDF5LibraryException; /** * H5Aopen opens an existing attribute, attr_name, that is attached to an object specified an object identifier, object_id. * * @param obj_id IN: Identifier for object to which attribute is attached * @param attr_name IN: Name of attribute to open * @param aapl_id IN: Attribute access property list identifier * * @return An attribute identifier if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - Name is null. **/ public static int H5Aopen(int obj_id, String attr_name, int aapl_id) throws HDF5LibraryException, NullPointerException { int id = _H5Aopen(obj_id, attr_name, aapl_id); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Aopen(int obj_id, String attr_name, int aapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Aopen_by_idx opens an existing attribute that is attached to an object specified by location and name, loc_id and obj_name, respectively * * @param loc_id IN: Location of object to which attribute is attached * @param obj_name IN: Name of object to which attribute is attached, relative to location * @param idx_type IN: Type of index * @param order IN: Index traversal order * @param n IN: Attribute's position in index * @param aapl_id IN: Attribute access property list * @param lapl_id IN: Link access property list * * @return An attribute identifier if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - Name is null. **/ public static int H5Aopen_by_idx(int loc_id, String obj_name, int idx_type, int order ,long n, int aapl_id, int lapl_id) throws HDF5LibraryException, NullPointerException { int id = _H5Aopen_by_idx(loc_id, obj_name, idx_type, order , n, aapl_id, lapl_id); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Aopen_by_idx(int loc_id, String obj_name, int idx_type, int order ,long n, int aapl_id, int lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Aopen_by_name Opens an attribute for an object by object name and attribute name * * @param loc_id IN: Location from which to find object to which attribute is attached * @param obj_name IN: Name of object to which attribute is attached, relative to loc_id * @param attr_name IN: Name of attribute to open * @param aapl_id IN: Attribute access property list * @param lapl_id IN: Link access property list identifier * * @return Returns an attribute identifier if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - obj_name is null. **/ public static int H5Aopen_by_name(int loc_id, String obj_name, String attr_name, int aapl_id, int lapl_id) throws HDF5LibraryException, NullPointerException { int id = _H5Aopen_by_name(loc_id, obj_name, attr_name, aapl_id, lapl_id); if (id > 0) OPEN_IDS.addElement(id); return id; } /** * H5Aopen_idx opens an attribute which is attached to the object specified * with loc_id. The location object may be either a group, dataset, or named * datatype, all of which may have any sort of attribute. * * @deprecated As of HDF5 1.8, replaced by {@link #H5Aopen_by_idx(int, String, int, int, long, int, int) } * * @param loc_id * IN: Identifier of the group, dataset, or named datatype attribute * @param idx * IN: Index of the attribute to open. * * @return attribute identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ @Deprecated public static int H5Aopen_idx(int loc_id, int idx) throws HDF5LibraryException { int id = _H5Aopen_idx(loc_id, idx); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Aopen_idx(int loc_id, int idx) throws HDF5LibraryException; /** * H5Aopen_name opens an attribute specified by its name, name, which is * attached to the object specified with loc_id. * * @deprecated As of HDF5 1.8, replaced by {@link #H5Aopen_by_name(int, String, String, int, int)} * * @param loc_id * IN: Identifier of a group, dataset, or named datatype atttribute * @param name * IN: Attribute name. * * @return attribute identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ @Deprecated public static int H5Aopen_name(int loc_id, String name) throws HDF5LibraryException, NullPointerException { int id = _H5Aopen_name(loc_id, name); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Aopen_name(int loc_id, String name) throws HDF5LibraryException, NullPointerException; /** * H5Aread reads an attribute, specified with attr_id. The attribute's * memory datatype is specified with mem_type_id. The entire attribute is * read into buf from the file. * * @param attr_id * IN: Identifier of an attribute to read. * @param mem_type_id * IN: Identifier of the attribute datatype (in memory). * @param buf * IN: Buffer for data to be read. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - data buffer is null. **/ public synchronized static native int H5Aread(int attr_id, int mem_type_id, byte[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Aread reads an attribute, specified with attr_id. The attribute's * memory datatype is specified with mem_type_id. The entire attribute is * read into data object from the file. * * @param attr_id * IN: Identifier of an attribute to read. * @param mem_type_id * IN: Identifier of the attribute datatype (in memory). * @param obj * IN: Object for data to be read. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - data buffer is null. See public synchronized static * native int H5Aread( ) **/ public synchronized static int H5Aread(int attr_id, int mem_type_id, Object obj) throws HDF5Exception, NullPointerException { HDFArray theArray = new HDFArray(obj); byte[] buf = theArray.emptyBytes(); // This will raise an exception if there is an error int status = H5Aread(attr_id, mem_type_id, buf); // No exception: status really ought to be OK if (status >= 0) { obj = theArray.arrayify(buf); } return status; } public synchronized static native int H5AreadVL(int attr_id, int mem_type_id, String[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Arename changes the name of attribute that is attached to the object specified by loc_id. * The attribute named old_attr_name is renamed new_attr_name. * * @param loc_id IN: Location or object identifier; may be dataset or group * @param old_attr_name IN: Prior attribute name * @param new_attr_name IN: New attribute name * * @return A non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - Name is null. **/ public synchronized static native int H5Arename(int loc_id, String old_attr_name, String new_attr_name) throws HDF5LibraryException, NullPointerException; /** * H5Arename_by_name changes the name of attribute that is attached to the object specified by loc_id and obj_name. * The attribute named old_attr_name is renamed new_attr_name. * * @param loc_id IN: Location or object identifier; may be dataset or group * @param obj_name IN: Name of object, relative to location, whose attribute is to be renamed * @param old_attr_name IN: Prior attribute name * @param new_attr_name IN: New attribute name * @param lapl_id IN: Link access property list * * @return A non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - Name is null. **/ public synchronized static native int H5Arename_by_name(int loc_id, String obj_name, String old_attr_name, String new_attr_name, int lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Awrite writes an attribute, specified with attr_id. The attribute's * memory datatype is specified with mem_type_id. The entire attribute is * written from buf to the file. * * @param attr_id * IN: Identifier of an attribute to write. * @param mem_type_id * IN: Identifier of the attribute datatype (in memory). * @param buf * IN: Data to be written. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - data is null. **/ public synchronized static native int H5Awrite(int attr_id, int mem_type_id, byte[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Awrite writes an attribute, specified with attr_id. The attribute's * memory datatype is specified with mem_type_id. The entire attribute is * written from data object to the file. * * @param attr_id * IN: Identifier of an attribute to write. * @param mem_type_id * IN: Identifier of the attribute datatype (in memory). * @param obj * IN: Data object to be written. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - data object is null. See public synchronized static * native int H5Awrite(int attr_id, int mem_type_id, byte[] * buf); **/ public synchronized static int H5Awrite(int attr_id, int mem_type_id, Object obj) throws HDF5Exception, NullPointerException { HDFArray theArray = new HDFArray(obj); byte[] buf = theArray.byteify(); int retVal = H5Awrite(attr_id, mem_type_id, buf); buf = null; theArray = null; return retVal; } public synchronized static native int H5AwriteVL(int attr_id, int mem_type_id, String[] buf) throws HDF5LibraryException, NullPointerException; ///////// unimplemented //////// //herr_t H5Aiterate2(hid_t loc_id, H5_index_t idx_type, H5_iter_order_t order, hsize_t *idx, H5A_operator2_t op, void *op_data); //herr_t H5Aiterate_by_name(hid_t loc_id, const char *obj_name, H5_index_t idx_type, // H5_iter_order_t order, hsize_t *idx, H5A_operator2_t op, void *op_data, hid_t lapd_id); ////////////////////////////////////////////////////////////// //// //H5D: Datasets Interface Functions // //// ////////////////////////////////////////////////////////////// public synchronized static native int H5Dchdir_ext(String dir_name) throws HDF5LibraryException, NullPointerException; /** * H5Dcopy copies the content of one dataset to another dataset. * * @param src_did * the identifier of the source dataset * @param dst_did * the identifier of the destinaiton dataset */ public synchronized static native int H5Dcopy(int src_did, int dst_did) throws HDF5LibraryException; /** * H5Dclose ends access to a dataset specified by dataset_id and releases * resources used by it. * * @param dataset_id * Identifier of the dataset to finish access to. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Dclose(int dataset_id) throws HDF5LibraryException { if (dataset_id < 0) return 0; // throw new HDF5LibraryException("Negative ID"); OPEN_IDS.removeElement(dataset_id); return _H5Dclose(dataset_id); } private synchronized static native int _H5Dclose(int dataset_id) throws HDF5LibraryException; /** * H5Dcreate creates a data set with a name, name, in the file or in the * group specified by the identifier loc_id. * * @deprecated As of HDF5 1.8, replaced by {@link #H5Dcreate(int, String, int, int, int, int, int) } * * @param loc_id * Identifier of the file or group to create the dataset within. * @param name * The name of the dataset to create. * @param type_id * Identifier of the datatype to use when creating the dataset. * @param space_id * Identifier of the dataspace to use when creating the dataset. * @param create_plist_id * Identifier of the set creation property list. * * @return a dataset identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ @Deprecated public static int H5Dcreate(int loc_id, String name, int type_id, int space_id, int create_plist_id) throws HDF5LibraryException, NullPointerException { int id = _H5Dcreate(loc_id, name, type_id, space_id, create_plist_id); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Dcreate(int loc_id, String name, int type_id, int space_id, int create_plist_id) throws HDF5LibraryException, NullPointerException; /** * H5Dcreate creates a new dataset named name at the * location specified by loc_id. * * @param loc_id IN: Location identifier * @param name IN: Dataset name * @param type_id IN: Datatype identifier * @param space_id IN: Dataspace identifier * @param lcpl_id IN: Identifier of link creation property list. * @param dcpl_id IN: Identifier of dataset creation property list. * @param dapl_id IN: Identifier of dataset access property list. * * @return a dataset identifier * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. **/ public static int H5Dcreate(int loc_id, String name, int type_id, int space_id, int lcpl_id, int dcpl_id, int dapl_id) throws HDF5LibraryException, NullPointerException { int id = _H5Dcreate2(loc_id, name, type_id, space_id, lcpl_id, dcpl_id, dapl_id); if (id > 0) OPEN_IDS.addElement(id); return id; } /** * H5Dcreate2 creates a new dataset named name at the * location specified by loc_id. * * @see public static int H5Dcreate(int loc_id, String name, int type_id, * int space_id, int lcpl_id, int dcpl_id, int dapl_id) **/ private synchronized static native int _H5Dcreate2(int loc_id, String name, int type_id, int space_id, int lcpl_id, int dcpl_id, int dapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Dcreate_anon creates a dataset in the file specified by loc_id. * * @param loc_id IN: Location identifier * @param type_id IN: Datatype identifier * @param space_id IN: Dataspace identifier * @param dcpl_id IN: Identifier of dataset creation property list. * @param dapl_id IN: Identifier of dataset access property list. * * @return a dataset identifier * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public static int H5Dcreate_anon(int loc_id, int type_id, int space_id, int dcpl_id, int dapl_id) throws HDF5LibraryException { int id = _H5Dcreate_anon(loc_id, type_id, space_id, dcpl_id, dapl_id); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Dcreate_anon(int loc_id, int type_id, int space_id, int dcpl_id, int dapl_id) throws HDF5LibraryException; /** * H5Dextend verifies that the dataset is at least of size size. * * @param dataset_id IN: Identifier of the dataset. * @param size IN: Array containing the new magnitude of each dimension. * * @return a non-negative value if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - size array is null. * * @deprecated As of HDF5 1.8, replaced by {@link #H5Dset_extent(int, long[]) } **/ @Deprecated public synchronized static native int H5Dextend(int dataset_id, byte[] size) throws HDF5LibraryException, NullPointerException; /** * H5Dextend verifies that the dataset is at least of size size. * * @param dataset_id IN: Identifier of the dataset. * @param size IN: Array containing the new magnitude of each dimension. * * @return a non-negative value if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - size array is null. * * @deprecated As of HDF5 1.8, replaced by {@link #H5Dset_extent(int, long[]) } **/ @Deprecated public synchronized static int H5Dextend(int dataset_id, long[] size) throws HDF5Exception, NullPointerException { int rval = -1; HDFArray theArray = new HDFArray(size); byte[] buf = theArray.byteify(); rval = H5Dextend(dataset_id, buf); buf = null; theArray = null; return rval; } /** * H5Dfill explicitly fills the dataspace selection in memory, space_id, * with the fill value specified in fill. * * @param fill IN: Pointer to the fill value to be used. * @param fill_type IN: Fill value datatype identifier. * @param buf IN/OUT: Pointer to the memory buffer containing the selection to be filled. * @param buf_type IN: Datatype of dataspace elements to be filled. * @param space IN: Dataspace describing memory buffer and containing the selection to be filled. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - buf is null. **/ public synchronized static native void H5Dfill(byte[] fill, int fill_type, byte[] buf, int buf_type, int space) throws HDF5LibraryException, NullPointerException; /** * H5Dget_access_plist returns an identifier for a copy of the * dataset access property list for a dataset. * * @param dset_id IN: Identifier of the dataset to query. * * @return a dataset access property list identifier * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native int H5Dget_access_plist(int dset_id) throws HDF5LibraryException; /** * H5Dget_create_plist returns an identifier for a copy of the dataset * creation property list for a dataset. * * @param dataset_id * Identifier of the dataset to query. * @return a dataset creation property list identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Dget_create_plist(int dataset_id) throws HDF5LibraryException { int id = _H5Dget_create_plist(dataset_id); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Dget_create_plist(int dataset_id) throws HDF5LibraryException; /** H5Dget_offset returns the address in the file of the dataset dset_id. * * @param dset_id IN: Identifier of the dataset in question * * @return the offset in bytes. * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native long H5Dget_offset(int dset_id) throws HDF5LibraryException; /** * H5Dget_space returns an identifier for a copy of the dataspace for a * dataset. * * @param dataset_id * Identifier of the dataset to query. * * @return a dataspace identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Dget_space(int dataset_id) throws HDF5LibraryException { int id = _H5Dget_space(dataset_id); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Dget_space(int dataset_id) throws HDF5LibraryException; /** * H5Dget_space_status determines whether space has been * allocated for the dataset dset_id. * * @param dset_id IN: Identifier of the dataset to query. * * @return the space allocation status * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native int H5Dget_space_status(int dset_id) throws HDF5LibraryException; /** * H5Dget_space_status determines whether space has been * allocated for the dataset dset_id. * * @param dset_id IN: Identifier of the dataset to query. * * @return the space allocation status * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public static int H5Dget_space_status(int dset_id, int[] status) throws HDF5LibraryException, NullPointerException { return _H5Dget_space_status(dset_id, status); } private synchronized static native int _H5Dget_space_status(int dset_id, int[] status) throws HDF5LibraryException, NullPointerException; /** * H5Dget_storage_size returns the amount of storage that is required for * the dataset. * * @param dataset_id * Identifier of the dataset in question * * @return he amount of storage space allocated for the dataset. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5Dget_storage_size(int dataset_id) throws HDF5LibraryException, IllegalArgumentException; /** * H5Dget_type returns an identifier for a copy of the datatype for a * dataset. * * @param dataset_id * Identifier of the dataset to query. * * @return a datatype identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Dget_type(int dataset_id) throws HDF5LibraryException { int id = _H5Dget_type(dataset_id); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Dget_type(int dataset_id) throws HDF5LibraryException; public synchronized static native int H5Dgetdir_ext(String[] dir_name, int size) throws HDF5LibraryException, NullPointerException; /** * H5Diterate iterates over all the data elements in the memory buffer buf, * executing the callback function operator once for each such data element. * * @param buf IN/OUT: Pointer to the memory containing the elements to iterate over. * @param buf_type IN: Buffer datatype identifier. * @param space IN: Dataspace describing memory buffer. * @param op IN: Callback function to operate on each value. * @param op_data IN/OUT: Pointer to any user-efined data for use by operator function. * * @return returns the return value of the first operator that returns a positive value, or zero if all members were * processed with no operator returning non-zero. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - buf is null. **/ public synchronized static native int H5Diterate(byte[] buf, int buf_type, int space, H5D_iterate_cb op, H5D_iterate_t op_data) throws HDF5LibraryException, NullPointerException; /** * H5Dopen opens the existing dataset specified by a location identifier * and name, loc_id and name, respectively. * * @deprecated As of HDF5 1.8, replaced by {@link #H5Dopen(int, String, int) } * * @param loc_id IN: Location identifier * @param name IN: Dataset name * * @return a dataset identifier if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. **/ @Deprecated public static int H5Dopen(int loc_id, String name) throws HDF5LibraryException, NullPointerException { int id = _H5Dopen(loc_id, name); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Dopen(int loc_id, String name) throws HDF5LibraryException, NullPointerException; /** * H5Dopen opens the existing dataset specified by a location identifier * and name, loc_id and name, respectively. * * @param loc_id IN: Location identifier * @param name IN: Dataset name * @param dapl_id IN: Identifier of dataset access property list. * * @return a dataset identifier if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. **/ public static int H5Dopen(int loc_id, String name, int dapl_id) throws HDF5LibraryException, NullPointerException { int id = _H5Dopen2(loc_id, name, dapl_id); if (id > 0) OPEN_IDS.addElement(id); return id; } /** * H5Dopen2 opens the existing dataset specified by a location identifier * and name, loc_id and name, respectively. * * @see public static int H5Dopen(int loc_id, String name, int dapl_id) **/ private synchronized static native int _H5Dopen2(int loc_id, String name, int dapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Dread reads a (partial) dataset, specified by its identifier * dataset_id, from the file into the application memory buffer buf. * * @param dataset_id * Identifier of the dataset read from. * @param mem_type_id * Identifier of the memory datatype. * @param mem_space_id * Identifier of the memory dataspace. * @param file_space_id * Identifier of the dataset's dataspace in the file. * @param xfer_plist_id * Identifier of a transfer property list for this I/O operation. * @param buf * Buffer to store data read from the file. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - data buffer is null. **/ public synchronized static native int H5Dread(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, byte[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; public synchronized static int H5Dread(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException { return H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } public synchronized static int H5Dread(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException { return H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, obj, true); } /** * H5Dread reads a (partial) dataset, specified by its identifier * dataset_id, from the file into the application data object. * * @param dataset_id * Identifier of the dataset read from. * @param mem_type_id * Identifier of the memory datatype. * @param mem_space_id * Identifier of the memory dataspace. * @param file_space_id * Identifier of the dataset's dataspace in the file. * @param xfer_plist_id * Identifier of a transfer property list for this I/O operation. * @param obj * Object to store data read from the file. * * @return a non-negative value if successful * * @exception HDF5Exception * - Failure in the data conversion. * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - data object is null. **/ public synchronized static int H5Dread(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, Object obj, boolean isCriticalPinning) throws HDF5Exception, HDF5LibraryException, NullPointerException { int status = -1; boolean is1D = false; Class dataClass = obj.getClass(); if (!dataClass.isArray()) { throw (new HDF5JavaException("H5Dread: data is not an array")); } String cname = dataClass.getName(); is1D = (cname.lastIndexOf('[') == cname.indexOf('[')); char dname = cname.charAt(cname.lastIndexOf("[") + 1); if (is1D && (dname == 'B')) { status = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (byte[]) obj, isCriticalPinning); } else if (is1D && (dname == 'S')) { status = H5Dread_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (short[]) obj, isCriticalPinning); } else if (is1D && (dname == 'I')) { status = H5Dread_int(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (int[]) obj, isCriticalPinning); } else if (is1D && (dname == 'J')) { status = H5Dread_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (long[]) obj); } else if (is1D && (dname == 'F')) { status = H5Dread_float(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (float[]) obj, isCriticalPinning); } else if (is1D && (dname == 'D')) { status = H5Dread_double(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (double[]) obj, isCriticalPinning); } else if (H5.H5Tequal(mem_type_id, HDF5Constants.H5T_STD_REF_DSETREG)) { status = H5Dread_reg_ref(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (String[]) obj); } else if (is1D && (dataClass.getComponentType() == String.class)) { // Rosetta Biosoftware - add support for // Strings (variable length) if (H5.H5Tis_variable_str(mem_type_id)) { status = H5DreadVL(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (Object[]) obj); } else { status = H5Dread_string(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (String[]) obj); } } else { // Create a data buffer to hold the data // into a Java Array HDFArray theArray = new HDFArray(obj); byte[] buf = theArray.emptyBytes(); // will raise exception if read fails status = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, isCriticalPinning); if (status >= 0) { // convert the data into a Java // Array */ obj = theArray.arrayify(buf); } // clean up these: assign 'null' as hint // to gc() */ buf = null; theArray = null; } return status; } public synchronized static native int H5Dread_double(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, double[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; public synchronized static int H5Dread_double(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, double[] buf) throws HDF5LibraryException, NullPointerException { return H5Dread_double(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } public synchronized static native int H5Dread_float(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, float[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; public synchronized static int H5Dread_float(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, float[] buf) throws HDF5LibraryException, NullPointerException { return H5Dread_float(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } public synchronized static native int H5Dread_int(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, int[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; public synchronized static int H5Dread_int(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, int[] buf) throws HDF5LibraryException, NullPointerException { return H5Dread_int(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } public synchronized static native int H5Dread_long(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, long[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; public synchronized static int H5Dread_long(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, long[] buf) throws HDF5LibraryException, NullPointerException { return H5Dread_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } public synchronized static native int H5Dread_reg_ref(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Dread_reg_ref_data(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Dread_short(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, short[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; public synchronized static int H5Dread_short(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, short[] buf) throws HDF5LibraryException, NullPointerException { return H5Dread_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } public synchronized static native int H5Dread_string(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5DreadVL(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, Object[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Dset_extent sets the current dimensions of the chunked dataset dset_id * to the sizes specified in size. * * @param dset_id IN: Chunked dataset identifier. * @param size IN: Array containing the new magnitude of each dimension of the dataset. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - size is null. **/ public synchronized static native void H5Dset_extent(int dset_id, long size[]) throws HDF5LibraryException, NullPointerException; private synchronized static native int _H5Aopen_by_name(int loc_id, String obj_name, String attr_name,int aapl_id, int lapl_id) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Dvlen_get_buf_size(int dataset_id, int type_id, int space_id, int[] size) throws HDF5LibraryException; /** * H5Dvlen_get_buf_size determines the number of bytes required to store the VL data from * the dataset, using the space_id for the selection in the dataset on disk and the * type_id for the memory representation of the VL data in memory. * * @param dset_id IN: Identifier of the dataset read from. * @param type_id IN: Identifier of the datatype. * @param space_id IN: Identifier of the dataspace. * * @return the size in bytes of the memory buffer required to store the VL data. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - buf is null. **/ public synchronized static native long H5Dvlen_get_buf_size_long(int dset_id, int type_id, int space_id) throws HDF5LibraryException; //int H5Dvlen_get_buf_size(int dset_id, int type_id, int space_id, LongByReference size); /** * * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - buf is null. **/ public synchronized static native int H5Dvlen_reclaim(int type_id, int space_id, int xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Dwrite writes a (partial) dataset, specified by its identifier * dataset_id, from the application memory buffer buf into the file. * * @param dataset_id * Identifier of the dataset read from. * @param mem_type_id * Identifier of the memory datatype. * @param mem_space_id * Identifier of the memory dataspace. * @param file_space_id * Identifier of the dataset's dataspace in the file. * @param xfer_plist_id * Identifier of a transfer property list for this I/O operation. * @param buf * Buffer with data to be written to the file. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native int H5Dwrite(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, byte[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; public synchronized static int H5Dwrite(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException { return H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } public synchronized static int H5Dwrite(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException { return H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, obj, true); } /** * H5Dwrite writes a (partial) dataset, specified by its identifier * dataset_id, from the application memory data object into the file. * * @param dataset_id * Identifier of the dataset read from. * @param mem_type_id * Identifier of the memory datatype. * @param mem_space_id * Identifier of the memory dataspace. * @param file_space_id * Identifier of the dataset's dataspace in the file. * @param xfer_plist_id * Identifier of a transfer property list for this I/O operation. * @param obj * Object with data to be written to the file. * * @return a non-negative value if successful * * @exception HDF5Exception * - Failure in the data conversion. * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - data object is null. **/ public synchronized static int H5Dwrite(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, Object obj, boolean isCriticalPinning) throws HDF5Exception, HDF5LibraryException, NullPointerException { int status = -1; boolean is1D = false; Class dataClass = obj.getClass(); if (!dataClass.isArray()) { throw (new HDF5JavaException("H5Dread: data is not an array")); } String cname = dataClass.getName(); is1D = (cname.lastIndexOf('[') == cname.indexOf('[')); char dname = cname.charAt(cname.lastIndexOf("[") + 1); if (is1D && (dname == 'B')) { status = H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (byte[]) obj, isCriticalPinning); } else if (is1D && (dname == 'S')) { status = H5Dwrite_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (short[]) obj, isCriticalPinning); } else if (is1D && (dname == 'I')) { status = H5Dwrite_int(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (int[]) obj, isCriticalPinning); } else if (is1D && (dname == 'J')) { status = H5Dwrite_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (long[]) obj, isCriticalPinning); } else if (is1D && (dname == 'F')) { status = H5Dwrite_float(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (float[]) obj, isCriticalPinning); } else if (is1D && (dname == 'D')) { status = H5Dwrite_double(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (double[]) obj, isCriticalPinning); } // Rosetta Biosoftware - call into H5DwriteString // for variable length Strings else if ((H5.H5Tget_class(mem_type_id) == HDF5Constants.H5T_STRING) && H5.H5Tis_variable_str(mem_type_id) && dataClass.isArray() && (dataClass.getComponentType() == String.class) && is1D) { status = H5DwriteString(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (String[]) obj); } else { HDFArray theArray = new HDFArray(obj); byte[] buf = theArray.byteify(); /* will raise exception on error */ status = H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, isCriticalPinning); // clean up these: assign 'null' as hint to // gc() */ buf = null; theArray = null; } return status; } public synchronized static native int H5Dwrite_double(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, double[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; public synchronized static int H5Dwrite_double(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, double[] buf) throws HDF5LibraryException, NullPointerException { return H5Dwrite_double(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } public synchronized static native int H5Dwrite_float(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, float[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; public synchronized static int H5Dwrite_float(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, float[] buf) throws HDF5LibraryException, NullPointerException { return H5Dwrite_float(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } public synchronized static native int H5Dwrite_int(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, int[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; public synchronized static int H5Dwrite_int(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, int[] buf) throws HDF5LibraryException, NullPointerException { return H5Dwrite_int(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } public synchronized static native int H5Dwrite_long(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, long[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; public synchronized static int H5Dwrite_long(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, long[] buf) throws HDF5LibraryException, NullPointerException { return H5Dwrite_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } public synchronized static native int H5Dwrite_short(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, short[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; public synchronized static int H5Dwrite_short(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, short[] buf) throws HDF5LibraryException, NullPointerException { return H5Dwrite_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } /** * H5DwriteString writes a (partial) variable length String dataset, * specified by its identifier dataset_id, from the application memory * buffer buf into the file. * * ---- contributed by Rosetta Biosoftware * * @param dataset_id * Identifier of the dataset read from. * @param mem_type_id * Identifier of the memory datatype. * @param mem_space_id * Identifier of the memory dataspace. * @param file_space_id * Identifier of the dataset's dataspace in the file. * @param xfer_plist_id * Identifier of a transfer property list for this I/O operation. * @param buf * Buffer with data to be written to the file. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native int H5DwriteString(int dataset_id, int mem_type_id, int mem_space_id, int file_space_id, int xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException; ///////// unimplemented //////// //herr_t H5Dgather(hid_t src_space_id, const void *src_buf, hid_t type_id, // size_t dst_buf_size, void *dst_buf, H5D_gather_func_t op, void *op_data); //herr_t H5Dscatter(H5D_scatter_func_t op, void *op_data, hid_t type_id, hid_t dst_space_id, void *dst_buf); ////////////////////////////////////////////////////////////// //// //H5E: Error Stack // //// ////////////////////////////////////////////////////////////// /** * H5Eauto_is_v2 determines whether the error auto reporting function for an * error stack conforms to the H5E_auto2_t typedef or the H5E_auto1_t * typedef. * * @param stack_id * IN: Error stack identifier. * * @return boolean true if the error stack conforms to H5E_auto2_t and false * if it conforms to H5E_auto1_t. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native boolean H5Eauto_is_v2(int stack_id) throws HDF5LibraryException; /** * H5Eclear clears the error stack for the current thread. H5Eclear can fail * if there are problems initializing the library. *

* This may be used by exception handlers to assure that the error condition * in the HDF-5 library has been reset. * * @return Returns a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Eclear() throws HDF5LibraryException { H5Eclear2(HDF5Constants.H5E_DEFAULT); return 0; } /** * H5Eclear clears the error stack specified by estack_id, or, if estack_id * is set to H5E_DEFAULT, the error stack for the current thread. * * @param stack_id * IN: Error stack identifier. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static void H5Eclear(int stack_id) throws HDF5LibraryException { H5Eclear2(stack_id); } /** * H5Eclear2 clears the error stack specified by estack_id, or, if estack_id * is set to H5E_DEFAULT, the error stack for the current thread. * * @see #H5Eclear **/ public synchronized static native void H5Eclear2(int stack_id) throws HDF5LibraryException; /** * H5Eclose_msg closes an error message identifier, which can be either a * major or minor message. * * @param err_id * IN: Error message identifier. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Eclose_msg(int err_id) throws HDF5LibraryException; /** * H5Eclose_stack closes the object handle for an error stack and releases * its resources. * * @param stack_id * IN: Error stack identifier. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Eclose_stack(int stack_id) throws HDF5LibraryException; /** * H5Ecreate_msg adds an error message to an error class defined by client * library or application program. * * @param cls_id * IN: Error class identifier. * @param msg_type * IN: The type of the error message. * @param msg * IN: The error message. * * @return a message identifier * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - msg is null. **/ public synchronized static native int H5Ecreate_msg(int cls_id, int msg_type, String msg) throws HDF5LibraryException, NullPointerException; /** * H5Ecreate_stack creates a new empty error stack and returns the new * stack's identifier. * * @return an error stack identifier * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Ecreate_stack() throws HDF5LibraryException; /** * H5Eget_class_name retrieves the name of the error class specified by the * class identifier. * * @param class_id * IN: Error class identifier. * * @return the name of the error class * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native String H5Eget_class_name(int class_id) throws HDF5LibraryException, NullPointerException; // long H5Eget_class_name(int class_id, String name, IntegerType size); /** * H5Eget_current_stack copies the current error stack and returns an error * stack identifier for the new copy. * * @return an error stack identifier * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Eget_current_stack() throws HDF5LibraryException; /** * H5Eset_current_stack replaces the content of the current error stack with * a copy of the content of the error stack specified by estack_id. * * @param stack_id * IN: Error stack identifier. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Eset_current_stack(int stack_id) throws HDF5LibraryException; /** * H5Eget_msg retrieves the error message including its length and type. * * @param msg_id * IN: Name of the error class. * @param type_list * OUT: The type of the error message. Valid values are H5E_MAJOR * and H5E_MINOR. * * @return the error message * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native String H5Eget_msg(int msg_id, int[] type_list) throws HDF5LibraryException; // long H5Eget_msg(int msg_id, H5E_TYPE type, String msg, IntegerType size); /** * H5Eget_num retrieves the number of error records in the error stack * specified by estack_id (including major, minor messages and description). * * @param stack_id * IN: Error stack identifier. * * @return the number of error messages * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5Eget_num(int stack_id) throws HDF5LibraryException, NullPointerException; /** * H5Eprint1 prints the error stack specified by estack_id on the specified * stream, stream. * * @param stream * IN: File pointer, or stderr if null. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * * @deprecated As of HDF5 1.8, replaced by {@link #H5Eprint2(int, Object)} **/ @Deprecated public synchronized static native void H5Eprint1(Object stream) throws HDF5LibraryException; /** * H5Eprint2 prints the error stack specified by estack_id on the specified * stream, stream. * * @param stack_id * IN: Error stack identifier.If the identifier is H5E_DEFAULT, * the current error stack will be printed. * @param stream * IN: File pointer, or stderr if null. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Eprint2(int stack_id, Object stream) throws HDF5LibraryException; /** * H5Epop deletes the number of error records specified in count from the * top of the error stack specified by estack_id (including major, minor * messages and description). * * @param stack_id * IN: Error stack identifier. * @param count * IN: Version of the client library or application to which the * error class belongs. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Epop(int stack_id, long count) throws HDF5LibraryException; /** * H5Eregister_class registers a client library or application program to * the HDF5 error API so that the client library or application program can * report errors together with HDF5 library. * * @param cls_name * IN: Name of the error class. * @param lib_name * IN: Name of the client library or application to which the * error class belongs. * @param version * IN: Version of the client library or application to which the * error class belongs. * * @return a class identifier * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native int H5Eregister_class(String cls_name, String lib_name, String version) throws HDF5LibraryException, NullPointerException; /** * H5Eunregister_class removes the error class specified by class_id. * * @param class_id * IN: Error class identifier. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Eunregister_class(int class_id) throws HDF5LibraryException; ///////// unimplemented //////// //public interface H5E_auto2_t extends Callback //{ // int callback(int estack, Pointer client_data); //} //int H5Eget_auto(int estack_id, H5E_auto2_t func, PointerByReference client_data); //{ // return H5Eget_auto2(estack_id, func, client_data); //} //int H5Eget_auto2(int estack_id, H5E_auto2_t func, PointerByReference client_data); //int H5Eset_auto(int estack_id, H5E_auto2_t func, Pointer client_data); //{ // return H5Eset_auto2(estack_id, func, client_data); //} //int H5Eset_auto2(int estack_id, H5E_auto2_t func, Pointer client_data); //public static int H5Epush(int err_stack, String file, String func, int line, // int cls_id, int maj_id, int min_id, String msg, ...) //{ // H5Epush2(err_stack, file, func, line, cls_id, maj_id, min_id, msg, ...); //} //public synchronized static native int H5Epush2(int err_stack, String file, String func, int line, // int cls_id, int maj_id, int min_id, String msg, ...); ////Error stack traversal callback function pointers //public interface H5E_walk2_t extends Callback //{ // int callback(int n, H5E_error2_t err_desc, Pointer client_data); //} //int H5Ewalk(int err_stack, H5E_direction_t direction, H5E_walk2_t func, Pointer client_data) //{ // return H5Ewalk2(err_stack, direction, func, client_data); //} //int H5Ewalk2(int err_stack, H5E_direction_t direction, H5E_walk2_t func, Pointer client_data); ////////////////////////////////////////////////////////////// //// //H5F: File Interface Functions // //// ////////////////////////////////////////////////////////////// /** * H5Fclose terminates access to an HDF5 file. * * @param file_id * Identifier of a file to terminate access to. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Fclose(int file_id) throws HDF5LibraryException { if (file_id <0) return 0; // throw new HDF5LibraryException("Negative ID");; OPEN_IDS.removeElement(file_id); return _H5Fclose(file_id); } private synchronized static native int _H5Fclose(int file_id) throws HDF5LibraryException; /** * H5Fopen opens an existing file and is the primary function for accessing * existing HDF5 files. * * @param name * Name of the file to access. * @param flags * File access flags. * @param access_id * Identifier for the file access properties list. * * @return a file identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public static int H5Fopen(String name, int flags, int access_id) throws HDF5LibraryException, NullPointerException { int id = _H5Fopen(name, flags, access_id); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Fopen(String name, int flags, int access_id) throws HDF5LibraryException, NullPointerException; /** * H5Freopen reopens an HDF5 file. * * @param file_id * Identifier of a file to terminate and reopen access to. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @return a new file identifier if successful **/ public static int H5Freopen(int file_id) throws HDF5LibraryException { int id = _H5Freopen(file_id); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Freopen(int file_id) throws HDF5LibraryException; /** * H5Fcreate is the primary function for creating HDF5 files. * * @param name * Name of the file to access. * @param flags * File access flags. Possible values include: *

    *
  • * H5F_ACC_RDWR Allow read and write access to file.
    • *
  • * H5F_ACC_RDONLY Allow read-only access to file.
    • *
  • * H5F_ACC_TRUNC Truncate file, if it already exists, erasing all * data previously stored in the file.
    • *
  • * H5F_ACC_EXCL Fail if file already exists.
    • *
  • * H5F_ACC_DEBUG Print debug information.
    • *
  • * H5P_DEFAULT Apply default file access and creation properties. *
    • *
* * @param create_id * File creation property list identifier, used when modifying * default file meta-data. Use H5P_DEFAULT for default access * properties. * @param access_id * File access property list identifier. If parallel file access * is desired, this is a collective call according to the * communicator stored in the access_id (not supported in Java). * Use H5P_DEFAULT for default access properties. * * @return a file identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public static int H5Fcreate(String name, int flags, int create_id, int access_id) throws HDF5LibraryException, NullPointerException { int id = _H5Fcreate(name, flags, create_id, access_id); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Fcreate(String name, int flags, int create_id, int access_id) throws HDF5LibraryException, NullPointerException; /** * H5Fflush causes all buffers associated with a file or object to be * immediately flushed (written) to disk without removing the data from the * (memory) cache. *

* After this call completes, the file (or object) is in a consistent state * and all data written to date is assured to be permanent. * * @param object_id * Identifier of object used to identify the file. * object_id can be any object associated with the file, * including the file itself, a dataset, a group, an attribute, * or a named data type. * @param scope * specifies the scope of the flushing action, in the case that * the HDF-5 file is not a single physical file. *

* Valid values are: *

    *
  • * H5F_SCOPE_GLOBAL Flushes the entire virtual file.
    • *
  • * H5F_SCOPE_LOCAL Flushes only the specified file.
    • *
* * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Fflush(int object_id, int scope) throws HDF5LibraryException; /** * H5Fget_access_plist returns the file access property list identifier of * the specified file. * * @param file_id * Identifier of file to get access property list of * * @return a file access property list identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Fget_access_plist(int file_id) throws HDF5LibraryException { int id = _H5Fget_access_plist(file_id); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Fget_access_plist(int file_id) throws HDF5LibraryException; /** * H5Fget_create_plist returns a file creation property list identifier * identifying the creation properties used to create this file. * * @param file_id * Identifier of the file to get creation property list * * @return a file creation property list identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Fget_create_plist(int file_id) throws HDF5LibraryException { int id = _H5Fget_create_plist(file_id); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Fget_create_plist(int file_id) throws HDF5LibraryException; public synchronized static native long H5Fget_filesize(int file_id) throws HDF5LibraryException; /** * H5Fget_freespace returns the amount of space that is unused by any * objects in the file. * * @param file_id * IN: File identifier for a currently-open HDF5 file * * @return the amount of free space in the file * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5Fget_freespace(int file_id) throws HDF5LibraryException; /** * H5Fget_intent retrieves the intended access mode flag passed with H5Fopen * when the file was opened. * * @param file_id * IN: File identifier for a currently-open HDF5 file * * @return the intended access mode flag, as originally passed with H5Fopen. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Fget_intent(int file_id) throws HDF5LibraryException; // int H5Fget_intent(int file_id, IntByReference intent); /** * H5Fget_mdc_hit_rate queries the metadata cache of the target file to * obtain its hit rate (cache hits / (cache hits + cache misses)) since the * last time hit rate statistics were reset. * * @param file_id * IN: Identifier of the target file. * * @return the double in which the hit rate is returned. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native double H5Fget_mdc_hit_rate(int file_id) throws HDF5LibraryException; /** * H5Fget_mdc_size queries the metadata cache of the target file for the * desired size information. * * @param file_id * IN: Identifier of the target file. * @param metadata_cache * OUT: Current metadata cache information *
    *
  • metadata_cache[0] = max_size_ptr // current cache maximum * size
    • *
  • metadata_cache[1] = min_clean_size_ptr // current cache * minimum clean size
    • *
  • metadata_cache[2] = cur_size_ptr // current cache size
    • *
* * @return current number of entries in the cache * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - metadata_cache is null. **/ public synchronized static native int H5Fget_mdc_size(int file_id, long[] metadata_cache) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Fget_name retrieves the name of the file to which the object obj_id * belongs. * * @param obj_id * IN: Identifier of the object for which the associated filename * is sought. * * @return the filename. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native String H5Fget_name(int obj_id) throws HDF5LibraryException; // long H5Fget_name(int obj_id, Buffer name/*out*/, long size); public synchronized static native String H5Fget_name(int obj_id, int size) throws HDF5LibraryException; /** * H5Fget_obj_count returns the number of open object identifiers for the * file. * * @param file_id * IN: File identifier for a currently-open HDF5 file * @param types * IN: Type of object for which identifiers are to be returned. *
    *
  • H5F_OBJ_FILE Files only
    • *
  • H5F_OBJ_DATASET Datasets only
    • *
  • H5F_OBJ_GROUP Groups only
    • *
  • H5F_OBJ_DATATYPE Named datatypes only
    • *
  • H5F_OBJ_ATTR Attributes only
    • *
  • H5F_OBJ_ALL All of the above
    • *
  • H5F_OBJ_LOCAL Restrict search to objects opened through * current file identifier.
    • *
* * @return the number of open objects. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Fget_obj_count(int file_id, int types) throws HDF5LibraryException; /** * H5Fget_obj_count returns the number of open object identifiers for the * file. * * @param file_id * IN: File identifier for a currently-open HDF5 file * @param types * IN: Type of object for which identifiers are to be returned. *
    *
  • H5F_OBJ_FILE Files only
    • *
  • H5F_OBJ_DATASET Datasets only
    • *
  • H5F_OBJ_GROUP Groups only
    • *
  • H5F_OBJ_DATATYPE Named datatypes only
    • *
  • H5F_OBJ_ATTR Attributes only
    • *
  • H5F_OBJ_ALL All of the above
    • *
  • H5F_OBJ_LOCAL Restrict search to objects opened through * current file identifier.
    • *
* * @return the number of open objects. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5Fget_obj_count_long(int file_id, int types) throws HDF5LibraryException; /** * H5Fget_obj_ids returns the list of identifiers for all open HDF5 objects * fitting the specified criteria. * * @param file_id * IN: File identifier for a currently-open HDF5 file * @param types * IN: Type of object for which identifiers are to be returned. * @param max_objs * IN: Maximum number of object identifiers to place into * obj_id_list. * @param obj_id_list * OUT: Pointer to the returned list of open object identifiers. * * @return the number of objects placed into obj_id_list. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - obj_id_list is null. **/ public synchronized static native int H5Fget_obj_ids(int file_id, int types, int max_objs, int[] obj_id_list) throws HDF5LibraryException, NullPointerException; /** * H5Fget_obj_ids returns the list of identifiers for all open HDF5 objects * fitting the specified criteria. * * @param file_id * IN: File identifier for a currently-open HDF5 file * @param types * IN: Type of object for which identifiers are to be returned. * @param max_objs * IN: Maximum number of object identifiers to place into * obj_id_list. * @param obj_id_list * OUT: Pointer to the returned list of open object identifiers. * * @return the number of objects placed into obj_id_list. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - obj_id_list is null. **/ public synchronized static native long H5Fget_obj_ids_long(int file_id, int types, long max_objs, int[] obj_id_list) throws HDF5LibraryException, NullPointerException; /** * H5Fis_hdf5 determines whether a file is in the HDF5 format. * * @param name * File name to check format. * * @return true if is HDF-5, false if not. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native boolean H5Fis_hdf5(String name) throws HDF5LibraryException, NullPointerException; /** * H5Fmount mounts the file specified by child_id onto the group specified * by loc_id and name using the mount properties plist_id. * * @param loc_id * The identifier for the group onto which the file specified by * child_id is to be mounted. * @param name * The name of the group onto which the file specified by * child_id is to be mounted. * @param child_id * The identifier of the file to be mounted. * @param plist_id * The identifier of the property list to be used. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native int H5Fmount(int loc_id, String name, int child_id, int plist_id) throws HDF5LibraryException, NullPointerException; /** * Given a mount point, H5Funmount dissassociates the mount point's file * from the file mounted there. * * @param loc_id * The identifier for the location at which the specified file is * to be unmounted. * @param name * The name of the file to be unmounted. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native int H5Funmount(int loc_id, String name) throws HDF5LibraryException, NullPointerException; /** * H5Freset_mdc_hit_rate_stats resets the hit rate statistics counters in * the metadata cache associated with the specified file. * * @param file_id * IN: Identifier of the target file. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Freset_mdc_hit_rate_stats( int file_id) throws HDF5LibraryException; ///////// unimplemented //////// //herr_t H5Fclear_elink_file_cache(hid_t file_id); //ssize_t H5Fget_file_image(hid_t file_id, void * buf_ptr, size_t buf_len); ///** //* H5Fget_info returns global information for the file associated with the //* object identifier obj_id. //* //* @param obj_id IN: Object identifier for any object in the file. //* //* @return the structure containing global file information. //* //* @exception HDF5LibraryException - Error from the HDF-5 Library. //**/ //public synchronized static native H5F_info_t H5Fget_info(int obj_id) //throws HDF5LibraryException, NullPointerException; //int H5Fget_info(int obj_id, H5F_info_t file_info); ///** //* H5Fget_mdc_config loads the current metadata cache configuration into //* the instance of H5AC_cache_config_t pointed to by the config_ptr //parameter. //* //* @param file_id IN: Identifier of the target file //* @param config_ptr IN/OUT: Pointer to the instance of //H5AC_cache_config_t in which the current metadata cache configuration is to be reported. //* //* @return none //* //* @exception HDF5LibraryException - Error from the HDF-5 Library. //* @exception NullPointerException - config_ptr is null. //**/ //public synchronized static native void H5Fget_mdc_config(int file_id, H5AC_cache_config_t config_ptr) //throws HDF5LibraryException, NullPointerException; ///** //* H5Fget_vfd_handle returns a pointer to the file handle from the //low-level file driver //* currently being used by the HDF5 library for file I/O. //* //* @param file_id IN: Identifier of the file to be queried. //* @param fapl IN: File access property list identifier. //* //* @return a pointer to the file handle being used by the low-level //virtual file driver. //* //* @exception HDF5LibraryException - Error from the HDF-5 Library. //**/ //public synchronized static native Pointer file_handle //H5Fget_vfd_handle(int file_id, int fapl) //throws HDF5LibraryException; ///** //* H5Fset_mdc_config attempts to configure the file's metadata cache //according to the configuration supplied. //* //* @param file_id IN: Identifier of the target file //* @param config_ptr IN: Pointer to the instance of H5AC_cache_config_t //containing the desired configuration. //* //* @return none //* //* @exception HDF5LibraryException - Error from the HDF-5 Library. //* @exception NullPointerException - config_ptr is null. //**/ //public synchronized static native int H5Fset_mdc_config(int file_id, //H5AC_cache_config_t config_ptr) //throws HDF5LibraryException, NullPointerException; // //////////////////////////////////////////////////////////// // // // H5G: Group Interface Functions // // // // //////////////////////////////////////////////////////////// /** * H5Gclose releases resources used by a group which was opened by a call to * H5Gcreate() or H5Gopen(). * * @param group_id * Group identifier to release. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Gclose(int group_id) throws HDF5LibraryException { if (group_id < 0) return 0; // throw new HDF5LibraryException("Negative ID");; OPEN_IDS.removeElement(group_id); return _H5Gclose(group_id); } private synchronized static native int _H5Gclose(int group_id) throws HDF5LibraryException; /** * H5Gcreate creates a new group with the specified name at the specified * location, loc_id. * * @deprecated As of HDF5 1.8, replaced by {@link #H5Gcreate(int, String, int, int, int) } * * @param loc_id * The file or group identifier. * @param name * The absolute or relative name of the new group. * @param size_hint * An optional parameter indicating the number of bytes to * reserve for the names that will appear in the group. * * @return a valid group identifier for the open group if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ @Deprecated public static int H5Gcreate(int loc_id, String name, long size_hint) throws HDF5LibraryException, NullPointerException { int id = _H5Gcreate(loc_id, name, size_hint); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Gcreate(int loc_id, String name, long size_hint) throws HDF5LibraryException, NullPointerException; /** * H5Gcreate creates a new group with the specified name at the specified * location, loc_id. * * @param loc_id * IN: The file or group identifier. * @param name * IN: The absolute or relative name of the new group. * @param lcpl_id * IN: Identifier of link creation property list. * @param gcpl_id * IN: Identifier of group creation property list. * @param gapl_id * IN: Identifier of group access property list. (No group access * properties have been implemented at this time; use * H5P_DEFAULT.) * * @return a valid group identifier * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public static int H5Gcreate(int loc_id, String name, int lcpl_id, int gcpl_id, int gapl_id) throws HDF5LibraryException, NullPointerException { int id = _H5Gcreate2(loc_id, name, lcpl_id, gcpl_id, gapl_id); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Gcreate2(int loc_id, String name, int lcpl_id, int gcpl_id, int gapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Gcreate_anon creates a new empty group in the file specified by loc_id. * * @param loc_id * IN: File or group identifier specifying the file in which the * new group is to be created. * @param gcpl_id * IN: Identifier of group creation property list. * @param gapl_id * IN: Identifier of group access property list. (No group access * properties have been implemented at this time; use * H5P_DEFAULT.) * * @return a valid group identifier * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Gcreate_anon(int loc_id, int gcpl_id, int gapl_id) throws HDF5LibraryException { int id = _H5Gcreate_anon(loc_id, gcpl_id, gapl_id); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Gcreate_anon(int loc_id, int gcpl_id, int gapl_id) throws HDF5LibraryException; /** * H5Gget_comment retrieves the comment for the the object name. The comment * is returned in the buffer comment. * * @param loc_id * IN: Identifier of the file, group, dataset, or datatype. * @param name * IN: Name of the object whose comment is to be set or reset. * @param bufsize * IN: Anticipated size of the buffer required to hold comment. * @param comment * OUT: The comment. * @return the number of characters in the comment, counting the null * terminator, if successful * * @exception ArrayIndexOutOfBoundsException * - JNI error writing back data * @exception ArrayStoreException * - JNI error writing back data * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. * @exception IllegalArgumentException * - size < 1, comment is invalid. * * @deprecated As of HDF5 1.8, replaced by {@link #H5Oget_comment(int)} **/ @Deprecated public synchronized static native int H5Gget_comment(int loc_id, String name, int bufsize, String[] comment) throws ArrayIndexOutOfBoundsException, ArrayStoreException, HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Gset_comment sets the comment for the the object name to comment. Any * previously existing comment is overwritten. * * @param loc_id * IN: Identifier of the file, group, dataset, or datatype. * @param name * IN: Name of the object whose comment is to be set or reset. * @param comment * IN: The new comment. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name or comment is null. * * @deprecated As of HDF5 1.8, replaced by {@link #H5Oset_comment(int, String)} **/ @Deprecated public synchronized static native int H5Gset_comment(int loc_id, String name, String comment) throws HDF5LibraryException, NullPointerException; /** * H5Gget_create_plist returns an identifier for the group creation property * list associated with the group specified by group_id. * * @param group_id * IN: Identifier of the group. * * @return an identifier for the group's creation property list * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Gget_create_plist(int group_id) throws HDF5LibraryException; /** * H5Gget_info retrieves information about the group specified by group_id. * The information is returned in the group_info struct. * * @param group_id * IN: Identifier of the group. * * @return a structure in which group information is returned * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native H5G_info_t H5Gget_info(int group_id) throws HDF5LibraryException; // int H5Gget_info(int loc_id, H5G_info_t ginfo); /** * H5Gget_info_by_idx retrieves information about a group, according to the * group's position within an index. * * @param group_id * IN: File or group identifier. * @param group_name * IN: Name of group for which information is to be retrieved. * @param idx_type * IN: Type of index by which objects are ordered * @param order * IN: Order of iteration within index * @param n * IN: Attribute's position in index * @param lapl_id * IN: Link access property list. * * @return a structure in which group information is returned * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native H5G_info_t H5Gget_info_by_idx( int group_id, String group_name, int idx_type, int order, long n, int lapl_id) throws HDF5LibraryException, NullPointerException; // int H5Gget_info_by_idx(int group_id, String group_name, // H5_index_t idx_type, H5_iter_order_t order, long n, H5G_info_t ginfo, int // lapl_id); /** * H5Gget_info_by_name retrieves information about the group group_name * located in the file or group specified by loc_id. * * @param group_id * IN: File or group identifier. * @param name * IN: Name of group for which information is to be retrieved. * @param lapl_id * IN: Link access property list. * * @return a structure in which group information is returned * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native H5G_info_t H5Gget_info_by_name( int group_id, String name, int lapl_id) throws HDF5LibraryException, NullPointerException; // int H5Gget_info_by_name(int group_id, String name, H5G_info_t ginfo, int // lapl_id); /** * H5Gget_linkval returns size characters of the link value through the * value argument if loc_id (a file or group identifier) and name specify a * symbolic link. * * @param loc_id * IN: Identifier of the file, group, dataset, or datatype. * @param name * IN: Name of the object whose link value is to be checked. * @param size * IN: Maximum number of characters of value to be returned. * @param value * OUT: Link value. * * @return a non-negative value, with the link value in value, if * successful. * * @exception ArrayIndexOutOfBoundsException * Copy back failed * @exception ArrayStoreException * Copy back failed * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. * @exception IllegalArgumentException * - size is invalid * * @deprecated As of HDF5 1.8, replaced by {@link #H5Lget_val(int, String, String[] , int)} **/ @Deprecated public synchronized static native int H5Gget_linkval(int loc_id, String name, int size, String[] value) throws ArrayIndexOutOfBoundsException, ArrayStoreException, HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * Returns number of objects in the group specified by its identifier * * @param loc_id * Identifier of the group or the file * @param num_obj * Number of objects in the group * @return positive value if successful; otherwise returns a negative value. * @throws HDF5LibraryException * @throws NullPointerException * * @deprecated As of HDF5 1.8, replaced by {@link #H5Gget_info(int)} */ @Deprecated public synchronized static native int H5Gget_num_objs(int loc_id, long[] num_obj) throws HDF5LibraryException, NullPointerException; /** * retrieves information of all objects under the group (name) located in * the file or group specified by loc_id. * * @param loc_id * IN: File or group identifier * @param name * IN: Name of group for which information is to be retrieved * @param objNames * OUT: Names of all objects under the group, name. * @param objTypes * OUT: Types of all objects under the group, name. * @param objRef * OUT: Reference number of all objects under the group, name. * * @return the number of items found * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. */ public synchronized static int H5Gget_obj_info_all(int loc_id, String name, String[] objNames, int[] objTypes, long[] objRef) throws HDF5LibraryException, NullPointerException { if (objNames == null) { throw new NullPointerException( "H5Gget_obj_info_all(): name array is null"); } return H5Gget_obj_info_all(loc_id, name, objNames, objTypes, null, null, objRef, HDF5Constants.H5_INDEX_NAME); } public synchronized static int H5Gget_obj_info_all(int loc_id, String name, String[] oname, int[] otype, int[] ltype, long[] ref, int indx_type) throws HDF5LibraryException, NullPointerException { return H5Gget_obj_info_full(loc_id, name, oname, otype, ltype, null, ref, indx_type, -1); } public synchronized static int H5Gget_obj_info_all(int loc_id, String name, String[] oname, int[] otype, int[] ltype, long[] fno, long[] ref, int indx_type) throws HDF5LibraryException, NullPointerException { return H5Gget_obj_info_full(loc_id, name, oname, otype, ltype, fno, ref, oname.length, indx_type, -1); } public synchronized static int H5Gget_obj_info_full(int loc_id, String name, String[] oname, int[] otype, int[] ltype, long[] fno, long[] ref, int indx_type, int indx_order) throws HDF5LibraryException, NullPointerException { if (oname == null) { throw new NullPointerException( "H5Gget_obj_info_full(): name array is null"); } if (otype == null) { throw new NullPointerException( "H5Gget_obj_info_full(): object type array is null"); } if (oname.length == 0) { throw new HDF5LibraryException( "H5Gget_obj_info_full(): array size is zero"); } if (oname.length != otype.length) { throw new HDF5LibraryException( "H5Gget_obj_info_full(): name and type array sizes are different"); } if (ltype == null) ltype = new int[otype.length]; if (fno == null) fno = new long[ref.length]; if (indx_type < 0) indx_type = HDF5Constants.H5_INDEX_NAME; if (indx_order < 0) indx_order = HDF5Constants.H5_ITER_INC; return H5Gget_obj_info_full(loc_id, name, oname, otype, ltype, fno, ref, oname.length, indx_type, indx_order); } private synchronized static native int H5Gget_obj_info_full(int loc_id, String name, String[] oname, int[] otype, int[] ltype, long[] fno, long[] ref, int n, int indx_type, int indx_order) throws HDF5LibraryException, NullPointerException; /** * H5Gget_obj_info_idx report the name and type of object with index 'idx' * in a Group. The 'idx' corresponds to the index maintained by H5Giterate. * Each link is returned, so objects with multiple links will be counted * once for each link. * * @param loc_id * IN: file or group ID. * @param name * IN: name of the group to iterate, relative to the loc_id * @param idx * IN: the index of the object to iterate. * @param oname * the name of the object [OUT] * @param type * the type of the object [OUT] * * @return non-negative if successful, -1 if not. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. */ public synchronized static int H5Gget_obj_info_idx(int loc_id, String name, int idx, String[] oname, int[] type) throws HDF5LibraryException, NullPointerException { long default_buf_size = 4096; String n[] = new String[1]; n[0] = new String(""); int grp_id = H5Gopen(loc_id, name); long val = H5Gget_objname_by_idx(grp_id, idx, n, default_buf_size); int type_code = H5Gget_objtype_by_idx(grp_id, idx); oname[0] = new String(n[0]); type[0] = type_code; int ret = (new Long(val)).intValue(); return ret; } /* * ////////////////////////////////////////////////////////////////////////// * /////// // // //Add these methods so that we don't need to call * //in a loop to get information for all the object * in a group, which takes //a lot of time to finish if the number of * objects is more than 10,000 // * /////////////////////////////////////////// * ////////////////////////////////////// */ /** * retrieves information of all objects (recurvisely) under the group (name) * located in the file or group specified by loc_id upto maximum specified * by objMax. * * @param loc_id * IN: File or group identifier * @param objNames * OUT: Names of all objects under the group, name. * @param objTypes * OUT: Types of all objects under the group, name. * @param lnkTypes * OUT: Types of all links under the group, name. * @param objRef * OUT: Reference number of all objects under the group, name. * @param objMax * IN: Maximum number of all objects under the group, name. * * @return the number of items found * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. */ public synchronized static int H5Gget_obj_info_max(int loc_id, String[] objNames, int[] objTypes, int[] lnkTypes, long[] objRef, int objMax) throws HDF5LibraryException, NullPointerException { if (objNames == null) { throw new NullPointerException( "H5Gget_obj_info_max(): name array is null"); } if (objTypes == null) { throw new NullPointerException( "H5Gget_obj_info_max(): object type array is null"); } if (lnkTypes == null) { throw new NullPointerException( "H5Gget_obj_info_max(): link type array is null"); } if (objNames.length <= 0) { throw new HDF5LibraryException( "H5Gget_obj_info_max(): array size is zero"); } if (objMax <= 0) { throw new HDF5LibraryException( "H5Gget_obj_info_max(): maximum array size is zero"); } if (objNames.length != objTypes.length) { throw new HDF5LibraryException( "H5Gget_obj_info_max(): name and type array sizes are different"); } return H5Gget_obj_info_max(loc_id, objNames, objTypes, lnkTypes, objRef, objMax, objNames.length); } private synchronized static native int H5Gget_obj_info_max(int loc_id, String[] oname, int[] otype, int[] ltype, long[] ref, int amax, int n) throws HDF5LibraryException, NullPointerException; /** * H5Gget_objinfo returns information about the specified object. * * @param loc_id * IN: File, group, dataset, or datatype identifier. * @param name * IN: Name of the object for which status is being sought. * @param follow_link * IN: Link flag. * @param fileno * OUT: file id numbers. * @param objno * OUT: object id numbers. * @param link_info * OUT: link information. * * 
 *          link_info[0] = nlink
 *          link_info[1] = type
 *          link_info[2] = linklen
 *
* @param mtime * OUT: modification time * * @return a non-negative value if successful, with the fields of link_info * and mtime (if non-null) initialized. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name or array is null. * @exception IllegalArgumentException * - bad argument. * * @deprecated As of HDF5 1.8, replaced by {@link #H5Lget_info(int, String, int) and #H5Oget_info(int)} **/ @Deprecated public synchronized static native int H5Gget_objinfo(int loc_id, String name, boolean follow_link, long[] fileno, long[] objno, int[] link_info, long[] mtime) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Gget_objinfo returns information about the specified object in an * HDF5GroupInfo object. * * @param loc_id * IN: File, group, dataset, or datatype identifier. * @param name * IN: Name of the object for which status is being sought. * @param follow_link * IN: Link flag. * @param info * OUT: the HDF5GroupInfo object to store the object infomation * * @return a non-negative value if successful, with the fields of * HDF5GroupInfo object (if non-null) initialized. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. * * @see ncsa.hdf.hdf5lib.HDF5GroupInfo See public synchronized static native * int H5Gget_objinfo(); * * @deprecated As of HDF5 1.8 **/ @Deprecated public synchronized static int H5Gget_objinfo(int loc_id, String name, boolean follow_link, HDF5GroupInfo info) throws HDF5LibraryException, NullPointerException { int status = -1; long[] fileno = new long[2]; long[] objno = new long[2]; int[] link_info = new int[3]; long[] mtime = new long[1]; status = H5Gget_objinfo(loc_id, name, follow_link, fileno, objno, link_info, mtime); if (status >= 0) { info.setGroupInfo(fileno, objno, link_info[0], link_info[1], mtime[0], link_info[2]); } return status; } /** * Returns a name of an object specified by an index. * * @param group_id * Group or file identifier * @param idx * Transient index identifying object * @param name * the object name * @param size * Name length * @return the size of the object name if successful, or 0 if no name is * associated with the group identifier. Otherwise returns a * negative value * @throws HDF5LibraryException * @throws NullPointerException * * @deprecated As of HDF5 1.8, replaced by {@link #H5Lget_name_by_idx(int, String, int, int, long, int)} */ @Deprecated public synchronized static native long H5Gget_objname_by_idx(int group_id, long idx, String[] name, long size) throws HDF5LibraryException, NullPointerException; /** * Returns the type of an object specified by an index. * * @param group_id * Group or file identifier. * @param idx * Transient index identifying object. * @return Returns the type of the object if successful. Otherwise returns a * negative value * @throws HDF5LibraryException * @throws NullPointerException * * @deprecated As of HDF5 1.8, replaced by {@link #H5Oget_info(int)} */ @Deprecated public synchronized static native int H5Gget_objtype_by_idx(int group_id, long idx) throws HDF5LibraryException, NullPointerException; /** * H5Glink creates a new name for an already existing object. * * @param loc_id * File, group, dataset, or datatype identifier. * @param link_type * Link type. Possible values are: *
    *
  • * H5G_LINK_HARD
    • *
  • * H5G_LINK_SOFT.
    • *
* @param current_name * A name of the existing object if link is a hard link. Can be * anything for the soft link. * @param new_name * New name for the object. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - current_name or name is null. * * @deprecated As of HDF5 1.8, replaced by * {@link #H5Lcreate_hard(int, String, int, String, int, int) * and #H5Lcreate_soft(String, int, String, int, int) } **/ @Deprecated public synchronized static native int H5Glink(int loc_id, int link_type, String current_name, String new_name) throws HDF5LibraryException, NullPointerException; /** * H5Glink creates a new name for an already existing object. * * @deprecated As of HDF5 1.8 **/ @Deprecated public synchronized static native int H5Glink2(int curr_loc_id, String current_name, int link_type, int new_loc_id, String new_name) throws HDF5LibraryException, NullPointerException; /** * H5Gunlink removes an association between a name and an object. * * @param loc_id * Identifier of the file containing the object. * @param name * Name of the object to unlink. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. * * @deprecated As of HDF5 1.8, replaced by {@link #H5Ldelete(int, String, int)} **/ @Deprecated public synchronized static native int H5Gunlink(int loc_id, String name) throws HDF5LibraryException, NullPointerException; /** * H5Gmove renames an object within an HDF5 file. The original name, src, is * unlinked from the group graph and the new name, dst, is inserted as an * atomic operation. Both names are interpreted relative to loc_id, which is * either a file or a group identifier. * * @param loc_id * File or group identifier. * @param src * Object's original name. * @param dst * Object's new name. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - src or dst is null. * * @deprecated As of HDF5 1.8, replaced by {@link #H5Lmove(int, String, int,String, int, int)} **/ @Deprecated public synchronized static native int H5Gmove(int loc_id, String src, String dst) throws HDF5LibraryException, NullPointerException; // Backward compatibility: // These functions have been replaced by new HDF5 library calls. // The interface is preserved as a convenience to existing code. /** * H5Gn_members report the number of objects in a Group. The 'objects' * include everything that will be visited by H5Giterate. Each link is * returned, so objects with multiple links will be counted once for each * link. * * @param loc_id * file or group ID. * @param name * name of the group to iterate, relative to the loc_id * * @return the number of members in the group or -1 if error. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. */ public synchronized static long H5Gn_members_long(int loc_id, String name) throws HDF5LibraryException, NullPointerException { int grp_id = H5Gopen(loc_id, name); long n = -1; try { H5G_info_t info = H5.H5Gget_info(grp_id); n = info.nlinks; } finally { H5Gclose(grp_id); } return n; } /** * H5Gn_members report the number of objects in a Group. The 'objects' * include everything that will be visited by H5Giterate. Each link is * returned, so objects with multiple links will be counted once for each * link. * * @param loc_id * file or group ID. * @param name * name of the group to iterate, relative to the loc_id * * @return the number of members in the group or -1 if error. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. */ public synchronized static int H5Gn_members(int loc_id, String name) throws HDF5LibraryException, NullPointerException { return (int) H5Gn_members_long(loc_id, name); } /** * H5Gopen opens an existing group with the specified name at the specified * location, loc_id. * * @deprecated As of HDF5 1.8, replaced by {@link #H5Gopen(int, String, int) } * * @param loc_id * File or group identifier within which group is to be open. * @param name * Name of group to open. * * @return a valid group identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ @Deprecated public static int H5Gopen(int loc_id, String name) throws HDF5LibraryException, NullPointerException { int id = _H5Gopen(loc_id, name); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Gopen(int loc_id, String name) throws HDF5LibraryException, NullPointerException; /** * H5Gopen opens an existing group, name, at the location specified by * loc_id. * * @param loc_id * IN: File or group identifier specifying the location of the * group to be opened. * @param name * IN: Name of group to open. * @param gapl_id * IN: Identifier of group access property list. (No group access * properties have been implemented at this time; use * H5P_DEFAULT.) * * @return a valid group identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public static int H5Gopen(int loc_id, String name, int gapl_id) throws HDF5LibraryException, NullPointerException { int id = _H5Gopen2(loc_id, name, gapl_id); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Gopen2(int loc_id, String name, int gapl_id) throws HDF5LibraryException, NullPointerException; ////////////////////////////////////////////////////////////// //// //H5I: HDF5 1.8 Identifier Interface API Functions // //// ////////////////////////////////////////////////////////////// public synchronized static native int H5Iget_file_id(int obj_id) throws HDF5LibraryException; public synchronized static native long H5Iget_name(int obj_id, String[] name, long size) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Iget_ref(int obj_id) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Idec_ref(int obj_id) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Iinc_ref(int obj_id) throws HDF5LibraryException, NullPointerException; /** * H5Iget_type retrieves the type of the object identified by obj_id. * * @param obj_id * IN: Object identifier whose type is to be determined. * * @return the object type if successful; otherwise H5I_BADID. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Iget_type(int obj_id) throws HDF5LibraryException; /** * H5Iget_type_ref retrieves the reference count on an ID type. The reference count is used by the library to indicate when an ID type can be destroyed. * * @param type * IN: The identifier of the type whose reference count is to be retrieved * * @return The current reference count on success, negative on failure. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Iget_type_ref(int type) throws HDF5LibraryException; /** * H5Inmembers returns the number of identifiers of the identifier type specified in type. * * @param type * IN: Identifier for the identifier type whose member count will be retrieved * * @return Number of identifiers of the specified identifier type * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Inmembers(int type) throws HDF5LibraryException; ///////// unimplemented //////// //herr_t H5Iclear_type(H5I_type_t type, hbool_t force); //int H5Idec_type_ref(H5I_type_t type); //herr_t H5Idestroy_type(H5I_type_t type); //int H5Iinc_type_ref(H5I_type_t type); //htri_t H5Iis_valid(hid_t id); //void *H5Iobject_verify(hid_t id, H5I_type_t id_type); //hid_t H5Iregister(H5I_type_t type, const void *object); //H5I_type_t H5Iregister_type(size_t hash_size, unsigned reserved, H5I_free_t free_func); //void *H5Iremove_verify(hid_t id, H5I_type_t id_type); //void *H5Isearch(H5I_type_t type, H5I_search_func_t func, void *key); //htri_t H5Itype_exists(H5I_type_t type); // ////////////////////////////////////////////////////////////////// // // // New APIs for HDF5Index // // October 10, 2005 // // ////////////////////////////////////////////////////////////////// public synchronized static native int H5INcreate(String grp_name, int grp_loc_id, int property_list, int data_loc_id, String data_loc_name, String field_name, long max_mem_size); public synchronized static native int H5INquery(int dset_id, String keys[], Object ubounds, Object lbounds, int nkeys); // ////////////////////////////////////////////////////////////////// // H5L: Link Interface Functions // // ////////////////////////////////////////////////////////////////// /** * H5Lcopy copies a link from one location to another. * * @param src_loc IN: Location identifier of the source link * @param src_name IN: Name of the link to be copied * @param dst_loc IN: Location identifier specifying the destination of the copy * @param dst_name IN: Name to be assigned to the new copy * @param lcpl_id IN: Link creation property list identifier * @param lapl_id IN: Link access property list identifier * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. **/ public synchronized static native void H5Lcopy(int src_loc, String src_name, int dst_loc, String dst_name, int lcpl_id, int lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Lcreate_external creates a new soft link to an external object, which is * an object in a different HDF5 file from the location of the link. * * @param file_name IN: Name of the target file containing the target object. * @param obj_name IN: Path within the target file to the target object. * @param link_loc_id IN: The file or group identifier for the new link. * @param link_name IN: The name of the new link. * @param lcpl_id IN: Link creation property list identifier * @param lapl_id IN: Link access property list identifier * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. **/ public synchronized static native void H5Lcreate_external(String file_name, String obj_name, int link_loc_id, String link_name, int lcpl_id, int lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Lcreate_hard creates a new hard link to a pre-existing object in an HDF5 file. * * @param cur_loc IN: The file or group identifier for the target object. * @param cur_name IN: Name of the target object, which must already exist. * @param dst_loc IN: The file or group identifier for the new link. * @param dst_name IN: The name of the new link. * @param lcpl_id IN: Link creation property list identifier * @param lapl_id IN: Link access property list identifier * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - cur_name or dst_name is null. **/ public synchronized static native void H5Lcreate_hard(int cur_loc, String cur_name, int dst_loc, String dst_name, int lcpl_id, int lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Lcreate_soft creates a new soft link to an object in an HDF5 file. * * @param link_target IN: Path to the target object, which is not required to exist. * @param link_loc_id IN: The file or group identifier for the new link. * @param link_name IN: The name of the new link. * @param lcpl_id IN: Link creation property list identifier * @param lapl_id IN: Link access property list identifier * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - link_name is null. **/ public synchronized static native void H5Lcreate_soft(String link_target, int link_loc_id, String link_name, int lcpl_id, int lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Ldelete removes the link specified from a group. * * @param loc_id IN: Identifier of the file or group containing the object. * @param name IN: Name of the link to delete. * @param lapl_id IN: Link access property list identifier * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. **/ public synchronized static native void H5Ldelete(int loc_id, String name, int lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Ldelete_by_idx removes the nth link in a group according to the specified order * and in the specified index. * * @param loc_id IN: File or group identifier specifying location of subject group * @param group_name IN: Name of subject group * @param idx_type IN: Index or field which determines the order * @param order IN: Order within field or index * @param n IN: Link for which to retrieve information * @param lapl_id IN: Link access property list identifier * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - group_name is null. **/ public synchronized static native void H5Ldelete_by_idx(int loc_id, String group_name, int idx_type, int order, long n, int lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Lexists checks if a link with a particular name exists in a group. * * @param loc_id IN: Identifier of the file or group to query. * @param name IN: The name of the link to check. * @param lapl_id IN: Link access property list identifier * * @return a boolean, true if the name exists, otherwise false. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. **/ public synchronized static native boolean H5Lexists(int loc_id, String name, int lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Lget_info returns information about the specified link. * * @param loc_id IN: Identifier of the file or group. * @param name IN: Name of the link for which information is being sought. * @param lapl_id IN: Link access property list identifier * * @return a buffer(H5L_info_t) for the link information. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. **/ public synchronized static native H5L_info_t H5Lget_info(int loc_id, String name, int lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Lget_info_by_idx opens a named datatype at the location specified * by loc_id and return an identifier for the datatype. * * @param loc_id IN: File or group identifier specifying location of subject group * @param group_name IN: Name of subject group * @param idx_type IN: Type of index * @param order IN: Order within field or index * @param n IN: Link for which to retrieve information * @param lapl_id IN: Link access property list identifier * * @return a buffer(H5L_info_t) for the link information. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - group_name is null. **/ public synchronized static native H5L_info_t H5Lget_info_by_idx(int loc_id, String group_name, int idx_type, int order, long n, int lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Lget_name_by_idx retrieves name of the nth link in a group, according to * the order within a specified field or index. * * @param loc_id IN: File or group identifier specifying location of subject group * @param group_name IN: Name of subject group * @param idx_type IN: Type of index * @param order IN: Order within field or index * @param n IN: Link for which to retrieve information * @param lapl_id IN: Link access property list identifier * * @return a String for the link name. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - group_name is null. **/ public synchronized static native String H5Lget_name_by_idx(int loc_id, String group_name, int idx_type, int order, long n, int lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Lget_val returns the link value of a symbolic link. * * @param loc_id IN: Identifier of the file or group containing the object. * @param name IN: Name of the symbolic link. * @param link_value OUT: Path of the symbolic link, or the file_name and path of an external file. * @param lapl_id IN: Link access property list identifier * * @return the link type * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. **/ public synchronized static native int H5Lget_val(int loc_id, String name, String[] link_value, int lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Lget_val_by_idx retrieves value of the nth link in a group, according to the order within an index. * * @param loc_id IN: File or group identifier specifying location of subject group * @param group_name IN: Name of subject group * @param idx_type IN: Type of index * @param order IN: Order within field or index * @param n IN: Link for which to retrieve information * @param link_value OUT: Path of the symbolic link, or the file_name and path of an external file. * @param lapl_id IN: Link access property list identifier * * @return the link type * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - group_name is null. **/ public synchronized static native int H5Lget_val_by_idx(int loc_id, String group_name, int idx_type, int order, long n, String[] link_value, int lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Literate iterates through links in a group. * * @param grp_id IN: Identifier specifying subject group * @param idx_type IN: Type of index * @param order IN: Order of iteration within index * @param idx IN: Iteration position at which to start * @param op IN: Callback function passing data regarding the link to the calling application * @param op_data IN: User-defined pointer to data required by the application for its processing of the link * * @return returns the return value of the first operator that returns a positive value, or zero if all members were * processed with no operator returning non-zero. * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native int H5Literate(int grp_id, int idx_type, int order, long idx, H5L_iterate_cb op, H5L_iterate_t op_data) throws HDF5LibraryException; /** * H5Literate_by_name iterates through links in a group. * * @param grp_id IN: Identifier specifying subject group * @param group_name IN: Name of subject group * @param idx_type IN: Type of index * @param order IN: Order of iteration within index * @param idx IN: Iteration position at which to start * @param op IN: Callback function passing data regarding the link to the calling application * @param op_data IN: User-defined pointer to data required by the application for its processing of the link * @param lapl_id IN: Link access property list identifier * * @return returns the return value of the first operator that returns a positive value, or zero if all members were * processed with no operator returning non-zero. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - group_name is null. **/ public synchronized static native int H5Literate_by_name(int grp_id, String group_name, int idx_type, int order, long idx, H5L_iterate_cb op, H5L_iterate_t op_data, int lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Lmove renames a link within an HDF5 file. * * @param src_loc IN: Original file or group identifier. * @param src_name IN: Original link name. * @param dst_loc IN: Destination file or group identifier. * @param dst_name IN: New link name. * @param lcpl_id IN: Link creation property list identifier to be associated with the new link. * @param lapl_id IN: Link access property list identifier to be associated with the new link. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. **/ public synchronized static native void H5Lmove(int src_loc, String src_name, int dst_loc, String dst_name, int lcpl_id, int lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Lvisit recursively visits all links starting from a specified group. * * @param grp_id IN: Identifier specifying subject group * @param idx_type IN: Type of index * @param order IN: Order of iteration within index * @param op IN: Callback function passing data regarding the link to the calling application * @param op_data IN: User-defined pointer to data required by the application for its processing of the link * * @return returns the return value of the first operator that returns a positive value, or zero if all members were * processed with no operator returning non-zero. * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native int H5Lvisit(int grp_id, int idx_type, int order, H5L_iterate_cb op, H5L_iterate_t op_data) throws HDF5LibraryException; /** * H5Lvisit_by_name recursively visits all links starting from a specified group. * * @param loc_id IN: Identifier specifying subject group * @param group_name IN: Name of subject group * @param idx_type IN: Type of index * @param order IN: Order of iteration within index * @param op IN: Callback function passing data regarding the link to the calling application * @param op_data IN: User-defined pointer to data required by the application for its processing of the link * * @return returns the return value of the first operator that returns a positive value, or zero if all members were * processed with no operator returning non-zero. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - group_name is null. **/ public synchronized static native int H5Lvisit_by_name(int loc_id, String group_name, int idx_type, int order, H5L_iterate_cb op, H5L_iterate_t op_data, int lapl_id) throws HDF5LibraryException, NullPointerException; ///////// unimplemented //////// //herr_t H5Lcreate_ud(hid_t link_loc_id, const char *link_name, // H5L_type_t link_type, const void *udata, size_t udata_size, hid_t lcpl_id, // hid_t lapl_id); //htri_t H5Lis_registered(H5L_type_t id); //herr_t H5Lregister(const H5L_class_t *cls); //herr_t H5Lunpack_elink_val(const void *ext_linkval/*in*/, size_t link_size, // unsigned *flags, const char **filename/*out*/, const char **obj_path /*out*/); //herr_t H5Lunregister(H5L_type_t id); ////////////////////////////////////////////////////////////// //// //H5O: HDF5 1.8 Object Interface API Functions // //// ////////////////////////////////////////////////////////////// /** * H5Oclose closes the group, dataset, or named datatype specified. * * @param object_id IN: Object identifier * * @return non-negative on success * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public static int H5Oclose(int object_id) throws HDF5LibraryException { if (object_id < 0) return 0; // throw new HDF5LibraryException("Negative ID");; OPEN_IDS.removeElement(object_id); return _H5Oclose(object_id); } private synchronized static native int _H5Oclose(int object_id) throws HDF5LibraryException; /** * H5Ocopy copies the group, dataset or named datatype specified from the file or * group specified by source location to the destination location. * * @param src_loc_id IN: Object identifier indicating the location of the source object to be copied * @param src_name IN: Name of the source object to be copied * @param dst_loc_id IN: Location identifier specifying the destination * @param dst_name IN: Name to be assigned to the new copy * @param ocpypl_id IN: Object copy property list * @param lcpl_id IN: Link creation property list for the new hard link * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. **/ public synchronized static native void H5Ocopy(int src_loc_id, String src_name, int dst_loc_id, String dst_name, int ocpypl_id, int lcpl_id) throws HDF5LibraryException, NullPointerException; /** * H5Oget_comment retrieves the comment for the specified object. * * @param obj_id IN: File or group identifier * * @return the comment * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native String H5Oget_comment(int obj_id) throws HDF5LibraryException; /** * H5Oset_comment sets the comment for the specified object. * * @param obj_id IN: Identifier of the target object * @param comment IN: The new comment. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * * @deprecated As of HDF5 1.8 in favor of object attributes. **/ @Deprecated public synchronized static native void H5Oset_comment(int obj_id, String comment) throws HDF5LibraryException; /** * H5Oget_comment_by_name retrieves the comment for an object. * * @param loc_id IN: Identifier of a file, group, dataset, or named datatype. * @param name IN: Relative name of the object whose comment is to be set or reset. * @param lapl_id IN: Link access property list identifier. * * @return the comment * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. **/ public synchronized static native String H5Oget_comment_by_name(int loc_id, String name, int lapl_id) throws HDF5LibraryException, NullPointerException; //long H5Oget_comment_by_name(int loc_id, String name, String comment, long bufsize, int lapl_id); /** * H5Oset_comment_by_name sets the comment for the specified object. * * @param loc_id IN: Identifier of a file, group, dataset, or named datatype. * @param name IN: Relative name of the object whose comment is to be set or reset. * @param comment IN: The new comment. * @param lapl_id IN: Link access property list identifier. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. * * @deprecated As of HDF5 1.8 in favor of object attributes. **/ @Deprecated public synchronized static native void H5Oset_comment_by_name(int loc_id, String name, String comment, int lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Oget_info retrieves the metadata for an object specified by an identifier. * * @param loc_id IN: Identifier for target object * * @return object information * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. **/ public synchronized static native H5O_info_t H5Oget_info(int loc_id) throws HDF5LibraryException, NullPointerException; /** * H5Oget_info_by_idx retrieves the metadata for an object, identifying the object by an index position. * * @param loc_id IN: File or group identifier * @param group_name IN: Name of group, relative to loc_id, in which object is located * @param idx_type IN: Type of index by which objects are ordered * @param order IN: Order of iteration within index * @param n IN: Object to open * @param lapl_id IN: Access property list identifier for the link pointing to the object (Not currently used; pass as H5P_DEFAULT.) * * @return object information * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. **/ public synchronized static native H5O_info_t H5Oget_info_by_idx(int loc_id, String group_name, int idx_type, int order, long n, int lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Oget_info_by_name retrieves the metadata for an object, identifying the object by location and relative name. * * @param loc_id IN: File or group identifier specifying location of group in which object is located * @param name IN: Relative name of group * @param lapl_id IN: Access property list identifier for the link pointing to the object (Not currently used; pass as H5P_DEFAULT.) * * @return object information * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. **/ public synchronized static native H5O_info_t H5Oget_info_by_name(int loc_id, String name, int lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Olink creates a new hard link to an object in an HDF5 file. * * @param obj_id IN: Object to be linked. * @param new_loc_id IN: File or group identifier specifying location at which object is to be linked. * @param new_name IN: Relative name of link to be created. * @param lcpl_id IN: Link creation property list identifier. * @param lapl_id IN: Access property list identifier. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. **/ public synchronized static native void H5Olink(int obj_id, int new_loc_id, String new_name, int lcpl_id, int lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Oopen opens a group, dataset, or named datatype specified by a location and a path name. * * @param loc_id IN: File or group identifier * @param name IN: Relative path to the object * @param lapl_id IN: Access property list identifier for the link pointing to the object * * @return an object identifier for the opened object * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. **/ public static int H5Oopen(int loc_id, String name, int lapl_id) throws HDF5LibraryException, NullPointerException { int id = _H5Oopen(loc_id, name, lapl_id); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Oopen(int loc_id, String name, int lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Ovisit recursively visits all objects accessible from a specified object. * * @param obj_id IN: Identifier of the object at which the recursive iteration begins. * @param idx_type IN: Type of index * @param order IN: Order of iteration within index * @param op IN: Callback function passing data regarding the object to the calling application * @param op_data IN: User-defined pointer to data required by the application for its processing of the object * * @return returns the return value of the first operator that returns a positive value, or zero if all members were processed with no operator returning non-zero. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. **/ public synchronized static native int H5Ovisit(int obj_id, int idx_type, int order, H5O_iterate_cb op, H5O_iterate_t op_data) throws HDF5LibraryException, NullPointerException; /** * H5Ovisit_by_name recursively visits all objects starting from a specified object. * * @param loc_id IN: File or group identifier * @param obj_name IN: Relative path to the object * @param idx_type IN: Type of index * @param order IN: Order of iteration within index * @param op IN: Callback function passing data regarding the object to the calling application * @param op_data IN: User-defined pointer to data required by the application for its processing of the object * @param lapl_id IN: Link access property list identifier * * @return returns the return value of the first operator that returns a positive value, or zero if all members were processed with no operator returning non-zero. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. **/ public synchronized static native int H5Ovisit_by_name(int loc_id, String obj_name, int idx_type, int order, H5O_iterate_cb op, H5O_iterate_t op_data, int lapl_id) throws HDF5LibraryException, NullPointerException; ///////// unimplemented //////// ///** //* H5Odecr_refcount decrements the hard link reference count for an object. //* //* @param object_id IN: Object identifier //* //* @return none //* //* @exception HDF5LibraryException - Error from the HDF-5 Library. //**/ //public synchronized static native void H5Odecr_refcount(int object_id) // throws HDF5LibraryException; ///** //* H5Oincr_refcount increments the hard link reference count for an object. //* //* @param object_id IN: Object identifier //* //* @return none //* //* @exception HDF5LibraryException - Error from the HDF-5 Library. //**/ //public synchronized static native void H5Oincr_refcount(int object_id) // throws HDF5LibraryException; ///** //* H5Oopen_by_addr opens a group, dataset, or named datatype using its address within an HDF5 file. //* //* @param loc_id IN: File or group identifier //* @param addr IN: Object's address in the file //* //* @return an object identifier for the opened object //* //* @exception HDF5LibraryException - Error from the HDF-5 Library. //**/ //public synchronized static native int H5Oopen_by_addr(int loc_id, long addr) // throws HDF5LibraryException; ///** //* H5Oopen_by_idx opens the nth object in the group specified. //* //* @param loc_id IN: File or group identifier //* @param group_name IN: Name of group, relative to loc_id, in which object is located //* @param idx_type IN: Type of index by which objects are ordered //* @param order IN: Order of iteration within index //* @param n IN: Object to open //* @param lapl_id IN: Access property list identifier for the link pointing to the object //* //* @return an object identifier for the opened object //* //* @exception HDF5LibraryException - Error from the HDF-5 Library. //* @exception NullPointerException - group_name is null. //**/ //public synchronized static native int H5Oopen_by_idx(int loc_id, String group_name, // H5_INDEX idx_type, H5_ITER order, long n, int lapl_id) // throws HDF5LibraryException, NullPointerException; ////////////////////////////////////////////////////////////// // // // H5P: Property List Interface Functions // // // ////////////////////////////////////////////////////////////// public synchronized static native boolean H5Pall_filters_avail(int dcpl_id) throws HDF5LibraryException, NullPointerException; /** * H5Pclose terminates access to a property list. * * @param plist * IN: Identifier of the property list to terminate access to. * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Pclose(int plist) throws HDF5LibraryException { if (plist < 0) return 0; // throw new HDF5LibraryException("Negative ID");; OPEN_IDS.removeElement(plist); return _H5Pclose(plist); } private synchronized static native int _H5Pclose(int plist) throws HDF5LibraryException; /** * Closes an existing property list class * * @param plid * IN: Property list class to close * @return a non-negative value if successful; a negative value if failed * @throws HDF5LibraryException */ public synchronized static native int H5Pclose_class(int plid) throws HDF5LibraryException; /** * H5Pcopy copies an existing property list to create a new property list. * * @param plist * IN: Identifier of property list to duplicate. * * @return a property list identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Pcopy(int plist) throws HDF5LibraryException { int id = _H5Pcopy(plist); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Pcopy(int plist) throws HDF5LibraryException; /** * H5Pcopy_prop copies a property from one property list or class to another * * @param dst_id * IN: Identifier of the destination property list or class * @param src_id * IN: Identifier of the source property list or class * @param name * IN: Name of the property to copy * @return a non-negative value if successful; a negative value if failed * @throws HDF5LibraryException */ public synchronized static native int H5Pcopy_prop(int dst_id, int src_id, String name) throws HDF5LibraryException; /** * H5Pcreate creates a new property as an instance of some property list * class. * * @param type * IN: The type of property list to create. * * @return a property list identifier (plist) if successful; otherwise Fail * (-1). * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Pcreate(int type) throws HDF5LibraryException { int id = _H5Pcreate(type); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Pcreate(int type) throws HDF5LibraryException; /** * H5Pequal determines if two property lists or classes are equal * * @param plid1 * IN: First property object to be compared * @param plid2 * IN: Second property object to be compared * @return positive value if equal; zero if unequal, a negative value if * failed * @throws HDF5LibraryException */ public synchronized static native int H5Pequal(int plid1, int plid2) throws HDF5LibraryException; public static boolean H5P_equal(int plid1, int plid2) throws HDF5LibraryException { if(H5Pequal(plid1, plid2)==1) return true; return false; } /** * H5Pexist determines whether a property exists within a property list or * class * * @param plid * IN: Identifier for the property to query * @param name * IN: Name of property to check for * @return a positive value if the property exists in the property object; * zero if the property does not exist; a negative value if failed * @throws HDF5LibraryException */ public synchronized static native int H5Pexist(int plid, String name) throws HDF5LibraryException; public synchronized static native int H5Pfill_value_defined(int plist_id, int[] status) throws HDF5LibraryException, NullPointerException; /** * H5Pget retrieves a copy of the value for a property in a property list * (support integer only) * * @param plid * IN: Identifier of property object to query * @param name * IN: Name of property to query * @return value for a property if successful; a negative value if failed * @throws HDF5LibraryException */ public synchronized static native int H5Pget(int plid, String name) throws HDF5LibraryException; /** * Sets a property list value (support integer only) * * @param plid * IN: Property list identifier to modify * @param name * IN: Name of property to modify * @param value * IN: value to set the property to * @return a non-negative value if successful; a negative value if failed * @throws HDF5LibraryException */ public synchronized static native int H5Pset(int plid, String name, int value) throws HDF5LibraryException; /** * H5Pget_alignment retrieves the current settings for alignment properties * from a file access property list. * * @param plist * IN: Identifier of a file access property list. * @param alignment * OUT: threshold value and alignment value. * * 
 *      alignment[0] = threshold // threshold value
 *      alignment[1] = alignment // alignment value
 *
* @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - aligment array is null. * @exception IllegalArgumentException * - aligment array is invalid. **/ public synchronized static native int H5Pget_alignment(int plist, long[] alignment) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Pset_alignment sets the alignment properties of a file access property * list so that any file object >= THRESHOLD bytes will be aligned on an * address which is a multiple of ALIGNMENT. * * @param plist * IN: Identifier for a file access property list. * @param threshold * IN: Threshold value. * @param alignment * IN: Alignment value. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_alignment(int plist, long threshold, long alignment) throws HDF5LibraryException; public synchronized static native int H5Pget_alloc_time(int plist_id, int[] alloc_time) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Pset_alloc_time(int plist_id, int alloc_time) throws HDF5LibraryException, NullPointerException; /** * H5Pget_attr_creation_order retrieves the settings for tracking and indexing attribute creation order on an object * @param ocpl_id IN: Object (group or dataset) creation property list identifier * * @return Flags specifying whether to track and index attribute creation order * * @exception HDF5LibraryException - Error from the HDF-5 Library. * **/ public synchronized static native int H5Pget_attr_creation_order(int ocpl_id) throws HDF5LibraryException; /** * H5Pset_attr_creation_order sets flags specifying whether to track and index attribute creation order on an object. * @param ocpl_id IN: Object creation property list identifier * @param crt_order_flags IN: Flags specifying whether to track and index attribute creation order * * @return Returns a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * **/ public synchronized static native int H5Pset_attr_creation_order(int ocpl_id, int crt_order_flags) throws HDF5LibraryException; /** * H5Pget_attr_phase_change retrieves attribute storage phase change thresholds. * @param ocpl_id IN: : Object (dataset or group) creation property list identifier * @param attributes * The maximun and minimum no. of attributes * to be stored. * * 
*      attributes[0] =  The maximum number of attributes to be stored in compact storage
*      attributes[1] =  The minimum number of attributes to be stored in dense storage 
*
* * @return Returns a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - size is null. * **/ public synchronized static native int H5Pget_attr_phase_change(int ocpl_id, int []attributes) throws HDF5LibraryException, NullPointerException; /** * H5Pget_btree_ratio Get the B-tree split ratios for a dataset transfer * property list. * * @param plist_id * IN Dataset transfer property list * @param left * OUT split ratio for leftmost nodes * @param right * OUT split ratio for righttmost nodes * @param middle * OUT split ratio for all other nodes * * @return non-negative if succeed * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - an input array is null. **/ public synchronized static native int H5Pget_btree_ratios(int plist_id, double[] left, double[] middle, double[] right) throws HDF5LibraryException, NullPointerException; /** * H5Pset_btree_ratio Sets B-tree split ratios for a dataset transfer * property list. The split ratios determine what percent of children go in * the first node when a node splits. * * @param plist_id * IN Dataset transfer property list * @param left * IN split ratio for leftmost nodes * @param right * IN split ratio for righttmost nodes * @param middle * IN split ratio for all other nodes * * @return non-negative if succeed * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_btree_ratios(int plist_id, double left, double middle, double right) throws HDF5LibraryException; /** * HH5Pget_buffer gets type conversion and background buffers. Returns * buffer size, in bytes, if successful; otherwise 0 on failure. * * @param plist * Identifier for the dataset transfer property list. * @param tconv * byte array of application-allocated type conversion buffer. * @param bkg * byte array of application-allocated background buffer. * * @return buffer size, in bytes, if successful; otherwise 0 on failure * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception IllegalArgumentException * - plist is invalid. **/ public synchronized static native int H5Pget_buffer(int plist, byte[] tconv, byte[] bkg) throws HDF5LibraryException, IllegalArgumentException; public synchronized static native long H5Pget_buffer_size(int plist) throws HDF5LibraryException, IllegalArgumentException; /** * H5Pset_buffer sets type conversion and background buffers. status to TRUE * or FALSE. * * Given a dataset transfer property list, H5Pset_buffer sets the maximum * size for the type conversion buffer and background buffer and optionally * supplies pointers to application-allocated buffers. If the buffer size is * smaller than the entire amount of data being transferred between the * application and the file, and a type conversion buffer or background * buffer is required, then strip mining will be used. * * Note that there are minimum size requirements for the buffer. Strip * mining can only break the data up along the first dimension, so the * buffer must be large enough to accommodate a complete slice that * encompasses all of the remaining dimensions. For example, when strip * mining a 100x200x300 hyperslab of a simple data space, the buffer must be * large enough to hold 1x200x300 data elements. When strip mining a * 100x200x300x150 hyperslab of a simple data space, the buffer must be * large enough to hold 1x200x300x150 data elements. * * @param plist * Identifier for the dataset transfer property list. * @param size * Size, in bytes, of the type conversion and background buffers. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception IllegalArgumentException * - plist is invalid. **/ public synchronized static native void H5Pset_buffer_size(int plist, long size) throws HDF5LibraryException, IllegalArgumentException; /** * Retrieves the maximum possible number of elements in the meta data cache * and the maximum possible number of bytes and the RDCC_W0 value in the raw * data chunk cache. * * @param plist IN: Identifier of the file access property list. * @param mdc_nelmts IN/OUT: No longer used, will be ignored. * @param rdcc_nelmts IN/OUT: Number of elements (objects) in the raw data chunk cache. * @param rdcc_nbytes IN/OUT: Total size of the raw data chunk cache, in bytes. * @param rdcc_w0 IN/OUT: Preemption policy. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - an array is null. **/ public synchronized static native int H5Pget_cache(int plist, int[] mdc_nelmts, long[] rdcc_nelmts, long[] rdcc_nbytes, double[] rdcc_w0) throws HDF5LibraryException, NullPointerException; /** * @deprecated As of HDF5 1.8, replaced by {@link #H5Pget_cache(int, int[], long[], long[], double[]) } * because of possible loss of precision **/ @Deprecated public static int H5Pget_cache(int plist, int[] mdc_nelmts, int[] rdcc_nelmts, int[] rdcc_nbytes, double[] rdcc_w0) throws HDF5LibraryException, NullPointerException { long[] rdcc_nelmts_l = {rdcc_nelmts[0]}; long[] rdcc_nbytes_l = {rdcc_nbytes[0]}; int retval = H5Pget_cache(plist, mdc_nelmts, rdcc_nelmts_l, rdcc_nbytes_l, rdcc_w0); rdcc_nelmts[0] = (int)rdcc_nelmts_l[0]; rdcc_nbytes[0] = (int)rdcc_nbytes_l[0]; return retval; } /** * H5Pset_cache sets the number of elements (objects) in the meta data cache * and the total number of bytes in the raw data chunk cache. * * @param plist IN: Identifier of the file access property list. * @param mdc_nelmts IN: No longer used, will be ignored. * @param rdcc_nelmts IN: Number of elements (objects) in the raw data chunk cache. * @param rdcc_nbytes IN: Total size of the raw data chunk cache, in bytes. * @param rdcc_w0 IN: Preemption policy. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_cache(int plist, int mdc_nelmts, long rdcc_nelmts, long rdcc_nbytes, double rdcc_w0) throws HDF5LibraryException; public synchronized static native int H5Pget_char_encoding(int plist_id) throws HDF5LibraryException; public synchronized static native void H5Pset_char_encoding(int plist_id, int encoding) throws HDF5LibraryException; /** * H5Pget_chunk retrieves the size of chunks for the raw data of a chunked * layout dataset. * * @param plist * IN: Identifier of property list to query. * @param max_ndims * IN: Size of the dims array. * @param dims * OUT: Array to store the chunk dimensions. * * @return chunk dimensionality successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - dims array is null. * @exception IllegalArgumentException * - max_ndims <=0 **/ public synchronized static native int H5Pget_chunk(int plist, int max_ndims, long[] dims) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Pset_chunk sets the size of the chunks used to store a chunked layout * dataset. * * @param plist * IN: Identifier for property list to query. * @param ndims * IN: The number of dimensions of each chunk. * @param dim * IN: An array containing the size of each chunk. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - dims array is null. * @exception IllegalArgumentException * - dims <=0 **/ public synchronized static native int H5Pset_chunk(int plist, int ndims, byte[] dim) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; public synchronized static int H5Pset_chunk(int plist, int ndims, long[] dim) throws HDF5Exception, NullPointerException, IllegalArgumentException { if (dim == null) { return -1; } HDFArray theArray = new HDFArray(dim); byte[] thedims = theArray.byteify(); int retVal = H5Pset_chunk(plist, ndims, thedims); thedims = null; theArray = null; return retVal; } /** * Retrieves the maximum possible number of elements in the meta data cache * and the maximum possible number of bytes and the RDCC_W0 value in the raw * data chunk cache on a per-datset basis. * * @param dapl_id IN: Identifier of the dataset access property list. * @param rdcc_nslots IN/OUT: Number of elements (objects) in the raw data chunk cache. * @param rdcc_nbytes IN/OUT: Total size of the raw data chunk cache, in bytes. * @param rdcc_w0 IN/OUT: Preemption policy. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - an array is null. **/ public synchronized static native void H5Pget_chunk_cache(int dapl_id, long[] rdcc_nslots, long[] rdcc_nbytes, double[] rdcc_w0) throws HDF5LibraryException, NullPointerException; /** * H5Pset_chunk_cache sets the number of elements (objects) in the meta data cache * and the total number of bytes in the raw data chunk cache on a per-datset basis. * * @param dapl_id IN: Identifier of the datset access property list. * @param rdcc_nslots IN: Number of elements (objects) in the raw data chunk cache. * @param rdcc_nbytes IN: Total size of the raw data chunk cache, in bytes. * @param rdcc_w0 IN: Preemption policy. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Pset_chunk_cache(int dapl_id, long rdcc_nslots, long rdcc_nbytes, double rdcc_w0) throws HDF5LibraryException; /** * H5Pget_class returns the property list class for the property list * identified by the plist parameter. * * @param plist * IN: Identifier of property list to query. * @return a property list class if successful. Otherwise returns * H5P_NO_CLASS (-1). * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Pget_class(int plist) throws HDF5LibraryException; /** * H5Pget_class_name retrieves the name of a generic property list class * * @param plid * IN: Identifier of property object to query * @return name of a property list if successful; null if failed * @throws HDF5LibraryException */ public synchronized static native String H5Pget_class_name(int plid) throws HDF5LibraryException; /** * H5Pget_class_parent retrieves an identifier for the parent class of a * property class * * @param plid * IN: Identifier of the property class to query * @return a valid parent class object identifier if successful; a negative * value if failed * @throws HDF5LibraryException */ public synchronized static native int H5Pget_class_parent(int plid) throws HDF5LibraryException; /** * H5Pget_copy_object retrieves the properties to be used when an object is copied. * @param ocp_plist_id IN: Object copy property list identifier * * @return Copy option(s) set in the object copy property list * * @exception HDF5LibraryException - Error from the HDF-5 Library. * **/ public synchronized static native int H5Pget_copy_object(int ocp_plist_id) throws HDF5LibraryException; /** * H5Pset_copy_object Sets properties to be used when an object is copied. * @param ocp_plist_id IN: Object copy property list identifier * @param copy_options IN: Copy option(s) to be set * * @exception HDF5LibraryException - Error from the HDF-5 Library. * **/ public synchronized static native void H5Pset_copy_object(int ocp_plist_id, int copy_options) throws HDF5LibraryException; /** * H5Pget_create_intermediate_group determines whether property is set to enable creating missing intermediate groups. * @param lcpl_id IN: Link creation property list identifier * * @return Boolean true or false * * @exception HDF5LibraryException - Error from the HDF-5 Library. * **/ public synchronized static native boolean H5Pget_create_intermediate_group(int lcpl_id) throws HDF5LibraryException; /** * H5Pset_create_intermediate_group specifies in property list whether to create missing intermediate groups * @param lcpl_id IN: Link creation property list identifier * @param crt_intermed_group IN: Flag specifying whether to create intermediate groups upon the creation of an object * * @return a non-negative valule if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * **/ public synchronized static native int H5Pset_create_intermediate_group(int lcpl_id, boolean crt_intermed_group) throws HDF5LibraryException; /** * H5Pget_data_transform retrieves the data transform expression previously set in the dataset transfer property list plist_id by H5Pset_data_transform. * @param plist_id IN: Identifier of the property list or class * @param size IN: Number of bytes of the transform expression to copy to * @param expression OUT: A data transform expression * * @return The size of the transform expression if successful; 0(zero) if no transform expression exists. Otherwise returns a negative value. * * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception IllegalArgumentException - Size is <= 0. * **/ public synchronized static native long H5Pget_data_transform( int plist_id, String[] expression, long size) throws HDF5LibraryException, IllegalArgumentException; /** * H5Pset_data_transform sets a data transform expression * @param plist_id IN: Identifier of the property list or class * @param expression IN: Pointer to the null-terminated data transform expression * * @return a non-negative valule if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - expression is null. * **/ public synchronized static native int H5Pset_data_transform(int plist_id, String expression) throws HDF5LibraryException, NullPointerException; /** * H5Pget_driver returns the identifier of the low-level file driver * associated with the file access property list or data transfer * property list plid. * * @param plid * IN: File access or data transfer property list identifier. * @return a valid low-level driver identifier if successful; a negative value if failed * @throws HDF5LibraryException */ public synchronized static native int H5Pget_driver(int plid) throws HDF5LibraryException; public synchronized static native int H5Pget_edc_check(int plist) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Pset_edc_check(int plist, int check) throws HDF5LibraryException, NullPointerException; /** * H5Pget_elink_acc_flags retrieves the external link traversal file access flag from the specified link access property list. * @param lapl_id IN: Link access property list identifier * * @return File access flag for link traversal. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * **/ public synchronized static native int H5Pget_elink_acc_flags(int lapl_id) throws HDF5LibraryException; /** * H5Pset_elink_acc_flags Sets the external link traversal file access flag in a link access property list. * @param lapl_id IN: Link access property list identifier * @param flags IN: The access flag for external link traversal. * * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception IllegalArgumentException - Invalid Flag values. * **/ public synchronized static native int H5Pset_elink_acc_flags(int lapl_id, int flags) throws HDF5LibraryException, IllegalArgumentException; /** * H5Pget_elink_fapl Retrieves the file access property list identifier associated with * the link access property list. * * @param lapl_id IN: Link access property list identifier * * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * **/ public static int H5Pget_elink_fapl(int lapl_id) throws HDF5LibraryException { int id = _H5Pget_elink_fapl(lapl_id); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Pget_elink_fapl(int lapl_id) throws HDF5LibraryException; /** * H5Pset_elink_fapl sets a file access property list for use in accessing a * file pointed to by an external link. * * @param lapl_id IN: Link access property list identifier * @param fapl_id IN: File access property list identifier * * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * **/ public synchronized static native int H5Pset_elink_fapl(int lapl_id, int fapl_id) throws HDF5LibraryException; /** * H5Pget_elink_file_cache_size retrieves the size of the external link open file cache. * @param fapl_id IN: File access property list identifier * * @return External link open file cache size in number of files. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * **/ public synchronized static native int H5Pget_elink_file_cache_size(int fapl_id) throws HDF5LibraryException; /** * H5Pset_elink_file_cache_size sets the number of files that can be held open in an external link open file cache. * @param fapl_id IN: File access property list identifier * @param efc_size IN: External link open file cache size in number of files. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * **/ public synchronized static native void H5Pset_elink_file_cache_size(int fapl_id, int efc_size) throws HDF5LibraryException; /** * H5Pget_elink_prefix Retrieves prefix applied to external link paths. * @param lapl_id IN: Link access property list identifier * @param prefix OUT: Prefix applied to external link paths * * @return If successful, returns a non-negative value specifying the size in bytes of the prefix without the NULL terminator; * otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - prefix is null. * **/ public synchronized static native long H5Pget_elink_prefix(int lapl_id, String[] prefix) throws HDF5LibraryException, NullPointerException; /** * H5Pset_elink_prefix Sets prefix to be applied to external link paths. * @param lapl_id IN: Link access property list identifier * @param prefix IN: Prefix to be applied to external link paths * * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - prefix is null. * **/ public synchronized static native int H5Pset_elink_prefix(int lapl_id, String prefix) throws HDF5LibraryException, NullPointerException; /** * H5Pget_est_link_info Queries data required to estimate required local heap or object header size. * @param gcpl_id IN: Group creation property list identifier * @param link_info * Estimated number of links to be inserted into group * And the estimated average length of link names * * 
*      link_info[0] =  Estimated number of links to be inserted into group
*      link_info[1] =  Estimated average length of link names   
*
* * @return Returns a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - link_info is null. * **/ public synchronized static native int H5Pget_est_link_info(int gcpl_id, int []link_info) throws HDF5LibraryException, NullPointerException; /** * H5Pset_est_link_info Sets estimated number of links and length of link names in a group. * @param gcpl_id IN: Group creation property list identifier * @param est_num_entries IN: Estimated number of links to be inserted into group * @param est_name_len IN: Estimated average length of link names * * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception IllegalArgumentException - Invalid values to est_num_entries and est_name_len. * **/ public synchronized static native int H5Pset_est_link_info(int gcpl_id, int est_num_entries, int est_name_len) throws HDF5LibraryException, IllegalArgumentException; /** * H5Pget_external returns information about an external file. * * @param plist * IN: Identifier of a dataset creation property list. * @param idx * IN: External file index. * @param name_size * IN: Maximum length of name array. * @param name * OUT: Name of the external file. * @param size * OUT: the offset value and the size of the external file data. * * 
 *      size[0] = offset // a location to return an offset value
 *      size[1] = size // a location to return the size of
 *                // the external file data.
 *
* * @return a non-negative value if successful * * @exception ArrayIndexOutOfBoundsException * Fatal error on Copyback * @exception ArrayStoreException * Fatal error on Copyback * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name or size is null. * @exception IllegalArgumentException * - name_size <= 0 . * **/ public synchronized static native int H5Pget_external(int plist, int idx, long name_size, String[] name, long[] size) throws ArrayIndexOutOfBoundsException, ArrayStoreException, HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Pset_external adds an external file to the list of external files. * * @param plist * IN: Identifier of a dataset creation property list. * @param name * IN: Name of an external file. * @param offset * IN: Offset, in bytes, from the beginning of the file to the * location in the file where the data starts. * @param size * IN: Number of bytes reserved in the file for the data. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native int H5Pset_external(int plist, String name, long offset, long size) throws HDF5LibraryException, NullPointerException; /** * H5Pget_external_count returns the number of external files for the * specified dataset. * * @param plist * IN: Identifier of a dataset creation property list. * * @return the number of external files if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Pget_external_count(int plist) throws HDF5LibraryException; public synchronized static native long H5Pget_family_offset(int fapl_id) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Pset_family_offset(int fapl_id, long offset) throws HDF5LibraryException, NullPointerException; public synchronized static native void H5Pget_fapl_core(int fapl_id, long[] increment, boolean[] backing_store) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Pset_fapl_core(int fapl_id, long increment, boolean backing_store) throws HDF5LibraryException, NullPointerException; /** * H5Pget_fapl_direct Retrieve direct I/O settings. * @param fapl_id IN: File access property list identifier * @param info OUT: Returned property list information * info[0] = alignment Required memory alignment boundary * info[1] = block_size File system block size * info[2] = cbuf_size Copy buffer size * * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * **/ public synchronized static native int H5Pget_fapl_direct(int fapl_id, long[]info) throws HDF5LibraryException; /** * H5Pset_fapl_direct Sets up use of the direct I/O driver. * @param fapl_id IN: File access property list identifier * @param alignment IN: Required memory alignment boundary * @param block_size IN: File system block size * @param cbuf_size IN: Copy buffer size * * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * **/ public synchronized static native int H5Pset_fapl_direct(int fapl_id, long alignment, long block_size, long cbuf_size) throws HDF5LibraryException; public synchronized static native int H5Pget_fapl_family(int fapl_id, long[] memb_size, int[] memb_fapl_id) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Pset_fapl_family(int fapl_id, long memb_size, int memb_fapl_id) throws HDF5LibraryException, NullPointerException; //herr_t H5Pget_fapl_mpio( int fapl_id, MPI_Comm *comm, MPI_Info *info ) //herr_t H5Pset_fapl_mpio( int fapl_id, MPI_Comm comm, MPI_Info info ) //herr_t H5Pget_fapl_mpiposix( int fapl_id, MPI_Comm *comm, hbool_t *use_gpfs_hints ) //herr_t H5Pset_fapl_mpiposix( int fapl_id, MPI_Comm comm, hbool_t use_gpfs_hints ) /** * H5Pget_fapl_multi Sets up use of the multi I/O driver. * @param fapl_id IN: File access property list identifier * @param memb_map IN: Maps memory usage types to other memory usage types. * @param memb_fapl IN: Property list for each memory usage type. * @param memb_name IN: Name generator for names of member files. * @param memb_addr IN: The offsets within the virtual address space, from 0 (zero) to HADDR_MAX, at which each type of data storage begins. * * @return a boolean value; Allows read-only access to incomplete file sets when TRUE. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - an array is null. * **/ public synchronized static native boolean H5Pget_fapl_multi(int fapl_id, int[] memb_map, int[] memb_fapl, String[] memb_name, long[] memb_addr) throws HDF5LibraryException, NullPointerException; /** * H5Pset_fapl_multi Sets up use of the multi I/O driver. * @param fapl_id IN: File access property list identifier * @param memb_map IN: Maps memory usage types to other memory usage types. * @param memb_fapl IN: Property list for each memory usage type. * @param memb_name IN: Name generator for names of member files. * @param memb_addr IN: The offsets within the virtual address space, from 0 (zero) to HADDR_MAX, at which each type of data storage begins. * @param relax IN: Allows read-only access to incomplete file sets when TRUE. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - an array is null. * **/ public synchronized static native void H5Pset_fapl_multi(int fapl_id, int[] memb_map, int[] memb_fapl, String[] memb_name, long[] memb_addr, boolean relax) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Pget_fclose_degree(int plist_id) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Pset_fclose_degree(int plist, int degree) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Pget_fill_time(int plist_id, int[] fill_time) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Pset_fill_time(int plist_id, int fill_time) throws HDF5LibraryException, NullPointerException; /** * H5Pget_fill_value queries the fill value property of a dataset creation * property list. * * @param plist_id * IN: Property list identifier. * @param type_id * IN: The datatype identifier of value. * @param value * IN: The fill value. * * @return a non-negative value if successful * **/ public synchronized static native int H5Pget_fill_value(int plist_id, int type_id, byte[] value) throws HDF5Exception; /** * H5Pget_fill_value queries the fill value property of a dataset creation * property list. * * @param plist_id * IN: Property list identifier. * @param type_id * IN: The datatype identifier of value. * @param obj * IN: The fill value. * * @return a non-negative value if successful * **/ public synchronized static int H5Pget_fill_value(int plist_id, int type_id, Object obj) throws HDF5Exception { HDFArray theArray = new HDFArray(obj); byte[] buf = theArray.emptyBytes(); int status = H5Pget_fill_value(plist_id, type_id, buf); if (status >= 0) { obj = theArray.arrayify(buf); } return status; } /** * H5Pset_fill_value sets the fill value for a dataset creation property * list. * * @param plist_id * IN: Property list identifier. * @param type_id * IN: The datatype identifier of value. * @param value * IN: The fill value. * * @return a non-negative value if successful * * @exception HDF5Exception * - Error converting data array **/ public synchronized static native int H5Pset_fill_value(int plist_id, int type_id, byte[] value) throws HDF5Exception; /** * H5Pset_fill_value sets the fill value for a dataset creation property * list. * * @param plist_id * IN: Property list identifier. * @param type_id * IN: The datatype identifier of value. * @param obj * IN: The fill value. * * @return a non-negative value if successful * * @exception HDF5Exception * - Error converting data array **/ public synchronized static int H5Pset_fill_value(int plist_id, int type_id, Object obj) throws HDF5Exception { HDFArray theArray = new HDFArray(obj); byte[] buf = theArray.byteify(); int retVal = H5Pset_fill_value(plist_id, type_id, buf); buf = null; theArray = null; return retVal; } /** * H5Pget_filter returns information about a filter, specified by its filter * number, in a filter pipeline, specified by the property list with which * it is associated. * * @deprecated As of HDF5 1.8, replaced by {@link #H5Pget_filter(int, int, int[], long[], int[], long, String[], int[]) } * * @param plist * IN: Property list identifier. * @param filter_number * IN: Sequence number within the filter pipeline of the filter * for which information is sought. * @param flags * OUT: Bit vector specifying certain general properties of the * filter. * @param cd_nelmts * IN/OUT: Number of elements in cd_values * @param cd_values * OUT: Auxiliary data for the filter. * @param namelen * IN: Anticipated number of characters in name. * @param name * OUT: Name of the filter. * * @return the filter identification number if successful. Otherwise returns * H5Z_FILTER_ERROR (-1). * * @exception ArrayIndexOutOfBoundsException * Fatal error on Copyback * @exception ArrayStoreException * Fatal error on Copyback * @exception NullPointerException * - name or an array is null. * **/ @Deprecated public synchronized static native int H5Pget_filter(int plist, int filter_number, int[] flags, int[] cd_nelmts, int[] cd_values, int namelen, String[] name) throws ArrayIndexOutOfBoundsException, ArrayStoreException, HDF5LibraryException, NullPointerException; /** * H5Pget_filter returns information about a filter, specified by its filter * number, in a filter pipeline, specified by the property list with which * it is associated. * * @param plist IN: Property list identifier. * @param filter_number IN: Sequence number within the filter pipeline of the filter * for which information is sought. * @param flags OUT: Bit vector specifying certain general properties of the * filter. * @param cd_nelmts IN/OUT: Number of elements in cd_values * @param cd_values OUT: Auxiliary data for the filter. * @param namelen IN: Anticipated number of characters in name. * @param name OUT: Name of the filter. * @param filter_config OUT:A bit field encoding the returned filter information * * @return the filter identification number if successful. Otherwise returns * H5Z_FILTER_ERROR (-1). * * @exception ArrayIndexOutOfBoundsException * Fatal error on Copyback * @exception ArrayStoreException * Fatal error on Copyback * @exception NullPointerException * - name or an array is null. * **/ public static int H5Pget_filter(int plist, int filter_number, int[] flags, long[] cd_nelmts, int[] cd_values, long namelen, String[] name, int[] filter_config) throws ArrayIndexOutOfBoundsException, ArrayStoreException, HDF5LibraryException, NullPointerException { return H5Pget_filter2(plist, filter_number, flags, cd_nelmts, cd_values, namelen, name, filter_config); } /** * H5Pget_filter2 returns information about a filter, specified by its filter * number, in a filter pipeline, specified by the property list with which * it is associated. * * @see public static int H5Pget_filter(int plist, int filter_number, int[] flags, * int[] cd_nelmts, int[] cd_values, int namelen, String[] name, int[] filter_config) * **/ private synchronized static native int H5Pget_filter2(int plist, int filter_number, int[] flags, long[] cd_nelmts, int[] cd_values, long namelen, String[] name, int[] filter_config) throws ArrayIndexOutOfBoundsException, ArrayStoreException, HDF5LibraryException, NullPointerException; /** * H5Pset_filter adds the specified filter and corresponding properties to * the end of an output filter pipeline. * * @param plist * IN: Property list identifier. * @param filter * IN: Filter to be added to the pipeline. * @param flags * IN: Bit vector specifying certain general properties of the * filter. * @param cd_nelmts * IN: Number of elements in cd_values * @param cd_values * IN: Auxiliary data for the filter. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_filter(int plist, int filter, int flags, long cd_nelmts, int[] cd_values) throws HDF5LibraryException; /** * H5Pget_filter_by_id returns information about the filter specified in filter_id, a * filter identifier. plist_id must be a dataset or group creation property list and * filter_id must be in the associated filter pipeline. The filter_id and flags parameters * are used in the same manner as described in the discussion of H5Pset_filter. Aside from * the fact that they are used for output, the parameters cd_nelmts and cd_values[] are * used in the same manner as described in the discussion of H5Pset_filter. On input, the * cd_nelmts parameter indicates the number of entries in the cd_values[] array allocated * by the calling program; on exit it contains the number of values defined by the filter. * On input, the namelen parameter indicates the number of characters allocated for the * filter name by the calling program in the array name[]. On exit name[] contains the name * of the filter with one character of the name in each element of the array. If the filter * specified in filter_id is not set for the property list, an error will be returned and * H5Pget_filter_by_id1 will fail. * * @deprecated As of HDF5 1.8, replaced by {@link #H5Pget_filter_by_id(int, int, int[], long[], int[], long, String[], int[]) } * * @param plist_id IN: Property list identifier. * @param filter_id IN: Filter identifier. * @param flags OUT: Bit vector specifying certain general properties of the * filter. * @param cd_nelmts IN/OUT: Number of elements in cd_values * @param cd_values OUT: Auxiliary data for the filter. * @param namelen IN: Anticipated number of characters in name. * @param name OUT: Name of the filter. * * @return the filter identification number if successful. Otherwise returns * H5Z_FILTER_ERROR (-1). * * @exception ArrayIndexOutOfBoundsException * Fatal error on Copyback * @exception ArrayStoreException * Fatal error on Copyback * @exception NullPointerException * - name or an array is null. * **/ @Deprecated public synchronized static native int H5Pget_filter_by_id(int plist_id, int filter_id, int[] flags, long[] cd_nelmts, int[] cd_values, long namelen, String[] name) throws HDF5LibraryException, NullPointerException; /** * H5Pget_filter_by_id returns information about the filter specified in filter_id, a * filter identifier. plist_id must be a dataset or group creation property list and * filter_id must be in the associated filter pipeline. The filter_id and flags parameters * are used in the same manner as described in the discussion of H5Pset_filter. Aside from * the fact that they are used for output, the parameters cd_nelmts and cd_values[] are * used in the same manner as described in the discussion of H5Pset_filter. On input, the * cd_nelmts parameter indicates the number of entries in the cd_values[] array allocated * by the calling program; on exit it contains the number of values defined by the filter. * On input, the namelen parameter indicates the number of characters allocated for the * filter name by the calling program in the array name[]. On exit name[] contains the name * of the filter with one character of the name in each element of the array. If the filter * specified in filter_id is not set for the property list, an error will be returned and * H5Pget_filter_by_id1 will fail. * * @param plist_id IN: Property list identifier. * @param filter_id IN: Filter identifier. * @param flags OUT: Bit vector specifying certain general properties of the * filter. * @param cd_nelmts N/OUT: Number of elements in cd_values * @param cd_values OUT: Auxiliary data for the filter. * @param namelen IN: Anticipated number of characters in name. * @param name OUT: Name of the filter. * @param filter_config OUT: A bit field encoding the returned filter information * * @return the filter identification number if successful. Otherwise returns * H5Z_FILTER_ERROR (-1). * * @exception ArrayIndexOutOfBoundsException * Fatal error on Copyback * @exception ArrayStoreException * Fatal error on Copyback * @exception NullPointerException * - name or an array is null. * **/ public static int H5Pget_filter_by_id(int plist_id, int filter_id, int[] flags, long[] cd_nelmts, int[] cd_values, long namelen, String[] name, int[] filter_config) throws ArrayIndexOutOfBoundsException, ArrayStoreException, HDF5LibraryException, NullPointerException { return H5Pget_filter_by_id2(plist_id, filter_id, flags, cd_nelmts, cd_values, namelen, name, filter_config); } /** * H5Pget_filter_by_id2 returns information about a filter, specified by its filter * id, in a filter pipeline, specified by the property list with which * it is associated. * * @see #H5Pget_filter_by_id **/ public synchronized static native int H5Pget_filter_by_id2(int plist_id, int filter_id, int[] flags, long[] cd_nelmts, int[] cd_values, long namelen, String[] name, int[] filter_config) throws HDF5LibraryException, NullPointerException; /** * H5Pget_gc_references Returns the current setting for the garbage * collection refernces property from a file access property list. *

* Note: this routine changed name with HDF5.1.2.2. If using an earlier * version, use 'configure --enable-hdf5_1_2_1' so this routine will link to * the old name. * * @param fapl_id * IN File access property list * @param gc_ref * OUT GC is on (true) or off (false) * * @return non-negative if succeed * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - array is null. **/ public synchronized static native int H5Pget_gc_references(int fapl_id, boolean[] gc_ref) throws HDF5LibraryException, NullPointerException; public synchronized static native boolean H5Pget_gcreferences(int fapl_id) throws HDF5LibraryException; /* * Earlier versions of the HDF5 library had a different name. This is * included as an alias. */ public synchronized static int H5Pget_gc_reference(int fapl_id, boolean[] gc_ref) throws HDF5LibraryException, NullPointerException { return H5Pget_gc_references(fapl_id, gc_ref); } /** * H5Pset_gc_references Sets the flag for garbage collecting references for * the file. Default value for garbage collecting references is off. * * @param fapl_id * IN File access property list * @param gc_ref * IN set GC on (true) or off (false) * * @return non-negative if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_gc_references(int fapl_id, boolean gc_ref) throws HDF5LibraryException; public synchronized static native int H5Pget_hyper_vector_size(int dxpl_id, long[] vector_size) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Pset_hyper_vector_size(int dxpl_id, long vector_size) throws HDF5LibraryException, NullPointerException; /** * H5Pget_istore_k queries the 1/2 rank of an indexed storage B-tree. * * @param plist * IN: Identifier of property list to query. * @param ik * OUT: Pointer to location to return the chunked storage B-tree * 1/2 rank. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - ik array is null. **/ public synchronized static native int H5Pget_istore_k(int plist, int[] ik) throws HDF5LibraryException, NullPointerException; /** * H5Pset_istore_k sets the size of the parameter used to control the * B-trees for indexing chunked datasets. * * @param plist * IN: Identifier of property list to query. * @param ik * IN: 1/2 rank of chunked storage B-tree. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_istore_k(int plist, int ik) throws HDF5LibraryException; /** * H5Pget_layout returns the layout of the raw data for a dataset. * * @param plist * IN: Identifier for property list to query. * * @return the layout type of a dataset creation property list if * successful. Otherwise returns H5D_LAYOUT_ERROR (-1). * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Pget_layout(int plist) throws HDF5LibraryException; /** * H5Pset_layout sets the type of storage used store the raw data for a * dataset. * * @param plist * IN: Identifier of property list to query. * @param layout * IN: Type of storage layout for raw data. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_layout(int plist, int layout) throws HDF5LibraryException; /** * H5Pget_libver_bounds retrieves the lower and upper bounds on the HDF5 Library versions that indirectly determine the object formats versions used when creating objects in the file. * @param fapl_id IN: File access property list identifier * @param libver * The earliest/latest version of the library that will be used for writing objects. * * 

*      libver[0] =  The earliest version of the library that will be used for writing objects
*      libver[1] =  The latest version of the library that will be used for writing objects.
*
* * @return Returns a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - size is null. * **/ public synchronized static native int H5Pget_libver_bounds(int fapl_id, int []libver) throws HDF5LibraryException, NullPointerException; /** * H5Pset_libver_bounds Sets bounds on library versions, and indirectly format versions, to be used when creating objects * @param fapl_id IN: File access property list identifier * @param low IN: The earliest version of the library that will be used for writing objects * @param high IN: The latest version of the library that will be used for writing objects. * * * @return Returns a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception IllegalArgumentException - Argument is Illegal * **/ public synchronized static native int H5Pset_libver_bounds(int fapl_id, int low, int high) throws HDF5LibraryException, IllegalArgumentException; /** * H5Pget_link_creation_order queries the group creation property list, gcpl_id, and returns a flag indicating whether link creation order is tracked and/or indexed in a group. * @param gcpl_id IN: Group creation property list identifier * * @return crt_order_flags -Creation order flag(s) * * @exception HDF5LibraryException - Error from the HDF-5 Library. * **/ public synchronized static native int H5Pget_link_creation_order(int gcpl_id) throws HDF5LibraryException; /** * H5Pset_link_creation_order Sets flags in a group creation property list, gcpl_id, for tracking and/or indexing links on creation order. * @param gcpl_id IN: Group creation property list identifier * @param crt_order_flags IN: Creation order flag(s) * * * @return Returns a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * **/ public synchronized static native int H5Pset_link_creation_order(int gcpl_id, int crt_order_flags) throws HDF5LibraryException; /** * H5Pget_link_phase_change Queries the settings for conversion between compact and dense groups. * @param gcpl_id IN: Group creation property list identifier * @param links * The max. no. of compact links & the min. no. of dense * links, which are used for storing groups * * 
*      links[0] =  The maximum number of links for compact storage
*      links[1] =  The minimum number of links for dense storage
*
* * @return Returns a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - size is null. * **/ public synchronized static native int H5Pget_link_phase_change(int gcpl_id, int []links) throws HDF5LibraryException, NullPointerException; /** * H5Pset_link_phase_change Sets the parameters for conversion between compact and dense groups. * @param gcpl_id IN: Group creation property list identifier * @param max_compact IN: Maximum number of links for compact storage(Default: 8) * @param min_dense IN: Minimum number of links for dense storage(Default: 6) * * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception IllegalArgumentException - Invalid values of max_compact and min_dense. * **/ public synchronized static native int H5Pset_link_phase_change(int gcpl_id, int max_compact, int min_dense) throws HDF5LibraryException, IllegalArgumentException; /** * H5Pget_local_heap_size_hint Retrieves the anticipated size of the local heap for original-style groups. * @param gcpl_id IN: Group creation property list identifier * * @return size_hint, the anticipated size of local heap * * @exception HDF5LibraryException - Error from the HDF-5 Library. * **/ public synchronized static native long H5Pget_local_heap_size_hint(int gcpl_id) throws HDF5LibraryException; /** * H5Pset_local_heap_size_hint Specifies the anticipated maximum size of a local heap. * @param gcpl_id IN: Group creation property list identifier * @param size_hint IN: Anticipated maximum size in bytes of local heap * * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * **/ public synchronized static native int H5Pset_local_heap_size_hint(int gcpl_id, long size_hint) throws HDF5LibraryException; /** * H5Pget_mdc_config gets the initial metadata cache configuration contained in a * file access property list and loads it into the instance of H5AC_cache_config_t * pointed to by the config_ptr parameter. This configuration is used when the file is opened. * * @param plist_id IN: Identifier of the file access property list. * * @return A buffer(H5AC_cache_config_t) for the current metadata cache configuration information * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native H5AC_cache_config_t H5Pget_mdc_config(int plist_id) throws HDF5LibraryException; public synchronized static native void H5Pset_mdc_config(int plist_id, H5AC_cache_config_t config_ptr) throws HDF5LibraryException; /** * H5Pget_meta_block_size the current metadata block size setting. * @param fapl_id IN: File access property list identifier * * @return the minimum size, in bytes, of metadata block allocations. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * **/ public synchronized static native long H5Pget_meta_block_size(int fapl_id) throws HDF5LibraryException; /** * H5Pset_meta_block_size sets the minimum metadata block size. * @param fapl_id IN: File access property list identifier * @param size IN: Minimum size, in bytes, of metadata block allocations. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * **/ public synchronized static native void H5Pset_meta_block_size(int fapl_id, long size) throws HDF5LibraryException; /** * H5Pget_nfilters returns the number of filters defined in the filter * pipeline associated with the property list plist. * * @param plist * IN: Property list identifier. * * @return the number of filters in the pipeline if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Pget_nfilters(int plist) throws HDF5LibraryException; /** * H5Pget_nlinks retrieves the maximum number of soft or user-defined link traversals allowed, nlinks, before the library assumes it has found a cycle and aborts the traversal. This value is retrieved from the link access property list lapl_id. * @param lapl_id IN: File access property list identifier * * @return Returns a Maximum number of links to traverse. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * **/ public synchronized static native long H5Pget_nlinks(int lapl_id) throws HDF5LibraryException; /** * H5Pset_nlinks sets the maximum number of soft or user-defined link traversals allowed, nlinks, before the library assumes it has found a cycle and aborts the traversal. This value is set in the link access property list lapl_id. * @param lapl_id IN: File access property list identifier * @param nlinks IN: Maximum number of links to traverse * * @return Returns a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception IllegalArgumentException - Argument is Illegal * **/ public synchronized static native int H5Pset_nlinks(int lapl_id, long nlinks) throws HDF5LibraryException, IllegalArgumentException; /** * H5Pget_nprops retrieves the number of properties in a property list or * class * * @param plid * IN: Identifier of property object to query * @return number of properties if successful; a negative value if failed * @throws HDF5LibraryException */ public synchronized static native long H5Pget_nprops(int plid) throws HDF5LibraryException; /** * H5Pget_preserve checks the status of the dataset transfer property list. * * @deprecated As of HDF5 1.8, compound datatype field preservation is now core functionality in the HDF5 Library. * * @param plist * IN: Identifier for the dataset transfer property list. * * @return TRUE or FALSE if successful; otherwise returns a negative value * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ @Deprecated public synchronized static native int H5Pget_preserve(int plist) throws HDF5LibraryException; /** * H5Pset_preserve sets the dataset transfer property list status to TRUE or * FALSE. * * @deprecated As of HDF5 1.8, compound datatype field preservation is now core functionality in the HDF5 Library. * * @param plist * IN: Identifier for the dataset transfer property list. * @param status * IN: Status of for the dataset transfer property list. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception IllegalArgumentException * - plist is invalid. **/ @Deprecated public synchronized static native int H5Pset_preserve(int plist, boolean status) throws HDF5LibraryException, IllegalArgumentException; /** * H5Pget_obj_track_times queries the object creation property list, ocpl_id, * to determine whether object times are being recorded. * * @param ocpl_id IN: Object creation property list identifier * * @return TRUE or FALSE, specifying whether object times are being recorded * * @exception HDF5LibraryException - Error from the HDF-5 Library. * **/ public synchronized static native boolean H5Pget_obj_track_times(int ocpl_id) throws HDF5LibraryException; /** * H5Pset_obj_track_times sets a property in the object creation property list, ocpl_id, * that governs the recording of times associated with an object. * * @param ocpl_id IN: Object creation property list identifier * * @param track_times IN: TRUE or FALSE, specifying whether object times are to be tracked * * @exception HDF5LibraryException - Error from the HDF-5 Library. * **/ public synchronized static native void H5Pset_obj_track_times(int ocpl_id, boolean track_times) throws HDF5LibraryException; /** * H5Pget_shared_mesg_index Retrieves the configuration settings for a shared message index. * @param fcpl_id IN: File creation property list identifier * @param index_num IN: Index being configured. * @param mesg_info * The message type and minimum message size * * 
*      mesg_info[0] =  Types of messages that may be stored in this index.
*      mesg_info[1] =  Minimum message size.  
*
* * @return Returns a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - mesg_info is null. * @exception IllegalArgumentException - Invalid value of nindexes * **/ public synchronized static native int H5Pget_shared_mesg_index(int fcpl_id, int index_num, int[] mesg_info) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Pset_shared_mesg_index Configures the specified shared object header message index * @param fcpl_id IN: File creation property list identifier. * @param index_num IN: Index being configured. * @param mesg_type_flags IN: Types of messages that should be stored in this index. * @param min_mesg_size IN: Minimum message size. * * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception IllegalArgumentException - Invalid value of nindexes * **/ public synchronized static native int H5Pset_shared_mesg_index(int fcpl_id, int index_num, int mesg_type_flags, int min_mesg_size) throws HDF5LibraryException, IllegalArgumentException; /** * H5Pget_shared_mesg_nindexes retrieves number of shared object header message indexes in file creation property list. * @param fcpl_id IN: : File creation property list identifier * * @return nindexes, the number of shared object header message indexes available in files created with this property list * * @exception HDF5LibraryException - Error from the HDF-5 Library. * **/ public synchronized static native int H5Pget_shared_mesg_nindexes(int fcpl_id) throws HDF5LibraryException; /** * H5Pset_shared_mesg_nindexes sets the number of shared object header message indexes in the specified file creation property list. * @param plist_id IN: File creation property list * @param nindexes IN: Number of shared object header message indexes to be available in files created with this property list * * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception IllegalArgumentException - Invalid value of nindexes * **/ public synchronized static native int H5Pset_shared_mesg_nindexes(int plist_id, int nindexes) throws HDF5LibraryException, IllegalArgumentException; /** * H5Pget_shared_mesg_phase_change retrieves shared object header message phase change information. * @param fcpl_id IN: : File creation property list identifier * @param size * The threshold values for storage of shared object header * message indexes in a file. * * 
*      size[0] =  Threshold above which storage of a shared object header message index shifts from list to B-tree 
*      size[1] =  Threshold below which storage of a shared object header message index reverts to list format  
*
* * @return Returns a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - size is null. * **/ public synchronized static native int H5Pget_shared_mesg_phase_change(int fcpl_id, int[] size) throws HDF5LibraryException, NullPointerException; /** * H5Pset_shared_mesg_phase_change sets shared object header message storage phase change thresholds. * @param fcpl_id IN: File creation property list identifier * @param max_list IN: Threshold above which storage of a shared object header message index shifts from list to B-tree * @param min_btree IN: Threshold below which storage of a shared object header message index reverts to list format * * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception IllegalArgumentException - Invalid values of max_list and min_btree. * **/ public synchronized static native int H5Pset_shared_mesg_phase_change(int fcpl_id, int max_list, int min_btree) throws HDF5LibraryException, IllegalArgumentException; public synchronized static native long H5Pget_sieve_buf_size(int fapl_id) throws HDF5LibraryException; public synchronized static native void H5Pset_sieve_buf_size(int fapl_id, long size) throws HDF5LibraryException; /** * H5Pget_size retrieves the size of a property's value in bytes * * @param plid * IN: Identifier of property object to query * @param name * IN: Name of property to query * @return size of a property's value if successful; a negative value if * failed * @throws HDF5LibraryException */ public synchronized static native long H5Pget_size(int plid, String name) throws HDF5LibraryException; /** * H5Pget_sizes retrieves the size of the offsets and lengths used in an * HDF5 file. This function is only valid for file creation property lists. * * @param plist * IN: Identifier of property list to query. * @param size * OUT: the size of the offsets and length. * * 
 *      size[0] = sizeof_addr // offset size in bytes
 *      size[1] = sizeof_size // length size in bytes
 *
* @return a non-negative value with the sizes initialized; if successful; * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - size is null. * @exception IllegalArgumentException * - size is invalid. **/ public synchronized static native int H5Pget_sizes(int plist, long[] size) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Pset_sizes sets the byte size of the offsets and lengths used to * address objects in an HDF5 file. * * @param plist * IN: Identifier of property list to modify. * @param sizeof_addr * IN: Size of an object offset in bytes. * @param sizeof_size * IN: Size of an object length in bytes. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_sizes(int plist, int sizeof_addr, int sizeof_size) throws HDF5LibraryException; /** * H5Pget_small_data_block_size retrieves the size of a block of small data * in a file creation property list. * * @param plist * IN: Identifier for property list to query. * @param size * OUT: Pointer to location to return block size. * * @return a non-negative value and the size of the user block; if * successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - size is null. **/ public synchronized static native int H5Pget_small_data_block_size( int plist, long[] size) throws HDF5LibraryException, NullPointerException; public synchronized static native long H5Pget_small_data_block_size_long( int plist) throws HDF5LibraryException; /** * H5Pset_small_data_block_size reserves blocks of size bytes for the * contiguous storage of the raw data portion of small datasets. * * @param plist * IN: Identifier of property list to modify. * @param size * IN: Size of the blocks in bytes. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_small_data_block_size( int plist, long size) throws HDF5LibraryException; /** * H5Pget_sym_k retrieves the size of the symbol table B-tree 1/2 rank and * the symbol table leaf node 1/2 size. * * @param plist * IN: Property list to query. * @param size * OUT: the symbol table's B-tree 1/2 rank and leaf node 1/2size. * * 
 *      size[0] = ik // the symbol table's B-tree 1/2 rank
 *      size[1] = lk // leaf node 1/2 size
 *
* * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - size is null. * @exception IllegalArgumentException * - size is invalid. **/ public synchronized static native int H5Pget_sym_k(int plist, int[] size) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Pset_sym_k sets the size of parameters used to control the symbol table * nodes. * * @param plist * IN: Identifier for property list to query. * @param ik * IN: Symbol table tree rank. * @param lk * IN: Symbol table node size. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_sym_k(int plist, int ik, int lk) throws HDF5LibraryException; /** * H5Pget_userblock retrieves the size of a user block in a file creation * property list. * * @param plist * IN: Identifier for property list to query. * @param size * OUT: Pointer to location to return user-block size. * * @return a non-negative value and the size of the user block; if * successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - size is null. **/ public synchronized static native int H5Pget_userblock(int plist, long[] size) throws HDF5LibraryException, NullPointerException; /** * H5Pset_userblock sets the user block size of a file creation property * list. * * @param plist * IN: Identifier of property list to modify. * @param size * IN: Size of the user-block in bytes. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_userblock(int plist, long size) throws HDF5LibraryException; /** * H5Pget_version retrieves the version information of various objects for a * file creation property list. * * @param plist * IN: Identifier of the file creation property list. * @param version_info * OUT: version information. * * 
 *      version_info[0] = boot  // boot block version number
 *      version_info[1] = freelist  // global freelist version
 *      version_info[2] = stab  // symbol tabl version number
 *      version_info[3] = shhdr  // hared object header version
 *
* @return a non-negative value, with the values of version_info * initialized, if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - version_info is null. * @exception IllegalArgumentException * - version_info is illegal. **/ public synchronized static native int H5Pget_version(int plist, int[] version_info) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Pisa_class checks to determine whether a property list is a member of * the specified class * * @param plist * IN: Identifier of the property list * @param pclass * IN: Identifier of the property class * @return a positive value if equal; zero if unequal; a negative value if * failed * @throws HDF5LibraryException */ public synchronized static native int H5Pisa_class(int plist, int pclass) throws HDF5LibraryException; public synchronized static native int H5Pmodify_filter(int plist, int filter, int flags, long cd_nelmts, int[] cd_values) throws HDF5LibraryException, NullPointerException; /** * H5Punregister removes a property from a property list class * * @param plid * IN: Property list class from which to remove permanent * property * @param name * IN: Name of property to remove * @return a non-negative value if successful; a negative value if failed * @throws HDF5LibraryException */ public synchronized static native int H5Punregister(int plid, String name) throws HDF5LibraryException; /** * H5Premove removes a property from a property list * * @param plid * IN: Identifier of the property list to modify * @param name * IN: Name of property to remove * @return a non-negative value if successful; a negative value if failed * @throws HDF5LibraryException */ public synchronized static native int H5Premove(int plid, String name) throws HDF5LibraryException; public synchronized static native int H5Premove_filter(int obj_id, int filter) throws HDF5LibraryException; /** * H5Pset_deflate sets the compression method for a dataset. * * @param plist * IN: Identifier for the dataset creation property list. * @param level * IN: Compression level. * * @return non-negative if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_deflate(int plist, int level) throws HDF5LibraryException; /** * H5Pset_fapl_log Sets up the logging virtual file driver (H5FD_LOG) for use. * H5Pset_fapl_log modifies the file access property list to use the logging driver, H5FD_LOG. * The logging virtual file driver (VFD) is a clone of the standard SEC2 (H5FD_SEC2) driver * with additional facilities for logging VFD metrics and activity to a file. * * @deprecated As of HDF5 1.8.7, replaced by {@link #H5Pset_fapl_log(int, String, long, long)} * * @param fapl_id IN: File access property list identifier. * @param logfile IN: logfile is the name of the file in which the logging entries are to be recorded. * @param flags IN: Flags specifying the types of logging activity. * @param buf_size IN: The size of the logging buffers, in bytes. * * @return a non-negative value if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - logfile is null. **/ @Deprecated public static int H5Pset_fapl_log(int fapl_id, String logfile, int flags, int buf_size) throws HDF5LibraryException, NullPointerException { H5Pset_fapl_log(fapl_id, logfile, (long)flags, (long)buf_size); return 1; } /** * H5Pset_fapl_log Sets up the logging virtual file driver (H5FD_LOG) for use. * H5Pset_fapl_log modifies the file access property list to use the logging driver, H5FD_LOG. * The logging virtual file driver (VFD) is a clone of the standard SEC2 (H5FD_SEC2) driver * with additional facilities for logging VFD metrics and activity to a file. * * @param fapl_id IN: File access property list identifier. * @param logfile IN: logfile is the name of the file in which the logging entries are to be recorded. * @param flags IN: Flags specifying the types of logging activity. * @param buf_size IN: The size of the logging buffers, in bytes. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - logfile is null. **/ public synchronized static native void H5Pset_fapl_log(int fapl_id, String logfile, long flags, long buf_size) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Pset_fapl_sec2(int fapl_id) throws HDF5LibraryException, NullPointerException; public synchronized static native void H5Pset_fapl_split(int fapl_id, String meta_ext, int meta_plist_id, String raw_ext, int raw_plist_id) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Pset_fapl_stdio(int fapl_id) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Pset_fapl_windows(int fapl_id) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Pset_fletcher32(int plist) throws HDF5LibraryException, NullPointerException; /** * H5Pset_nbit Sets up the use of the N-Bit filter. * @param plist_id IN: Dataset creation property list identifier. * * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * **/ public synchronized static native int H5Pset_nbit(int plist_id) throws HDF5LibraryException; /** * H5Pset_scaleoffset sets the Scale-Offset filter for a dataset. * @param plist_id IN: Dataset creation property list identifier. * @param scale_type IN: Flag indicating compression method. * @param scale_factor IN: Parameter related to scale. * * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception IllegalArgumentException - Invalid arguments * **/ public synchronized static native int H5Pset_scaleoffset(int plist_id, int scale_type, int scale_factor) throws HDF5LibraryException, IllegalArgumentException; public synchronized static native int H5Pset_shuffle(int plist_id) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Pset_szip(int plist, int options_mask, int pixels_per_block) throws HDF5LibraryException, NullPointerException; ///////// unimplemented //////// //herr_t H5Padd_merge_committed_dtype_path(hid_t plist_id, const char *path); //hid_t H5Pcreate_class( hid_t parent_class, const char *name, H5P_cls_create_func_t create, void *create_data, H5P_cls_copy_func_t copy, void *copy_data, H5P_cls_close_func_t close, void *close_data ) //herr_t H5Pfree_merge_committed_dtype_paths(hid_t plist_id); //void *H5Pget_driver_info( hid_t plist_id ) //herr_t H5Pget_elink_cb( hid_t lapl_id, H5L_elink_traverse_t *func, void **op_data ) //herr_t H5Pset_elink_cb( hid_t lapl_id, H5L_elink_traverse_t func, void *op_data ) //herr_t H5Pget_file_image(hid_t fapl_id, void **buf_ptr_ptr, size_t *buf_len_ptr); //herr_t H5Pset_file_image(hid_t fapl_id, void *buf_ptr, size_t buf_len); //herr_t H5Pget_file_image_callbacks(hid_t fapl_id, // H5FD_file_image_callbacks_t *callbacks_ptr); //herr_t H5Pset_file_image_callbacks(hid_t fapl_id, // H5FD_file_image_callbacks_t *callbacks_ptr); //herr_t H5Pget_mcdt_search_cb(hid_t plist_id, H5O_mcdt_search_cb_t *func, void **op_data); //herr_t H5Pset_mcdt_search_cb(hid_t plist_id, H5O_mcdt_search_cb_t func, void *op_data); //herr_t H5Pget_multi_type ( hid_t fapl_id, H5FD_mem_t *type ) //herr_t H5Pset_multi_type ( hid_t fapl_id, H5FD_mem_t type ) //herr_t H5Pget_type_conv_cb(hid_t plist, H5T_conv_except_func_t *func, void **op_data) //herr_t H5Pset_type_conv_cb( hid_t plist, H5T_conv_except_func_t func, void *op_data) //herr_t H5Pget_vlen_mem_manager(hid_t plist, H5MM_allocate_t *alloc, void **alloc_info, H5MM_free_t *free, void **free_info ) //herr_t H5Pset_vlen_mem_manager(hid_t plist, H5MM_allocate_t alloc, void *alloc_info, H5MM_free_t free, void *free_info ) //herr_t H5Pinsert( hid_t plid, const char *name, size_t size, void *value, H5P_prp_set_func_t set, H5P_prp_get_func_t get, H5P_prp_delete_func_t delete, H5P_prp_copy_func_t copy, H5P_prp_compare_func_t compare, H5P_prp_close_func_t close )] //herr_t H5Pinsert2( hid_t plid, const char *name, size_t size, void *value, H5P_prp_set_func_t set, H5P_prp_get_func_t get, H5P_prp_delete_func_t delete, H5P_prp_copy_func_t copy, H5P_prp_compare_func_t compare, H5P_prp_close_func_t close ) //int H5Piterate( hid_t id, int * idx, H5P_iterate_t iter_func, void * iter_data ) //herr_t H5Pregister( hid_t class, const char * name, size_t size, void * default, H5P_prp_create_func_t create, H5P_prp_set_func_t set, H5P_prp_get_func_t get, H5P_prp_delete_func_t delete, H5P_prp_copy_func_t copy, H5P_prp_compare_func_t compare, H5P_prp_close_func_t close ) //herr_t H5Pregister2( hid_t class, const char * name, size_t size, void * default, H5P_prp_create_func_t create, H5P_prp_set_func_t set, H5P_prp_get_func_t get, H5P_prp_delete_func_t delete, H5P_prp_copy_func_t copy, H5P_prp_compare_func_t compare, H5P_prp_close_func_t close ) //herr_t H5Pset_attr_phase_change( hid_t ocpl_id, unsigned max_compact, unsigned min_dense ) //herr_t H5Pset_buffer(hid_t plist_id, size_t size, void *tconv, void *bkg); //herr_t H5Pset_driver( hid_t plist_id, hid_t new_driver_id, const void *new_driver_info ) //herr_t H5Pset_filter_callback(hid_t plist, H5Z_filter_func_t func, void *op_data) //herr_t H5Pget_dxpl_mpio( hid_t dxpl_id, H5FD_mpio_xfer_t *xfer_mode ) //herr_t H5Pset_dxpl_mpio( hid_t dxpl_id, H5FD_mpio_xfer_t xfer_mode ) //herr_t H5Pset_dxpl_mpio_chunk_opt (hid_t dxpl_id, H5FD_mpio_chunk_opt_t opt_mode) //herr_t H5Pset_dxpl_mpio_chunk_opt_num (hid_t dxpl_id, unsigned num_chunk_per_proc) //herr_t H5Pset_dxpl_mpio_chunk_opt_ratio (hid_t dxpl_id, unsigned percent_proc_per_chunk) //herr_t H5Pset_dxpl_mpio_collective_opt (hid_t dxpl_id, H5FD_mpio_collective_opt_t opt_mode) ////////////////////////////////////////////////////////////// //// //H5R: HDF5 1.8 Reference API Functions // //// ////////////////////////////////////////////////////////////// private synchronized static native int H5Rcreate(byte[] ref, int loc_id, String name, int ref_type, int space_id) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Rcreate creates the reference, ref, of the type specified in ref_type, * pointing to the object name located at loc_id. * * @param loc_id * IN: Location identifier used to locate the object being * pointed to. * @param name * IN: Name of object at location loc_id. * @param ref_type * IN: Type of reference. * @param space_id * IN: Dataspace identifier with selection. * * @return the reference (byte[]) if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - an input array is null. * @exception IllegalArgumentException * - an input array is invalid. **/ public synchronized static byte[] H5Rcreate(int loc_id, String name, int ref_type, int space_id) throws HDF5LibraryException, NullPointerException, IllegalArgumentException { /* These sizes are correct for HDF5.1.2 */ int ref_size = 8; if (ref_type == HDF5Constants.H5R_DATASET_REGION) { ref_size = 12; } byte rbuf[] = new byte[ref_size]; /* will raise an exception if fails */ H5Rcreate(rbuf, loc_id, name, ref_type, space_id); return rbuf; } /** * Given a reference to some object, H5Rdereference opens that object and * return an identifier. * * @param dataset * IN: Dataset containing reference object. * @param ref_type * IN: The reference type of ref. * @param ref * IN: reference to an object * * @return valid identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - output array is null. * @exception IllegalArgumentException * - output array is invalid. **/ public static int H5Rdereference(int dataset, int ref_type, byte[] ref) throws HDF5LibraryException, NullPointerException, IllegalArgumentException { int id = _H5Rdereference(dataset, ref_type, ref); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Rdereference(int dataset, int ref_type, byte[] ref) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Rget_name retrieves a name for the object identified by ref. * @param loc_id IN: Identifier for the dataset containing the reference or for the group that dataset is in. * @param ref_type IN: Type of reference. * @param ref IN: An object or dataset region reference. * @param name OUT: A name associated with the referenced object or dataset region. * @param size IN: The size of the name buffer. * * @return Returns the length of the name if successful, returning 0 (zero) if no name is associated with the identifier. Otherwise returns a negative value. * * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - size is null. * @exception IllegalArgumentException - Argument is illegal. * **/ public synchronized static native long H5Rget_name( int loc_id, int ref_type, byte[] ref, String[] name, long size) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /* * [NOTE: This function is only supported in HDF5 Releases 1.4.x. It has * been replaced in Release 1.6 by the function H5Rget_obj_type public * synchronized static native int H5Rget_object_type(int loc_id, byte ref[]) * throws HDF5LibraryException, NullPointerException, * IllegalArgumentException; */ /** * Given a reference to an object ref, H5Rget_obj_type returns the type of * the object pointed to. * * @deprecated As of HDF5 1.8, replaced by {@link #H5Rget_obj_type(int, int, byte[], int[]) } * * @param loc_id * IN: loc_id of the reference object. * @param ref_type * IN: Type of reference to query. * * @param ref * IN: the reference * * @return a valid object type if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - array is null. * @exception IllegalArgumentException * - array is invalid. **/ @Deprecated public synchronized static native int H5Rget_obj_type(int loc_id, int ref_type, byte ref[]) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Rget_obj_type Given a reference to an object ref, H5Rget_obj_type returns the type of * the object pointed to. * * @param loc_id IN: loc_id of the reference object. * @param ref_type IN: Type of reference to query. * @param ref IN: the reference * @param obj_type OUT:Type of referenced object * * @return Returns the object type, which is the same as obj_type[0]. The return value is * the same as the HDF5 1.6 version. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - array is null. * @exception IllegalArgumentException * - array is invalid. **/ public static int H5Rget_obj_type(int loc_id, int ref_type, byte ref[], int [] obj_type) throws HDF5LibraryException, NullPointerException, IllegalArgumentException { return H5Rget_obj_type2(loc_id, ref_type, ref, obj_type); } /** * H5Rget_obj_type2 Retrieves the type of object that an object reference points to. * * @see public static int H5Rget_obj_type(int loc_id, int ref_type, byte ref[], int [] obj_type) **/ private synchronized static native int H5Rget_obj_type2(int loc_id, int ref_type, byte ref[], int [] obj_type) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * Given a reference to an object ref, H5Rget_region creates a copy of the * dataspace of the dataset pointed to and defines a selection in the copy * which is the region pointed to. * * @param loc_id * IN: loc_id of the reference object. * @param ref_type * IN: The reference type of ref. * @param ref * OUT: the reference to the object and region * * @return a valid identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - output array is null. * @exception IllegalArgumentException * - output array is invalid. **/ public static int H5Rget_region(int loc_id, int ref_type, byte[] ref) throws HDF5LibraryException, NullPointerException, IllegalArgumentException { int id = _H5Rget_region(loc_id, ref_type, ref); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Rget_region(int loc_id, int ref_type, byte[] ref) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; ////////////////////////////////////////////////////////////// // // //H5S: Dataspace Interface Functions // // // ////////////////////////////////////////////////////////////// /** * H5Sclose releases a dataspace. * * @param space_id * Identifier of dataspace to release. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Sclose(int space_id) throws HDF5LibraryException { if (space_id < 0) return 0; // throw new HDF5LibraryException("Negative ID");; OPEN_IDS.removeElement(space_id); return _H5Sclose(space_id); } private synchronized static native int _H5Sclose(int space_id) throws HDF5LibraryException; /** * H5Scopy creates a new dataspace which is an exact copy of the dataspace * identified by space_id. * * @param space_id * Identifier of dataspace to copy. * @return a dataspace identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Scopy(int space_id) throws HDF5LibraryException { int id = _H5Scopy(space_id); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Scopy(int space_id) throws HDF5LibraryException; /** * H5Screate creates a new dataspace of a particular type. * * @param type IN: The type of dataspace to be created. * @return a dataspace identifier * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public static int H5Screate(int type) throws HDF5LibraryException { int id = _H5Screate(type); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Screate(int type) throws HDF5LibraryException; /** * H5Screate_simple creates a new simple data space and opens * it for access. * * @param rank IN: Number of dimensions of dataspace. * @param dims IN: An array of the size of each dimension. * @param maxdims IN: An array of the maximum size of each dimension. * * @return a dataspace identifier * * @exception HDF5Exception - Error from the HDF-5 Library. * @exception NullPointerException - dims or maxdims is null. **/ public static int H5Screate_simple(int rank, long[] dims, long[] maxdims) throws HDF5Exception, NullPointerException { int id = _H5Screate_simple(rank, dims, maxdims); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Screate_simple(int rank, long[] dims, long[] maxdims) throws HDF5Exception, NullPointerException; /** * @deprecated use H5Screate_simple(int rank, long[] dims, long[] maxdims) **/ @Deprecated public static int H5Screate_simple(int rank, byte[] dims, byte[] maxdims) throws HDF5Exception, NullPointerException { ByteBuffer dimsbb = ByteBuffer.wrap(dims); long[] ladims = (dimsbb.asLongBuffer()).array(); ByteBuffer maxdimsbb = ByteBuffer.wrap(maxdims); long[] lamaxdims = (maxdimsbb.asLongBuffer()).array(); int id = _H5Screate_simple(rank, ladims, lamaxdims); if (id > 0) OPEN_IDS.addElement(id); return id; } /** * H5Sdecode reconstructs the HDF5 data space object and returns a * new object handle for it. * * @param buf IN: Buffer for the data space object to be decoded. * * @return a new object handle * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - buf is null. **/ public synchronized static native int H5Sdecode(byte[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Sencode converts a data space description into binary form in a buffer. * * @param obj_id IN: Identifier of the object to be encoded. * * @return the buffer for the object to be encoded into. * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native byte[] H5Sencode(int obj_id) throws HDF5LibraryException, NullPointerException; /** * H5Sextent_copy copies the extent from source_space_id to dest_space_id. * This action may change the type of the dataspace. * * @param dest_space_id * IN: The identifier for the dataspace from which the extent is * copied. * @param source_space_id * IN: The identifier for the dataspace to which the extent is * copied. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Sextent_copy(int dest_space_id, int source_space_id) throws HDF5LibraryException; /** * H5Sextent_equal determines whether the dataspace extents of two dataspaces, * space1_id and space2_id, are equal. * * @param first_space_id * IN: The identifier for the first dataspace. * @param second_space_id * IN: The identifier for the seconddataspace. * * @return true if successful, else false * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native boolean H5Sextent_equal(int first_space_id, int second_space_id) throws HDF5LibraryException; /** * H5Sget_select_bounds retrieves the coordinates of the bounding box * containing the current selection and places them into user-supplied * buffers. *

* The start and end buffers must be large enough to hold the dataspace rank * number of coordinates. * * @param spaceid * Identifier of dataspace to release. * @param start * coordinates of lowest corner of bounding box. * @param end * coordinates of highest corner of bounding box. * * @return a non-negative value if successful,with start and end * initialized. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - start or end is null. **/ public synchronized static native int H5Sget_select_bounds(int spaceid, long[] start, long[] end) throws HDF5LibraryException, NullPointerException; /** * H5Sget_select_elem_npoints returns the number of element points in the * current dataspace selection. * * @param spaceid * Identifier of dataspace to release. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5Sget_select_elem_npoints( int spaceid) throws HDF5LibraryException; /** * H5Sget_select_elem_pointlist returns an array of of element points in the * current dataspace selection. The point coordinates have the same * dimensionality (rank) as the dataspace they are located within, one * coordinate per point. * * @param spaceid * Identifier of dataspace to release. * @param startpoint * first point to retrieve * @param numpoints * number of points to retrieve * @param buf * returns points startblock to startblock+num-1, each points is * rank longs. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - buf is null. **/ public synchronized static native int H5Sget_select_elem_pointlist( int spaceid, long startpoint, long numpoints, long[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Sget_select_hyper_blocklist returns an array of hyperslab blocks. The * block coordinates have the same dimensionality (rank) as the dataspace * they are located within. The list of blocks is formatted as follows: * * 

 *    <"start" coordinate>, immediately followed by
 *    <"opposite" corner coordinate>, followed by
 *   the next "start" and "opposite" coordinates,
 *   etc.
 *   until all of the selected blocks have been listed.
 *
* * @param spaceid * Identifier of dataspace to release. * @param startblock * first block to retrieve * @param numblocks * number of blocks to retrieve * @param buf * returns blocks startblock to startblock+num-1, each block is * rank * 2 (corners) longs. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - buf is null. **/ public synchronized static native int H5Sget_select_hyper_blocklist( int spaceid, long startblock, long numblocks, long[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Sget_select_hyper_nblocks returns the number of hyperslab blocks in the * current dataspace selection. * * @param spaceid * Identifier of dataspace to release. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5Sget_select_hyper_nblocks( int spaceid) throws HDF5LibraryException; /** * H5Sget_select_npoints determines the number of elements in the current * selection of a dataspace. * * @param space_id IN: Identifier of the dataspace object to query * * @return the number of elements in the selection if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native long H5Sget_select_npoints(int space_id) throws HDF5LibraryException; /** * H5Sget_select_type retrieves the type of selection currently defined for the dataspace space_id. * * @param space_id IN: Identifier of the dataspace object to query * * @return the dataspace selection type if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native int H5Sget_select_type(int space_id) throws HDF5LibraryException; /** * H5Sget_simple_extent_dims returns the size and maximum sizes of each * dimension of a dataspace through the dims and maxdims parameters. * * @param space_id IN: Identifier of the dataspace object to query * @param dims OUT: Pointer to array to store the size of each dimension. * @param maxdims OUT: Pointer to array to store the maximum size of each * dimension. * * @return the number of dimensions in the dataspace if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - dims or maxdims is null. **/ public synchronized static native int H5Sget_simple_extent_dims( int space_id, long[] dims, long[] maxdims) throws HDF5LibraryException, NullPointerException; /** * H5Sget_simple_extent_ndims determines the dimensionality (or rank) of a * dataspace. * * @param space_id IN: Identifier of the dataspace * * @return the number of dimensions in the dataspace if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native int H5Sget_simple_extent_ndims( int space_id) throws HDF5LibraryException; /** * H5Sget_simple_extent_npoints determines the number of elements in a * dataspace. * * @param space_id * ID of the dataspace object to query * @return the number of elements in the dataspace if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5Sget_simple_extent_npoints( int space_id) throws HDF5LibraryException; /** * H5Sget_simple_extent_type queries a dataspace to determine the current * class of a dataspace. * * @param space_id * Dataspace identifier. * * @return a dataspace class name if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Sget_simple_extent_type(int space_id) throws HDF5LibraryException; /** * H5Sis_simple determines whether a dataspace is a simple dataspace. * * @param space_id * Identifier of the dataspace to query * * @return true if is a simple dataspace * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native boolean H5Sis_simple(int space_id) throws HDF5LibraryException; /** * H5Soffset_simple sets the offset of a simple dataspace space_id. * * @param space_id * IN: The identifier for the dataspace object to reset. * @param offset * IN: The offset at which to position the selection. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - offset array is null. **/ public synchronized static native int H5Soffset_simple(int space_id, byte[] offset) throws HDF5LibraryException, NullPointerException; public synchronized static int H5Soffset_simple(int space_id, long[] offset) throws HDF5Exception, NullPointerException { if (offset == null) { return -1; } HDFArray theArray = new HDFArray(offset); byte[] theArr = theArray.byteify(); int retVal = H5Soffset_simple(space_id, theArr); theArr = null; theArray = null; return retVal; } /** * H5Sselect_all selects the entire extent of the dataspace space_id. * * @param space_id * IN: The identifier of the dataspace to be selected. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Sselect_all(int space_id) throws HDF5LibraryException; /** * H5Sselect_elements selects array elements to be included in the selection * for the space_id dataspace. * * @param space_id * Identifier of the dataspace. * @param op * operator specifying how the new selection is combined. * @param num_elements * Number of elements to be selected. * @param coord * A 2-dimensional array specifying the coordinates of the * elements. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ private synchronized static native int H5Sselect_elements(int space_id, int op, int num_elements, byte[] coord) throws HDF5LibraryException, NullPointerException; /** * H5Sselect_elements selects array elements to be included in the selection * for the space_id dataspace. * * @param space_id * Identifier of the dataspace. * @param op * operator specifying how the new selection is combined. * @param num_elements * Number of elements to be selected. * @param coord2D * A 2-dimensional array specifying the coordinates of the * elements. * * @return a non-negative value if successful * * @exception HDF5Exception * - Error in the data conversion * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - cord array is **/ public synchronized static int H5Sselect_elements(int space_id, int op, int num_elements, long[][] coord2D) throws HDF5Exception, HDF5LibraryException, NullPointerException { if (coord2D == null) { return -1; } HDFArray theArray = new HDFArray(coord2D); byte[] coord = theArray.byteify(); int retVal = H5Sselect_elements(space_id, op, num_elements, coord); coord = null; theArray = null; return retVal; } ///** //* H5Sselect_hyperslab selects a hyperslab region to add to //* the current selected region for the dataspace specified //* by space_id. The start, stride, count, and block arrays //* must be the same size as the rank of the dataspace. //* //* @param space_id IN: Identifier of dataspace selection to modify //* @param op IN: Operation to perform on current selection. //* @param start IN: Offset of start of hyperslab //* @param count IN: Number of blocks included in hyperslab. //* @param stride IN: Hyperslab stride. //* @param block IN: Size of block in hyperslab. //* //* @return none //* //* @exception HDF5LibraryException - Error from the HDF-5 Library. //* @exception NullPointerException - an input array is null. //* @exception IllegalArgumentException - an input array is invalid. //**/ //public synchronized static native void H5Sselect_hyperslab(int space_id, H5S_SELECT_OPER op, // long start[], long _stride[], long count[], long _block[]) // throws HDF5LibraryException, NullPointerException, IllegalArgumentException; //public synchronized static native int H5Scombine_hyperslab(int space_id, H5S_SELECT_OPER op, // const long start[], const long _stride[], // const long count[], const long _block[]) // throws HDF5LibraryException, NullPointerException; //public synchronized static native int H5Sselect_select(int space1_id, H5S_SELECT_OPER op, // int space2_id) // throws HDF5LibraryException, NullPointerException; //public synchronized static native int H5Scombine_select(int space1_id, H5S_SELECT_OPER op, // int space2_id) // throws HDF5LibraryException, NullPointerException; /** * H5Sselect_hyperslab selects a hyperslab region to add to the current * selected region for the dataspace specified by space_id. The start, * stride, count, and block arrays must be the same size as the rank of the * dataspace. * * @param space_id * IN: Identifier of dataspace selection to modify * @param op * IN: Operation to perform on current selection. * @param start * IN: Offset of start of hyperslab * @param stride * IN: Hyperslab stride. * @param count * IN: Number of blocks included in hyperslab. * @param block * IN: Size of block in hyperslab. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - an input array is null. * @exception NullPointerException * - an input array is invalid. **/ public synchronized static int H5Sselect_hyperslab(int space_id, int op, byte[] start, byte[] stride, byte[] count, byte[] block) throws HDF5LibraryException, NullPointerException, IllegalArgumentException { ByteBuffer startbb = ByteBuffer.wrap(start); long[] lastart = (startbb.asLongBuffer()).array(); ByteBuffer stridebb = ByteBuffer.wrap(stride); long[] lastride = (stridebb.asLongBuffer()).array(); ByteBuffer countbb = ByteBuffer.wrap(count); long[] lacount = (countbb.asLongBuffer()).array(); ByteBuffer blockbb = ByteBuffer.wrap(block); long[] lablock = (blockbb.asLongBuffer()).array(); return H5Sselect_hyperslab(space_id, op, lastart, lastride, lacount, lablock); } public synchronized static native int H5Sselect_hyperslab(int space_id, int op, long[] start, long[] stride, long[] count, long[] block) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Sselect_none resets the selection region for the dataspace space_id to * include no elements. * * @param space_id * IN: The identifier of the dataspace to be reset. * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Sselect_none(int space_id) throws HDF5LibraryException; /** * H5Sselect_valid verifies that the selection for the dataspace. * * @param space_id * The identifier for the dataspace in which the selection is * being reset. * * @return true if the selection is contained within the extent and FALSE if * it is not or is an error. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native boolean H5Sselect_valid(int space_id) throws HDF5LibraryException; /** * H5Sset_extent_none removes the extent from a dataspace and sets the type * to H5S_NONE. * * @param space_id * The identifier for the dataspace from which the extent is to * be removed. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Sset_extent_none(int space_id) throws HDF5LibraryException; /** * H5Sset_extent_simple sets or resets the size of an existing dataspace. * * @param space_id * Dataspace identifier. * @param rank * Rank, or dimensionality, of the dataspace. * @param current_size * Array containing current size of dataspace. * @param maximum_size * Array containing maximum size of dataspace. * * @return a dataspace identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Sset_extent_simple(int space_id, int rank, long[] current_size, long[] maximum_size) throws HDF5LibraryException, NullPointerException; public synchronized static int H5Sset_extent_simple(int space_id, int rank, byte[] current_size, byte[] maximum_size) throws HDF5LibraryException, NullPointerException { ByteBuffer csbb = ByteBuffer.wrap(current_size); long[] lacs = (csbb.asLongBuffer()).array(); ByteBuffer maxsbb = ByteBuffer.wrap(maximum_size); long[] lamaxs = (maxsbb.asLongBuffer()).array(); return H5Sset_extent_simple(space_id, rank, lacs, lamaxs); } ////////////////////////////////////////////////////////////// //// //H5T: Datatype Interface Functions // //// ////////////////////////////////////////////////////////////// /** * H5Tarray_create creates a new array datatype object. * * @deprecated As of HDF5 1.8, replaced by {@link #H5Tarray_create(int, int, long[])} * * @param base IN: Datatype identifier for the array base datatype. * @param rank IN: Rank of the array. * @param dims IN: Size of each array dimension. * @param perms IN: Dimension permutation. (Currently not implemented.) * * @return a valid datatype identifier * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - dims is null. **/ @Deprecated public static int H5Tarray_create(int base, int rank, int[] dims, int[] perms) throws HDF5LibraryException, NullPointerException { int id = _H5Tarray_create(base, rank, dims, perms); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Tarray_create(int base, int rank, int[] dims, int[] perms) throws HDF5LibraryException, NullPointerException; /** * H5Tarray_create creates a new array datatype object. * * @param base_id IN: Datatype identifier for the array base datatype. * @param ndims IN: Rank of the array. * @param dim IN: Size of each array dimension. * * @return a valid datatype identifier * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - dim is null. **/ public static int H5Tarray_create(int base_id, int ndims, long[] dim) throws HDF5LibraryException, NullPointerException { int id = _H5Tarray_create2(base_id, ndims, dim); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Tarray_create2(int base_id, int ndims, long[] dim) throws HDF5LibraryException, NullPointerException; /** * H5Tclose releases a datatype. * * @param type_id IN: Identifier of datatype to release. * * @return a non-negative value if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public static int H5Tclose(int type_id) throws HDF5LibraryException { if (type_id < 0) return 0; // throw new HDF5LibraryException("Negative ID");; OPEN_IDS.removeElement(type_id); return _H5Tclose(type_id); } private synchronized static native int _H5Tclose(int type_id) throws HDF5LibraryException; /** * H5Tcommit commits a transient datatype (not immutable) to a file, turned * it into a named datatype. * * @deprecated As of HDF5 1.8, replaced by {@link #H5Tcommit(int, String, int, int, int, int)} * * @param loc_id IN: Location identifier. * @param name IN: Name given to committed datatype. * @param type_id IN: Identifier of datatype to be committed. * * @return a non-negative value if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. **/ @Deprecated public static int H5Tcommit(int loc_id, String name, int type_id) throws HDF5LibraryException, NullPointerException { return H5Tcommit1(loc_id, name, type_id); } @Deprecated public synchronized static native int H5Tcommit1(int loc_id, String name, int type) throws HDF5LibraryException, NullPointerException; /** * H5Tcommit saves a transient datatype as an immutable named datatype in a file. * * @param loc_id IN: Location identifier. * @param name IN: Name given to committed datatype. * @param type_id IN: Identifier of datatype to be committed. * @param lcpl_id IN: Link creation property list. * @param tcpl_id IN: Datatype creation property list. * @param tapl_id IN: Datatype access property list. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. **/ public synchronized static native void H5Tcommit(int loc_id, String name, int type_id, int lcpl_id, int tcpl_id, int tapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Tcommit_anon commits a transient datatype (not immutable) to a file, * turning it into a named datatype with the specified creation and property lists. * * @param loc_id IN: Location identifier. * @param type_id IN: Identifier of datatype to be committed. * @param tcpl_id IN: Datatype creation property list. * @param tapl_id IN: Datatype access property list. * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native void H5Tcommit_anon(int loc_id, int type_id, int tcpl_id, int tapl_id) throws HDF5LibraryException; /** * H5Tcommitted queries a type to determine whether the type specified by * the type identifier is a named type or a transient type. * * @param type_id IN: Identifier of datatype. * * @return true the datatype has been committed * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native boolean H5Tcommitted(int type_id) throws HDF5LibraryException; /** * H5Tcompiler_conv finds out whether the library's conversion function from * type src_id to type dst_id is a compiler (hard) conversion. * * @param src_id IN: Identifier of source datatype. * @param dst_id IN: Identifier of destination datatype. * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native void H5Tcompiler_conv(int src_id, int dst_id) throws HDF5LibraryException; /** ** H5Tconvert converts nelmts elements from the type specified by the src_id identifier to type dst_id. * * @param src_id IN: Identifier of source datatype. * @param dst_id IN: Identifier of destination datatype. * @param nelmts IN: Size of array buf. * @param buf IN: Array containing pre- and post-conversion values. * @param background IN: Optional background buffer. * @param plist_id IN: Dataset transfer property list identifier. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - buf is null. **/ public synchronized static native void H5Tconvert(int src_id, int dst_id, long nelmts, byte[] buf, byte[] background, int plist_id) throws HDF5LibraryException, NullPointerException; // int H5Tconvert(int src_id, int dst_id, long nelmts, Pointer buf, Pointer background, int plist_id); /** * H5Tcopy copies an existing datatype. The returned type is * always transient and unlocked. * * @param type_id IN: Identifier of datatype to copy. Can be a datatype * identifier, a predefined datatype (defined in * H5Tpublic.h), or a dataset Identifier. * * @return a datatype identifier if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public static int H5Tcopy(int type_id) throws HDF5LibraryException { int id = _H5Tcopy(type_id); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Tcopy(int type_id) throws HDF5LibraryException; /** * H5Tcreate creates a new dataype of the specified class with the specified * number of bytes. * * @param dclass IN: Class of datatype to create. * @param size IN: The number of bytes in the datatype to create. * * @return datatype identifier if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public static int H5Tcreate(int dclass, int size) throws HDF5LibraryException { return H5Tcreate(dclass, (long)size); } /** * H5Tcreate creates a new dataype of the specified class with * the specified number of bytes. * * @param tclass IN: Class of datatype to create. * @param size IN: The number of bytes in the datatype to create. * * @return datatype identifier * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public static int H5Tcreate(int tclass, long size) throws HDF5LibraryException { int id = _H5Tcreate(tclass, size); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Tcreate(int type, long size) throws HDF5LibraryException; /** * H5Tdecode reconstructs the HDF5 data type object and * returns a new object handle for it. * * @param buf IN: Buffer for the data type object to be decoded. * * @return a new object handle * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - buf is null. **/ public synchronized static native int H5Tdecode(byte[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Tdetect_class determines whether the datatype specified in dtype_id contains * any datatypes of the datatype class specified in dtype_class. * * @param type_id IN: Identifier of datatype to query. * @param cls IN: Identifier of datatype cls. * * @return true if the datatype specified in dtype_id contains any datatypes of the datatype class * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native boolean H5Tdetect_class(int type_id, int cls) throws HDF5LibraryException; /** * H5Tencode converts a data type description into binary form in a buffer. * * @param obj_id IN: Identifier of the object to be encoded. * @param buf OUT: Buffer for the object to be encoded into. * If the provided buffer is NULL, only the * size of buffer needed is returned. * @param nalloc IN: The size of the allocated buffer. * * @return the size needed for the allocated buffer. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - buf is null. **/ public synchronized static native int H5Tencode(int obj_id, byte[] buf, long nalloc) throws HDF5LibraryException, NullPointerException; ///** // * H5Tencode converts a data type description into binary form in a buffer. // * // * @param obj_id IN: Identifier of the object to be encoded. // * // * @return the buffer for the object to be encoded into. // * // * @exception HDF5LibraryException - Error from the HDF-5 Library. // **/ //public synchronized static native byte[] H5Tencode(int obj_id) //throws HDF5LibraryException; /** * H5Tenum_create creates a new enumeration datatype based on the specified * base datatype, parent_id, which must be an integer type. * * @param base_id IN: Identifier of the parent datatype to release. * * @return the datatype identifier for the new enumeration datatype * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public static int H5Tenum_create(int base_id) throws HDF5LibraryException { int id = _H5Tenum_create(base_id); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Tenum_create(int base_id) throws HDF5LibraryException; /** * H5Tenum_insert inserts a new enumeration datatype member * into an enumeration datatype. * * @param type IN: Identifier of datatype. * @param name IN: The name of the member * @param value IN: The value of the member, data of the correct type * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. **/ public synchronized static native void H5Tenum_insert(int type, String name, byte[] value) throws HDF5LibraryException, NullPointerException; /** * H5Tenum_insert inserts a new enumeration datatype member into an * enumeration datatype. * * @param type IN: Identifier of datatype. * @param name IN: The name of the member * @param value IN: The value of the member, data of the correct type * * @return a non-negative value if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. **/ public static int H5Tenum_insert(int type, String name, int[] value) throws HDF5LibraryException, NullPointerException { return H5Tenum_insert_int(type, name, value); } public static int H5Tenum_insert(int type, String name, int value) throws HDF5LibraryException, NullPointerException { int[] val = { value }; return H5Tenum_insert_int(type, name, val); } private synchronized static native int H5Tenum_insert_int(int type, String name, int[] value) throws HDF5LibraryException, NullPointerException; /** * H5Tenum_nameof finds the symbol name that corresponds * to the specified value of the enumeration datatype type. * * @param type IN: Identifier of datatype. * @param value IN: The value of the member, data of the correct * @param size IN: The probable length of the name * * @return the symbol name. * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - value is null. **/ public synchronized static native String H5Tenum_nameof(int type, byte[] value, long size) throws HDF5LibraryException, NullPointerException; //int H5Tenum_nameof(int type, Pointer value, Buffer name/* out */, long size); /** * H5Tenum_nameof finds the symbol name that corresponds to the specified * value of the enumeration datatype type. * * @param type IN: Identifier of datatype. * @param value IN: The value of the member, data of the correct * @param name OUT: The name of the member * @param size IN: The max length of the name * * @return a non-negative value if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. **/ public static int H5Tenum_nameof(int type, int[] value, String[] name, int size) throws HDF5LibraryException, NullPointerException { return H5Tenum_nameof_int(type, value, name, size); } private synchronized static native int H5Tenum_nameof_int(int type, int[] value, String[] name, int size) throws HDF5LibraryException, NullPointerException; /** * H5Tenum_valueof finds the value that corresponds to * the specified name of the enumeration datatype type. * * @param type IN: Identifier of datatype. * @param name IN: The name of the member * @param value OUT: The value of the member * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native void H5Tenum_valueof(int type, String name, byte[] value) throws HDF5LibraryException, NullPointerException; /** * H5Tenum_valueof finds the value that corresponds to the specified name of * the enumeration datatype type. * * @param type IN: Identifier of datatype. * @param name IN: The name of the member * @param value OUT: The value of the member * * @return a non-negative value if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. **/ public static int H5Tenum_valueof(int type, String name, int[] value) throws HDF5LibraryException, NullPointerException { return H5Tenum_valueof_int(type, name, value); } private synchronized static native int H5Tenum_valueof_int(int type, String name, int[] value) throws HDF5LibraryException, NullPointerException; /** * H5Tequal determines whether two datatype identifiers refer * to the same datatype. * * @param type_id1 IN: Identifier of datatype to compare. * @param type_id2 IN: Identifier of datatype to compare. * * @return true if the datatype identifiers refer to the * same datatype, else false. * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native boolean H5Tequal(int type_id1, int type_id2) throws HDF5LibraryException; /** * H5Tget_array_dims returns the sizes of the dimensions of the specified array datatype object. * * @deprecated As of HDF5 1.8 * * @param type_id IN: Datatype identifier of array object. * @param dims OUT: Sizes of array dimensions. * @param perm OUT: Dimension permutations. (This parameter is not used.) * * @return the non-negative number of dimensions of the array type * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - dims is null. **/ @Deprecated public synchronized static native int H5Tget_array_dims(int type_id, int[] dims, int[] perm) throws HDF5LibraryException, NullPointerException; /** * H5Tget_array_dims returns the sizes of the dimensions of the specified array datatype object. * * @deprecated As of HDF5 1.8, replaced by {@link #H5Tget_array_dims(int, long[])} * * @param type_id IN: Datatype identifier of array object. * @param dims OUT: Sizes of array dimensions. * @param perm OUT: Dimension permutation. (Currently not implemented.) * * @return the non-negative number of dimensions of the array type * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ @Deprecated public static int H5Tget_array_dims(int type_id, long[] dims, int[] perm) throws HDF5LibraryException, NullPointerException { return H5Tget_array_dims1(type_id, dims, perm); } /** * H5Tget_array_dims1 returns the sizes of the dimensions of the specified array datatype object. * * @deprecated As of HDF5 1.8, replaced by {@link #H5Tget_array_dims2(int, long[])} * * @see public static int H5Tget_array_dims(int type_id, long[] dims, int[] perm) **/ @Deprecated private synchronized static native int H5Tget_array_dims1(int type_id, long[] dims, int[] perm) throws HDF5LibraryException, NullPointerException; /** * H5Tget_array_dims returns the sizes of the dimensions of the specified array datatype object. * * @param type_id IN: Datatype identifier of array object. * @param dims OUT: Sizes of array dimensions. * * @return the non-negative number of dimensions of the array type * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - dims is null. **/ public static int H5Tget_array_dims(int type_id, long[] dims) throws HDF5LibraryException, NullPointerException { return H5Tget_array_dims2(type_id, dims); } /** * H5Tget_array_dims2 returns the sizes of the dimensions of the specified array datatype object. * * @see #H5Tget_array_dims **/ public synchronized static native int H5Tget_array_dims2(int type_id, long[] dims) throws HDF5LibraryException, NullPointerException; /** * H5Tget_array_ndims returns the rank, the number of dimensions, of an array datatype object. * * @param type_id IN: Datatype identifier of array object. * * @return the rank of the array * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_array_ndims(int type_id) throws HDF5LibraryException; /** * H5Tget_class returns the datatype class identifier. * * @param type_id IN: Identifier of datatype to query. * * @return datatype class identifier if successful; otherwise H5T_NO_CLASS(-1). * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_class(int type_id) throws HDF5LibraryException; /** * H5Tget_class_name returns the datatype class identifier. * * @param class_id IN: Identifier of class from H5Tget_class. * * @return class name if successful; otherwise H5T_NO_CLASS. * **/ public static String H5Tget_class_name(int class_id) { String retValue = null; if(HDF5Constants.H5T_INTEGER==class_id) /*integer types */ retValue = "H5T_INTEGER"; else if(HDF5Constants.H5T_FLOAT==class_id) /*floating-point types */ retValue = "H5T_FLOAT"; else if(HDF5Constants.H5T_TIME==class_id) /*date and time types */ retValue = "H5T_TIME"; else if(HDF5Constants.H5T_STRING==class_id) /*character string types */ retValue = "H5T_STRING"; else if(HDF5Constants.H5T_BITFIELD==class_id) /*bit field types */ retValue = "H5T_BITFIELD"; else if(HDF5Constants.H5T_OPAQUE==class_id) /*opaque types */ retValue = "H5T_OPAQUE"; else if(HDF5Constants.H5T_COMPOUND==class_id) /*compound types */ retValue = "H5T_COMPOUND"; else if(HDF5Constants.H5T_REFERENCE==class_id)/*reference types */ retValue = "H5T_REFERENCE"; else if(HDF5Constants.H5T_ENUM==class_id) /*enumeration types */ retValue = "H5T_ENUM"; else if(HDF5Constants.H5T_VLEN==class_id) /*Variable-Length types */ retValue = "H5T_VLEN"; else if(HDF5Constants.H5T_ARRAY==class_id) /*Array types */ retValue = "H5T_ARRAY"; else retValue = "H5T_NO_CLASS"; return retValue; } /** * H5Tget_create_plist returns a property list identifier for the datatype * creation property list associated with the datatype specified by type_id. * * @param type_id IN: Identifier of datatype. * * @return a datatype property list identifier. * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_create_plist(int type_id) throws HDF5LibraryException; /** * H5Tget_cset retrieves the character set type of a string datatype. * * @param type_id IN: Identifier of datatype to query. * * @return a valid character set type if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_cset(int type_id) throws HDF5LibraryException; /** * H5Tset_cset the character set to be used. * * @param type_id IN: Identifier of datatype to modify. * @param cset IN: Character set type. * * @return a non-negative value if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native int H5Tset_cset(int type_id, int cset) throws HDF5LibraryException; /** * H5Tget_ebias retrieves the exponent bias of a floating-point type. * * @param type_id * Identifier of datatype to query. * * @return the bias if successful; otherwise 0. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_ebias(int type_id) throws HDF5LibraryException; /** * H5Tset_ebias sets the exponent bias of a floating-point type. * * @param type_id * Identifier of datatype to set. * @param ebias * Exponent bias value. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Tset_ebias(int type_id, int ebias) throws HDF5LibraryException { H5Tset_ebias(type_id, (long)ebias); return 0; } /** * H5Tget_ebias retrieves the exponent bias of a * floating-point type. * * @param type_id IN: Identifier of datatype to query. * * @return the bias * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native long H5Tget_ebias_long(int type_id) throws HDF5LibraryException; /** * H5Tset_ebias sets the exponent bias of a floating-point type. * * @param type_id IN: Identifier of datatype to set. * @param ebias IN: Exponent bias value. * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native void H5Tset_ebias(int type_id, long ebias) throws HDF5LibraryException; /** * H5Tget_fields retrieves information about the locations of * the various bit fields of a floating point datatype. * * @param type_id IN: Identifier of datatype to query. * @param fields OUT: location of size and bit-position. *
    *
  • fields[0] = spos OUT: location to return size of in bits.
    • *
  • fields[1] = epos OUT: location to return exponent bit-position.
    • *
  • fields[2] = esize OUT: location to return size of exponent in bits.
    • *
  • fields[3] = mpos OUT: location to return mantissa bit-position.
    • *
  • fields[4] = msize OUT: location to return size of mantissa in bits.
    • *
* * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - fields is null. * @exception IllegalArgumentException - fields array is invalid. **/ public synchronized static native void H5Tget_fields(int type_id, long[] fields) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Tget_fields retrieves information about the locations of the various * bit fields of a floating point datatype. * * @param type_id IN: Identifier of datatype to query. * @param fields OUT: location of size and bit-position. * * 
 *      fields[0] = spos  OUT: location to return size of in bits.
 *      fields[1] = epos  OUT: location to return exponent bit-position.
 *      fields[2] = esize OUT: location to return size of exponent in bits.
 *      fields[3] = mpos  OUT: location to return mantissa bit-position.
 *      fields[4] = msize OUT: location to return size of mantissa in bits.
 *
* * @return a non-negative value if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - fields is null. * @exception IllegalArgumentException - fields array is invalid. **/ public static int H5Tget_fields(int type_id, int[] fields) throws HDF5LibraryException, NullPointerException, IllegalArgumentException { return H5Tget_fields_int(type_id, fields); } private synchronized static native int H5Tget_fields_int(int type_id, int[] fields) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Tset_fields sets the locations and sizes of the various * floating point bit fields. * * @param type_id IN: Identifier of datatype to set. * @param spos IN: Size position. * @param epos IN: Exponent bit position. * @param esize IN: Size of exponent in bits. * @param mpos IN: Mantissa bit position. * @param msize IN: Size of mantissa in bits. * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native void H5Tset_fields(int type_id, long spos, long epos, long esize, long mpos, long msize) throws HDF5LibraryException; /** * H5Tset_fields sets the locations and sizes of the various floating point * bit fields. * * @param type_id * Identifier of datatype to set. * @param spos * Size position. * @param epos * Exponent bit position. * @param esize * Size of exponent in bits. * @param mpos * Mantissa bit position. * @param msize * Size of mantissa in bits. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Tset_fields(int type_id, int spos, int epos, int esize, int mpos, int msize) throws HDF5LibraryException { H5Tset_fields(type_id, (long)spos, (long)epos, (long)esize, (long)mpos, (long)msize); return 0; } /** * H5Tget_inpad retrieves the internal padding type for unused bits in * floating-point datatypes. * * @param type_id IN: Identifier of datatype to query. * * @return a valid padding type if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_inpad(int type_id) throws HDF5LibraryException; /** * If any internal bits of a floating point type are unused (that is, those * significant bits which are not part of the sign, exponent, or mantissa), * then H5Tset_inpad will be filled according to the value of the padding * value property inpad. * * @param type_id IN: Identifier of datatype to modify. * @param inpad IN: Padding type. * * @return a non-negative value if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native int H5Tset_inpad(int type_id, int inpad) throws HDF5LibraryException; /** * H5Tget_member_class returns the datatype of the specified member. * * @param type_id IN: Datatype identifier of compound object. * @param membno IN: Compound object member number. * * @return the identifier of a copy of the datatype of the field if successful; * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_member_class(int type_id, int membno) throws HDF5LibraryException; /** * H5Tget_member_index retrieves the index of a field of a compound * datatype. * * @param type_id IN: Identifier of datatype to query. * @param field_name IN: Field name of the field index to retrieve. * * @return if field is defined, the index; else negative. * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_member_index(int type_id, String field_name); /** * H5Tget_member_name retrieves the name of a field of a compound datatype or * an element of an enumeration datatype. * * @param type_id IN: Identifier of datatype to query. * @param field_idx IN: Field index (0-based) of the field name to retrieve. * * @return a valid pointer to the name if successful; otherwise null. * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native String H5Tget_member_name(int type_id, int field_idx); /** * H5Tget_member_offset returns the byte offset of the specified member of * the compound datatype. This is the byte offset in the HDF-5 file/library, * NOT the offset of any Java object which might be mapped to this data * item. * * @param type_id IN: Identifier of datatype to query. * @param membno IN: Field index (0-based) of the field type to retrieve. * * @return the offset of the member. * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native long H5Tget_member_offset(int type_id, int membno) throws HDF5LibraryException; /** * H5Tget_member_type returns the datatype of the specified member. * * @param type_id IN: Identifier of datatype to query. * @param field_idx IN: Field index (0-based) of the field type to retrieve. * * @return the identifier of a copy of the datatype of the field if * successful; * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public static int H5Tget_member_type(int type_id, int field_idx) throws HDF5LibraryException { int id = _H5Tget_member_type(type_id, field_idx); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Tget_member_type(int type_id, int field_idx) throws HDF5LibraryException; /** * H5Tget_member_value returns the value of the enumeration datatype member memb_no. * * @param type_id IN: Datatype identifier for the enumeration datatype. * @param membno IN: Number of the enumeration datatype member. * @param value OUT: The value of the member * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - value is null. **/ public synchronized static native void H5Tget_member_value(int type_id, int membno, byte[] value) throws HDF5LibraryException, NullPointerException; /** * H5Tget_member_value returns the value of the enumeration datatype member * memb_no. * * @param type_id IN: Identifier of datatype. * @param membno IN: The name of the member * @param value OUT: The value of the member * * @return a non-negative value if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - value is null. **/ public static int H5Tget_member_value(int type_id, int membno, int[] value) throws HDF5LibraryException, NullPointerException { return H5Tget_member_value_int(type_id, membno, value); } private synchronized static native int H5Tget_member_value_int(int type_id, int membno, int[] value) throws HDF5LibraryException, NullPointerException; /** * H5Tget_native_type returns the equivalent native datatype for the datatype specified in type_id. * * @param type_id IN: Identifier of datatype to query. * Direction of search is assumed to be in ascending order. * * @return the native datatype identifier for the specified dataset datatype. * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static int H5Tget_native_type(int type_id) throws HDF5LibraryException { return H5Tget_native_type(type_id, HDF5Constants.H5T_DIR_ASCEND); } /** * H5Tget_native_type returns the equivalent native datatype for the datatype specified in type_id. * * @param type_id IN: Identifier of datatype to query. * @param direction IN: Direction of search. * * @return the native datatype identifier for the specified dataset datatype. * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public static int H5Tget_native_type(int type_id, int direction) throws HDF5LibraryException { int id = _H5Tget_native_type(type_id, direction); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Tget_native_type(int tid, int direction) throws HDF5LibraryException; /** * H5Tget_nmembers retrieves the number of fields a compound datatype has. * * @param type_id IN: Identifier of datatype to query. * * @return number of members datatype has if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_nmembers(int type_id) throws HDF5LibraryException; /** * H5Tget_norm retrieves the mantissa normalization of a floating-point * datatype. * * @param type_id IN: Identifier of datatype to query. * * @return a valid normalization type if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_norm(int type_id) throws HDF5LibraryException; /** * H5Tset_norm sets the mantissa normalization of a floating-point datatype. * * @param type_id IN: Identifier of datatype to set. * @param norm IN: Mantissa normalization type. * * @return a non-negative value if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native int H5Tset_norm(int type_id, int norm) throws HDF5LibraryException; /** * H5Tget_offset retrieves the bit offset of the first significant bit. * * @param type_id IN: Identifier of datatype to query. * * @return a positive offset value if successful; otherwise 0. * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_offset(int type_id) throws HDF5LibraryException; /** * H5Tset_offset sets the bit offset of the first significant bit. * * @param type_id * Identifier of datatype to set. * @param offset * Offset of first significant bit. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Tset_offset(int type_id, int offset) throws HDF5LibraryException { H5Tset_offset(type_id, (long)offset); return 0; } /** * H5Tset_offset sets the bit offset of the first significant bit. * * @param type_id IN: Identifier of datatype to set. * @param offset IN: Offset of first significant bit. * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native void H5Tset_offset(int type_id, long offset) throws HDF5LibraryException; /** * H5Tget_order returns the byte order of an atomic datatype. * * @param type_id IN: Identifier of datatype to query. * * @return a byte order constant if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_order(int type_id) throws HDF5LibraryException; /** * H5Tset_order sets the byte ordering of an atomic datatype. * * @param type_id IN: Identifier of datatype to set. * @param order IN: Byte ordering constant. * * @return a non-negative value if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native int H5Tset_order(int type_id, int order) throws HDF5LibraryException; /** * H5Tget_pad retrieves the padding type of the least and most-significant * bit padding. * * @param type_id IN: Identifier of datatype to query. * @param pad OUT: locations to return least-significant and * most-significant bit padding type. * * 
 *      pad[0] = lsb // least-significant bit padding type
 *      pad[1] = msb // most-significant bit padding type
 *
* * @return a non-negative value if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - pad is null. **/ public synchronized static native int H5Tget_pad(int type_id, int[] pad) throws HDF5LibraryException, NullPointerException; /** * H5Tset_pad sets the least and most-significant bits padding types. * * @param type_id IN: Identifier of datatype to set. * @param lsb IN: Padding type for least-significant bits. * @param msb IN: Padding type for most-significant bits. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Tset_pad(int type_id, int lsb, int msb) throws HDF5LibraryException; /** * H5Tget_precision returns the precision of an atomic datatype. * * @param type_id * Identifier of datatype to query. * * @return the number of significant bits if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_precision(int type_id) throws HDF5LibraryException; /** * H5Tset_precision sets the precision of an atomic datatype. * * @param type_id * Identifier of datatype to set. * @param precision * Number of bits of precision for datatype. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Tset_precision(int type_id, int precision) throws HDF5LibraryException { H5Tset_precision(type_id, (long)precision); return 0; } /** * H5Tget_precision returns the precision of an atomic datatype. * * @param type_id IN: Identifier of datatype to query. * * @return the number of significant bits if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native long H5Tget_precision_long(int type_id) throws HDF5LibraryException; /** * H5Tset_precision sets the precision of an atomic datatype. * * @param type_id IN: Identifier of datatype to set. * @param precision IN: Number of bits of precision for datatype. * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native void H5Tset_precision(int type_id, long precision) throws HDF5LibraryException; /** * H5Tget_sign retrieves the sign type for an integer type. * * @param type_id IN: Identifier of datatype to query. * * @return a valid sign type if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_sign(int type_id) throws HDF5LibraryException; /** * H5Tset_sign sets the sign proprety for an integer type. * * @param type_id IN: Identifier of datatype to set. * @param sign IN: Sign type. * * @return a non-negative value if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native int H5Tset_sign(int type_id, int sign) throws HDF5LibraryException; /** * H5Tget_size returns the size of a datatype in bytes. * * @param type_id * Identifier of datatype to query. * * @return the size of the datatype in bytes if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_size(int type_id) throws HDF5LibraryException; /** * H5Tset_size sets the total size in bytes, size, for an atomic datatype * (this operation is not permitted on compound datatypes). * * @param type_id * Identifier of datatype to change size. * @param size * Size in bytes to modify datatype. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Tset_size(int type_id, int size) throws HDF5LibraryException { H5Tset_size(type_id, (long)size); return 0; } /** * H5Tget_size returns the size of a datatype in bytes. * * @param type_id IN: Identifier of datatype to query. * * @return the size of the datatype in bytes * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native long H5Tget_size_long(int type_id) throws HDF5LibraryException; /** * H5Tset_size sets the total size in bytes, size, for an * atomic datatype (this operation is not permitted on * compound datatypes). * * @param type_id IN: Identifier of datatype to change size. * @param size IN: Size in bytes to modify datatype. * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native void H5Tset_size(int type_id, long size) throws HDF5LibraryException; /** * H5Tget_strpad retrieves the string padding method for a string datatype. * * @param type_id IN: Identifier of datatype to query. * * @return a valid string padding type if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_strpad(int type_id) throws HDF5LibraryException; /** * H5Tset_strpad defines the storage mechanism for the string. * * @param type_id IN: Identifier of datatype to modify. * @param strpad IN: String padding type. * * @return a non-negative value if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native int H5Tset_strpad(int type_id, int strpad) throws HDF5LibraryException; /** * H5Tget_super returns the type from which TYPE is derived. * * @param type IN: Identifier of datatype. * * @return the parent type * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public static int H5Tget_super(int type) throws HDF5LibraryException { int id = _H5Tget_super(type); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Tget_super(int type) throws HDF5LibraryException; /** * H5Tget_tag returns the tag associated with datatype type_id. * * @param type IN: Identifier of datatype. * * @return the tag * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native String H5Tget_tag(int type) throws HDF5LibraryException; /** * H5Tset_tag tags an opaque datatype type_id with a unique ASCII identifier * tag. * * @param type IN: Datatype identifier for the opaque datatype to be tagged. * @param tag IN: Descriptive ASCII string with which the opaque datatype is to be tagged. * * @return a non-negative value if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native int H5Tset_tag(int type, String tag) throws HDF5LibraryException; /** * H5Tinsert adds another member to the compound datatype type_id. * * @param type_id IN: Identifier of compound datatype to modify. * @param name IN: Name of the field to insert. * @param offset IN: Offset in memory structure of the field to insert. * @param field_id IN: Datatype identifier of the field to insert. * * @return a non-negative value if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. **/ public synchronized static native int H5Tinsert(int type_id, String name, long offset, int field_id) throws HDF5LibraryException, NullPointerException; /** * H5Tis_variable_str determines whether the datatype identified in type_id is a variable-length string. * * @param type_id IN: Identifier of datatype to query. * * @return true if type_id is a variable-length string. * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native boolean H5Tis_variable_str(int type_id) throws HDF5LibraryException; /** * H5Tlock locks the datatype specified by the type_id identifier, making it * read-only and non-destrucible. * * @param type_id IN: Identifier of datatype to lock. * * @return a non-negative value if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native int H5Tlock(int type_id) throws HDF5LibraryException; /** * H5Topen opens a named datatype at the location specified * by loc_id and return an identifier for the datatype. * * @deprecated As of HDF5 1.8, replaced by {@link #H5Topen(int, String, int)} * * @param loc_id IN: A file, group, or datatype identifier. * @param name IN: A datatype name, defined within the file or group identified by loc_id. * * @return a named datatype identifier if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. **/ @Deprecated public static int H5Topen(int loc_id, String name) throws HDF5LibraryException, NullPointerException { int id = _H5Topen(loc_id, name); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Topen(int loc_id, String name) throws HDF5LibraryException, NullPointerException; /** * H5Topen opens a named datatype at the location specified * by loc_id and return an identifier for the datatype. * * @param loc_id IN: A file, group, or datatype identifier. * @param name IN: A datatype name, defined within the file or group identified by loc_id. * @param tapl_id IN: Datatype access property list. * * @return a named datatype identifier if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - name is null. **/ public static int H5Topen(int loc_id, String name, int tapl_id) throws HDF5LibraryException, NullPointerException { int id = _H5Topen2(loc_id, name, tapl_id); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Topen2(int loc_id, String name, int tapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Tpack recursively removes padding from within a compound datatype to * make it more efficient (space-wise) to store that data. *

* WARNING: This call only affects the C-data, even if it succeeds, * there may be no visible effect on Java objects. * * @param type_id IN: Identifier of datatype to modify. * * @return a non-negative value if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native int H5Tpack(int type_id) throws HDF5LibraryException; /** * H5Tvlen_create creates a new variable-length (VL) dataype. * * @param base_id IN: Identifier of parent datatype. * * @return a non-negative value if successful * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public static int H5Tvlen_create(int base_id) throws HDF5LibraryException { int id = _H5Tvlen_create(base_id); if (id > 0) OPEN_IDS.addElement(id); return id; } private synchronized static native int _H5Tvlen_create(int base_id) throws HDF5LibraryException; ///////// unimplemented //////// //H5T_conv_t H5Tfind(int src_id, int dst_id, H5T_cdata_t *pcdata); //public synchronized static native int H5Tregister(H5T_pers_t pers, String name, int src_id, int dst_id, // H5T_conv_t func) // throws HDF5LibraryException, NullPointerException; //public synchronized static native int H5Tunregister(H5T_pers_t pers, String name, int src_id, int dst_id, // H5T_conv_t func) // throws HDF5LibraryException, NullPointerException; ////////////////////////////////////////////////////////////// //// //H5Z: Filter Interface Functions // //// ////////////////////////////////////////////////////////////// public synchronized static native int H5Zfilter_avail(int filter) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Zget_filter_info(int filter) throws HDF5LibraryException; public synchronized static native int H5Zunregister(int filter) throws HDF5LibraryException, NullPointerException; } ///////// unimplemented //////// //herr_t H5Zregister(const void *cls); libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/HDF5Constants.java000077500000000000000000002170451256564762100255650ustar00rootroot00000000000000/**************************************************************************** * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF Java Products. The full HDF Java copyright * * notice, including terms governing use, modification, and redistribution, * * is contained in the file, COPYING. COPYING can be found at the root of * * the source code distribution tree. You can also access it online at * * http://www.hdfgroup.org/products/licenses.html. If you do not have * * access to the file, you may request a copy from help@hdfgroup.org. * ****************************************************************************/ package ncsa.hdf.hdf5lib; /** * /** This class contains C constants and enumerated types of HDF5 library. The * values of these constants are obtained from the library by calling J2C(int * jconstant), where jconstant is any of the private constants which start their * name with "JH5" need to be converted. *

* Do not edit this file! * * See also: ncsa.hdf.hdf5lib.HDF5Library */ public class HDF5Constants { static { H5.loadH5Lib(); } // ///////////////////////////////////////////////////////////////////////// // Get the HDF5 constants from the library // // ///////////////////////////////////////////////////////////////////////// public static final long H5_QUARTER_HADDR_MAX = H5_QUARTER_HADDR_MAX(); public static final int H5_SZIP_MAX_PIXELS_PER_BLOCK = H5_SZIP_MAX_PIXELS_PER_BLOCK(); public static final int H5_SZIP_NN_OPTION_MASK = H5_SZIP_NN_OPTION_MASK(); public static final int H5_SZIP_EC_OPTION_MASK = H5_SZIP_EC_OPTION_MASK(); public static final int H5_SZIP_ALLOW_K13_OPTION_MASK = H5_SZIP_ALLOW_K13_OPTION_MASK(); public static final int H5_SZIP_CHIP_OPTION_MASK = H5_SZIP_CHIP_OPTION_MASK(); public static final int H5_INDEX_UNKNOWN = H5_INDEX_UNKNOWN(); public static final int H5_INDEX_NAME = H5_INDEX_NAME(); public static final int H5_INDEX_CRT_ORDER = H5_INDEX_CRT_ORDER(); public static final int H5_INDEX_N = H5_INDEX_N(); public static final int H5_ITER_UNKNOWN = H5_ITER_UNKNOWN(); public static final int H5_ITER_INC = H5_ITER_INC(); public static final int H5_ITER_DEC = H5_ITER_DEC(); public static final int H5_ITER_NATIVE = H5_ITER_NATIVE(); public static final int H5_ITER_N = H5_ITER_N(); public static final int H5AC_CURR_CACHE_CONFIG_VERSION = H5AC_CURR_CACHE_CONFIG_VERSION(); public static final int H5AC_MAX_TRACE_FILE_NAME_LEN = H5AC_MAX_TRACE_FILE_NAME_LEN(); public static final int H5AC_METADATA_WRITE_STRATEGY_PROCESS_ZERO_ONLY = H5AC_METADATA_WRITE_STRATEGY_PROCESS_ZERO_ONLY(); public static final int H5AC_METADATA_WRITE_STRATEGY_DISTRIBUTED = H5AC_METADATA_WRITE_STRATEGY_DISTRIBUTED(); public static final int H5C_incr_off = H5C_incr_off(); public static final int H5C_incr_threshold = H5C_incr_threshold(); public static final int H5C_flash_incr_off = H5C_flash_incr_off(); public static final int H5C_flash_incr_add_space = H5C_flash_incr_add_space(); public static final int H5C_decr_off = H5C_decr_off(); public static final int H5C_decr_threshold = H5C_decr_threshold(); public static final int H5C_decr_age_out = H5C_decr_age_out(); public static final int H5C_decr_age_out_with_threshold = H5C_decr_age_out_with_threshold(); public static final int H5D_CHUNK_BTREE = H5D_CHUNK_BTREE(); public static final int H5D_ALLOC_TIME_DEFAULT = H5D_ALLOC_TIME_DEFAULT(); public static final int H5D_ALLOC_TIME_EARLY = H5D_ALLOC_TIME_EARLY(); public static final int H5D_ALLOC_TIME_ERROR = H5D_ALLOC_TIME_ERROR(); public static final int H5D_ALLOC_TIME_INCR = H5D_ALLOC_TIME_INCR(); public static final int H5D_ALLOC_TIME_LATE = H5D_ALLOC_TIME_LATE(); public static final int H5D_FILL_TIME_ERROR = H5D_FILL_TIME_ERROR(); public static final int H5D_FILL_TIME_ALLOC = H5D_FILL_TIME_ALLOC(); public static final int H5D_FILL_TIME_NEVER = H5D_FILL_TIME_NEVER(); public static final int H5D_FILL_TIME_IFSET = H5D_FILL_TIME_IFSET(); public static final int H5D_FILL_VALUE_DEFAULT = H5D_FILL_VALUE_DEFAULT(); public static final int H5D_FILL_VALUE_ERROR = H5D_FILL_VALUE_ERROR(); public static final int H5D_FILL_VALUE_UNDEFINED = H5D_FILL_VALUE_UNDEFINED(); public static final int H5D_FILL_VALUE_USER_DEFINED = H5D_FILL_VALUE_USER_DEFINED(); public static final int H5D_LAYOUT_ERROR = H5D_LAYOUT_ERROR(); public static final int H5D_CHUNKED = H5D_CHUNKED(); public static final int H5D_COMPACT = H5D_COMPACT(); public static final int H5D_CONTIGUOUS = H5D_CONTIGUOUS(); public static final int H5D_NLAYOUTS = H5D_NLAYOUTS(); public static final int H5D_SPACE_STATUS_ALLOCATED = H5D_SPACE_STATUS_ALLOCATED(); public static final int H5D_SPACE_STATUS_ERROR = H5D_SPACE_STATUS_ERROR(); public static final int H5D_SPACE_STATUS_NOT_ALLOCATED = H5D_SPACE_STATUS_NOT_ALLOCATED(); public static final int H5D_SPACE_STATUS_PART_ALLOCATED = H5D_SPACE_STATUS_PART_ALLOCATED(); public static final int H5E_ALIGNMENT = H5E_ALIGNMENT(); public static final int H5E_ALREADYEXISTS = H5E_ALREADYEXISTS(); public static final int H5E_ALREADYINIT = H5E_ALREADYINIT(); public static final int H5E_ARGS = H5E_ARGS(); public static final int H5E_ATOM = H5E_ATOM(); public static final int H5E_ATTR = H5E_ATTR(); public static final int H5E_BADATOM = H5E_BADATOM(); public static final int H5E_BADFILE = H5E_BADFILE(); public static final int H5E_BADGROUP = H5E_BADGROUP(); public static final int H5E_BADMESG = H5E_BADMESG(); public static final int H5E_BADRANGE = H5E_BADRANGE(); public static final int H5E_BADSELECT = H5E_BADSELECT(); public static final int H5E_BADSIZE = H5E_BADSIZE(); public static final int H5E_BADTYPE = H5E_BADTYPE(); public static final int H5E_BADVALUE = H5E_BADVALUE(); public static final int H5E_BTREE = H5E_BTREE(); public static final int H5E_CACHE = H5E_CACHE(); public static final int H5E_CALLBACK = H5E_CALLBACK(); public static final int H5E_CANAPPLY = H5E_CANAPPLY(); // public static final int H5E_CANTALLOC = H5E_CANTALLOC(); public static final int H5E_CANTCLIP = H5E_CANTCLIP(); public static final int H5E_CANTCLOSEFILE = H5E_CANTCLOSEFILE(); public static final int H5E_CANTCONVERT = H5E_CANTCONVERT(); public static final int H5E_CANTCOPY = H5E_CANTCOPY(); public static final int H5E_CANTCOUNT = H5E_CANTCOUNT(); public static final int H5E_CANTCREATE = H5E_CANTCREATE(); public static final int H5E_CANTDEC = H5E_CANTDEC(); public static final int H5E_CANTDECODE = H5E_CANTDECODE(); public static final int H5E_CANTDELETE = H5E_CANTDELETE(); public static final int H5E_CANTENCODE = H5E_CANTENCODE(); public static final int H5E_CANTFLUSH = H5E_CANTFLUSH(); public static final int H5E_CANTFREE = H5E_CANTFREE(); public static final int H5E_CANTGET = H5E_CANTGET(); public static final int H5E_CANTINC = H5E_CANTINC(); public static final int H5E_CANTINIT = H5E_CANTINIT(); public static final int H5E_CANTINSERT = H5E_CANTINSERT(); public static final int H5E_CANTLIST = H5E_CANTLIST(); public static final int H5E_CANTLOAD = H5E_CANTLOAD(); public static final int H5E_CANTLOCK = H5E_CANTLOCK(); public static final int H5E_CANTNEXT = H5E_CANTNEXT(); public static final int H5E_CANTOPENFILE = H5E_CANTOPENFILE(); public static final int H5E_CANTOPENOBJ = H5E_CANTOPENOBJ(); // public static final int H5E_CANTRECV = H5E_CANTRECV(); public static final int H5E_CANTREGISTER = H5E_CANTREGISTER(); public static final int H5E_CANTRELEASE = H5E_CANTRELEASE(); public static final int H5E_CANTSELECT = H5E_CANTSELECT(); public static final int H5E_CANTSET = H5E_CANTSET(); public static final int H5E_CANTSPLIT = H5E_CANTSPLIT(); public static final int H5E_CANTUNLOCK = H5E_CANTUNLOCK(); public static final int H5E_CLOSEERROR = H5E_CLOSEERROR(); public static final int H5E_COMPLEN = H5E_COMPLEN(); public static final int H5E_DATASET = H5E_DATASET(); public static final int H5E_DATASPACE = H5E_DATASPACE(); public static final int H5E_DATATYPE = H5E_DATATYPE(); public static final int H5E_DEFAULT = H5E_DEFAULT(); public static final int H5E_DUPCLASS = H5E_DUPCLASS(); public static final int H5E_EFL = H5E_EFL(); public static final int H5E_EXISTS = H5E_EXISTS(); public static final int H5E_FCNTL = H5E_FCNTL(); public static final int H5E_FILE = H5E_FILE(); public static final int H5E_FILEEXISTS = H5E_FILEEXISTS(); public static final int H5E_FILEOPEN = H5E_FILEOPEN(); public static final int H5E_FUNC = H5E_FUNC(); public static final int H5E_HEAP = H5E_HEAP(); public static final int H5E_INTERNAL = H5E_INTERNAL(); public static final int H5E_IO = H5E_IO(); public static final int H5E_LINK = H5E_LINK(); public static final int H5E_LINKCOUNT = H5E_LINKCOUNT(); public static final int H5E_MAJOR = H5E_MAJOR(); public static final int H5E_MINOR = H5E_MINOR(); public static final int H5E_MOUNT = H5E_MOUNT(); public static final int H5E_MPI = H5E_MPI(); public static final int H5E_MPIERRSTR = H5E_MPIERRSTR(); public static final int H5E_NOFILTER = H5E_NOFILTER(); public static final int H5E_NOIDS = H5E_NOIDS(); public static final int H5E_NONE_MAJOR = H5E_NONE_MAJOR(); public static final int H5E_NONE_MINOR = H5E_NONE_MINOR(); public static final int H5E_NOSPACE = H5E_NOSPACE(); public static final int H5E_NOTCACHED = H5E_NOTCACHED(); public static final int H5E_NOTFOUND = H5E_NOTFOUND(); public static final int H5E_NOTHDF5 = H5E_NOTHDF5(); public static final int H5E_OHDR = H5E_OHDR(); public static final int H5E_OVERFLOW = H5E_OVERFLOW(); public static final int H5E_PLINE = H5E_PLINE(); public static final int H5E_PLIST = H5E_PLIST(); public static final int H5E_PROTECT = H5E_PROTECT(); public static final int H5E_READERROR = H5E_READERROR(); public static final int H5E_REFERENCE = H5E_REFERENCE(); public static final int H5E_RESOURCE = H5E_RESOURCE(); public static final int H5E_RS = H5E_RS(); public static final int H5E_SEEKERROR = H5E_SEEKERROR(); public static final int H5E_SETLOCAL = H5E_SETLOCAL(); public static final int H5E_STORAGE = H5E_STORAGE(); public static final int H5E_SYM = H5E_SYM(); public static final int H5E_TRUNCATED = H5E_TRUNCATED(); public static final int H5E_TST = H5E_TST(); public static final int H5E_UNINITIALIZED = H5E_UNINITIALIZED(); public static final int H5E_UNSUPPORTED = H5E_UNSUPPORTED(); public static final int H5E_VERSION = H5E_VERSION(); public static final int H5E_VFL = H5E_VFL(); public static final int H5E_WALK_DOWNWARD = H5E_WALK_DOWNWARD(); public static final int H5E_WALK_UPWARD = H5E_WALK_UPWARD(); public static final int H5E_WRITEERROR = H5E_WRITEERROR(); public static final int H5F_ACC_CREAT = H5F_ACC_CREAT(); public static final int H5F_ACC_DEBUG = H5F_ACC_DEBUG(); public static final int H5F_ACC_EXCL = H5F_ACC_EXCL(); public static final int H5F_ACC_RDONLY = H5F_ACC_RDONLY(); public static final int H5F_ACC_RDWR = H5F_ACC_RDWR(); public static final int H5F_ACC_TRUNC = H5F_ACC_TRUNC(); public static final int H5F_ACC_DEFAULT = H5F_ACC_DEFAULT(); public static final int H5F_CLOSE_DEFAULT = H5F_CLOSE_DEFAULT(); public static final int H5F_CLOSE_SEMI = H5F_CLOSE_SEMI(); public static final int H5F_CLOSE_STRONG = H5F_CLOSE_STRONG(); public static final int H5F_CLOSE_WEAK = H5F_CLOSE_WEAK(); public static final int H5F_LIBVER_EARLIEST = H5F_LIBVER_EARLIEST(); public static final int H5F_LIBVER_LATEST = H5F_LIBVER_LATEST(); public static final int H5F_OBJ_ALL = H5F_OBJ_ALL(); public static final int H5F_OBJ_ATTR = H5F_OBJ_ATTR(); public static final int H5F_OBJ_DATASET = H5F_OBJ_DATASET(); public static final int H5F_OBJ_DATATYPE = H5F_OBJ_DATATYPE(); public static final int H5F_OBJ_FILE = H5F_OBJ_FILE(); public static final int H5F_OBJ_GROUP = H5F_OBJ_GROUP(); public static final int H5F_OBJ_LOCAL = H5F_OBJ_LOCAL(); public static final int H5F_SCOPE_GLOBAL = H5F_SCOPE_GLOBAL(); public static final int H5F_SCOPE_LOCAL = H5F_SCOPE_LOCAL(); public static final int H5F_UNLIMITED = H5F_UNLIMITED(); public static final int H5FD_CORE = H5FD_CORE(); public static final int H5FD_DIRECT = H5FD_DIRECT(); public static final int H5FD_FAMILY = H5FD_FAMILY(); public static final int H5FD_LOG = H5FD_LOG(); public static final int H5FD_MPIO = H5FD_MPIO(); public static final int H5FD_MULTI = H5FD_MULTI(); public static final int H5FD_SEC2 = H5FD_SEC2(); public static final int H5FD_STDIO = H5FD_STDIO(); public static final int H5FD_WINDOWS = H5FD_WINDOWS(); public static final int H5FD_LOG_LOC_READ = H5FD_LOG_LOC_READ(); public static final int H5FD_LOG_LOC_WRITE = H5FD_LOG_LOC_WRITE(); public static final int H5FD_LOG_LOC_SEEK = H5FD_LOG_LOC_SEEK(); public static final int H5FD_LOG_LOC_IO = H5FD_LOG_LOC_IO(); public static final int H5FD_LOG_FILE_READ = H5FD_LOG_FILE_READ(); public static final int H5FD_LOG_FILE_WRITE = H5FD_LOG_FILE_WRITE(); public static final int H5FD_LOG_FILE_IO = H5FD_LOG_FILE_IO(); public static final int H5FD_LOG_FLAVOR = H5FD_LOG_FLAVOR(); public static final int H5FD_LOG_NUM_READ = H5FD_LOG_NUM_READ(); public static final int H5FD_LOG_NUM_WRITE = H5FD_LOG_NUM_WRITE(); public static final int H5FD_LOG_NUM_SEEK = H5FD_LOG_NUM_SEEK(); public static final int H5FD_LOG_NUM_TRUNCATE = H5FD_LOG_NUM_TRUNCATE(); public static final int H5FD_LOG_NUM_IO = H5FD_LOG_NUM_IO(); public static final int H5FD_LOG_TIME_OPEN = H5FD_LOG_TIME_OPEN(); public static final int H5FD_LOG_TIME_STAT = H5FD_LOG_TIME_STAT(); public static final int H5FD_LOG_TIME_READ = H5FD_LOG_TIME_READ(); public static final int H5FD_LOG_TIME_WRITE = H5FD_LOG_TIME_WRITE(); public static final int H5FD_LOG_TIME_SEEK = H5FD_LOG_TIME_SEEK(); public static final int H5FD_LOG_TIME_CLOSE = H5FD_LOG_TIME_CLOSE(); public static final int H5FD_LOG_TIME_IO = H5FD_LOG_TIME_IO(); public static final int H5FD_LOG_ALLOC = H5FD_LOG_ALLOC(); public static final int H5FD_LOG_ALL = H5FD_LOG_ALL(); public static final int H5FD_MEM_NOLIST = H5FD_MEM_NOLIST(); public static final int H5FD_MEM_DEFAULT = H5FD_MEM_DEFAULT(); public static final int H5FD_MEM_SUPER = H5FD_MEM_SUPER(); public static final int H5FD_MEM_BTREE = H5FD_MEM_BTREE(); public static final int H5FD_MEM_DRAW = H5FD_MEM_DRAW(); public static final int H5FD_MEM_GHEAP = H5FD_MEM_GHEAP(); public static final int H5FD_MEM_LHEAP = H5FD_MEM_LHEAP(); public static final int H5FD_MEM_OHDR = H5FD_MEM_OHDR(); public static final int H5FD_MEM_NTYPES = H5FD_MEM_NTYPES(); public static final long H5FD_DEFAULT_HADDR_SIZE = H5FD_DEFAULT_HADDR_SIZE(); public static final int H5G_DATASET = H5G_DATASET(); public static final int H5G_GROUP = H5G_GROUP(); public static final int H5G_LINK = H5G_LINK(); public static final int H5G_UDLINK = H5G_UDLINK(); public static final int H5G_LINK_ERROR = H5G_LINK_ERROR(); public static final int H5G_LINK_HARD = H5G_LINK_HARD(); public static final int H5G_LINK_SOFT = H5G_LINK_SOFT(); public static final int H5G_NLIBTYPES = H5G_NLIBTYPES(); public static final int H5G_NTYPES = H5G_NTYPES(); public static final int H5G_NUSERTYPES = H5G_NUSERTYPES(); public static final int H5G_RESERVED_5 = H5G_RESERVED_5(); public static final int H5G_RESERVED_6 = H5G_RESERVED_6(); public static final int H5G_RESERVED_7 = H5G_RESERVED_7(); public static final int H5G_SAME_LOC = H5G_SAME_LOC(); public static final int H5G_STORAGE_TYPE_UNKNOWN = H5G_STORAGE_TYPE_UNKNOWN(); public static final int H5G_STORAGE_TYPE_SYMBOL_TABLE = H5G_STORAGE_TYPE_SYMBOL_TABLE(); public static final int H5G_STORAGE_TYPE_COMPACT = H5G_STORAGE_TYPE_COMPACT(); public static final int H5G_STORAGE_TYPE_DENSE = H5G_STORAGE_TYPE_DENSE(); public static final int H5G_TYPE = H5G_TYPE(); public static final int H5G_UNKNOWN = H5G_UNKNOWN(); public static final int H5I_ATTR = H5I_ATTR(); public static final int H5I_BADID = H5I_BADID(); public static final int H5I_DATASET = H5I_DATASET(); public static final int H5I_DATASPACE = H5I_DATASPACE(); public static final int H5I_DATATYPE = H5I_DATATYPE(); public static final int H5I_FILE = H5I_FILE(); public static final int H5I_GENPROP_CLS = H5I_GENPROP_CLS(); public static final int H5I_GENPROP_LST = H5I_GENPROP_LST(); public static final int H5I_GROUP = H5I_GROUP(); public static final int H5I_INVALID_HID = H5I_INVALID_HID(); public static final int H5I_REFERENCE = H5I_REFERENCE(); public static final int H5I_VFL = H5I_VFL(); public static final int H5L_TYPE_ERROR = H5L_TYPE_ERROR(); public static final int H5L_TYPE_HARD = H5L_TYPE_HARD(); public static final int H5L_TYPE_SOFT = H5L_TYPE_SOFT(); public static final int H5L_TYPE_EXTERNAL = H5L_TYPE_EXTERNAL(); public static final int H5L_TYPE_MAX = H5L_TYPE_MAX(); public static final int H5O_COPY_SHALLOW_HIERARCHY_FLAG = H5O_COPY_SHALLOW_HIERARCHY_FLAG(); public static final int H5O_COPY_EXPAND_SOFT_LINK_FLAG = H5O_COPY_EXPAND_SOFT_LINK_FLAG(); public static final int H5O_COPY_EXPAND_EXT_LINK_FLAG = H5O_COPY_EXPAND_EXT_LINK_FLAG(); public static final int H5O_COPY_EXPAND_REFERENCE_FLAG = H5O_COPY_EXPAND_REFERENCE_FLAG(); public static final int H5O_COPY_WITHOUT_ATTR_FLAG = H5O_COPY_WITHOUT_ATTR_FLAG(); public static final int H5O_COPY_PRESERVE_NULL_FLAG = H5O_COPY_PRESERVE_NULL_FLAG(); public static final int H5O_SHMESG_NONE_FLAG = H5O_SHMESG_NONE_FLAG(); public static final int H5O_SHMESG_SDSPACE_FLAG = H5O_SHMESG_SDSPACE_FLAG(); public static final int H5O_SHMESG_DTYPE_FLAG = H5O_SHMESG_DTYPE_FLAG(); public static final int H5O_SHMESG_FILL_FLAG = H5O_SHMESG_FILL_FLAG(); public static final int H5O_SHMESG_PLINE_FLAG = H5O_SHMESG_PLINE_FLAG(); public static final int H5O_SHMESG_ATTR_FLAG = H5O_SHMESG_ATTR_FLAG(); public static final int H5O_SHMESG_ALL_FLAG = H5O_SHMESG_ALL_FLAG(); public static final int H5O_TYPE_UNKNOWN = H5O_TYPE_UNKNOWN(); public static final int H5O_TYPE_GROUP = H5O_TYPE_GROUP(); public static final int H5O_TYPE_DATASET = H5O_TYPE_DATASET(); public static final int H5O_TYPE_NAMED_DATATYPE = H5O_TYPE_NAMED_DATATYPE(); public static final int H5O_TYPE_NTYPES = H5O_TYPE_NTYPES(); public static final int H5P_ROOT = H5P_ROOT(); public static final int H5P_OBJECT_CREATE = H5P_OBJECT_CREATE(); public static final int H5P_FILE_CREATE = H5P_FILE_CREATE(); public static final int H5P_FILE_ACCESS = H5P_FILE_ACCESS(); public static final int H5P_DATASET_CREATE = H5P_DATASET_CREATE(); public static final int H5P_DATASET_ACCESS = H5P_DATASET_ACCESS(); public static final int H5P_DATASET_XFER = H5P_DATASET_XFER(); public static final int H5P_FILE_MOUNT = H5P_FILE_MOUNT(); public static final int H5P_GROUP_CREATE = H5P_GROUP_CREATE(); public static final int H5P_GROUP_ACCESS = H5P_GROUP_ACCESS(); public static final int H5P_DATATYPE_CREATE = H5P_DATATYPE_CREATE(); public static final int H5P_DATATYPE_ACCESS = H5P_DATATYPE_ACCESS(); public static final int H5P_STRING_CREATE = H5P_STRING_CREATE(); public static final int H5P_ATTRIBUTE_CREATE = H5P_ATTRIBUTE_CREATE(); public static final int H5P_OBJECT_COPY = H5P_OBJECT_COPY(); public static final int H5P_LINK_CREATE = H5P_LINK_CREATE(); public static final int H5P_LINK_ACCESS = H5P_LINK_ACCESS(); public static final int H5P_FILE_CREATE_DEFAULT = H5P_FILE_CREATE_DEFAULT(); public static final int H5P_FILE_ACCESS_DEFAULT = H5P_FILE_ACCESS_DEFAULT(); public static final int H5P_DATASET_CREATE_DEFAULT = H5P_DATASET_CREATE_DEFAULT(); public static final int H5P_DATASET_ACCESS_DEFAULT = H5P_DATASET_ACCESS_DEFAULT(); public static final int H5P_DATASET_XFER_DEFAULT = H5P_DATASET_XFER_DEFAULT(); public static final int H5P_FILE_MOUNT_DEFAULT = H5P_FILE_MOUNT_DEFAULT(); public static final int H5P_GROUP_CREATE_DEFAULT = H5P_GROUP_CREATE_DEFAULT(); public static final int H5P_GROUP_ACCESS_DEFAULT = H5P_GROUP_ACCESS_DEFAULT(); public static final int H5P_DATATYPE_CREATE_DEFAULT = H5P_DATATYPE_CREATE_DEFAULT(); public static final int H5P_DATATYPE_ACCESS_DEFAULT = H5P_DATATYPE_ACCESS_DEFAULT(); public static final int H5P_ATTRIBUTE_CREATE_DEFAULT = H5P_ATTRIBUTE_CREATE_DEFAULT(); public static final int H5P_OBJECT_COPY_DEFAULT = H5P_OBJECT_COPY_DEFAULT(); public static final int H5P_LINK_CREATE_DEFAULT = H5P_LINK_CREATE_DEFAULT(); public static final int H5P_LINK_ACCESS_DEFAULT = H5P_LINK_ACCESS_DEFAULT(); public static final int H5P_CRT_ORDER_TRACKED = H5P_CRT_ORDER_TRACKED(); public static final int H5P_CRT_ORDER_INDEXED = H5P_CRT_ORDER_INDEXED(); public static final int H5P_DEFAULT = H5P_DEFAULT(); public static final int H5P_NO_CLASS = H5P_NO_CLASS(); public static final int H5R_BADTYPE = H5R_BADTYPE(); public static final int H5R_DATASET_REGION = H5R_DATASET_REGION(); public static final int H5R_MAXTYPE = H5R_MAXTYPE(); public static final int H5R_OBJ_REF_BUF_SIZE = H5R_OBJ_REF_BUF_SIZE(); public static final int H5R_OBJECT = H5R_OBJECT(); public static final int H5S_ALL = H5S_ALL(); public static final int H5S_MAX_RANK = H5S_MAX_RANK(); public static final int H5S_NO_CLASS = H5S_NO_CLASS(); public static final int H5S_NULL = H5S_NULL(); public static final int H5S_SCALAR = H5S_SCALAR(); public static final int H5S_SEL_ALL = H5S_SEL_ALL(); public static final int H5S_SEL_ERROR = H5S_SEL_ERROR(); public static final int H5S_SEL_HYPERSLABS = H5S_SEL_HYPERSLABS(); public static final int H5S_SEL_N = H5S_SEL_N(); public static final int H5S_SEL_NONE = H5S_SEL_NONE(); public static final int H5S_SEL_POINTS = H5S_SEL_POINTS(); public static final int H5S_SELECT_AND = H5S_SELECT_AND(); public static final int H5S_SELECT_APPEND = H5S_SELECT_APPEND(); public static final int H5S_SELECT_INVALID = H5S_SELECT_INVALID(); public static final int H5S_SELECT_NOOP = H5S_SELECT_NOOP(); public static final int H5S_SELECT_NOTA = H5S_SELECT_NOTA(); public static final int H5S_SELECT_NOTB = H5S_SELECT_NOTB(); public static final int H5S_SELECT_OR = H5S_SELECT_OR(); public static final int H5S_SELECT_PREPEND = H5S_SELECT_PREPEND(); public static final int H5S_SELECT_SET = H5S_SELECT_SET(); public static final int H5S_SELECT_XOR = H5S_SELECT_XOR(); public static final int H5S_SIMPLE = H5S_SIMPLE(); public static final int H5S_UNLIMITED = H5S_UNLIMITED(); public static final int H5T_ALPHA_B16 = H5T_ALPHA_B16(); public static final int H5T_ALPHA_B32 = H5T_ALPHA_B32(); public static final int H5T_ALPHA_B64 = H5T_ALPHA_B64(); public static final int H5T_ALPHA_B8 = H5T_ALPHA_B8(); public static final int H5T_ALPHA_F32 = H5T_ALPHA_F32(); public static final int H5T_ALPHA_F64 = H5T_ALPHA_F64(); public static final int H5T_ALPHA_I16 = H5T_ALPHA_I16(); public static final int H5T_ALPHA_I32 = H5T_ALPHA_I32(); public static final int H5T_ALPHA_I64 = H5T_ALPHA_I64(); public static final int H5T_ALPHA_I8 = H5T_ALPHA_I8(); public static final int H5T_ALPHA_U16 = H5T_ALPHA_U16(); public static final int H5T_ALPHA_U32 = H5T_ALPHA_U32(); public static final int H5T_ALPHA_U64 = H5T_ALPHA_U64(); public static final int H5T_ALPHA_U8 = H5T_ALPHA_U8(); public static final int H5T_ARRAY = H5T_ARRAY(); public static final int H5T_BITFIELD = H5T_BITFIELD(); public static final int H5T_BKG_NO = H5T_BKG_NO(); public static final int H5T_BKG_YES = H5T_BKG_YES(); public static final int H5T_C_S1 = H5T_C_S1(); public static final int H5T_COMPOUND = H5T_COMPOUND(); public static final int H5T_CONV_CONV = H5T_CONV_CONV(); public static final int H5T_CONV_FREE = H5T_CONV_FREE(); public static final int H5T_CONV_INIT = H5T_CONV_INIT(); public static final int H5T_CSET_ERROR = H5T_CSET_ERROR(); public static final int H5T_CSET_ASCII = H5T_CSET_ASCII(); public static final int H5T_CSET_UTF8 = H5T_CSET_UTF8(); public static final int H5T_CSET_RESERVED_10 = H5T_CSET_RESERVED_10(); public static final int H5T_CSET_RESERVED_11 = H5T_CSET_RESERVED_11(); public static final int H5T_CSET_RESERVED_12 = H5T_CSET_RESERVED_12(); public static final int H5T_CSET_RESERVED_13 = H5T_CSET_RESERVED_13(); public static final int H5T_CSET_RESERVED_14 = H5T_CSET_RESERVED_14(); public static final int H5T_CSET_RESERVED_15 = H5T_CSET_RESERVED_15(); public static final int H5T_CSET_RESERVED_2 = H5T_CSET_RESERVED_2(); public static final int H5T_CSET_RESERVED_3 = H5T_CSET_RESERVED_3(); public static final int H5T_CSET_RESERVED_4 = H5T_CSET_RESERVED_4(); public static final int H5T_CSET_RESERVED_5 = H5T_CSET_RESERVED_5(); public static final int H5T_CSET_RESERVED_6 = H5T_CSET_RESERVED_6(); public static final int H5T_CSET_RESERVED_7 = H5T_CSET_RESERVED_7(); public static final int H5T_CSET_RESERVED_8 = H5T_CSET_RESERVED_8(); public static final int H5T_CSET_RESERVED_9 = H5T_CSET_RESERVED_9(); public static final int H5T_DIR_ASCEND = H5T_DIR_ASCEND(); public static final int H5T_DIR_DEFAULT = H5T_DIR_DEFAULT(); public static final int H5T_DIR_DESCEND = H5T_DIR_DESCEND(); public static final int H5T_ENUM = H5T_ENUM(); public static final int H5T_FLOAT = H5T_FLOAT(); public static final int H5T_FORTRAN_S1 = H5T_FORTRAN_S1(); public static final int H5T_IEEE_F32BE = H5T_IEEE_F32BE(); public static final int H5T_IEEE_F32LE = H5T_IEEE_F32LE(); public static final int H5T_IEEE_F64BE = H5T_IEEE_F64BE(); public static final int H5T_IEEE_F64LE = H5T_IEEE_F64LE(); public static final int H5T_INTEGER = H5T_INTEGER(); public static final int H5T_INTEL_B16 = H5T_INTEL_B16(); public static final int H5T_INTEL_B32 = H5T_INTEL_B32(); public static final int H5T_INTEL_B64 = H5T_INTEL_B64(); public static final int H5T_INTEL_B8 = H5T_INTEL_B8(); public static final int H5T_INTEL_F32 = H5T_INTEL_F32(); public static final int H5T_INTEL_F64 = H5T_INTEL_F64(); public static final int H5T_INTEL_I16 = H5T_INTEL_I16(); public static final int H5T_INTEL_I32 = H5T_INTEL_I32(); public static final int H5T_INTEL_I64 = H5T_INTEL_I64(); public static final int H5T_INTEL_I8 = H5T_INTEL_I8(); public static final int H5T_INTEL_U16 = H5T_INTEL_U16(); public static final int H5T_INTEL_U32 = H5T_INTEL_U32(); public static final int H5T_INTEL_U64 = H5T_INTEL_U64(); public static final int H5T_INTEL_U8 = H5T_INTEL_U8(); public static final int H5T_MIPS_B16 = H5T_MIPS_B16(); public static final int H5T_MIPS_B32 = H5T_MIPS_B32(); public static final int H5T_MIPS_B64 = H5T_MIPS_B64(); public static final int H5T_MIPS_B8 = H5T_MIPS_B8(); public static final int H5T_MIPS_F32 = H5T_MIPS_F32(); public static final int H5T_MIPS_F64 = H5T_MIPS_F64(); public static final int H5T_MIPS_I16 = H5T_MIPS_I16(); public static final int H5T_MIPS_I32 = H5T_MIPS_I32(); public static final int H5T_MIPS_I64 = H5T_MIPS_I64(); public static final int H5T_MIPS_I8 = H5T_MIPS_I8(); public static final int H5T_MIPS_U16 = H5T_MIPS_U16(); public static final int H5T_MIPS_U32 = H5T_MIPS_U32(); public static final int H5T_MIPS_U64 = H5T_MIPS_U64(); public static final int H5T_MIPS_U8 = H5T_MIPS_U8(); public static final int H5T_NATIVE_B16 = H5T_NATIVE_B16(); public static final int H5T_NATIVE_B32 = H5T_NATIVE_B32(); public static final int H5T_NATIVE_B64 = H5T_NATIVE_B64(); public static final int H5T_NATIVE_B8 = H5T_NATIVE_B8(); public static final int H5T_NATIVE_CHAR = H5T_NATIVE_CHAR(); public static final int H5T_NATIVE_DOUBLE = H5T_NATIVE_DOUBLE(); public static final int H5T_NATIVE_FLOAT = H5T_NATIVE_FLOAT(); public static final int H5T_NATIVE_HADDR = H5T_NATIVE_HADDR(); public static final int H5T_NATIVE_HBOOL = H5T_NATIVE_HBOOL(); public static final int H5T_NATIVE_HERR = H5T_NATIVE_HERR(); public static final int H5T_NATIVE_HSIZE = H5T_NATIVE_HSIZE(); public static final int H5T_NATIVE_HSSIZE = H5T_NATIVE_HSSIZE(); public static final int H5T_NATIVE_INT = H5T_NATIVE_INT(); public static final int H5T_NATIVE_INT_FAST16 = H5T_NATIVE_INT_FAST16(); public static final int H5T_NATIVE_INT_FAST32 = H5T_NATIVE_INT_FAST32(); public static final int H5T_NATIVE_INT_FAST64 = H5T_NATIVE_INT_FAST64(); public static final int H5T_NATIVE_INT_FAST8 = H5T_NATIVE_INT_FAST8(); public static final int H5T_NATIVE_INT_LEAST16 = H5T_NATIVE_INT_LEAST16(); public static final int H5T_NATIVE_INT_LEAST32 = H5T_NATIVE_INT_LEAST32(); public static final int H5T_NATIVE_INT_LEAST64 = H5T_NATIVE_INT_LEAST64(); public static final int H5T_NATIVE_INT_LEAST8 = H5T_NATIVE_INT_LEAST8(); public static final int H5T_NATIVE_INT16 = H5T_NATIVE_INT16(); public static final int H5T_NATIVE_INT32 = H5T_NATIVE_INT32(); public static final int H5T_NATIVE_INT64 = H5T_NATIVE_INT64(); public static final int H5T_NATIVE_INT8 = H5T_NATIVE_INT8(); public static final int H5T_NATIVE_LDOUBLE = H5T_NATIVE_LDOUBLE(); public static final int H5T_NATIVE_LLONG = H5T_NATIVE_LLONG(); public static final int H5T_NATIVE_LONG = H5T_NATIVE_LONG(); public static final int H5T_NATIVE_OPAQUE = H5T_NATIVE_OPAQUE(); public static final int H5T_NATIVE_SCHAR = H5T_NATIVE_SCHAR(); public static final int H5T_NATIVE_SHORT = H5T_NATIVE_SHORT(); public static final int H5T_NATIVE_UCHAR = H5T_NATIVE_UCHAR(); public static final int H5T_NATIVE_UINT = H5T_NATIVE_UINT(); public static final int H5T_NATIVE_UINT_FAST16 = H5T_NATIVE_UINT_FAST16(); public static final int H5T_NATIVE_UINT_FAST32 = H5T_NATIVE_UINT_FAST32(); public static final int H5T_NATIVE_UINT_FAST64 = H5T_NATIVE_UINT_FAST64(); public static final int H5T_NATIVE_UINT_FAST8 = H5T_NATIVE_UINT_FAST8(); public static final int H5T_NATIVE_UINT_LEAST16 = H5T_NATIVE_UINT_LEAST16(); public static final int H5T_NATIVE_UINT_LEAST32 = H5T_NATIVE_UINT_LEAST32(); public static final int H5T_NATIVE_UINT_LEAST64 = H5T_NATIVE_UINT_LEAST64(); public static final int H5T_NATIVE_UINT_LEAST8 = H5T_NATIVE_UINT_LEAST8(); public static final int H5T_NATIVE_UINT16 = H5T_NATIVE_UINT16(); public static final int H5T_NATIVE_UINT32 = H5T_NATIVE_UINT32(); public static final int H5T_NATIVE_UINT64 = H5T_NATIVE_UINT64(); public static final int H5T_NATIVE_UINT8 = H5T_NATIVE_UINT8(); public static final int H5T_NATIVE_ULLONG = H5T_NATIVE_ULLONG(); public static final int H5T_NATIVE_ULONG = H5T_NATIVE_ULONG(); public static final int H5T_NATIVE_USHORT = H5T_NATIVE_USHORT(); public static final int H5T_NCLASSES = H5T_NCLASSES(); public static final int H5T_NO_CLASS = H5T_NO_CLASS(); public static final int H5T_NORM_ERROR = H5T_NORM_ERROR(); public static final int H5T_NORM_IMPLIED = H5T_NORM_IMPLIED(); public static final int H5T_NORM_MSBSET = H5T_NORM_MSBSET(); public static final int H5T_NORM_NONE = H5T_NORM_NONE(); public static final int H5T_NPAD = H5T_NPAD(); public static final int H5T_NSGN = H5T_NSGN(); public static final int H5T_OPAQUE = H5T_OPAQUE(); public static final int H5T_OPAQUE_TAG_MAX = H5T_OPAQUE_TAG_MAX(); /* 1.6.5 */ public static final int H5T_ORDER_BE = H5T_ORDER_BE(); public static final int H5T_ORDER_ERROR = H5T_ORDER_ERROR(); public static final int H5T_ORDER_LE = H5T_ORDER_LE(); public static final int H5T_ORDER_NONE = H5T_ORDER_NONE(); public static final int H5T_ORDER_VAX = H5T_ORDER_VAX(); public static final int H5T_PAD_BACKGROUND = H5T_PAD_BACKGROUND(); public static final int H5T_PAD_ERROR = H5T_PAD_ERROR(); public static final int H5T_PAD_ONE = H5T_PAD_ONE(); public static final int H5T_PAD_ZERO = H5T_PAD_ZERO(); public static final int H5T_PERS_DONTCARE = H5T_PERS_DONTCARE(); public static final int H5T_PERS_HARD = H5T_PERS_HARD(); public static final int H5T_PERS_SOFT = H5T_PERS_SOFT(); public static final int H5T_REFERENCE = H5T_REFERENCE(); public static final int H5T_SGN_2 = H5T_SGN_2(); public static final int H5T_SGN_ERROR = H5T_SGN_ERROR(); public static final int H5T_SGN_NONE = H5T_SGN_NONE(); public static final int H5T_STD_B16BE = H5T_STD_B16BE(); public static final int H5T_STD_B16LE = H5T_STD_B16LE(); public static final int H5T_STD_B32BE = H5T_STD_B32BE(); public static final int H5T_STD_B32LE = H5T_STD_B32LE(); public static final int H5T_STD_B64BE = H5T_STD_B64BE(); public static final int H5T_STD_B64LE = H5T_STD_B64LE(); public static final int H5T_STD_B8BE = H5T_STD_B8BE(); public static final int H5T_STD_B8LE = H5T_STD_B8LE(); public static final int H5T_STD_I16BE = H5T_STD_I16BE(); public static final int H5T_STD_I16LE = H5T_STD_I16LE(); public static final int H5T_STD_I32BE = H5T_STD_I32BE(); public static final int H5T_STD_I32LE = H5T_STD_I32LE(); public static final int H5T_STD_I64BE = H5T_STD_I64BE(); public static final int H5T_STD_I64LE = H5T_STD_I64LE(); public static final int H5T_STD_I8BE = H5T_STD_I8BE(); public static final int H5T_STD_I8LE = H5T_STD_I8LE(); public static final int H5T_STD_REF_DSETREG = H5T_STD_REF_DSETREG(); public static final int H5T_STD_REF_OBJ = H5T_STD_REF_OBJ(); public static final int H5T_STD_U16BE = H5T_STD_U16BE(); public static final int H5T_STD_U16LE = H5T_STD_U16LE(); public static final int H5T_STD_U32BE = H5T_STD_U32BE(); public static final int H5T_STD_U32LE = H5T_STD_U32LE(); public static final int H5T_STD_U64BE = H5T_STD_U64BE(); public static final int H5T_STD_U64LE = H5T_STD_U64LE(); public static final int H5T_STD_U8BE = H5T_STD_U8BE(); public static final int H5T_STD_U8LE = H5T_STD_U8LE(); public static final int H5T_STR_ERROR = H5T_STR_ERROR(); public static final int H5T_STR_NULLPAD = H5T_STR_NULLPAD(); public static final int H5T_STR_NULLTERM = H5T_STR_NULLTERM(); public static final int H5T_STR_RESERVED_10 = H5T_STR_RESERVED_10(); public static final int H5T_STR_RESERVED_11 = H5T_STR_RESERVED_11(); public static final int H5T_STR_RESERVED_12 = H5T_STR_RESERVED_12(); public static final int H5T_STR_RESERVED_13 = H5T_STR_RESERVED_13(); public static final int H5T_STR_RESERVED_14 = H5T_STR_RESERVED_14(); public static final int H5T_STR_RESERVED_15 = H5T_STR_RESERVED_15(); public static final int H5T_STR_RESERVED_3 = H5T_STR_RESERVED_3(); public static final int H5T_STR_RESERVED_4 = H5T_STR_RESERVED_4(); public static final int H5T_STR_RESERVED_5 = H5T_STR_RESERVED_5(); public static final int H5T_STR_RESERVED_6 = H5T_STR_RESERVED_6(); public static final int H5T_STR_RESERVED_7 = H5T_STR_RESERVED_7(); public static final int H5T_STR_RESERVED_8 = H5T_STR_RESERVED_8(); public static final int H5T_STR_RESERVED_9 = H5T_STR_RESERVED_9(); public static final int H5T_STR_SPACEPAD = H5T_STR_SPACEPAD(); public static final int H5T_STRING = H5T_STRING(); public static final int H5T_TIME = H5T_TIME(); public static final int H5T_UNIX_D32BE = H5T_UNIX_D32BE(); public static final int H5T_UNIX_D32LE = H5T_UNIX_D32LE(); public static final int H5T_UNIX_D64BE = H5T_UNIX_D64BE(); public static final int H5T_UNIX_D64LE = H5T_UNIX_D64LE(); public static final int H5T_VARIABLE = H5T_VARIABLE(); public static final int H5T_VLEN = H5T_VLEN(); public static final int H5Z_CB_CONT = H5Z_CB_CONT(); public static final int H5Z_CB_ERROR = H5Z_CB_ERROR(); public static final int H5Z_CB_FAIL = H5Z_CB_FAIL(); public static final int H5Z_CB_NO = H5Z_CB_NO(); public static final int H5Z_DISABLE_EDC = H5Z_DISABLE_EDC(); public static final int H5Z_ENABLE_EDC = H5Z_ENABLE_EDC(); public static final int H5Z_ERROR_EDC = H5Z_ERROR_EDC(); public static final int H5Z_FILTER_DEFLATE = H5Z_FILTER_DEFLATE(); public static final int H5Z_FILTER_ERROR = H5Z_FILTER_ERROR(); public static final int H5Z_FILTER_FLETCHER32 = H5Z_FILTER_FLETCHER32(); public static final int H5Z_FILTER_MAX = H5Z_FILTER_MAX(); public static final int H5Z_FILTER_NBIT = H5Z_FILTER_NBIT(); public static final int H5Z_FILTER_NONE = H5Z_FILTER_NONE(); public static final int H5Z_FILTER_RESERVED = H5Z_FILTER_RESERVED(); public static final int H5Z_FILTER_SCALEOFFSET = H5Z_FILTER_SCALEOFFSET(); public static final int H5Z_FILTER_SHUFFLE = H5Z_FILTER_SHUFFLE(); public static final int H5Z_FILTER_SZIP = H5Z_FILTER_SZIP(); public static final int H5Z_FLAG_DEFMASK = H5Z_FLAG_DEFMASK(); public static final int H5Z_FLAG_INVMASK = H5Z_FLAG_INVMASK(); public static final int H5Z_FLAG_MANDATORY = H5Z_FLAG_MANDATORY(); public static final int H5Z_FLAG_OPTIONAL = H5Z_FLAG_OPTIONAL(); public static final int H5Z_FLAG_REVERSE = H5Z_FLAG_REVERSE(); public static final int H5Z_FLAG_SKIP_EDC = H5Z_FLAG_SKIP_EDC(); public static final int H5Z_MAX_NFILTERS = H5Z_MAX_NFILTERS(); public static final int H5Z_NO_EDC = H5Z_NO_EDC(); public static final int H5Z_FILTER_CONFIG_ENCODE_ENABLED = H5Z_FILTER_CONFIG_ENCODE_ENABLED(); public static final int H5Z_FILTER_CONFIG_DECODE_ENABLED = H5Z_FILTER_CONFIG_DECODE_ENABLED(); public static final int H5Z_SO_INT_MINBITS_DEFAULT = H5Z_SO_INT_MINBITS_DEFAULT(); public static final int H5Z_SO_FLOAT_DSCALE = H5Z_SO_FLOAT_DSCALE(); public static final int H5Z_SO_FLOAT_ESCALE = H5Z_SO_FLOAT_ESCALE(); public static final int H5Z_SO_INT = H5Z_SO_INT(); public static final int H5Z_SHUFFLE_USER_NPARMS = H5Z_SHUFFLE_USER_NPARMS(); public static final int H5Z_SHUFFLE_TOTAL_NPARMS = H5Z_SHUFFLE_TOTAL_NPARMS(); public static final int H5Z_SZIP_USER_NPARMS = H5Z_SZIP_USER_NPARMS(); public static final int H5Z_SZIP_TOTAL_NPARMS = H5Z_SZIP_TOTAL_NPARMS(); public static final int H5Z_SZIP_PARM_MASK = H5Z_SZIP_PARM_MASK(); public static final int H5Z_SZIP_PARM_PPB = H5Z_SZIP_PARM_PPB(); public static final int H5Z_SZIP_PARM_BPP = H5Z_SZIP_PARM_BPP(); public static final int H5Z_SZIP_PARM_PPS = H5Z_SZIP_PARM_PPS(); public static final int H5Z_NBIT_USER_NPARMS = H5Z_NBIT_USER_NPARMS(); public static final int H5Z_SCALEOFFSET_USER_NPARMS = H5Z_SCALEOFFSET_USER_NPARMS(); public static final int H5Z_FILTER_ALL = H5Z_FILTER_ALL(); // ///////////////////////////////////////////////////////////////////////// // List of private native variables to get constant values from C // // DO NOT EDIT THE LIST UNLESS YOU KNOW WHAT YOU DO!!! // // ///////////////////////////////////////////////////////////////////////// private static native final long H5_QUARTER_HADDR_MAX(); private static native final int H5_SZIP_MAX_PIXELS_PER_BLOCK(); private static native final int H5_SZIP_NN_OPTION_MASK(); private static native final int H5_SZIP_EC_OPTION_MASK(); private static native final int H5_SZIP_ALLOW_K13_OPTION_MASK(); private static native final int H5_SZIP_CHIP_OPTION_MASK(); private static native final int H5_INDEX_UNKNOWN(); private static native final int H5_INDEX_NAME(); private static native final int H5_INDEX_CRT_ORDER(); private static native final int H5_INDEX_N(); private static native final int H5_ITER_UNKNOWN(); private static native final int H5_ITER_INC(); private static native final int H5_ITER_DEC(); private static native final int H5_ITER_NATIVE(); private static native final int H5_ITER_N(); private static native final int H5AC_CURR_CACHE_CONFIG_VERSION(); private static native final int H5AC_MAX_TRACE_FILE_NAME_LEN(); private static native final int H5AC_METADATA_WRITE_STRATEGY_PROCESS_ZERO_ONLY(); private static native final int H5AC_METADATA_WRITE_STRATEGY_DISTRIBUTED(); private static native final int H5C_incr_off(); private static native final int H5C_incr_threshold(); private static native final int H5C_flash_incr_off(); private static native final int H5C_flash_incr_add_space(); private static native final int H5C_decr_off(); private static native final int H5C_decr_threshold(); private static native final int H5C_decr_age_out(); private static native final int H5C_decr_age_out_with_threshold(); private static native final int H5D_CHUNK_BTREE(); private static native final int H5D_ALLOC_TIME_DEFAULT(); private static native final int H5D_ALLOC_TIME_EARLY(); private static native final int H5D_ALLOC_TIME_ERROR(); private static native final int H5D_ALLOC_TIME_INCR(); private static native final int H5D_ALLOC_TIME_LATE(); private static native final int H5D_FILL_TIME_ERROR(); private static native final int H5D_FILL_TIME_ALLOC(); private static native final int H5D_FILL_TIME_NEVER(); private static native final int H5D_FILL_TIME_IFSET(); private static native final int H5D_FILL_VALUE_DEFAULT(); private static native final int H5D_FILL_VALUE_ERROR(); private static native final int H5D_FILL_VALUE_UNDEFINED(); private static native final int H5D_FILL_VALUE_USER_DEFINED(); private static native final int H5D_LAYOUT_ERROR(); private static native final int H5D_CHUNKED(); private static native final int H5D_COMPACT(); private static native final int H5D_CONTIGUOUS(); private static native final int H5D_NLAYOUTS(); private static native final int H5D_SPACE_STATUS_ALLOCATED(); private static native final int H5D_SPACE_STATUS_ERROR(); private static native final int H5D_SPACE_STATUS_NOT_ALLOCATED(); private static native final int H5D_SPACE_STATUS_PART_ALLOCATED(); private static native final int H5E_ALIGNMENT(); private static native final int H5E_ALREADYEXISTS(); private static native final int H5E_ALREADYINIT(); private static native final int H5E_ARGS(); private static native final int H5E_ATOM(); private static native final int H5E_ATTR(); private static native final int H5E_BADATOM(); private static native final int H5E_BADFILE(); private static native final int H5E_BADGROUP(); private static native final int H5E_BADMESG(); private static native final int H5E_BADRANGE(); private static native final int H5E_BADSELECT(); private static native final int H5E_BADSIZE(); private static native final int H5E_BADTYPE(); private static native final int H5E_BADVALUE(); private static native final int H5E_BTREE(); private static native final int H5E_CACHE(); private static native final int H5E_CALLBACK(); private static native final int H5E_CANAPPLY(); // private static native final int H5E_CANTALLOC(); private static native final int H5E_CANTCLIP(); private static native final int H5E_CANTCLOSEFILE(); private static native final int H5E_CANTCONVERT(); private static native final int H5E_CANTCOPY(); private static native final int H5E_CANTCOUNT(); private static native final int H5E_CANTCREATE(); private static native final int H5E_CANTDEC(); private static native final int H5E_CANTDECODE(); private static native final int H5E_CANTDELETE(); private static native final int H5E_CANTENCODE(); private static native final int H5E_CANTFLUSH(); private static native final int H5E_CANTFREE(); private static native final int H5E_CANTGET(); private static native final int H5E_CANTINC(); private static native final int H5E_CANTINIT(); private static native final int H5E_CANTINSERT(); private static native final int H5E_CANTLIST(); private static native final int H5E_CANTLOAD(); private static native final int H5E_CANTLOCK(); private static native final int H5E_CANTNEXT(); private static native final int H5E_CANTOPENFILE(); private static native final int H5E_CANTOPENOBJ(); // private static native final int H5E_CANTRECV(); private static native final int H5E_CANTREGISTER(); private static native final int H5E_CANTRELEASE(); private static native final int H5E_CANTSELECT(); private static native final int H5E_CANTSET(); private static native final int H5E_CANTSPLIT(); private static native final int H5E_CANTUNLOCK(); private static native final int H5E_CLOSEERROR(); private static native final int H5E_COMPLEN(); private static native final int H5E_DATASET(); private static native final int H5E_DATASPACE(); private static native final int H5E_DATATYPE(); private static native final int H5E_DEFAULT(); private static native final int H5E_DUPCLASS(); private static native final int H5E_EFL(); private static native final int H5E_EXISTS(); private static native final int H5E_FCNTL(); private static native final int H5E_FILE(); private static native final int H5E_FILEEXISTS(); private static native final int H5E_FILEOPEN(); private static native final int H5E_FUNC(); private static native final int H5E_HEAP(); private static native final int H5E_INTERNAL(); private static native final int H5E_IO(); private static native final int H5E_LINK(); private static native final int H5E_LINKCOUNT(); private static native final int H5E_MAJOR(); private static native final int H5E_MINOR(); private static native final int H5E_MOUNT(); private static native final int H5E_MPI(); private static native final int H5E_MPIERRSTR(); private static native final int H5E_NOFILTER(); private static native final int H5E_NOIDS(); private static native final int H5E_NONE_MAJOR(); private static native final int H5E_NONE_MINOR(); private static native final int H5E_NOSPACE(); private static native final int H5E_NOTCACHED(); private static native final int H5E_NOTFOUND(); private static native final int H5E_NOTHDF5(); private static native final int H5E_OHDR(); private static native final int H5E_OVERFLOW(); private static native final int H5E_PLINE(); private static native final int H5E_PLIST(); private static native final int H5E_PROTECT(); private static native final int H5E_READERROR(); private static native final int H5E_REFERENCE(); private static native final int H5E_RESOURCE(); private static native final int H5E_RS(); private static native final int H5E_SEEKERROR(); private static native final int H5E_SETLOCAL(); private static native final int H5E_STORAGE(); private static native final int H5E_SYM(); private static native final int H5E_TRUNCATED(); private static native final int H5E_TST(); private static native final int H5E_UNINITIALIZED(); private static native final int H5E_UNSUPPORTED(); private static native final int H5E_VERSION(); private static native final int H5E_VFL(); private static native final int H5E_WALK_DOWNWARD(); private static native final int H5E_WALK_UPWARD(); private static native final int H5E_WRITEERROR(); private static native final int H5F_ACC_CREAT(); private static native final int H5F_ACC_DEBUG(); private static native final int H5F_ACC_EXCL(); private static native final int H5F_ACC_RDONLY(); private static native final int H5F_ACC_RDWR(); private static native final int H5F_ACC_TRUNC(); private static native final int H5F_ACC_DEFAULT(); private static native final int H5F_CLOSE_DEFAULT(); private static native final int H5F_CLOSE_SEMI(); private static native final int H5F_CLOSE_STRONG(); private static native final int H5F_CLOSE_WEAK(); private static native final int H5F_LIBVER_EARLIEST(); private static native final int H5F_LIBVER_LATEST(); private static native final int H5F_OBJ_ALL(); private static native final int H5F_OBJ_ATTR(); private static native final int H5F_OBJ_DATASET(); private static native final int H5F_OBJ_DATATYPE(); private static native final int H5F_OBJ_FILE(); private static native final int H5F_OBJ_GROUP(); private static native final int H5F_OBJ_LOCAL(); /* 1.6.5 */ private static native final int H5F_SCOPE_DOWN(); private static native final int H5F_SCOPE_GLOBAL(); private static native final int H5F_SCOPE_LOCAL(); private static native final int H5F_UNLIMITED(); private static native final int H5FD_CORE(); private static native final int H5FD_DIRECT(); private static native final int H5FD_FAMILY(); private static native final int H5FD_LOG(); private static native final int H5FD_MPIO(); private static native final int H5FD_MULTI(); private static native final int H5FD_SEC2(); private static native final int H5FD_STDIO(); private static native final int H5FD_WINDOWS(); private static native final int H5FD_LOG_LOC_READ(); private static native final int H5FD_LOG_LOC_WRITE(); private static native final int H5FD_LOG_LOC_SEEK(); private static native final int H5FD_LOG_LOC_IO(); private static native final int H5FD_LOG_FILE_READ(); private static native final int H5FD_LOG_FILE_WRITE(); private static native final int H5FD_LOG_FILE_IO(); private static native final int H5FD_LOG_FLAVOR(); private static native final int H5FD_LOG_NUM_READ(); private static native final int H5FD_LOG_NUM_WRITE(); private static native final int H5FD_LOG_NUM_SEEK(); private static native final int H5FD_LOG_NUM_TRUNCATE(); private static native final int H5FD_LOG_NUM_IO(); private static native final int H5FD_LOG_TIME_OPEN(); private static native final int H5FD_LOG_TIME_STAT(); private static native final int H5FD_LOG_TIME_READ(); private static native final int H5FD_LOG_TIME_WRITE(); private static native final int H5FD_LOG_TIME_SEEK(); private static native final int H5FD_LOG_TIME_CLOSE(); private static native final int H5FD_LOG_TIME_IO(); private static native final int H5FD_LOG_ALLOC(); private static native final int H5FD_LOG_ALL(); private static native final int H5FD_MEM_NOLIST(); private static native final int H5FD_MEM_DEFAULT(); private static native final int H5FD_MEM_SUPER(); private static native final int H5FD_MEM_BTREE(); private static native final int H5FD_MEM_DRAW(); private static native final int H5FD_MEM_GHEAP(); private static native final int H5FD_MEM_LHEAP(); private static native final int H5FD_MEM_OHDR(); private static native final int H5FD_MEM_NTYPES(); private static native final long H5FD_DEFAULT_HADDR_SIZE(); private static native final int H5G_DATASET(); private static native final int H5G_GROUP(); private static native final int H5G_LINK(); private static native final int H5G_UDLINK(); private static native final int H5G_LINK_ERROR(); private static native final int H5G_LINK_HARD(); private static native final int H5G_LINK_SOFT(); private static native final int H5G_NLIBTYPES(); private static native final int H5G_NTYPES(); private static native final int H5G_NUSERTYPES(); private static native final int H5G_RESERVED_5(); private static native final int H5G_RESERVED_6(); private static native final int H5G_RESERVED_7(); private static native final int H5G_SAME_LOC(); private static native final int H5G_STORAGE_TYPE_UNKNOWN(); private static native final int H5G_STORAGE_TYPE_SYMBOL_TABLE(); private static native final int H5G_STORAGE_TYPE_COMPACT(); private static native final int H5G_STORAGE_TYPE_DENSE(); private static native final int H5G_TYPE(); private static native final int H5G_UNKNOWN(); private static native final int H5I_ATTR(); private static native final int H5I_BADID(); private static native final int H5I_DATASET(); private static native final int H5I_DATASPACE(); private static native final int H5I_DATATYPE(); private static native final int H5I_FILE(); private static native final int H5I_GENPROP_CLS(); private static native final int H5I_GENPROP_LST(); private static native final int H5I_GROUP(); private static native final int H5I_INVALID_HID(); private static native final int H5I_REFERENCE(); private static native final int H5I_VFL(); private static native final int H5L_TYPE_ERROR(); private static native final int H5L_TYPE_HARD(); private static native final int H5L_TYPE_SOFT(); private static native final int H5L_TYPE_EXTERNAL(); private static native final int H5L_TYPE_MAX(); private static native final int H5O_COPY_SHALLOW_HIERARCHY_FLAG(); private static native final int H5O_COPY_EXPAND_SOFT_LINK_FLAG(); private static native final int H5O_COPY_EXPAND_EXT_LINK_FLAG(); private static native final int H5O_COPY_EXPAND_REFERENCE_FLAG(); private static native final int H5O_COPY_WITHOUT_ATTR_FLAG(); private static native final int H5O_COPY_PRESERVE_NULL_FLAG(); private static native final int H5O_SHMESG_NONE_FLAG(); private static native final int H5O_SHMESG_SDSPACE_FLAG(); private static native final int H5O_SHMESG_DTYPE_FLAG(); private static native final int H5O_SHMESG_FILL_FLAG(); private static native final int H5O_SHMESG_PLINE_FLAG(); private static native final int H5O_SHMESG_ATTR_FLAG(); private static native final int H5O_SHMESG_ALL_FLAG(); private static native final int H5O_TYPE_UNKNOWN(); private static native final int H5O_TYPE_GROUP(); private static native final int H5O_TYPE_DATASET(); private static native final int H5O_TYPE_NAMED_DATATYPE(); private static native final int H5O_TYPE_NTYPES(); private static native final int H5P_ROOT(); private static native final int H5P_OBJECT_CREATE(); private static native final int H5P_FILE_CREATE(); private static native final int H5P_FILE_ACCESS(); private static native final int H5P_DATASET_CREATE(); private static native final int H5P_DATASET_ACCESS(); private static native final int H5P_DATASET_XFER(); private static native final int H5P_FILE_MOUNT(); private static native final int H5P_GROUP_CREATE(); private static native final int H5P_GROUP_ACCESS(); private static native final int H5P_DATATYPE_CREATE(); private static native final int H5P_DATATYPE_ACCESS(); private static native final int H5P_STRING_CREATE(); private static native final int H5P_ATTRIBUTE_CREATE(); private static native final int H5P_OBJECT_COPY(); private static native final int H5P_LINK_CREATE(); private static native final int H5P_LINK_ACCESS(); private static native final int H5P_FILE_CREATE_DEFAULT(); private static native final int H5P_FILE_ACCESS_DEFAULT(); private static native final int H5P_DATASET_CREATE_DEFAULT(); private static native final int H5P_DATASET_ACCESS_DEFAULT(); private static native final int H5P_DATASET_XFER_DEFAULT(); private static native final int H5P_FILE_MOUNT_DEFAULT(); private static native final int H5P_GROUP_CREATE_DEFAULT(); private static native final int H5P_GROUP_ACCESS_DEFAULT(); private static native final int H5P_DATATYPE_CREATE_DEFAULT(); private static native final int H5P_DATATYPE_ACCESS_DEFAULT(); private static native final int H5P_ATTRIBUTE_CREATE_DEFAULT(); private static native final int H5P_OBJECT_COPY_DEFAULT(); private static native final int H5P_LINK_CREATE_DEFAULT(); private static native final int H5P_LINK_ACCESS_DEFAULT(); private static native final int H5P_CRT_ORDER_TRACKED(); private static native final int H5P_CRT_ORDER_INDEXED(); private static native final int H5P_DEFAULT(); private static native final int H5P_NO_CLASS(); private static native final int H5R_BADTYPE(); private static native final int H5R_DATASET_REGION(); private static native final int H5R_MAXTYPE(); private static native final int H5R_OBJ_REF_BUF_SIZE(); private static native final int H5R_OBJECT(); private static native final int H5S_ALL(); private static native final int H5S_MAX_RANK(); private static native final int H5S_NO_CLASS(); private static native final int H5S_NULL(); private static native final int H5S_SCALAR(); private static native final int H5S_SEL_ALL(); private static native final int H5S_SEL_ERROR(); private static native final int H5S_SEL_HYPERSLABS(); private static native final int H5S_SEL_N(); private static native final int H5S_SEL_NONE(); private static native final int H5S_SEL_POINTS(); private static native final int H5S_SELECT_AND(); private static native final int H5S_SELECT_APPEND(); private static native final int H5S_SELECT_INVALID(); private static native final int H5S_SELECT_NOOP(); private static native final int H5S_SELECT_NOTA(); private static native final int H5S_SELECT_NOTB(); private static native final int H5S_SELECT_OR(); private static native final int H5S_SELECT_PREPEND(); private static native final int H5S_SELECT_SET(); private static native final int H5S_SELECT_XOR(); private static native final int H5S_SIMPLE(); private static native final int H5S_UNLIMITED(); private static native final int H5T_ALPHA_B16(); private static native final int H5T_ALPHA_B32(); private static native final int H5T_ALPHA_B64(); private static native final int H5T_ALPHA_B8(); private static native final int H5T_ALPHA_F32(); private static native final int H5T_ALPHA_F64(); private static native final int H5T_ALPHA_I16(); private static native final int H5T_ALPHA_I32(); private static native final int H5T_ALPHA_I64(); private static native final int H5T_ALPHA_I8(); private static native final int H5T_ALPHA_U16(); private static native final int H5T_ALPHA_U32(); private static native final int H5T_ALPHA_U64(); private static native final int H5T_ALPHA_U8(); private static native final int H5T_ARRAY(); private static native final int H5T_BITFIELD(); private static native final int H5T_BKG_NO(); private static native final int H5T_BKG_YES(); private static native final int H5T_C_S1(); private static native final int H5T_COMPOUND(); private static native final int H5T_CONV_CONV(); private static native final int H5T_CONV_FREE(); private static native final int H5T_CONV_INIT(); private static native final int H5T_CSET_ERROR(); private static native final int H5T_CSET_ASCII(); private static native final int H5T_CSET_UTF8(); private static native final int H5T_CSET_RESERVED_10(); private static native final int H5T_CSET_RESERVED_11(); private static native final int H5T_CSET_RESERVED_12(); private static native final int H5T_CSET_RESERVED_13(); private static native final int H5T_CSET_RESERVED_14(); private static native final int H5T_CSET_RESERVED_15(); private static native final int H5T_CSET_RESERVED_2(); private static native final int H5T_CSET_RESERVED_3(); private static native final int H5T_CSET_RESERVED_4(); private static native final int H5T_CSET_RESERVED_5(); private static native final int H5T_CSET_RESERVED_6(); private static native final int H5T_CSET_RESERVED_7(); private static native final int H5T_CSET_RESERVED_8(); private static native final int H5T_CSET_RESERVED_9(); private static native final int H5T_DIR_ASCEND(); private static native final int H5T_DIR_DEFAULT(); private static native final int H5T_DIR_DESCEND(); private static native final int H5T_ENUM(); private static native final int H5T_FLOAT(); private static native final int H5T_FORTRAN_S1(); private static native final int H5T_IEEE_F32BE(); private static native final int H5T_IEEE_F32LE(); private static native final int H5T_IEEE_F64BE(); private static native final int H5T_IEEE_F64LE(); private static native final int H5T_INTEGER(); private static native final int H5T_INTEL_B16(); private static native final int H5T_INTEL_B32(); private static native final int H5T_INTEL_B64(); private static native final int H5T_INTEL_B8(); private static native final int H5T_INTEL_F32(); private static native final int H5T_INTEL_F64(); private static native final int H5T_INTEL_I16(); private static native final int H5T_INTEL_I32(); private static native final int H5T_INTEL_I64(); private static native final int H5T_INTEL_I8(); private static native final int H5T_INTEL_U16(); private static native final int H5T_INTEL_U32(); private static native final int H5T_INTEL_U64(); private static native final int H5T_INTEL_U8(); private static native final int H5T_MIPS_B16(); private static native final int H5T_MIPS_B32(); private static native final int H5T_MIPS_B64(); private static native final int H5T_MIPS_B8(); private static native final int H5T_MIPS_F32(); private static native final int H5T_MIPS_F64(); private static native final int H5T_MIPS_I16(); private static native final int H5T_MIPS_I32(); private static native final int H5T_MIPS_I64(); private static native final int H5T_MIPS_I8(); private static native final int H5T_MIPS_U16(); private static native final int H5T_MIPS_U32(); private static native final int H5T_MIPS_U64(); private static native final int H5T_MIPS_U8(); private static native final int H5T_NATIVE_B16(); private static native final int H5T_NATIVE_B32(); private static native final int H5T_NATIVE_B64(); private static native final int H5T_NATIVE_B8(); private static native final int H5T_NATIVE_CHAR(); private static native final int H5T_NATIVE_DOUBLE(); private static native final int H5T_NATIVE_FLOAT(); private static native final int H5T_NATIVE_HADDR(); private static native final int H5T_NATIVE_HBOOL(); private static native final int H5T_NATIVE_HERR(); private static native final int H5T_NATIVE_HSIZE(); private static native final int H5T_NATIVE_HSSIZE(); private static native final int H5T_NATIVE_INT(); private static native final int H5T_NATIVE_INT_FAST16(); private static native final int H5T_NATIVE_INT_FAST32(); private static native final int H5T_NATIVE_INT_FAST64(); private static native final int H5T_NATIVE_INT_FAST8(); private static native final int H5T_NATIVE_INT_LEAST16(); private static native final int H5T_NATIVE_INT_LEAST32(); private static native final int H5T_NATIVE_INT_LEAST64(); private static native final int H5T_NATIVE_INT_LEAST8(); private static native final int H5T_NATIVE_INT16(); private static native final int H5T_NATIVE_INT32(); private static native final int H5T_NATIVE_INT64(); private static native final int H5T_NATIVE_INT8(); private static native final int H5T_NATIVE_LDOUBLE(); private static native final int H5T_NATIVE_LLONG(); private static native final int H5T_NATIVE_LONG(); private static native final int H5T_NATIVE_OPAQUE(); private static native final int H5T_NATIVE_SCHAR(); private static native final int H5T_NATIVE_SHORT(); private static native final int H5T_NATIVE_UCHAR(); private static native final int H5T_NATIVE_UINT(); private static native final int H5T_NATIVE_UINT_FAST16(); private static native final int H5T_NATIVE_UINT_FAST32(); private static native final int H5T_NATIVE_UINT_FAST64(); private static native final int H5T_NATIVE_UINT_FAST8(); private static native final int H5T_NATIVE_UINT_LEAST16(); private static native final int H5T_NATIVE_UINT_LEAST32(); private static native final int H5T_NATIVE_UINT_LEAST64(); private static native final int H5T_NATIVE_UINT_LEAST8(); private static native final int H5T_NATIVE_UINT16(); private static native final int H5T_NATIVE_UINT32(); private static native final int H5T_NATIVE_UINT64(); private static native final int H5T_NATIVE_UINT8(); private static native final int H5T_NATIVE_ULLONG(); private static native final int H5T_NATIVE_ULONG(); private static native final int H5T_NATIVE_USHORT(); private static native final int H5T_NCLASSES(); private static native final int H5T_NO_CLASS(); private static native final int H5T_NORM_ERROR(); private static native final int H5T_NORM_IMPLIED(); private static native final int H5T_NORM_MSBSET(); private static native final int H5T_NORM_NONE(); private static native final int H5T_NPAD(); private static native final int H5T_NSGN(); private static native final int H5T_OPAQUE(); private static native final int H5T_OPAQUE_TAG_MAX(); private static native final int H5T_ORDER_BE(); private static native final int H5T_ORDER_ERROR(); private static native final int H5T_ORDER_LE(); private static native final int H5T_ORDER_NONE(); private static native final int H5T_ORDER_VAX(); private static native final int H5T_PAD_BACKGROUND(); private static native final int H5T_PAD_ERROR(); private static native final int H5T_PAD_ONE(); private static native final int H5T_PAD_ZERO(); private static native final int H5T_PERS_DONTCARE(); private static native final int H5T_PERS_HARD(); private static native final int H5T_PERS_SOFT(); private static native final int H5T_REFERENCE(); private static native final int H5T_SGN_2(); private static native final int H5T_SGN_ERROR(); private static native final int H5T_SGN_NONE(); private static native final int H5T_STD_B16BE(); private static native final int H5T_STD_B16LE(); private static native final int H5T_STD_B32BE(); private static native final int H5T_STD_B32LE(); private static native final int H5T_STD_B64BE(); private static native final int H5T_STD_B64LE(); private static native final int H5T_STD_B8BE(); private static native final int H5T_STD_B8LE(); private static native final int H5T_STD_I16BE(); private static native final int H5T_STD_I16LE(); private static native final int H5T_STD_I32BE(); private static native final int H5T_STD_I32LE(); private static native final int H5T_STD_I64BE(); private static native final int H5T_STD_I64LE(); private static native final int H5T_STD_I8BE(); private static native final int H5T_STD_I8LE(); private static native final int H5T_STD_REF_DSETREG(); private static native final int H5T_STD_REF_OBJ(); private static native final int H5T_STD_U16BE(); private static native final int H5T_STD_U16LE(); private static native final int H5T_STD_U32BE(); private static native final int H5T_STD_U32LE(); private static native final int H5T_STD_U64BE(); private static native final int H5T_STD_U64LE(); private static native final int H5T_STD_U8BE(); private static native final int H5T_STD_U8LE(); private static native final int H5T_STR_ERROR(); private static native final int H5T_STR_NULLPAD(); private static native final int H5T_STR_NULLTERM(); private static native final int H5T_STR_RESERVED_10(); private static native final int H5T_STR_RESERVED_11(); private static native final int H5T_STR_RESERVED_12(); private static native final int H5T_STR_RESERVED_13(); private static native final int H5T_STR_RESERVED_14(); private static native final int H5T_STR_RESERVED_15(); private static native final int H5T_STR_RESERVED_3(); private static native final int H5T_STR_RESERVED_4(); private static native final int H5T_STR_RESERVED_5(); private static native final int H5T_STR_RESERVED_6(); private static native final int H5T_STR_RESERVED_7(); private static native final int H5T_STR_RESERVED_8(); private static native final int H5T_STR_RESERVED_9(); private static native final int H5T_STR_SPACEPAD(); private static native final int H5T_STRING(); private static native final int H5T_TIME(); private static native final int H5T_UNIX_D32BE(); private static native final int H5T_UNIX_D32LE(); private static native final int H5T_UNIX_D64BE(); private static native final int H5T_UNIX_D64LE(); private static native final int H5T_VARIABLE(); private static native final int H5T_VLEN(); private static native final int H5Z_CB_CONT(); private static native final int H5Z_CB_ERROR(); private static native final int H5Z_CB_FAIL(); private static native final int H5Z_CB_NO(); private static native final int H5Z_DISABLE_EDC(); private static native final int H5Z_ENABLE_EDC(); private static native final int H5Z_ERROR_EDC(); private static native final int H5Z_FILTER_DEFLATE(); private static native final int H5Z_FILTER_ERROR(); private static native final int H5Z_FILTER_FLETCHER32(); private static native final int H5Z_FILTER_MAX(); private static native final int H5Z_FILTER_NBIT(); private static native final int H5Z_FILTER_NONE(); private static native final int H5Z_FILTER_RESERVED(); private static native final int H5Z_FILTER_SCALEOFFSET(); private static native final int H5Z_FILTER_SHUFFLE(); private static native final int H5Z_FILTER_SZIP(); private static native final int H5Z_FLAG_DEFMASK(); private static native final int H5Z_FLAG_INVMASK(); private static native final int H5Z_FLAG_MANDATORY(); private static native final int H5Z_FLAG_OPTIONAL(); private static native final int H5Z_FLAG_REVERSE(); private static native final int H5Z_FLAG_SKIP_EDC(); private static native final int H5Z_MAX_NFILTERS(); private static native final int H5Z_NO_EDC(); private static native final int H5Z_FILTER_CONFIG_ENCODE_ENABLED(); private static native final int H5Z_FILTER_CONFIG_DECODE_ENABLED(); private static native final int H5Z_SO_INT_MINBITS_DEFAULT(); private static native final int H5Z_SO_FLOAT_DSCALE(); private static native final int H5Z_SO_FLOAT_ESCALE(); private static native final int H5Z_SO_INT(); private static native final int H5Z_SHUFFLE_USER_NPARMS(); private static native final int H5Z_SHUFFLE_TOTAL_NPARMS(); private static native final int H5Z_SZIP_USER_NPARMS(); private static native final int H5Z_SZIP_TOTAL_NPARMS(); private static native final int H5Z_SZIP_PARM_MASK(); private static native final int H5Z_SZIP_PARM_PPB(); private static native final int H5Z_SZIP_PARM_BPP(); private static native final int H5Z_SZIP_PARM_PPS(); private static native final int H5Z_NBIT_USER_NPARMS(); private static native final int H5Z_SCALEOFFSET_USER_NPARMS(); private static native final int H5Z_FILTER_ALL(); } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/HDF5GroupInfo.java000066400000000000000000000117711256564762100255140ustar00rootroot00000000000000/**************************************************************************** * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF Java Products. The full HDF Java copyright * * notice, including terms governing use, modification, and redistribution, * * is contained in the file, COPYING. COPYING can be found at the root of * * the source code distribution tree. You can also access it online at * * http://www.hdfgroup.org/products/licenses.html. If you do not have * * access to the file, you may request a copy from help@hdfgroup.org. * ****************************************************************************/ package ncsa.hdf.hdf5lib; /** *

* This class is a container for the information reported about an HDF5 Object * from the H5Gget_obj_info() method. *

* The fileno and objno fields contain four values which uniquely identify an * object among those HDF5 files which are open: if all four values are the same * between two objects, then the two objects are the same (provided both files * are still open). The nlink field is the number of hard links to the object or * zero when information is being returned about a symbolic link (symbolic links * do not have hard links but all other objects always have at least one). The * type field contains the type of the object, one of H5G_GROUP, H5G_DATASET, or * H5G_LINK. The mtime field contains the modification time. If information is * being returned about a symbolic link then linklen will be the length of the * link value (the name of the pointed-to object with the null terminator); * otherwise linklen will be zero. Other fields may be added to this structure * in the future. *

* For details of the HDF5 libraries, see the HDF5 Documentation at: http://hdf.ncsa.uiuc.edu/HDF5/doc/ */ public class HDF5GroupInfo { long[] fileno; long[] objno; int nlink; int type; long mtime; int linklen; public HDF5GroupInfo() { fileno = new long[2]; objno = new long[2]; nlink = -1; type = -1; mtime = 0; linklen = 0; } /** * Sets the HDF5 group information. Used by the JHI5. * * @param fn * File id number * @param on * Object id number * @param nl * Number of links * @param t * Type of the object * @param mt * Modification time * @param len * Length of link **/ public void setGroupInfo(long[] fn, long[] on, int nl, int t, long mt, int len) { fileno = fn; objno = on; nlink = nl; type = t; mtime = mt; linklen = len; } /** Resets all the group information to defaults. */ public void reset() { fileno[0] = 0; fileno[1] = 0; objno[0] = 0; objno[1] = 0; nlink = -1; type = -1; mtime = 0; linklen = 0; } /* accessors */ public long[] getFileno() { return fileno; } public long[] getObjno() { return objno; } public int getType() { return type; } public int getNlink() { return nlink; } public long getMtime() { return mtime; } public int getLinklen() { return linklen; } /** * The fileno and objno fields contain four values which uniquely identify * an object among those HDF5 files. */ @Override public boolean equals(Object obj) { if (!(obj instanceof HDF5GroupInfo)) { return false; } HDF5GroupInfo target = (HDF5GroupInfo) obj; if ((fileno[0] == target.fileno[0]) && (fileno[1] == target.fileno[1]) && (objno[0] == target.objno[0]) && (objno[1] == target.objno[1])) { return true; } else { return false; } } /** * Returns the object id. */ public long getOID() { return objno[0]; } /** * /** Converts this object to a String representation. * * @return a string representation of this object */ @Override public String toString() { String fileStr = "fileno=null"; String objStr = "objno=null"; if (fileno != null) { fileStr = "fileno[0]=" + fileno[0] + ",fileno[1]=" + fileno[1]; } if (objno != null) { objStr = "objno[0]=" + objno[0] + ",objno[1]=" + objno[1]; } return getClass().getName() + "[" + fileStr + "," + objStr + ",type=" + type + ",nlink=" + nlink + ",mtime=" + mtime + ",linklen=" + linklen + "]"; } } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/HDFArray.java000077500000000000000000001301221256564762100245700ustar00rootroot00000000000000/**************************************************************************** * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF Java Products. The full HDF Java copyright * * notice, including terms governing use, modification, and redistribution, * * is contained in the file, COPYING. COPYING can be found at the root of * * the source code distribution tree. You can also access it online at * * http://www.hdfgroup.org/products/licenses.html. If you do not have * * access to the file, you may request a copy from help@hdfgroup.org. * ****************************************************************************/ package ncsa.hdf.hdf5lib; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; /** * This is a class for handling multidimensional arrays for HDF. *

* The purpose is to allow the storage and retrieval of arbitrary array types * containing scientific data. *

* The methods support the conversion of an array to and from Java to a * one-dimensional array of bytes suitable for I/O by the C library. *

* This class heavily uses the HDFNativeData class to * convert between Java and C representations. */ public class HDFArray { private Object _theArray = null; private ArrayDescriptor _desc = null; private byte[] _barray = null; // public HDFArray() {} /** * The input must be a Java Array (possibly multidimensional) of primitive * numbers or sub-classes of Number. *

* The input is analysed to determine the number of dimensions and size of * each dimension, as well as the type of the elements. *

* The description is saved in private variables, and used to convert data. * * @exception ncsa.hdf.hdf5lib.exceptions.HDF5Exception * object is not an array. */ public HDFArray(Object anArray) throws HDF5Exception { if (anArray == null) { HDF5JavaException ex = new HDF5JavaException( "HDFArray: array is null?: "); throw (ex); } Class tc = anArray.getClass(); if (tc.isArray() == false) { /* exception: not an array */ HDF5JavaException ex = new HDF5JavaException( "HDFArray: not an array?: "); throw (ex); } _theArray = anArray; _desc = new ArrayDescriptor(_theArray); /* extra error checking -- probably not needed */ if (_desc == null) { HDF5JavaException ex = new HDF5JavaException( "HDFArray: internal error: array description failed?: "); throw (ex); } } /** * Allocate a one-dimensional array of bytes sufficient to store the array. * * @return A one-D array of bytes, filled with zeroes. The bytes are * sufficient to hold the data of the Array passed to the * constructor. * @exception ncsa.hdf.hdf5lib.exceptions.HDF5JavaException * Allocation failed. */ public byte[] emptyBytes() throws HDF5Exception { byte[] b = null; if ((ArrayDescriptor.dims == 1) && (ArrayDescriptor.NT == 'B')) { b = (byte[]) _theArray; } else { b = new byte[ArrayDescriptor.totalSize]; } if (b == null) { HDF5JavaException ex = new HDF5JavaException( "HDFArray: emptyBytes: allocation failed"); throw (ex); } return (b); } /** * Given a Java array of numbers, convert it to a one-dimensional array of * bytes in correct native order. * * @return A one-D array of bytes, constructed from the Array passed to the * constructor. * @exception ncsa.hdf.hdf5lib.exceptions.HDF5Exception * thrown for errors in HDF5 * @exception ncsa.hdf.hdf5lib.exceptions.HDF5JavaException * the object not an array or other internal error. */ public byte[] byteify() throws HDF5Exception { if (_barray != null) { return _barray; } if (_theArray == null) { /* exception: not an array */ HDF5JavaException ex = new HDF5JavaException( "HDFArray: byteify not an array?: "); throw (ex); } if (ArrayDescriptor.dims == 1) { /* special case */ if (ArrayDescriptor.NT == 'B') { /* really special case! */ _barray = (byte[]) _theArray; return _barray; } else { try { _barray = new byte[ArrayDescriptor.totalSize]; byte[] therow; if (ArrayDescriptor.NT == 'I') { therow = HDFNativeData.intToByte(0, ArrayDescriptor.dimlen[1], (int[]) _theArray); } else if (ArrayDescriptor.NT == 'S') { therow = HDFNativeData.shortToByte(0, ArrayDescriptor.dimlen[1], (short[]) _theArray); } else if (ArrayDescriptor.NT == 'F') { therow = HDFNativeData.floatToByte(0, ArrayDescriptor.dimlen[1], (float[]) _theArray); } else if (ArrayDescriptor.NT == 'J') { therow = HDFNativeData.longToByte(0, ArrayDescriptor.dimlen[1], (long[]) _theArray); } else if (ArrayDescriptor.NT == 'D') { therow = HDFNativeData .doubleToByte(0, ArrayDescriptor.dimlen[1], (double[]) _theArray); } else if (ArrayDescriptor.NT == 'L') { if (ArrayDescriptor.className.equals("java.lang.Byte")) { therow = ByteObjToByte((Byte[]) _theArray); } else if (ArrayDescriptor.className .equals("java.lang.Integer")) { therow = IntegerToByte((Integer[]) _theArray); } else if (ArrayDescriptor.className .equals("java.lang.Short")) { therow = ShortToByte((Short[]) _theArray); } else if (ArrayDescriptor.className .equals("java.lang.Float")) { therow = FloatObjToByte((Float[]) _theArray); } else if (ArrayDescriptor.className .equals("java.lang.Double")) { therow = DoubleObjToByte((Double[]) _theArray); } else if (ArrayDescriptor.className .equals("java.lang.Long")) { therow = LongObjToByte((Long[]) _theArray); } else { HDF5JavaException ex = new HDF5JavaException( "HDFArray: unknown type of Object?"); throw (ex); } } else { HDF5JavaException ex = new HDF5JavaException( "HDFArray: unknown type of data?"); throw (ex); } System .arraycopy( therow, 0, _barray, 0, (ArrayDescriptor.dimlen[1] * ArrayDescriptor.NTsize)); return _barray; } catch (OutOfMemoryError err) { HDF5JavaException ex = new HDF5JavaException( "HDFArray: byteify array too big?"); throw (ex); } } } try { _barray = new byte[ArrayDescriptor.totalSize]; } catch (OutOfMemoryError err) { HDF5JavaException ex = new HDF5JavaException( "HDFArray: byteify array too big?"); throw (ex); } Object oo = _theArray; int n = 0; /* the current byte */ int index = 0; int i; while (n < ArrayDescriptor.totalSize) { oo = ArrayDescriptor.objs[0]; index = n / ArrayDescriptor.bytetoindex[0]; index %= ArrayDescriptor.dimlen[0]; for (i = 0; i < (ArrayDescriptor.dims); i++) { index = n / ArrayDescriptor.bytetoindex[i]; index %= ArrayDescriptor.dimlen[i]; if (index == ArrayDescriptor.currentindex[i]) { /* then use cached copy */ oo = ArrayDescriptor.objs[i]; } else { /* check range of index */ if (index > (ArrayDescriptor.dimlen[i] - 1)) { throw new java.lang.IndexOutOfBoundsException( "HDFArray: byteify index OOB?"); } oo = java.lang.reflect.Array.get(oo, index); ArrayDescriptor.currentindex[i] = index; ArrayDescriptor.objs[i] = oo; } } /* byte-ify */ byte arow[]; try { if (ArrayDescriptor.NT == 'J') { arow = HDFNativeData .longToByte( 0, ArrayDescriptor.dimlen[ArrayDescriptor.dims], (long[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); arow = HDFNativeData .longToByte( 0, ArrayDescriptor.dimlen[ArrayDescriptor.dims], (long[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.NT == 'I') { arow = HDFNativeData .intToByte( 0, ArrayDescriptor.dimlen[ArrayDescriptor.dims], (int[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.NT == 'S') { arow = HDFNativeData .shortToByte( 0, ArrayDescriptor.dimlen[ArrayDescriptor.dims], (short[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.NT == 'B') { arow = (byte[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]; } else if (ArrayDescriptor.NT == 'F') { /* 32 bit float */ arow = HDFNativeData .floatToByte( 0, ArrayDescriptor.dimlen[ArrayDescriptor.dims], (float[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.NT == 'D') { /* 64 bit float */ arow = HDFNativeData .doubleToByte( 0, ArrayDescriptor.dimlen[ArrayDescriptor.dims], (double[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.NT == 'L') { if (ArrayDescriptor.className.equals("java.lang.Byte")) { arow = ByteObjToByte((Byte[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.className .equals("java.lang.Integer")) { arow = IntegerToByte((Integer[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.className .equals("java.lang.Short")) { arow = ShortToByte((Short[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.className .equals("java.lang.Float")) { arow = FloatObjToByte((Float[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.className .equals("java.lang.Double")) { arow = DoubleObjToByte((Double[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else if (ArrayDescriptor.className.equals("java.lang.Long")) { arow = LongObjToByte((Long[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]); } else { HDF5JavaException ex = new HDF5JavaException( "HDFArray: byteify Object type not implemented?"); throw (ex); } } else { HDF5JavaException ex = new HDF5JavaException( "HDFArray: byteify unknown type not implemented?"); throw (ex); } System .arraycopy( arow, 0, _barray, n, (ArrayDescriptor.dimlen[ArrayDescriptor.dims] * ArrayDescriptor.NTsize)); n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1]; } catch (OutOfMemoryError err) { HDF5JavaException ex = new HDF5JavaException( "HDFArray: byteify array too big?"); throw (ex); } } /* assert: the whole array is completed--currentindex should == len - 1 */ /* error checks */ if (n < ArrayDescriptor.totalSize) { throw new java.lang.InternalError(new String( "HDFArray::byteify: Panic didn't complete all input data: n= " + n + " size = " + ArrayDescriptor.totalSize)); } for (i = 0; i < ArrayDescriptor.dims; i++) { if (ArrayDescriptor.currentindex[i] != ArrayDescriptor.dimlen[i] - 1) { throw new java.lang.InternalError(new String( "Panic didn't complete all data: currentindex[" + i + "] = " + ArrayDescriptor.currentindex[i] + " (should be " + (ArrayDescriptor.dimlen[i] - 1) + " ?)")); } } return _barray; } /** * Given a one-dimensional array of bytes representing numbers, convert it * to a java array of the shape and size passed to the constructor. * * @param bytes * The bytes to construct the Array. * @return An Array (possibly multidimensional) of primitive or number * objects. * @exception ncsa.hdf.hdf5lib.exceptions.HDF5Exception * thrown for errors in HDF5 * @exception ncsa.hdf.hdf5lib.exceptions.HDF5JavaException * the object not an array or other internal error. */ public Object arrayify(byte[] bytes) throws HDF5Exception { if (_theArray == null) { /* exception: not an array */ HDF5JavaException ex = new HDF5JavaException( "arrayify: not an array?: "); throw (ex); } if (java.lang.reflect.Array.getLength(bytes) != ArrayDescriptor.totalSize) { /* exception: array not right size */ HDF5JavaException ex = new HDF5JavaException( "arrayify: array is wrong size?: "); throw (ex); } _barray = bytes; /* hope that the bytes are correct.... */ if (ArrayDescriptor.dims == 1) { /* special case */ /* 2 data copies here! */ try { if (ArrayDescriptor.NT == 'I') { int[] x = HDFNativeData.byteToInt(_barray); System.arraycopy(x, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } else if (ArrayDescriptor.NT == 'S') { short[] x = HDFNativeData.byteToShort(_barray); System.arraycopy(x, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } else if (ArrayDescriptor.NT == 'F') { float x[] = HDFNativeData.byteToFloat(_barray); System.arraycopy(x, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } else if (ArrayDescriptor.NT == 'J') { long x[] = HDFNativeData.byteToLong(_barray); System.arraycopy(x, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } else if (ArrayDescriptor.NT == 'D') { double x[] = HDFNativeData.byteToDouble(_barray); System.arraycopy(x, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } else if (ArrayDescriptor.NT == 'B') { System.arraycopy(_barray, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } else if (ArrayDescriptor.NT == 'L') { if (ArrayDescriptor.className.equals("java.lang.Byte")) { Byte I[] = ByteToByteObj(_barray); System.arraycopy(I, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } else if (ArrayDescriptor.className .equals("java.lang.Integer")) { Integer I[] = ByteToInteger(_barray); System.arraycopy(I, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } else if (ArrayDescriptor.className .equals("java.lang.Short")) { Short I[] = ByteToShort(_barray); System.arraycopy(I, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } else if (ArrayDescriptor.className .equals("java.lang.Float")) { Float I[] = ByteToFloatObj(_barray); System.arraycopy(I, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } else if (ArrayDescriptor.className .equals("java.lang.Double")) { Double I[] = ByteToDoubleObj(_barray); System.arraycopy(I, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } else if (ArrayDescriptor.className.equals("java.lang.Long")) { Long I[] = ByteToLongObj(_barray); System.arraycopy(I, 0, _theArray, 0, ArrayDescriptor.dimlen[1]); return _theArray; } else { HDF5JavaException ex = new HDF5JavaException( "arrayify: Object type not implemented yet..."); throw (ex); } } else { HDF5JavaException ex = new HDF5JavaException( "arrayify: unknown type not implemented yet..."); throw (ex); } } catch (OutOfMemoryError err) { HDF5JavaException ex = new HDF5JavaException( "HDFArray: arrayify array too big?"); throw (ex); } } /* Assert dims >= 2 */ Object oo = _theArray; int n = 0; /* the current byte */ int index = 0; int i; while (n < ArrayDescriptor.totalSize) { oo = ArrayDescriptor.objs[0]; index = n / ArrayDescriptor.bytetoindex[0]; index %= ArrayDescriptor.dimlen[0]; for (i = 0; i < (ArrayDescriptor.dims); i++) { index = n / ArrayDescriptor.bytetoindex[i]; index %= ArrayDescriptor.dimlen[i]; if (index == ArrayDescriptor.currentindex[i]) { /* then use cached copy */ oo = ArrayDescriptor.objs[i]; } else { /* check range of index */ if (index > (ArrayDescriptor.dimlen[i] - 1)) { System.out.println("out of bounds?"); return null; } oo = java.lang.reflect.Array.get(oo, index); ArrayDescriptor.currentindex[i] = index; ArrayDescriptor.objs[i] = oo; } } /* array-ify */ try { if (ArrayDescriptor.NT == 'J') { long[] arow = HDFNativeData.byteToLong(n, ArrayDescriptor.dimlen[ArrayDescriptor.dims], _barray); java.lang.reflect.Array .set( ArrayDescriptor.objs[ArrayDescriptor.dims - 2], (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]), arow); n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1]; ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++; } else if (ArrayDescriptor.NT == 'I') { int[] arow = HDFNativeData.byteToInt(n, ArrayDescriptor.dimlen[ArrayDescriptor.dims], _barray); java.lang.reflect.Array .set( ArrayDescriptor.objs[ArrayDescriptor.dims - 2], (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]), arow); n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1]; ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++; } else if (ArrayDescriptor.NT == 'S') { short[] arow = HDFNativeData.byteToShort(n, ArrayDescriptor.dimlen[ArrayDescriptor.dims], _barray); java.lang.reflect.Array .set( ArrayDescriptor.objs[ArrayDescriptor.dims - 2], (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]), arow); n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1]; ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++; } else if (ArrayDescriptor.NT == 'B') { System.arraycopy(_barray, n, ArrayDescriptor.objs[ArrayDescriptor.dims - 1], 0, ArrayDescriptor.dimlen[ArrayDescriptor.dims]); n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1]; } else if (ArrayDescriptor.NT == 'F') { float arow[] = HDFNativeData.byteToFloat(n, ArrayDescriptor.dimlen[ArrayDescriptor.dims], _barray); java.lang.reflect.Array .set( ArrayDescriptor.objs[ArrayDescriptor.dims - 2], (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]), arow); n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1]; ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++; } else if (ArrayDescriptor.NT == 'D') { double[] arow = HDFNativeData.byteToDouble(n, ArrayDescriptor.dimlen[ArrayDescriptor.dims], _barray); java.lang.reflect.Array .set( ArrayDescriptor.objs[ArrayDescriptor.dims - 2], (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]), arow); n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1]; ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++; } else if (ArrayDescriptor.NT == 'L') { if (ArrayDescriptor.className.equals("java.lang.Byte")) { Byte I[] = ByteToByteObj(n, ArrayDescriptor.dimlen[ArrayDescriptor.dims], _barray); java.lang.reflect.Array .set( ArrayDescriptor.objs[ArrayDescriptor.dims - 2], (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]), I); n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1]; ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++; } else if (ArrayDescriptor.className .equals("java.lang.Integer")) { Integer I[] = ByteToInteger(n, ArrayDescriptor.dimlen[ArrayDescriptor.dims], _barray); java.lang.reflect.Array .set( ArrayDescriptor.objs[ArrayDescriptor.dims - 2], (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]), I); n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1]; ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++; } else if (ArrayDescriptor.className .equals("java.lang.Short")) { Short I[] = ByteToShort(n, ArrayDescriptor.dimlen[ArrayDescriptor.dims], _barray); java.lang.reflect.Array .set( ArrayDescriptor.objs[ArrayDescriptor.dims - 2], (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]), I); n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1]; ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++; } else if (ArrayDescriptor.className .equals("java.lang.Float")) { Float I[] = ByteToFloatObj(n, ArrayDescriptor.dimlen[ArrayDescriptor.dims], _barray); java.lang.reflect.Array .set( ArrayDescriptor.objs[ArrayDescriptor.dims - 2], (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]), I); n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1]; ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++; } else if (ArrayDescriptor.className .equals("java.lang.Double")) { Double I[] = ByteToDoubleObj(n, ArrayDescriptor.dimlen[ArrayDescriptor.dims], _barray); java.lang.reflect.Array .set( ArrayDescriptor.objs[ArrayDescriptor.dims - 2], (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]), I); n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1]; ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++; } else if (ArrayDescriptor.className.equals("java.lang.Long")) { Long I[] = ByteToLongObj(n, ArrayDescriptor.dimlen[ArrayDescriptor.dims], _barray); java.lang.reflect.Array .set( ArrayDescriptor.objs[ArrayDescriptor.dims - 2], (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]), I); n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1]; ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++; } else { HDF5JavaException ex = new HDF5JavaException( "HDFArray: unsupported Object type: " + ArrayDescriptor.NT); throw (ex); } } else { HDF5JavaException ex = new HDF5JavaException( "HDFArray: unknown or unsupported type: " + ArrayDescriptor.NT); throw (ex); } } catch (OutOfMemoryError err) { HDF5JavaException ex = new HDF5JavaException( "HDFArray: arrayify array too big?"); throw (ex); } } /* assert: the whole array is completed--currentindex should == len - 1 */ /* error checks */ if (n < ArrayDescriptor.totalSize) { throw new java.lang.InternalError(new String( "HDFArray::arrayify Panic didn't complete all input data: n= " + n + " size = " + ArrayDescriptor.totalSize)); } for (i = 0; i <= ArrayDescriptor.dims - 2; i++) { if (ArrayDescriptor.currentindex[i] != ArrayDescriptor.dimlen[i] - 1) { throw new java.lang.InternalError(new String( "HDFArray::arrayify Panic didn't complete all data: currentindex[" + i + "] = " + ArrayDescriptor.currentindex[i] + " (should be " + (ArrayDescriptor.dimlen[i] - 1) + "?")); } } if (ArrayDescriptor.NT != 'B') { if (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1] != ArrayDescriptor.dimlen[ArrayDescriptor.dims - 1]) { throw new java.lang.InternalError(new String( "HDFArray::arrayify Panic didn't complete all data: currentindex[" + i + "] = " + ArrayDescriptor.currentindex[i] + " (should be " + (ArrayDescriptor.dimlen[i]) + "?")); } } else { if (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1] != (ArrayDescriptor.dimlen[ArrayDescriptor.dims - 1] - 1)) { throw new java.lang.InternalError(new String( "HDFArray::arrayify Panic didn't complete all data: currentindex[" + i + "] = " + ArrayDescriptor.currentindex[i] + " (should be " + (ArrayDescriptor.dimlen[i] - 1) + "?")); } } return _theArray; } private byte[] IntegerToByte(Integer in[]) { int nelems = java.lang.reflect.Array.getLength(in); int[] out = new int[nelems]; for (int i = 0; i < nelems; i++) { out[i] = in[i].intValue(); } return HDFNativeData.intToByte(0, nelems, out); } private Integer[] ByteToInteger(byte[] bin) { int in[] = HDFNativeData.byteToInt(bin); int nelems = java.lang.reflect.Array.getLength(in); Integer[] out = new Integer[nelems]; for (int i = 0; i < nelems; i++) { out[i] = new Integer(in[i]); } return out; } private Integer[] ByteToInteger(int start, int len, byte[] bin) { int in[] = HDFNativeData.byteToInt(start, len, bin); int nelems = java.lang.reflect.Array.getLength(in); Integer[] out = new Integer[nelems]; for (int i = 0; i < nelems; i++) { out[i] = new Integer(in[i]); } return out; } private byte[] ShortToByte(Short in[]) { int nelems = java.lang.reflect.Array.getLength(in); short[] out = new short[nelems]; for (int i = 0; i < nelems; i++) { out[i] = in[i].shortValue(); } return HDFNativeData.shortToByte(0, nelems, out); } private Short[] ByteToShort(byte[] bin) { short in[] = HDFNativeData.byteToShort(bin); int nelems = java.lang.reflect.Array.getLength(in); Short[] out = new Short[nelems]; for (int i = 0; i < nelems; i++) { out[i] = new Short(in[i]); } return out; } private Short[] ByteToShort(int start, int len, byte[] bin) { short in[] = HDFNativeData.byteToShort(start, len, bin); int nelems = java.lang.reflect.Array.getLength(in); Short[] out = new Short[nelems]; for (int i = 0; i < nelems; i++) { out[i] = new Short(in[i]); } return out; } private byte[] ByteObjToByte(Byte in[]) { int nelems = java.lang.reflect.Array.getLength(in); byte[] out = new byte[nelems]; for (int i = 0; i < nelems; i++) { out[i] = in[i].byteValue(); } return out; } private Byte[] ByteToByteObj(byte[] bin) { int nelems = java.lang.reflect.Array.getLength(bin); Byte[] out = new Byte[nelems]; for (int i = 0; i < nelems; i++) { out[i] = new Byte(bin[i]); } return out; } private Byte[] ByteToByteObj(int start, int len, byte[] bin) { Byte[] out = new Byte[len]; for (int i = 0; i < len; i++) { out[i] = new Byte(bin[i]); } return out; } private byte[] FloatObjToByte(Float in[]) { int nelems = java.lang.reflect.Array.getLength(in); float[] out = new float[nelems]; for (int i = 0; i < nelems; i++) { out[i] = in[i].floatValue(); } return HDFNativeData.floatToByte(0, nelems, out); } private Float[] ByteToFloatObj(byte[] bin) { float in[] = HDFNativeData.byteToFloat(bin); int nelems = java.lang.reflect.Array.getLength(in); Float[] out = new Float[nelems]; for (int i = 0; i < nelems; i++) { out[i] = new Float(in[i]); } return out; } private Float[] ByteToFloatObj(int start, int len, byte[] bin) { float in[] = HDFNativeData.byteToFloat(start, len, bin); int nelems = java.lang.reflect.Array.getLength(in); Float[] out = new Float[nelems]; for (int i = 0; i < nelems; i++) { out[i] = new Float(in[i]); } return out; } private byte[] DoubleObjToByte(Double in[]) { int nelems = java.lang.reflect.Array.getLength(in); double[] out = new double[nelems]; for (int i = 0; i < nelems; i++) { out[i] = in[i].doubleValue(); } return HDFNativeData.doubleToByte(0, nelems, out); } private Double[] ByteToDoubleObj(byte[] bin) { double in[] = HDFNativeData.byteToDouble(bin); int nelems = java.lang.reflect.Array.getLength(in); Double[] out = new Double[nelems]; for (int i = 0; i < nelems; i++) { out[i] = new Double(in[i]); } return out; } private Double[] ByteToDoubleObj(int start, int len, byte[] bin) { double in[] = HDFNativeData.byteToDouble(start, len, bin); int nelems = java.lang.reflect.Array.getLength(in); Double[] out = new Double[nelems]; for (int i = 0; i < nelems; i++) { out[i] = new Double(in[i]); } return out; } private byte[] LongObjToByte(Long in[]) { int nelems = java.lang.reflect.Array.getLength(in); long[] out = new long[nelems]; for (int i = 0; i < nelems; i++) { out[i] = in[i].longValue(); } return HDFNativeData.longToByte(0, nelems, out); } private Long[] ByteToLongObj(byte[] bin) { long in[] = HDFNativeData.byteToLong(bin); int nelems = java.lang.reflect.Array.getLength(in); Long[] out = new Long[nelems]; for (int i = 0; i < nelems; i++) { out[i] = new Long(in[i]); } return out; } private Long[] ByteToLongObj(int start, int len, byte[] bin) { long in[] = HDFNativeData.byteToLong(start, len, bin); int nelems = java.lang.reflect.Array.getLength(in); Long[] out = new Long[nelems]; for (int i = 0; i < nelems; i++) { out[i] = new Long(in[i]); } return out; } } /** * This private class is used by HDFArray to discover the shape and type of an * arbitrary array. *

* We use java.lang.reflection here. */ class ArrayDescriptor { static String theType = ""; static Class theClass = null; static int[] dimlen = null; static int[] dimstart = null; static int[] currentindex = null; static int[] bytetoindex = null; static int totalSize = 0; static Object[] objs = null; static char NT = ' '; /* must be B,S,I,L,F,D, else error */ static int NTsize = 0; static int dims = 0; static String className; public ArrayDescriptor(Object anArray) throws HDF5Exception { Class tc = anArray.getClass(); if (tc.isArray() == false) { /* exception: not an array */ HDF5Exception ex = new HDF5JavaException( "ArrayDescriptor: not an array?: "); throw (ex); } theClass = tc; /* * parse the type descriptor to discover the shape of the array */ String ss = tc.toString(); theType = ss; int n = 6; dims = 0; char c = ' '; while (n < ss.length()) { c = ss.charAt(n); n++; if (c == '[') { dims++; } } String css = ss.substring(ss.lastIndexOf('[') + 1); NT = c; /* must be B,S,I,L,F,D, else error */ if (NT == 'B') { NTsize = 1; } else if (NT == 'S') { NTsize = 2; } else if ((NT == 'I') || (NT == 'F')) { NTsize = 4; } else if ((NT == 'J') || (NT == 'D')) { NTsize = 8; } else if (css.startsWith("Ljava.lang.Byte")) { NT = 'L'; className = "java.lang.Byte"; NTsize = 1; } else if (css.startsWith("Ljava.lang.Short")) { NT = 'L'; className = "java.lang.Short"; NTsize = 2; } else if (css.startsWith("Ljava.lang.Integer")) { NT = 'L'; className = "java.lang.Integer"; NTsize = 4; } else if (css.startsWith("Ljava.lang.Float")) { NT = 'L'; className = "java.lang.Float"; NTsize = 4; } else if (css.startsWith("Ljava.lang.Double")) { NT = 'L'; className = "java.lang.Double"; NTsize = 8; } else if (css.startsWith("Ljava.lang.Long")) { NT = 'L'; className = "java.lang.Long"; NTsize = 8; } else if (css.startsWith("Ljava.lang.String")) { throw new HDF5JavaException(new String( "ArrayDesciptor: Error: String array not supported yet")); } else { /* * exception: not a numeric type */ throw new HDF5JavaException(new String( "ArrayDesciptor: Error: array is not numeric (type is " + css + ") ?")); } /* fill in the table */ dimlen = new int[dims + 1]; dimstart = new int[dims + 1]; currentindex = new int[dims + 1]; bytetoindex = new int[dims + 1]; objs = new Object[dims + 1]; Object o = anArray; objs[0] = o; dimlen[0] = 1; dimstart[0] = 0; currentindex[0] = 0; int i; for (i = 1; i <= dims; i++) { dimlen[i] = java.lang.reflect.Array.getLength(o); o = java.lang.reflect.Array.get(o, 0); objs[i] = o; dimstart[i] = 0; currentindex[i] = 0; } int j; int dd; bytetoindex[dims] = NTsize; for (i = dims; i >= 0; i--) { dd = NTsize; for (j = i; j < dims; j++) { dd *= dimlen[j + 1]; } bytetoindex[i] = dd; } totalSize = bytetoindex[0]; } /** * Debug dump */ public void dumpInfo() { System.out.println("Type: " + theType); System.out.println("Class: " + theClass); System.out.println("NT: " + NT + " NTsize: " + NTsize); System.out.println("Array has " + dims + " dimensions (" + totalSize + " bytes)"); int i; for (i = 0; i <= dims; i++) { Class tc = objs[i].getClass(); String ss = tc.toString(); System.out.println(i + ": start " + dimstart[i] + ": len " + dimlen[i] + " current " + currentindex[i] + " bytetoindex " + bytetoindex[i] + " object " + objs[i] + " otype " + ss); } } } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/HDFNativeData.java000066400000000000000000000354221256564762100255360ustar00rootroot00000000000000/**************************************************************************** * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF Java Products. The full HDF Java copyright * * notice, including terms governing use, modification, and redistribution, * * is contained in the file, COPYING. COPYING can be found at the root of * * the source code distribution tree. You can also access it online at * * http://www.hdfgroup.org/products/licenses.html. If you do not have * * access to the file, you may request a copy from help@hdfgroup.org. * ****************************************************************************/ package ncsa.hdf.hdf5lib; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; /** * This class encapsulates native methods to deal with arrays of numbers, * converting from numbers to bytes and bytes to numbers. *

* These routines are used by class HDFArray to pass data to and from the * HDF-5 library. *

* Methods xxxToByte() convert a Java array of primitive numbers (int, short, * ...) to a Java array of bytes. Methods byteToXxx() convert from a Java array * of bytes into a Java array of primitive numbers (int, short, ...) *

* Variant interfaces convert a section of an array, and also can convert to * sub-classes of Java Number. *

* See also: ncsa.hdf.hdf5lib.HDFArray. */ public class HDFNativeData { /** * Convert an array of bytes into an array of ints * * @param data * The input array of bytes * @return an array of int */ public synchronized static native int[] byteToInt(byte[] data); /** * Convert an array of bytes into an array of floats * * @param data * The input array of bytes * @return an array of float */ public synchronized static native float[] byteToFloat(byte[] data); /** * Convert an array of bytes into an array of shorts * * @param data * The input array of bytes * @return an array of short */ public synchronized static native short[] byteToShort(byte[] data); /** * Convert an array of bytes into an array of long * * @param data * The input array of bytes * @return an array of long */ /* * does this really work? C 'long' is 32 bits, Java 'long' is 64-bits. What * does this routine actually do? */ public synchronized static native long[] byteToLong(byte[] data); /** * Convert an array of bytes into an array of double * * @param data * The input array of bytes * @return an array of double */ public synchronized static native double[] byteToDouble(byte[] data); /** * Convert a range from an array of bytes into an array of int * * @param start * The position in the input array of bytes to start * @param len * The number of 'int' to convert * @param data * The input array of bytes * @return an array of 'len' int */ public synchronized static native int[] byteToInt(int start, int len, byte[] data); /** * Convert 4 bytes from an array of bytes into a single int * * @param start * The position in the input array of bytes to start * @param data * The input array of bytes * @return The integer value of the bytes. */ public synchronized static int byteToInt(byte[] data, int start) { int[] ival = new int[1]; ival = byteToInt(start, 1, data); return (ival[0]); } /** * Convert a range from an array of bytes into an array of short * * @param start * The position in the input array of bytes to start * @param len * The number of 'short' to convert * @param data * The input array of bytes * @return an array of 'len' short */ public synchronized static native short[] byteToShort(int start, int len, byte[] data); /** * Convert 2 bytes from an array of bytes into a single short * * @param start * The position in the input array of bytes to start * @param data * The input array of bytes * @return The short value of the bytes. */ public synchronized static short byteToShort(byte[] data, int start) { short[] sval = new short[1]; sval = byteToShort(start, 1, data); return (sval[0]); } /** * Convert a range from an array of bytes into an array of float * * @param start * The position in the input array of bytes to start * @param len * The number of 'float' to convert * @param data * The input array of bytes * @return an array of 'len' float */ public synchronized static native float[] byteToFloat(int start, int len, byte[] data); /** * Convert 4 bytes from an array of bytes into a single float * * @param start * The position in the input array of bytes to start * @param data * The input array of bytes * @return The float value of the bytes. */ public synchronized static float byteToFloat(byte[] data, int start) { float[] fval = new float[1]; fval = byteToFloat(start, 1, data); return (fval[0]); } /** * Convert a range from an array of bytes into an array of long * * @param start * The position in the input array of bytes to start * @param len * The number of 'long' to convert * @param data * The input array of bytes * @return an array of 'len' long */ public synchronized static native long[] byteToLong(int start, int len, byte[] data); /** * Convert 8 bytes from an array of bytes into a single long * * @param start * The position in the input array of bytes to start * @param data * The input array of bytes * @return The long value of the bytes. */ public synchronized static long byteToLong(byte[] data, int start) { long[] lval = new long[1]; lval = byteToLong(start, 1, data); return (lval[0]); } /** * Convert a range from an array of bytes into an array of double * * @param start * The position in the input array of bytes to start * @param len * The number of 'double' to convert * @param data * The input array of bytes * @return an array of 'len' double */ public synchronized static native double[] byteToDouble(int start, int len, byte[] data); /** * Convert 8 bytes from an array of bytes into a single double * * @param start * The position in the input array of bytes to start * @param data * The input array of bytes * @return The double value of the bytes. */ public synchronized static double byteToDouble(byte[] data, int start) { double[] dval = new double[1]; dval = byteToDouble(start, 1, data); return (dval[0]); } /** * Convert a range from an array of int into an array of bytes. * * @param start * The position in the input array of int to start * @param len * The number of 'int' to convert * @param data * The input array of int * @return an array of bytes */ public synchronized static native byte[] intToByte(int start, int len, int[] data); /** * Convert a range from an array of short into an array of bytes. * * @param start * The position in the input array of int to start * @param len * The number of 'short' to convert * @param data * The input array of short * @return an array of bytes */ public synchronized static native byte[] shortToByte(int start, int len, short[] data); /** * Convert a range from an array of float into an array of bytes. * * @param start * The position in the input array of int to start * @param len * The number of 'float' to convert * @param data * The input array of float * @return an array of bytes */ public synchronized static native byte[] floatToByte(int start, int len, float[] data); /** * Convert a range from an array of long into an array of bytes. * * @param start * The position in the input array of int to start * @param len * The number of 'long' to convert * @param data * The input array of long * @return an array of bytes */ public synchronized static native byte[] longToByte(int start, int len, long[] data); /** * Convert a range from an array of double into an array of bytes. * * @param start * The position in the input array of double to start * @param len * The number of 'double' to convert * @param data * The input array of double * @return an array of bytes */ public synchronized static native byte[] doubleToByte(int start, int len, double[] data); /** * Convert a single byte into an array of one byte. *

* (This is a trivial method.) * * @param data * The input byte * @return an array of bytes */ public synchronized static native byte[] byteToByte(byte data); /** * Convert a single Byte object into an array of one byte. *

* (This is an almost trivial method.) * * @param data * The input Byte * @return an array of bytes */ public synchronized static byte[] byteToByte(Byte data) { return byteToByte(data.byteValue()); } /** * Convert a single int into an array of 4 bytes. * * @param data * The input int * @return an array of bytes */ public synchronized static native byte[] intToByte(int data); /** * Convert a single Integer object into an array of 4 bytes. * * @param data * The input Integer * @return an array of bytes */ public synchronized static byte[] intToByte(Integer data) { return intToByte(data.intValue()); } /** * Convert a single short into an array of 2 bytes. * * @param data * The input short * @return an array of bytes */ public synchronized static native byte[] shortToByte(short data); /** * Convert a single Short object into an array of 2 bytes. * * @param data * The input Short * @return an array of bytes */ public synchronized static byte[] shortToByte(Short data) { return shortToByte(data.shortValue()); } /** * Convert a single float into an array of 4 bytes. * * @param data * The input float * @return an array of bytes */ public synchronized static native byte[] floatToByte(float data); /** * Convert a single Float object into an array of 4 bytes. * * @param data * The input Float * @return an array of bytes */ public synchronized static byte[] floatToByte(Float data) { return floatToByte(data.floatValue()); } /** * Convert a single long into an array of 8 bytes. * * @param data * The input long * @return an array of bytes */ public synchronized static native byte[] longToByte(long data); /** * Convert a single Long object into an array of 8 bytes. * * @param data * The input Long * @return an array of bytes */ public synchronized static byte[] longToByte(Long data) { return longToByte(data.longValue()); } /** * Convert a single double into an array of 8 bytes. * * @param data * The input double * @return an array of bytes */ public synchronized static native byte[] doubleToByte(double data); /** * Convert a single Double object into an array of 8 bytes. * * @param data * The input Double * @return an array of bytes */ public synchronized static byte[] doubleToByte(Double data) { return doubleToByte(data.doubleValue()); } /** * Create a Number object from an array of bytes. * * @param barray * The bytes to be converted * @param obj * Input object of the desired output class. Must be a sub-class * of Number. * @return A Object of the type of obj. */ public synchronized static Object byteToNumber(byte[] barray, Object obj) throws HDF5Exception { Class theClass = obj.getClass(); String type = theClass.getName(); Object retobj = null; if (type.equals("java.lang.Integer")) { int[] i = ncsa.hdf.hdf5lib.HDFNativeData.byteToInt(0, 1, barray); retobj = new Integer(i[0]); } else if (type.equals("java.lang.Byte")) { retobj = new Byte(barray[0]); } else if (type.equals("java.lang.Short")) { short[] f = ncsa.hdf.hdf5lib.HDFNativeData .byteToShort(0, 1, barray); retobj = new Short(f[0]); } else if (type.equals("java.lang.Float")) { float[] f = ncsa.hdf.hdf5lib.HDFNativeData .byteToFloat(0, 1, barray); retobj = new Float(f[0]); } else if (type.equals("java.lang.Long")) { long[] f = ncsa.hdf.hdf5lib.HDFNativeData.byteToLong(0, 1, barray); retobj = new Long(f[0]); } else if (type.equals("java.lang.Double")) { double[] f = ncsa.hdf.hdf5lib.HDFNativeData.byteToDouble(0, 1, barray); retobj = new Double(f[0]); } else { /* exception: unsupported type */ HDF5Exception ex = new HDF5JavaException( "byteToNumber: setfield bad type: " + obj + " " + type); throw (ex); } return (retobj); } } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/callbacks/000077500000000000000000000000001256564762100242425ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/callbacks/Callbacks.java000066400000000000000000000015111256564762100267620ustar00rootroot00000000000000package ncsa.hdf.hdf5lib.callbacks; /** All callback definitions must derive from this interface. Any * derived interfaces must define a single public method named "callback". * You are responsible for deregistering your callback (if necessary) * in its {@link Object#finalize} method. If native code attempts to call * a callback which has been GC'd, you will likely crash the VM. If * there is no method to deregister the callback (e.g. atexit * in the C library), you must ensure that you always keep a live reference * to the callback object.

* A callback should generally never throw an exception, since it doesn't * necessarily have an encompassing Java environment to catch it. Any * exceptions thrown will be passed to the default callback exception * handler. */ public interface Callbacks { } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/callbacks/H5D_iterate_cb.java000066400000000000000000000022441256564762100276500ustar00rootroot00000000000000/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF Java Products. The full HDF Java copyright * * notice, including terms governing use, modification, and redistribution, * * is contained in the file, COPYING. COPYING can be found at the root of * * the source code distribution tree. You can also access it online at * * http://www.hdfgroup.org/products/licenses.html. If you do not have * * access to the file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package ncsa.hdf.hdf5lib.callbacks; //Information class for link callback(for H5Diterate) public interface H5D_iterate_cb extends Callbacks { int callback(byte[] elem, int elem_type, int ndim, long[] point, H5D_iterate_t op_data); } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/callbacks/H5D_iterate_t.java000066400000000000000000000003151256564762100275240ustar00rootroot00000000000000package ncsa.hdf.hdf5lib.callbacks; public interface H5D_iterate_t { /** public ArrayList iterdata = new ArrayList(); * Any derived interfaces must define the single public varaible as above. */ } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/callbacks/H5L_iterate_cb.java000066400000000000000000000023251256564762100276600ustar00rootroot00000000000000/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF Java Products. The full HDF Java copyright * * notice, including terms governing use, modification, and redistribution, * * is contained in the file, COPYING. COPYING can be found at the root of * * the source code distribution tree. You can also access it online at * * http://www.hdfgroup.org/products/licenses.html. If you do not have * * access to the file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package ncsa.hdf.hdf5lib.callbacks; import ncsa.hdf.hdf5lib.structs.H5L_info_t; //Information class for link callback(for H5Lvisit/H5Lvisit_by_name) public interface H5L_iterate_cb extends Callbacks { int callback(int group, String name, H5L_info_t info, H5L_iterate_t op_data); } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/callbacks/H5L_iterate_t.java000066400000000000000000000003151256564762100275340ustar00rootroot00000000000000package ncsa.hdf.hdf5lib.callbacks; public interface H5L_iterate_t { /** public ArrayList iterdata = new ArrayList(); * Any derived interfaces must define the single public varaible as above. */ } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/callbacks/H5O_iterate_cb.java000066400000000000000000000023251256564762100276630ustar00rootroot00000000000000/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF Java Products. The full HDF Java copyright * * notice, including terms governing use, modification, and redistribution, * * is contained in the file, COPYING. COPYING can be found at the root of * * the source code distribution tree. You can also access it online at * * http://www.hdfgroup.org/products/licenses.html. If you do not have * * access to the file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package ncsa.hdf.hdf5lib.callbacks; import ncsa.hdf.hdf5lib.structs.H5O_info_t; //Information class for link callback(for H5Ovisit/H5Ovisit_by_name) public interface H5O_iterate_cb extends Callbacks { int callback(int group, String name, H5O_info_t info, H5O_iterate_t op_data); } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/callbacks/H5O_iterate_t.java000066400000000000000000000003151256564762100275370ustar00rootroot00000000000000package ncsa.hdf.hdf5lib.callbacks; public interface H5O_iterate_t { /** public ArrayList iterdata = new ArrayList(); * Any derived interfaces must define the single public varaible as above. */ } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/exceptions/000077500000000000000000000000001256564762100245045ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/exceptions/HDF5AtomException.java000066400000000000000000000034331256564762100305400ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF5 * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ package ncsa.hdf.hdf5lib.exceptions; /** * The class HDF5LibraryException returns errors raised by the HDF5 library. *

* This sub-class represents HDF-5 major error code H5E_ATOM */ public class HDF5AtomException extends HDF5LibraryException { private static final long serialVersionUID = 1L; /** * Constructs an HDF5AtomException with the specified detail message. * * @param majorErrorNumber The major error number of the HDF5 library. * @param majorErrorMessage The error message for the major error number of the HDF5 library. * @param minorErrorNumber The minor error number of the HDF5 library. * @param minorErrorMessage The error message for the minor error number of the HDF5 library. */ public HDF5AtomException(final int majorErrorNumber, final String majorErrorMessage, final int minorErrorNumber, final String minorErrorMessage) { super(majorErrorNumber, majorErrorMessage, minorErrorNumber, minorErrorMessage); } } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/exceptions/HDF5AttributeException.java000066400000000000000000000034501256564762100316020ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF5 * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ package ncsa.hdf.hdf5lib.exceptions; /** * The class HDF5LibraryException returns errors raised by the HDF5 library. *

* This sub-class represents HDF-5 major error code H5E_ATTR */ public class HDF5AttributeException extends HDF5LibraryException { private static final long serialVersionUID = 1L; /** * Constructs an HDF5AttributeException with the specified detail message. * * @param majorErrorNumber The major error number of the HDF5 library. * @param majorErrorMessage The error message for the major error number of the HDF5 library. * @param minorErrorNumber The minor error number of the HDF5 library. * @param minorErrorMessage The error message for the minor error number of the HDF5 library. */ public HDF5AttributeException(final int majorErrorNumber, final String majorErrorMessage, final int minorErrorNumber, final String minorErrorMessage) { super(majorErrorNumber, majorErrorMessage, minorErrorNumber, minorErrorMessage); } } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/exceptions/HDF5BtreeException.java000066400000000000000000000034351256564762100307030ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF5 * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ package ncsa.hdf.hdf5lib.exceptions; /** * The class HDF5LibraryException returns errors raised by the HDF5 library. *

* This sub-class represents HDF-5 major error code H5E_BTREE */ public class HDF5BtreeException extends HDF5LibraryException { private static final long serialVersionUID = 1L; /** * Constructs an HDF5BtreeException with the specified detail message. * * @param majorErrorNumber The major error number of the HDF5 library. * @param majorErrorMessage The error message for the major error number of the HDF5 library. * @param minorErrorNumber The minor error number of the HDF5 library. * @param minorErrorMessage The error message for the minor error number of the HDF5 library. */ public HDF5BtreeException(final int majorErrorNumber, final String majorErrorMessage, final int minorErrorNumber, final String minorErrorMessage) { super(majorErrorNumber, majorErrorMessage, minorErrorNumber, minorErrorMessage); } } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/exceptions/HDF5DataFiltersException.java000066400000000000000000000034571256564762100320500ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF5 * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ package ncsa.hdf.hdf5lib.exceptions; /** * The class HDF5LibraryException returns errors raised by the HDF5 library. *

* This sub-class represents HDF-5 major error code H5E_PLINE */ public class HDF5DataFiltersException extends HDF5LibraryException { private static final long serialVersionUID = 1L; /** * Constructs an HDF5DataFiltersException with the specified detail message. * * @param majorErrorNumber The major error number of the HDF5 library. * @param majorErrorMessage The error message for the major error number of the HDF5 library. * @param minorErrorNumber The minor error number of the HDF5 library. * @param minorErrorMessage The error message for the minor error number of the HDF5 library. */ public HDF5DataFiltersException(final int majorErrorNumber, final String majorErrorMessage, final int minorErrorNumber, final String minorErrorMessage) { super(majorErrorNumber, majorErrorMessage, minorErrorNumber, minorErrorMessage); } } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/exceptions/HDF5DataStorageException.java000066400000000000000000000034621256564762100320400ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF5 * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ package ncsa.hdf.hdf5lib.exceptions; /** * The class HDF5LibraryException returns errors raised by the HDF5 library. *

* This sub-class represents HDF-5 major error code H5E_STORAGE */ public class HDF5DataStorageException extends HDF5LibraryException { private static final long serialVersionUID = 1L; /** * Constructs an HDF5DataStorageException with the specified detail message. * * @param majorErrorNumber The major error number of the HDF5 library. * @param majorErrorMessage The error message for the major error number of the HDF5 library. * @param minorErrorNumber The minor error number of the HDF5 library. * @param minorErrorMessage The error message for the minor error number of the HDF5 library. */ public HDF5DataStorageException(final int majorErrorNumber, final String majorErrorMessage, final int minorErrorNumber, final String minorErrorMessage) { super(majorErrorNumber, majorErrorMessage, minorErrorNumber, minorErrorMessage); } } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/exceptions/HDF5DatasetInterfaceException.java000066400000000000000000000035001256564762100330410ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF5 * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ package ncsa.hdf.hdf5lib.exceptions; /** * The class HDF5LibraryException returns errors raised by the HDF5 library. *

* This sub-class represents HDF-5 major error code H5E_DATASET */ public class HDF5DatasetInterfaceException extends HDF5LibraryException { private static final long serialVersionUID = 1L; /** * Constructs an HDF5DatasetInterfaceException with the specified detail message. * * @param majorErrorNumber The major error number of the HDF5 library. * @param majorErrorMessage The error message for the major error number of the HDF5 library. * @param minorErrorNumber The minor error number of the HDF5 library. * @param minorErrorMessage The error message for the minor error number of the HDF5 library. */ public HDF5DatasetInterfaceException(final int majorErrorNumber, final String majorErrorMessage, final int minorErrorNumber, final String minorErrorMessage) { super(majorErrorNumber, majorErrorMessage, minorErrorNumber, minorErrorMessage); } } HDF5DataspaceInterfaceException.java000066400000000000000000000035111256564762100332640ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/exceptions/**************************************************************************** * NCSA HDF5 * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ package ncsa.hdf.hdf5lib.exceptions; /** * The class HDF5LibraryException returns errors raised by the HDF5 library. *

* This sub-class represents HDF-5 major error code H5E_DATASPACE */ public class HDF5DataspaceInterfaceException extends HDF5LibraryException { private static final long serialVersionUID = 1L; /** * Constructs an HDF5DataspaceInterfaceException with the specified detail message. * * @param majorErrorNumber The major error number of the HDF5 library. * @param majorErrorMessage The error message for the major error number of the HDF5 library. * @param minorErrorNumber The minor error number of the HDF5 library. * @param minorErrorMessage The error message for the minor error number of the HDF5 library. */ public HDF5DataspaceInterfaceException(final int majorErrorNumber, final String majorErrorMessage, final int minorErrorNumber, final String minorErrorMessage) { super(majorErrorNumber, majorErrorMessage, minorErrorNumber, minorErrorMessage); } } HDF5DatatypeInterfaceException.java000066400000000000000000000035051256564762100331550ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/exceptions/**************************************************************************** * NCSA HDF5 * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ package ncsa.hdf.hdf5lib.exceptions; /** * The class HDF5LibraryException returns errors raised by the HDF5 library. *

* This sub-class represents HDF-5 major error code H5E_DATATYPE */ public class HDF5DatatypeInterfaceException extends HDF5LibraryException { private static final long serialVersionUID = 1L; /** * Constructs an HDF5DatatypeInterfaceException with the specified detail message. * * @param majorErrorNumber The major error number of the HDF5 library. * @param majorErrorMessage The error message for the major error number of the HDF5 library. * @param minorErrorNumber The minor error number of the HDF5 library. * @param minorErrorMessage The error message for the minor error number of the HDF5 library. */ public HDF5DatatypeInterfaceException(final int majorErrorNumber, final String majorErrorMessage, final int minorErrorNumber, final String minorErrorMessage) { super(majorErrorNumber, majorErrorMessage, minorErrorNumber, minorErrorMessage); } } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/exceptions/HDF5Exception.java000066400000000000000000000041541256564762100277200ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF5 * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ package ncsa.hdf.hdf5lib.exceptions; /** *

* The class HDF5Exception returns errors from the Java HDF5 Interface. *

* Two sub-classes of HDF5Exception are defined: *

*

    *
  1. HDF5LibraryException -- errors raised the HDF5 library code *
  2. HDF5JavaException -- errors raised the HDF5 Java wrapper code *
*

* These exceptions are sub-classed to represent specific error conditions, as needed. In particular, * HDF5LibraryException has a sub-class for each major error code returned by the HDF5 library. */ public class HDF5Exception extends RuntimeException { private static final long serialVersionUID = 1L; protected String detailMessage; /** * Constructs an HDF5Exception with no specified detail message. */ public HDF5Exception() { super(); } /** * Constructs an HDF5Exception with the specified detail message. * * @param message the detail message. */ public HDF5Exception(final String message) { super(); detailMessage = message; } /** * Returns the detail message of this exception * * @return the detail message or null if this object does not have a detail message. */ @Override public String getMessage() { return detailMessage; } } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/exceptions/HDF5ExternalFileListException.java000066400000000000000000000034751256564762100330640ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF5 * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ package ncsa.hdf.hdf5lib.exceptions; /** * The class HDF5LibraryException returns errors raised by the HDF5 library. *

* This sub-class represents HDF-5 major error code H5E_EFL */ public class HDF5ExternalFileListException extends HDF5LibraryException { private static final long serialVersionUID = 1L; /** * Constructs an HDF5ExternalFileListException with the specified detail message. * * @param majorErrorNumber The major error number of the HDF5 library. * @param majorErrorMessage The error message for the major error number of the HDF5 library. * @param minorErrorNumber The minor error number of the HDF5 library. * @param minorErrorMessage The error message for the minor error number of the HDF5 library. */ public HDF5ExternalFileListException(final int majorErrorNumber, final String majorErrorMessage, final int minorErrorNumber, final String minorErrorMessage) { super(majorErrorNumber, majorErrorMessage, minorErrorNumber, minorErrorMessage); } } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/exceptions/HDF5FileInterfaceException.java000066400000000000000000000034651256564762100323450ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF5 * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ package ncsa.hdf.hdf5lib.exceptions; /** * The class HDF5LibraryException returns errors raised by the HDF5 library. *

* This sub-class represents HDF-5 major error code H5E_FILE */ public class HDF5FileInterfaceException extends HDF5LibraryException { private static final long serialVersionUID = 1L; /** * Constructs an HDF5FileInterfaceException with the specified detail message. * * @param majorErrorNumber The major error number of the HDF5 library. * @param majorErrorMessage The error message for the major error number of the HDF5 library. * @param minorErrorNumber The minor error number of the HDF5 library. * @param minorErrorMessage The error message for the minor error number of the HDF5 library. */ public HDF5FileInterfaceException(final int majorErrorNumber, final String majorErrorMessage, final int minorErrorNumber, final String minorErrorMessage) { super(majorErrorNumber, majorErrorMessage, minorErrorNumber, minorErrorMessage); } } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/exceptions/HDF5FileNotFoundException.java000066400000000000000000000021511256564762100321700ustar00rootroot00000000000000/* * Copyright 2011 ETH Zuerich, CISD * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ncsa.hdf.hdf5lib.exceptions; import java.io.File; /** *

* The class HDF5JavaException returns errors from the Java wrapper of theHDF5 library. *

* This exception communicates that a file is not found or cannot be opened. * * @author Bernd Rinn */ public class HDF5FileNotFoundException extends HDF5JavaException { private static final long serialVersionUID = 1L; public HDF5FileNotFoundException(File file, String msg) { super(msg + " (" + file.getAbsolutePath() + ")"); } } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/exceptions/HDF5FunctionArgumentException.java000066400000000000000000000034761256564762100331370ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF5 * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ package ncsa.hdf.hdf5lib.exceptions; /** * The class HDF5LibraryException returns errors raised by the HDF5 library. *

* This sub-class represents HDF-5 major error code H5E_ARGS */ public class HDF5FunctionArgumentException extends HDF5LibraryException { private static final long serialVersionUID = 1L; /** * Constructs an HDF5FunctionArgumentException with the specified detail message. * * @param majorErrorNumber The major error number of the HDF5 library. * @param majorErrorMessage The error message for the major error number of the HDF5 library. * @param minorErrorNumber The minor error number of the HDF5 library. * @param minorErrorMessage The error message for the minor error number of the HDF5 library. */ public HDF5FunctionArgumentException(final int majorErrorNumber, final String majorErrorMessage, final int minorErrorNumber, final String minorErrorMessage) { super(majorErrorNumber, majorErrorMessage, minorErrorNumber, minorErrorMessage); } } HDF5FunctionEntryExitException.java000066400000000000000000000035011256564762100332160ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/exceptions/**************************************************************************** * NCSA HDF5 * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ package ncsa.hdf.hdf5lib.exceptions; /** * The class HDF5LibraryException returns errors raised by the HDF5 library. *

* This sub-class represents HDF-5 major error code H5E_FUNC */ public class HDF5FunctionEntryExitException extends HDF5LibraryException { private static final long serialVersionUID = 1L; /** * Constructs an HDF5FunctionEntryExitException with the specified detail message. * * @param majorErrorNumber The major error number of the HDF5 library. * @param majorErrorMessage The error message for the major error number of the HDF5 library. * @param minorErrorNumber The minor error number of the HDF5 library. * @param minorErrorMessage The error message for the minor error number of the HDF5 library. */ public HDF5FunctionEntryExitException(final int majorErrorNumber, final String majorErrorMessage, final int minorErrorNumber, final String minorErrorMessage) { super(majorErrorNumber, majorErrorMessage, minorErrorNumber, minorErrorMessage); } } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/exceptions/HDF5HeapException.java000066400000000000000000000034321256564762100305140ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF5 * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ package ncsa.hdf.hdf5lib.exceptions; /** * The class HDF5LibraryException returns errors raised by the HDF5 library. *

* This sub-class represents HDF-5 major error code H5E_HEAP */ public class HDF5HeapException extends HDF5LibraryException { private static final long serialVersionUID = 1L; /** * Constructs an HDF5HeapException with the specified detail message. * * @param majorErrorNumber The major error number of the HDF5 library. * @param majorErrorMessage The error message for the major error number of the HDF5 library. * @param minorErrorNumber The minor error number of the HDF5 library. * @param minorErrorMessage The error message for the minor error number of the HDF5 library. */ public HDF5HeapException(final int majorErrorNumber, final String majorErrorMessage, final int minorErrorNumber, final String minorErrorMessage) { super(majorErrorNumber, majorErrorMessage, minorErrorNumber, minorErrorMessage); } } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/exceptions/HDF5InternalErrorException.java000066400000000000000000000033721256564762100324300ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF5 * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ package ncsa.hdf.hdf5lib.exceptions; /** * The class HDF5LibraryException returns errors raised by the HDF5 library. *

* This sub-class represents HDF-5 major error code H5E_INTERNAL */ public class HDF5InternalErrorException extends HDF5LibraryException { private static final long serialVersionUID = 1L; /** * Constructs an HDF5InternalErrorException with the specified detail message. * * @param majorErrorNumber The major error number of the HDF5 library. * @param majorErrorMessage The error message for the major error number of the HDF5 library. * @param minorErrorNumber The minor error number of the HDF5 library. * @param minorErrorMessage The error message for the minor error number of the HDF5 library. */ public HDF5InternalErrorException(final int majorErrorNumber, final String majorErrorMessage, final int minorErrorNumber, final String minorErrorMessage) { super(majorErrorNumber, majorErrorMessage, minorErrorNumber, minorErrorMessage); } } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/exceptions/HDF5JavaException.java000066400000000000000000000027631256564762100305260ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF5 * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ package ncsa.hdf.hdf5lib.exceptions; /** *

* The class HDF5JavaException returns errors from the Java wrapper of theHDF5 library. *

* These errors include Java configuration errors, security violations, and resource exhaustion. */ public class HDF5JavaException extends HDF5Exception { private static final long serialVersionUID = 1L; /** * Constructs an HDF5JavaException with no specified detail message. */ public HDF5JavaException() { super(); } /** * Constructs an HDF5JavaException with the specified detail message. * * @param s the detail message. */ public HDF5JavaException(final String s) { super(s); } } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/exceptions/HDF5LibraryException.java000066400000000000000000000201421256564762100312400ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF5 * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ package ncsa.hdf.hdf5lib.exceptions; import static ch.systemsx.cisd.hdf5.hdf5lib.H5General.H5open; import java.io.File; import java.io.IOException; import org.apache.commons.io.FileUtils; /** *

* The class HDF5LibraryException returns errors raised by the HDF5 library. *

* Each major error code from the HDF-5 Library is represented by a sub-class of this class, and by * default the 'detailedMessage' is set according to the minor error code from the HDF-5 Library. *

* For major and minor error codes, see H5Epublic.h in the HDF-5 library. *

*/ public class HDF5LibraryException extends HDF5Exception { private static final int UNKNOWN = -1; private static final long serialVersionUID = 1L; private final int majorErrorNumber; private final int minorErrorNumber; private final String majorErrorMessage; private final String minorErrorMessage; private final String hdf5ErrorStackString; private final String hdf5ErrorStackLastElementString; /** * Constructs an HDF5LibraryException with the specified detail message. * * @param majorErrorNumber The major error number of the HDF5 library. * @param majorErrorMessage The error message for the major error number of the HDF5 library. * @param minorErrorNumber The minor error number of the HDF5 library. * @param minorErrorMessage The error message for the minor error number of the HDF5 library. */ public HDF5LibraryException(final int majorErrorNumber, final String majorErrorMessage, final int minorErrorNumber, final String minorErrorMessage) { super(majorErrorMessage + ":" + minorErrorMessage); // this code forces the loading of the HDF-5 library // to assure that the native methods are available try { H5open(); } catch (final Exception e) { } this.majorErrorNumber = majorErrorNumber; this.majorErrorMessage = majorErrorMessage; this.minorErrorNumber = minorErrorNumber; this.minorErrorMessage = minorErrorMessage; this.hdf5ErrorStackString = retrieveHDF5ErrorStackAsString(); this.hdf5ErrorStackLastElementString = getLastErrorStackElement(hdf5ErrorStackString); } private static String getLastErrorStackElement(String hdf5ErrorStackString) { int idx = hdf5ErrorStackString.length() - 3; int lastLineBreakIdx = hdf5ErrorStackString.length(); while (--idx > 0) { if (hdf5ErrorStackString.charAt(idx) == '\n') { lastLineBreakIdx = idx; } if (hdf5ErrorStackString.substring(idx - 1, idx + 3).equals("\n #")) { idx += 3; while (idx < hdf5ErrorStackString.length() && hdf5ErrorStackString.charAt(idx) != ' ') { ++idx; } return hdf5ErrorStackString.substring(idx + 1, lastLineBreakIdx); } } return null; } /** * Constructs an HDF5LibraryException with the specified detail message. * * @param errorMessage The error message for the minor error number of the HDF5 library. */ public HDF5LibraryException(final String errorMessage) { super(errorMessage); // this code forces the loading of the HDF-5 library // to assure that the native methods are available try { H5open(); } catch (final Exception e) { } this.majorErrorNumber = UNKNOWN; this.majorErrorMessage = errorMessage; this.minorErrorNumber = UNKNOWN; this.minorErrorMessage = ""; this.hdf5ErrorStackString = "No error stack"; this.hdf5ErrorStackLastElementString = null; } @Override public String getMessage() { if (hdf5ErrorStackLastElementString != null) { return super.getMessage() + " [\"" + hdf5ErrorStackLastElementString + "\"]"; } else { return super.getMessage(); } } /** * Get the major error number of the first error on the HDF5 library error stack. * * @return the major error number */ public int getMajorErrorNumber() { return majorErrorNumber; } /** * Return a error message for the major error number of this exception. *

* These messages come from H5Epublic.h. * * @return the string of the minor error */ public String getMajorError() { return majorErrorMessage; } /** * Get the minor error number of the first error on the HDF5 library error stack. * * @return the minor error number */ public int getMinorErrorNumber() { return minorErrorNumber; } /** * Return a error message for the minor error number of this exception. *

* These messages come from H5Epublic.h. * * @return the string of the minor error */ public String getMinorError() { return minorErrorMessage; } /** * Returns the error stack as retrieved from the HDF5 library as a string. */ private String retrieveHDF5ErrorStackAsString() { try { final File tempFile = File.createTempFile("HDF5_error_stack", ".txt"); try { printStackTrace0(tempFile.getPath()); return FileUtils.readFileToString(tempFile).trim(); } finally { tempFile.delete(); } } catch (IOException ex) { System.err.println("Cannot create error stack file."); ex.printStackTrace(); return null; } } /** * Returns the error stack from the HDF5 library as a string. */ public String getHDF5ErrorStackAsString() { return hdf5ErrorStackString; } /** * Prints this HDF5LibraryException, the HDF-5 Library error stack, and and the * Java stack trace to the standard error stream. */ @Override public void printStackTrace() { System.err.println(getHDF5ErrorStackAsString()); // the HDF-5 Library error stack super.printStackTrace(); // the Java stack trace } /** * Prints this HDF5LibraryException the HDF-5 Library error stack, and and the Java * stack trace to the specified print stream. */ public void printStackTrace(final java.io.File f) { if ((f == null) || !f.exists() || f.isDirectory() || !f.canWrite()) { printStackTrace(); } else { try { final java.io.FileOutputStream o = new java.io.FileOutputStream(f); final java.io.PrintWriter p = new java.io.PrintWriter(o); p.println(getHDF5ErrorStackAsString()); // the HDF-5 Library error stack super.printStackTrace(p); // the Java stack trace p.close(); } catch (final Exception ex) { System.err.println(this); } } } /* * This private method calls the HDF-5 library to extract the error codes and error stack. */ private native void printStackTrace0(String s); } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/exceptions/HDF5LowLevelIOException.java000066400000000000000000000034521256564762100316220ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF5 * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ package ncsa.hdf.hdf5lib.exceptions; /** * The class HDF5LibraryException returns errors raised by the HDF5 library. *

* This sub-class represents HDF-5 major error code H5E_IO */ public class HDF5LowLevelIOException extends HDF5LibraryException { private static final long serialVersionUID = 1L; /** * Constructs an HDF5LowLevelIOException with the specified detail message. * * @param majorErrorNumber The major error number of the HDF5 library. * @param majorErrorMessage The error message for the major error number of the HDF5 library. * @param minorErrorNumber The minor error number of the HDF5 library. * @param minorErrorMessage The error message for the minor error number of the HDF5 library. */ public HDF5LowLevelIOException(final int majorErrorNumber, final String majorErrorMessage, final int minorErrorNumber, final String minorErrorMessage) { super(majorErrorNumber, majorErrorMessage, minorErrorNumber, minorErrorMessage); } } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/exceptions/HDF5MetaDataCacheException.java000066400000000000000000000034661256564762100322520ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF5 * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ package ncsa.hdf.hdf5lib.exceptions; /** * The class HDF5LibraryException returns errors raised by the HDF5 library. *

* This sub-class represents HDF-5 major error code H5E_CACHE */ public class HDF5MetaDataCacheException extends HDF5LibraryException { private static final long serialVersionUID = 1L; /** * Constructs an HDF5MetaDataCacheException with the specified detail message. * * @param majorErrorNumber The major error number of the HDF5 library. * @param majorErrorMessage The error message for the major error number of the HDF5 library. * @param minorErrorNumber The minor error number of the HDF5 library. * @param minorErrorMessage The error message for the minor error number of the HDF5 library. */ public HDF5MetaDataCacheException(final int majorErrorNumber, final String majorErrorMessage, final int minorErrorNumber, final String minorErrorMessage) { super(majorErrorNumber, majorErrorMessage, minorErrorNumber, minorErrorMessage); } } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/exceptions/HDF5ObjectHeaderException.java000066400000000000000000000034621256564762100321610ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF5 * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ package ncsa.hdf.hdf5lib.exceptions; /** * The class HDF5LibraryException returns errors raised by the HDF5 library. *

* This sub-class represents HDF-5 major error code H5E_OHDR */ public class HDF5ObjectHeaderException extends HDF5LibraryException { private static final long serialVersionUID = 1L; /** * Constructs an HDF5ObjectHeaderException with the specified detail message. * * @param majorErrorNumber The major error number of the HDF5 library. * @param majorErrorMessage The error message for the major error number of the HDF5 library. * @param minorErrorNumber The minor error number of the HDF5 library. * @param minorErrorMessage The error message for the minor error number of the HDF5 library. */ public HDF5ObjectHeaderException(final int majorErrorNumber, final String majorErrorMessage, final int minorErrorNumber, final String minorErrorMessage) { super(majorErrorNumber, majorErrorMessage, minorErrorNumber, minorErrorMessage); } } HDF5PropertyListInterfaceException.java000066400000000000000000000035161256564762100340640ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/exceptions/**************************************************************************** * NCSA HDF5 * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ package ncsa.hdf.hdf5lib.exceptions; /** * The class HDF5LibraryException returns errors raised by the HDF5 library. *

* This sub-class represents HDF-5 major error code H5E_PLIST */ public class HDF5PropertyListInterfaceException extends HDF5LibraryException { private static final long serialVersionUID = 1L; /** * Constructs an HDF5PropertyListInterfaceException with the specified detail message. * * @param majorErrorNumber The major error number of the HDF5 library. * @param majorErrorMessage The error message for the major error number of the HDF5 library. * @param minorErrorNumber The minor error number of the HDF5 library. * @param minorErrorMessage The error message for the minor error number of the HDF5 library. */ public HDF5PropertyListInterfaceException(final int majorErrorNumber, final String majorErrorMessage, final int minorErrorNumber, final String minorErrorMessage) { super(majorErrorNumber, majorErrorMessage, minorErrorNumber, minorErrorMessage); } } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/exceptions/HDF5ReferenceException.java000066400000000000000000000032101256564762100315270ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF5 * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ package ncsa.hdf.hdf5lib.exceptions; public class HDF5ReferenceException extends HDF5LibraryException { private static final long serialVersionUID = 1L; /** * Constructs an HDF5ReferenceException with the specified detail message. * * @param majorErrorNumber The major error number of the HDF5 library. * @param majorErrorMessage The error message for the major error number of the HDF5 library. * @param minorErrorNumber The minor error number of the HDF5 library. * @param minorErrorMessage The error message for the minor error number of the HDF5 library. */ public HDF5ReferenceException(final int majorErrorNumber, final String majorErrorMessage, final int minorErrorNumber, final String minorErrorMessage) { super(majorErrorNumber, majorErrorMessage, minorErrorNumber, minorErrorMessage); } } HDF5ResourceUnavailableException.java000066400000000000000000000035101256564762100335100ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/exceptions/**************************************************************************** * NCSA HDF5 * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ package ncsa.hdf.hdf5lib.exceptions; /** * The class HDF5LibraryException returns errors raised by the HDF5 library. *

* This sub-class represents HDF-5 major error code H5E_RESOURCE */ public class HDF5ResourceUnavailableException extends HDF5LibraryException { private static final long serialVersionUID = 1L; /** * Constructs an HDF5FunctionArgumentException with the specified detail message. * * @param majorErrorNumber The major error number of the HDF5 library. * @param majorErrorMessage The error message for the major error number of the HDF5 library. * @param minorErrorNumber The minor error number of the HDF5 library. * @param minorErrorMessage The error message for the minor error number of the HDF5 library. */ public HDF5ResourceUnavailableException(final int majorErrorNumber, final String majorErrorMessage, final int minorErrorNumber, final String minorErrorMessage) { super(majorErrorNumber, majorErrorMessage, minorErrorNumber, minorErrorMessage); } } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/exceptions/HDF5SpaceRankMismatch.java000066400000000000000000000026361256564762100313220ustar00rootroot00000000000000/* * Copyright 2014 ETH Zuerich, SIS * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ncsa.hdf.hdf5lib.exceptions; /** * An exception for signaling that the data space of a data set has an unexpected rank. * * @author Bernd Rinn */ public class HDF5SpaceRankMismatch extends HDF5JavaException { private static final long serialVersionUID = 1L; private final int spaceRankExpected; private final int spaceRankFound; public HDF5SpaceRankMismatch(int spaceRankExpected, int spaceRankFound) { super("Data Set is expected to be of rank " + spaceRankExpected + " (rank=" + spaceRankFound + ")"); this.spaceRankExpected = spaceRankExpected; this.spaceRankFound = spaceRankFound; } public int getSpaceRankExpected() { return spaceRankExpected; } public int getSpaceRankFound() { return spaceRankFound; } } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/exceptions/HDF5SymbolTableException.java000066400000000000000000000034561256564762100320620ustar00rootroot00000000000000/**************************************************************************** * NCSA HDF5 * * National Comptational Science Alliance * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf-java/COPYING file. * * * ****************************************************************************/ package ncsa.hdf.hdf5lib.exceptions; /** * The class HDF5LibraryException returns errors raised by the HDF5 library. *

* This sub-class represents HDF-5 major error code H5E_SYM */ public class HDF5SymbolTableException extends HDF5LibraryException { private static final long serialVersionUID = 1L; /** * Constructs an HDF5SymbolTableException with the specified detail message. * * @param majorErrorNumber The major error number of the HDF5 library. * @param majorErrorMessage The error message for the major error number of the HDF5 library. * @param minorErrorNumber The minor error number of the HDF5 library. * @param minorErrorMessage The error message for the minor error number of the HDF5 library. */ public HDF5SymbolTableException(final int majorErrorNumber, final String majorErrorMessage, final int minorErrorNumber, final String minorErrorMessage) { super(majorErrorNumber, majorErrorMessage, minorErrorNumber, minorErrorMessage); } } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/structs/000077500000000000000000000000001256564762100240325ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/structs/H5AC_cache_config_t.java000066400000000000000000000116451256564762100303570ustar00rootroot00000000000000/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF Java Products. The full HDF Java copyright * * notice, including terms governing use, modification, and redistribution, * * is contained in the file, COPYING. COPYING can be found at the root of * * the source code distribution tree. You can also access it online at * * http://www.hdfgroup.org/products/licenses.html. If you do not have * * access to the file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package ncsa.hdf.hdf5lib.structs; import java.io.Serializable; //Information struct for H5Pget_mdc_config/H5Pset_mdc_config public class H5AC_cache_config_t implements Serializable{ private static final long serialVersionUID = -6748085696476149972L; // general configuration fields: public int version; public boolean rpt_fcn_enabled; public boolean open_trace_file; public boolean close_trace_file; public String trace_file_name; public boolean evictions_enabled; public boolean set_initial_size; public long initial_size; public double min_clean_fraction; public long max_size; public long min_size; public long epoch_length; // size increase control fields: public int incr_mode; // H5C_cache_incr_mode public double lower_hr_threshold; public double increment; public boolean apply_max_increment; public long max_increment; public int flash_incr_mode; // H5C_cache_flash_incr_mode public double flash_multiple; public double flash_threshold; // size decrease control fields: public int decr_mode; // H5C_cache_decr_mode public double upper_hr_threshold; public double decrement; public boolean apply_max_decrement; public long max_decrement; public int epochs_before_eviction; public boolean apply_empty_reserve; public double empty_reserve; // parallel configuration fields: public int dirty_bytes_threshold; public int metadata_write_strategy; public H5AC_cache_config_t (int version, boolean rpt_fcn_enabled, boolean open_trace_file, boolean close_trace_file, String trace_file_name, boolean evictions_enabled, boolean set_initial_size, long initial_size, double min_clean_fraction, long max_size, long min_size, long epoch_length, int incr_mode, double lower_hr_threshold, double increment, boolean apply_max_increment, long max_increment, int flash_incr_mode, double flash_multiple, double flash_threshold, int decr_mode, double upper_hr_threshold, double decrement, boolean apply_max_decrement, long max_decrement, int epochs_before_eviction, boolean apply_empty_reserve, double empty_reserve, int dirty_bytes_threshold, int metadata_write_strategy) { this.version = version; this.rpt_fcn_enabled = rpt_fcn_enabled; this.open_trace_file = open_trace_file; this.close_trace_file = close_trace_file; this.trace_file_name = trace_file_name; this.evictions_enabled = evictions_enabled; this.set_initial_size = set_initial_size; this.initial_size = initial_size; this.min_clean_fraction = min_clean_fraction; this.max_size = max_size; this.min_size = min_size; this.epoch_length = epoch_length; this.incr_mode = incr_mode; this.lower_hr_threshold = lower_hr_threshold; this.increment = increment; this.apply_max_increment = apply_max_increment; this.max_increment = flash_incr_mode; this.flash_incr_mode = flash_incr_mode; this.flash_multiple = flash_multiple; this.flash_threshold = flash_threshold; this.decr_mode = decr_mode; this.upper_hr_threshold = upper_hr_threshold; this.decrement = decrement; this.apply_max_decrement = apply_max_decrement; this.max_decrement = max_decrement; this.epochs_before_eviction = epochs_before_eviction; this.apply_empty_reserve = apply_empty_reserve; this.empty_reserve = empty_reserve; this.dirty_bytes_threshold = dirty_bytes_threshold; this.metadata_write_strategy = metadata_write_strategy; } } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/structs/H5A_info_t.java000066400000000000000000000032161256564762100266120ustar00rootroot00000000000000/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF Java Products. The full HDF Java copyright * * notice, including terms governing use, modification, and redistribution, * * is contained in the file, COPYING. COPYING can be found at the root of * * the source code distribution tree. You can also access it online at * * http://www.hdfgroup.org/products/licenses.html. If you do not have * * access to the file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package ncsa.hdf.hdf5lib.structs; import java.io.Serializable; //Information struct for Attribute (For H5Aget_info/H5Aget_info_by_idx/H5Aget_info_by_name) public class H5A_info_t implements Serializable{ private static final long serialVersionUID = 2791443594041667613L; public boolean corder_valid; // Indicate if creation order is valid public long corder; // Creation order of attribute public int cset; // Character set of attribute name public long data_size; // Size of raw data H5A_info_t(boolean corder_valid, long corder, int cset, long data_size) { this.corder_valid = corder_valid; this.corder = corder; this.cset = cset; this.data_size = data_size; } } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/structs/H5G_info_t.java000066400000000000000000000027221256564762100266210ustar00rootroot00000000000000/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF Java Products. The full HDF Java copyright * * notice, including terms governing use, modification, and redistribution, * * is contained in the file, COPYING. COPYING can be found at the root of * * the source code distribution tree. You can also access it online at * * http://www.hdfgroup.org/products/licenses.html. If you do not have * * access to the file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package ncsa.hdf.hdf5lib.structs; import java.io.Serializable; //Information struct for group (for H5Gget_info/H5Gget_info_by_name/H5Gget_info_by_idx) public class H5G_info_t implements Serializable{ private static final long serialVersionUID = -3746463015312132912L; public int storage_type; // Type of storage for links in group public long nlinks; // Number of links in group public long max_corder; // Current max. creation order value for group public boolean mounted; // Whether group has a file mounted on it } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/structs/H5L_info_t.java000066400000000000000000000031561256564762100266300ustar00rootroot00000000000000/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF Java Products. The full HDF Java copyright * * notice, including terms governing use, modification, and redistribution, * * is contained in the file, COPYING. COPYING can be found at the root of * * the source code distribution tree. You can also access it online at * * http://www.hdfgroup.org/products/licenses.html. If you do not have * * access to the file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package ncsa.hdf.hdf5lib.structs; import java.io.Serializable; //Information struct for link (for H5Lget_info/H5Lget_info_by_idx) public class H5L_info_t implements Serializable{ private static final long serialVersionUID = -4754320605310155033L; public int type; public boolean corder_valid; public long corder; public int cset; public long address_val_size; H5L_info_t (int type, boolean corder_valid, long corder, int cset, long address_val_size) { this.type = type; this.corder_valid = corder_valid; this.corder = corder; this.cset = cset; this.address_val_size = address_val_size; } } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/structs/H5O_hdr_info_t.java000066400000000000000000000050471256564762100274710ustar00rootroot00000000000000/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF Java Products. The full HDF Java copyright * * notice, including terms governing use, modification, and redistribution, * * is contained in the file, COPYING. COPYING can be found at the root of * * the source code distribution tree. You can also access it online at * * http://www.hdfgroup.org/products/licenses.html. If you do not have * * access to the file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package ncsa.hdf.hdf5lib.structs; import java.io.Serializable; // Information struct for object header metadata (for H5Oget_info/H5Oget_info_by_name/H5Oget_info_by_idx) public class H5O_hdr_info_t implements Serializable{ private static final long serialVersionUID = 7883826382952577189L; public int version; /* Version number of header format in file */ public int nmesgs; /* Number of object header messages */ public int nchunks; /* Number of object header chunks */ public int flags; /* Object header status flags */ public long space_total; /* Total space for storing object header in file */ public long space_meta; /* Space within header for object header metadata information */ public long space_mesg; /* Space within header for actual message information */ public long space_free; /* Free space within object header */ public long mesg_present; /* Flags to indicate presence of message type in header */ public long mesg_shared; /* Flags to indicate message type is shared in header */ H5O_hdr_info_t (int version, int nmesgs, int nchunks, int flags, long space_total, long space_meta, long space_mesg, long space_free, long mesg_present, long mesg_shared) { this.version = version; this.nmesgs = nmesgs; this.nchunks = nchunks; this.flags = flags; this.space_total = space_total; this.space_meta = space_meta; this.space_mesg = space_mesg; this.space_free = space_free; this.mesg_present = mesg_present; this.mesg_shared = mesg_shared; } } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/structs/H5O_info_t.java000066400000000000000000000052741256564762100266360ustar00rootroot00000000000000/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF Java Products. The full HDF Java copyright * * notice, including terms governing use, modification, and redistribution, * * is contained in the file, COPYING. COPYING can be found at the root of * * the source code distribution tree. You can also access it online at * * http://www.hdfgroup.org/products/licenses.html. If you do not have * * access to the file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package ncsa.hdf.hdf5lib.structs; import java.io.Serializable; //Information struct for object (for H5Oget_info/H5Oget_info_by_name/H5Oget_info_by_idx) public class H5O_info_t implements Serializable{ private static final long serialVersionUID = 4691681163544054518L; public long fileno; /* File number that object is located in */ public long addr; /* Object address in file */ public int type; /* Basic object type (group, dataset, etc.) */ public int rc; /* Reference count of object */ public long atime; /* Access time */ public long mtime; /* Modification time */ public long ctime; /* Change time */ public long btime; /* Birth time */ public long num_attrs; /* # of attributes attached to object */ public H5O_hdr_info_t hdr; /* Object header information */ /* Extra metadata storage for obj & attributes */ public H5_ih_info_t meta_size_obj; /* v1/v2 B-tree & local/fractal heap for groups, B-tree for chunked datasets */ public H5_ih_info_t meta_size_attr; /* v2 B-tree & heap for attributes */ public H5O_info_t (long fileno, long addr, int type, int rc, long num_attrs, long atime, long mtime, long ctime, long btime, H5O_hdr_info_t hdr, H5_ih_info_t meta_size_obj, H5_ih_info_t meta_size_attr) { this.fileno = fileno; this.addr = addr; this.type = type; this.rc = rc; this.num_attrs = num_attrs; this.atime = atime; this.mtime = mtime; this.ctime = ctime; this.btime = btime; this.hdr = hdr; this.meta_size_obj = meta_size_obj; this.meta_size_attr = meta_size_attr; } } libsis-jhdf5-java-14.12.1/source/java/ncsa/hdf/hdf5lib/structs/H5_ih_info_t.java000066400000000000000000000026661256564762100272010ustar00rootroot00000000000000/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF Java Products. The full HDF Java copyright * * notice, including terms governing use, modification, and redistribution, * * is contained in the file, COPYING. COPYING can be found at the root of * * the source code distribution tree. You can also access it online at * * http://www.hdfgroup.org/products/licenses.html. If you do not have * * access to the file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package ncsa.hdf.hdf5lib.structs; import java.io.Serializable; //Information struct for group (for H5Gget_info/H5Gget_info_by_name/H5Gget_info_by_idx) public class H5_ih_info_t implements Serializable { private static final long serialVersionUID = -142238015615462707L; public long index_size; /* btree and/or list */ public long heap_size; H5_ih_info_t (long index_size, long heap_size) { this.index_size = index_size; this.heap_size = heap_size; } } libsis-jhdf5-java-14.12.1/sourceTest/000077500000000000000000000000001256564762100172405ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/sourceTest/java/000077500000000000000000000000001256564762100201615ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/sourceTest/java/ch/000077500000000000000000000000001256564762100205535ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/000077500000000000000000000000001256564762100224525ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/000077500000000000000000000000001256564762100233745ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/000077500000000000000000000000001256564762100242225ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/BitSetConversionTest.java000066400000000000000000000075021256564762100311710ustar00rootroot00000000000000/* * Copyright 2007 ETH Zuerich, CISD * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertTrue; import java.util.Arrays; import java.util.BitSet; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; import ch.rinn.restrictions.Friend; import ch.systemsx.cisd.base.mdarray.MDLongArray; /** * Test cases for the BitSet conversion from / to storage form. * * @author Bernd Rinn */ @Friend(toClasses = BitSetConversionUtils.class) public class BitSetConversionTest { private BitSet create(final Integer... indices) { final BitSet bs = new BitSet(); for (final int index : indices) { bs.set(index); } return bs; } private BitSet[] create2D(final int length, final Integer... indices) { final BitSet[] bs = new BitSet[length]; for (int i = 0; i < bs.length; ++i) { bs[i] = new BitSet(); for (final int index : indices) { bs[i].set(index); } } return bs; } @DataProvider public Object[][] createBitSets() { final BitSet full4w = new BitSet(); full4w.set(0, 256); return new Object[][] { { create() }, { create(0) }, { create(31) }, { create(64) }, { create(128) }, { create(63, 191) }, { create(64, 192) }, { create(17, 88, 155) }, { full4w }, }; } @Test(dataProvider = "createBitSets") public void testBitSetRoundTripGeneric(final BitSet bs) { final long[] bsArray = BitSetConversionUtils.toStorageFormGeneric(bs); final BitSet bs2 = BitSetConversionUtils.fromStorageFormGeneric(bsArray, 0, bsArray.length); assertEquals(bs, bs2); } @Test(dataProvider = "createBitSets") public void testBitSetRoundTrip(final BitSet bs) { final long[] bsArray = BitSetConversionUtils.toStorageForm(bs); final BitSet bs2 = BitSetConversionUtils.fromStorageForm(bsArray); assertEquals(bs, bs2); } @DataProvider public Object[][] createBitSetArrays() { final BitSet[] full4w = new BitSet[] { new BitSet(), new BitSet(), new BitSet(), }; full4w[0].set(0, 256); full4w[1].set(0, 256); full4w[2].set(0, 256); return new Object[][] { { create2D(3) }, { create2D(3, 0) }, { create2D(3, 31) }, { create2D(3, 64) }, { create2D(3, 128) }, { create2D(3, 63, 191) }, { create2D(1, 64, 192) }, { create2D(2, 17, 88, 155) }, { full4w }, }; } @Test(dataProvider = "createBitSetArrays") public void testBitSetArrayRoundTrip(final BitSet[] bs) { final int maxLength = BitSetConversionUtils.getMaxLength(bs); final long[] bsArray = BitSetConversionUtils.toStorageForm(bs, maxLength); final BitSet bs2[] = BitSetConversionUtils.fromStorageForm2D(new MDLongArray(bsArray, new int[] { maxLength, bs.length })); assertTrue(Arrays.equals(bs, bs2)); } } libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/Dir2HDF5.java000066400000000000000000000037431256564762100263030ustar00rootroot00000000000000/* * Copyright 2007 ETH Zuerich, CISD * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.io.File; import java.io.IOException; import org.apache.commons.lang.time.StopWatch; import ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator.FileFormat; import ch.systemsx.cisd.hdf5.h5ar.HDF5ArchiverFactory; import ch.systemsx.cisd.hdf5.h5ar.IArchiveEntryVisitor; import ch.systemsx.cisd.hdf5.h5ar.IHDF5Archiver; /** * Creates a HDF5 file from a directory. * * @author Bernd Rinn */ public class Dir2HDF5 { public static void main(String[] args) throws IOException { if (args.length == 0) { System.err.println("Syntax: Dir2HDF5 [ ...]"); System.exit(1); } final File hdf5File = new File(args[0]); final StopWatch watch = new StopWatch(); watch.start(); final IHDF5Archiver archiver = HDF5ArchiverFactory.open(hdf5File, true, FileFormat.ALLOW_1_8, null); if (args.length > 1) { for (int i = 1; i < args.length; ++i) { archiver.archiveFromFilesystem(new File(args[i]), IArchiveEntryVisitor.NONVERBOSE_VISITOR); } } else { archiver.archiveFromFilesystem(new File("."), IArchiveEntryVisitor.NONVERBOSE_VISITOR); } archiver.close(); watch.stop(); System.out.println("Creating hdf5 archive took " + watch); } } libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/HDF52Dir.java000066400000000000000000000036631256564762100263040ustar00rootroot00000000000000/* * Copyright 2007 ETH Zuerich, CISD * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.io.File; import java.io.IOException; import org.apache.commons.lang.time.StopWatch; import ch.systemsx.cisd.hdf5.h5ar.HDF5ArchiverFactory; import ch.systemsx.cisd.hdf5.h5ar.IHDF5ArchiveReader; import ch.systemsx.cisd.hdf5.h5ar.IArchiveEntryVisitor; /** * @author Bernd Rinn */ public class HDF52Dir { public static void main(String[] args) throws IOException { if (args.length != 1 && args.length != 2 && args.length != 3) { System.err.println("Syntax: HDF52Dir [] []"); System.exit(1); } final File hdf5File = new File(args[0]); final String pathInFile = (args.length > 1) ? args[1] : "/"; final File rootDir = new File((args.length > 2) ? args[2] : "."); if (rootDir.isDirectory() == false) { System.err.println("Path '" + rootDir + "' is not a directory."); System.exit(1); } final StopWatch watch = new StopWatch(); watch.start(); final IHDF5ArchiveReader reader = HDF5ArchiverFactory.openForReading(hdf5File); reader.extractToFilesystem(rootDir, pathInFile, IArchiveEntryVisitor.NONVERBOSE_VISITOR); reader.close(); watch.stop(); System.out.println("Extracting hdf5 file took " + watch); } } libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/HDF5ArrayTypeFloatWriter.java000066400000000000000000000230051256564762100315770ustar00rootroot00000000000000/* * Copyright 2009 ETH Zuerich, CISD * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.hdf5lib.H5A.H5Aclose; import static ch.systemsx.cisd.hdf5.hdf5lib.H5A.H5Acreate; import static ch.systemsx.cisd.hdf5.hdf5lib.H5D.H5Dwrite; import static ch.systemsx.cisd.hdf5.hdf5lib.H5S.H5Sclose; import static ch.systemsx.cisd.hdf5.hdf5lib.H5S.H5Screate_simple; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_ALL; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_IEEE_F32BE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_IEEE_F32LE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_IEEE_F64BE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_DOUBLE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_FLOAT; import ch.systemsx.cisd.base.mdarray.MDFloatArray; import ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator.FileFormat; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; import ch.systemsx.cisd.hdf5.hdf5lib.HDFNativeData; /** * A writer for array type data sets. * * @author Bernd Rinn */ public class HDF5ArrayTypeFloatWriter { private final HDF5BaseWriter baseWriter; HDF5ArrayTypeFloatWriter(HDF5Writer writer) { baseWriter = writer.getBaseWriter(); } public void writeFloatArrayBigEndian(final String objectPath, final float[] data, final HDF5FloatStorageFeatures features) { assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, H5T_IEEE_F32BE, new long[] { data.length }, 4, features, registry); H5Dwrite(dataSetId, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } public void writeDoubleArrayBigEndian(final String objectPath, final double[] data, final HDF5FloatStorageFeatures features) { assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, H5T_IEEE_F64BE, new long[] { data.length }, 4, features, registry); H5Dwrite(dataSetId, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } public void writeFloatArrayArrayType(final String objectPath, final float[] data) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int memoryTypeId = baseWriter.h5.createArrayType(H5T_NATIVE_FLOAT, data.length, registry); final int storageTypeId = baseWriter.h5.createArrayType(H5T_IEEE_F32LE, data.length, registry); final int dataSetId = baseWriter.h5.createScalarDataSet(baseWriter.fileId, storageTypeId, objectPath, true, registry); H5Dwrite(dataSetId, memoryTypeId, H5S_ALL, H5S_ALL, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } public void writeFloatArrayArrayType(final String objectPath, final MDFloatArray data) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int memoryTypeId = baseWriter.h5.createArrayType(H5T_NATIVE_FLOAT, data.dimensions(), registry); final int storageTypeId = baseWriter.h5.createArrayType(H5T_IEEE_F32LE, data.dimensions(), registry); final int dataSetId = baseWriter.h5.createScalarDataSet(baseWriter.fileId, storageTypeId, objectPath, true, registry); H5Dwrite(dataSetId, memoryTypeId, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } public void writeFloat2DArrayArrayType1DSpace1d(final String objectPath, final MDFloatArray data) { assert objectPath != null; assert data != null; assert data.rank() == 2; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int memoryTypeId = baseWriter.h5.createArrayType(H5T_NATIVE_FLOAT, data.dimensions()[1], registry); final int storageTypeId = baseWriter.h5.createArrayType(H5T_IEEE_F32LE, data.dimensions()[1], registry); final int dataSetId = baseWriter.h5.createDataSet(baseWriter.fileId, new long[] { data.dimensions()[0] }, null, storageTypeId, HDF5FloatStorageFeatures.FLOAT_CONTIGUOUS, objectPath, HDF5StorageLayout.CONTIGUOUS, FileFormat.ALLOW_1_8, registry); H5Dwrite(dataSetId, memoryTypeId, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } public void setFloatArrayAttributeDimensional(final String objectPath, final String name, final float[] value) { assert objectPath != null; assert name != null; assert value != null; baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] dimensions = new long[] { value.length }; final int dataSpaceId = H5Screate_simple(dimensions.length, dimensions, dimensions); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Sclose(dataSpaceId); } }); final int objectId = baseWriter.h5.openObject(baseWriter.fileId, objectPath, registry); final int attributeId = createAttribute(objectId, name, H5T_IEEE_F32LE, dataSpaceId, registry); baseWriter.h5.writeAttribute(attributeId, H5T_NATIVE_FLOAT, HDFNativeData.floatToByte(value)); return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } private int createAttribute(int locationId, String attributeName, int dataTypeId, int dataSpaceId, ICleanUpRegistry registry) { final int attributeId = H5Acreate(locationId, attributeName, dataTypeId, dataSpaceId, H5P_DEFAULT, H5P_DEFAULT); registry.registerCleanUp(new Runnable() { @Override public void run() { H5Aclose(attributeId); } }); return attributeId; } } libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/HDF5Extract.java000066400000000000000000000030471256564762100271120ustar00rootroot00000000000000/* * Copyright 2007 ETH Zuerich, CISD. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.io.File; import java.io.IOException; import org.apache.commons.io.FileUtils; import org.apache.commons.lang.time.StopWatch; /** * @author Bernd Rinn */ public class HDF5Extract { public static void main(String[] args) throws IOException { if (args.length != 2) { System.err.println("Syntax: HDF5Extract "); System.exit(1); } final File hdf5File = new File(args[0]); final File file = new File(args[1]); final StopWatch watch = new StopWatch(); watch.start(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(hdf5File); final byte[] data = reader.int8().readArray(file.getAbsolutePath()); FileUtils.writeByteArrayToFile(new File(file.getName()), data); reader.close(); watch.stop(); System.out.println("Extracting hdf5 file took " + watch); } } libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/HDF5ReadTest.java000066400000000000000000000106341256564762100272130ustar00rootroot00000000000000/* * Copyright 2007 ETH Zuerich, CISD. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.io.File; import java.util.BitSet; import java.util.List; import ch.systemsx.cisd.base.convert.NativeData; import ch.systemsx.cisd.hdf5.hdf5lib.HDFNativeData; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; /** * @author Bernd Rinn */ public class HDF5ReadTest { public static void main(String[] args) { try { IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(new File("test.h5")); System.out.println(reader.object().getGroupMemberPaths("/")); describe(reader, "/Group1/MyBitSet", null); describe(reader, "/Group1/MyDataSet", null); byte[] bsb = reader.readAsByteArray("/Group1/MyBitSet"); long[] bsl = HDFNativeData.byteToLong(bsb, 0, bsb.length / NativeData.LONG_SIZE); System.out.println("length of /Group1/MyBitSet=" + bsl.length); for (long l : bsl) { System.out.print(l + " "); } System.out.println(); BitSet bs = reader.readBitField("/Group1/MyBitSet"); System.out.println(bs); System.out.println(reader.float64().getAttr("/", "version")); List members = reader.object().getGroupMemberPaths("/Group1"); for (String m : members) { System.out.println(" " + m); } listAttributes(reader, "/Group1"); listAttributes(reader, "/Group1/MyDataSet"); describe(reader, "/Group1/MyDataSet", "foo"); describe(reader, "/Group1", "active"); System.out.println(reader.bool().getAttr("/Group1", "active")); System.out.println(reader.string().getAttr("/Group1/MyDataSet", "foo")); System.out.println(reader.string().getAttr("/Group1/SubGroup1/MyDataSet", "foo")); System.out.println(reader.float64().readMatrix("/Group1/MyDataSet")[1][0]); System.out.println(reader.float32().readMatrix("/Group1/SubGroup1/MyDataSet")[1][2]); System.out.println(reader.string().read("/Group1/MyString").length()); listAttributes(reader, "empty"); } catch (HDF5LibraryException ex) { System.err.println(ex.getHDF5ErrorStackAsString()); ex.printStackTrace(); } } private static void listAttributes(IHDF5Reader reader, String objectName) { final List attributeNames = reader.object().getAttributeNames(objectName); System.out.printf("Found %d attributes for object '%s':\n", attributeNames.size(), objectName); for (String a : attributeNames) { System.out.println(a); } } private static void describe(IHDF5Reader reader, String objectName, String attributeNameOrNull) { HDF5DataSetInformation dsInfo; HDF5DataTypeInformation dtInfo; if (attributeNameOrNull == null) { dsInfo = reader.getDataSetInformation(objectName); dtInfo = dsInfo.getTypeInformation(); } else { dsInfo = null; dtInfo = reader.object().getAttributeInformation(objectName, attributeNameOrNull); } System.out.printf("%s%s, class=%s, elemSize=%d", objectName, attributeNameOrNull != null ? "#" + attributeNameOrNull : "", dtInfo.getDataClass(), dtInfo.getElementSize()); if (dsInfo != null) { System.out.printf(", rank=%d, scalar=%s, variant=%s\n", dsInfo.getRank(), Boolean .toString(dsInfo.isScalar()), dsInfo.tryGetTypeVariant()); for (long dim : dsInfo.getDimensions()) { System.out.println(" DIM " + dim); } } else { System.out.println(); } } } libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/HDF5RoundtripTest.java000066400000000000000000017201451256564762100303340ustar00rootroot00000000000000/* * Copyright 2007 ETH Zuerich, CISD * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.HDF5CompoundMemberMapping.mapping; import static ch.systemsx.cisd.hdf5.HDF5FloatStorageFeatures.FLOAT_CHUNKED; import static ch.systemsx.cisd.hdf5.HDF5FloatStorageFeatures.FLOAT_DEFLATE; import static ch.systemsx.cisd.hdf5.HDF5FloatStorageFeatures.FLOAT_SCALING1_DEFLATE; import static ch.systemsx.cisd.hdf5.HDF5GenericStorageFeatures.GENERIC_DEFLATE; import static ch.systemsx.cisd.hdf5.HDF5GenericStorageFeatures.GENERIC_DEFLATE_MAX; import static ch.systemsx.cisd.hdf5.HDF5IntStorageFeatures.INT_AUTO_SCALING; import static ch.systemsx.cisd.hdf5.HDF5IntStorageFeatures.INT_AUTO_SCALING_DEFLATE; import static ch.systemsx.cisd.hdf5.HDF5IntStorageFeatures.INT_CHUNKED; import static ch.systemsx.cisd.hdf5.HDF5IntStorageFeatures.INT_DEFLATE; import static ch.systemsx.cisd.hdf5.HDF5IntStorageFeatures.INT_SHUFFLE_DEFLATE; import static ch.systemsx.cisd.hdf5.UnsignedIntUtils.toInt8; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_FLOAT; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_INTEGER; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_REFERENCE; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_ENUM; import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertFalse; import static org.testng.AssertJUnit.assertNotNull; import static org.testng.AssertJUnit.assertNull; import static org.testng.AssertJUnit.assertTrue; import static org.testng.AssertJUnit.fail; import static ch.systemsx.cisd.hdf5.UnsignedIntUtils.*; import java.io.File; import java.io.IOException; import java.lang.reflect.Array; import java.util.Arrays; import java.util.BitSet; import java.util.Date; import java.util.HashMap; import java.util.HashSet; import java.util.List; import java.util.Map; import java.util.Random; import java.util.Set; import ncsa.hdf.hdf5lib.exceptions.HDF5DatatypeInterfaceException; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import ncsa.hdf.hdf5lib.exceptions.HDF5SymbolTableException; import org.apache.commons.io.FileUtils; import org.apache.commons.lang.ArrayUtils; import org.apache.commons.lang.StringUtils; import org.apache.commons.lang.builder.EqualsBuilder; import org.apache.commons.lang.builder.HashCodeBuilder; import org.apache.commons.lang.builder.ToStringBuilder; import org.testng.annotations.BeforeSuite; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; import ch.systemsx.cisd.base.convert.NativeData; import ch.systemsx.cisd.base.convert.NativeData.ByteOrder; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MDByteArray; import ch.systemsx.cisd.base.mdarray.MDDoubleArray; import ch.systemsx.cisd.base.mdarray.MDFloatArray; import ch.systemsx.cisd.base.mdarray.MDIntArray; import ch.systemsx.cisd.base.mdarray.MDLongArray; import ch.systemsx.cisd.base.utilities.OSUtilities; import ch.systemsx.cisd.hdf5.HDF5CompoundMappingHints.EnumReturnType; import ch.systemsx.cisd.hdf5.HDF5DataTypeInformation.DataTypeInfoOptions; import ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator.FileFormat; import ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator.SyncMode; import ch.systemsx.cisd.hdf5.hdf5lib.H5General; import ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants; import ch.systemsx.cisd.hdf5.hdf5lib.HDFNativeData; /** * Test cases for {@link IHDF5Writer} and {@link IHDF5Reader}, doing "round-trips" to the HDF5 disk * format and back. * * @author Bernd Rinn */ public class HDF5RoundtripTest { private static final File rootDirectory = new File("targets", "unit-test-wd"); private static final File workingDirectory = new File(rootDirectory, "hdf5-roundtrip-wd"); @BeforeSuite public void init() { workingDirectory.mkdirs(); assertTrue(workingDirectory.isDirectory()); workingDirectory.deleteOnExit(); rootDirectory.deleteOnExit(); } @Override protected void finalize() throws Throwable { // Delete the working directory if (workingDirectory.exists() && workingDirectory.canWrite()) { workingDirectory.delete(); } // Delete root directory if (rootDirectory.exists() && rootDirectory.canWrite()) { rootDirectory.delete(); } super.finalize(); } public static void main(String[] args) throws Throwable { // Print Java Version System.out.println("Java Version: " + System.getProperty("java.version")); // Print OS Version System.out.println("Platform: " + OSUtilities.getComputerPlatform()); HDF5RoundtripTest test = new HDF5RoundtripTest(); test.init(); // Print Library Version final int[] libversion = new int[3]; H5General.H5get_libversion(libversion); System.out.println("HDF5 Version: " + libversion[0] + "." + libversion[1] + "." + libversion[2]); // Tests test.testStrangeDataSetName(); test.testCreateSomeDeepGroup(); test.testGetGroupMembersIteratively(); test.testScalarValues(); test.testUnsignedInt8ValuesArray(); test.testUnsignedInt16ValuesArray(); test.testOverwriteScalar(); test.testOverwriteScalarKeepDataSet(); test.testDataSets(); test.testDataTypeInfoOptions(); test.testCompactDataset(); test.testCreateEmptyFixedSizeDataSets(); test.testCreateEmptyDefaultFixedSizeDataSets(); test.testCreateEmptyGrowableDataSets(); test.testCreateZeroLengthGrowableDataSets(); test.testExtendChunkedDataset(); test.testMaxPathLength(); test.testExceedMaxPathLength(); test.testAccessClosedReaderWriter(); test.testDataSetsNonExtendable(); test.testOverwriteContiguousDataSet(); test.testScaleOffsetFilterInt(); test.testScaleOffsetFilterFloat(); test.testBooleanArray(); test.testBooleanArrayBlock(); test.testBitFieldArray(); test.testBitFieldArrayBlockWise(); test.testSmallString(); test.testReadStringAttributeAsByteArray(); test.testReadStringAsByteArray(); test.testReadStringVLAsByteArray(); test.testStringAttributeFixedLength(); test.testStringAttributeFixedLengthExplicitlySaveLength(); test.testStringAttributeLength0(); test.testStringAttributeFixedLengthOverwriteWithShorter(); test.testStringAttributeUTF8FixedLength(); test.testStringArrayAttributeLengthFitsValue(); test.testStringArrayAttributeFixedLength(); test.testStringArrayAttributeUTF8LengthFitsValue(); test.testStringArrayAttributeUTF8FixedLength(); test.testStringMDArrayAttributeFixedLength(); test.testStringMDArrayAttributeUTF8LengthFitsValue(); test.testStringMDArrayAttributeUTF8FixedLength(); test.testVeryLargeString(); test.testOverwriteString(); test.testOverwriteStringWithLarge(); test.testOverwriteStringWithLargeKeepCompact(); test.testStringCompact(); test.testStringContiguous(); test.testStringUnicode(); test.testStringVariableLength(); test.testStringArray(); test.testStringArrayUTF8(); test.testStringArrayUTF8WithZeroChar(); test.testStringArrayWithNullStrings(); test.testStringMDArrayWithNullStrings(); test.testStringArrayBlock(); test.testStringArrayBlockCompact(); test.testStringArrayCompact(); test.testStringCompression(); test.testStringArrayCompression(); test.testStringVLArray(); test.testStringArrayBlockVL(); test.testStringArrayMD(); test.testStringArrayMDBlocks(); test.testStringMDArrayVL(); test.testStringMDArrayVLBlocks(); test.testMDIntArrayDifferentSizesElementType(); test.testMDIntArrayDifferentSizesElementTypeUnsignedByte(); test.testReadMDFloatArrayWithSlicing(); test.testReadToFloatMDArray(); test.testFloatArrayTypeDataSet(); test.testFloatArrayTypeDataSetOverwrite(); test.testFloatArrayCreateCompactOverwriteBlock(); test.testFloatMDArrayTypeDataSet(); test.testIterateOverFloatArrayInNaturalBlocks(10, 99); test.testIterateOverFloatArrayInNaturalBlocks(10, 100); test.testIterateOverFloatArrayInNaturalBlocks(10, 101); test.testIterateOverStringArrayInNaturalBlocks(10, 99); test.testIterateOverStringArrayInNaturalBlocks(10, 100); test.testIterateOverStringArrayInNaturalBlocks(10, 101); test.testReadToFloatMDArrayBlockWithOffset(); test.testReadToTimeDurationMDArrayBlockWithOffset(); test.testIterateOverMDFloatArrayInNaturalBlocks(new int[] { 2, 2 }, new long[] { 4, 3 }, new float[] { 0f, 2f, 6f, 8f }, new int[][] { { 2, 2 }, { 2, 1 }, { 2, 2 }, { 2, 1 } }); test.testIterateOverMDFloatArrayInNaturalBlocks(new int[] { 2, 2 }, new long[] { 4, 4 }, new float[] { 0f, 2f, 8f, 10f }, new int[][] { { 2, 2 }, { 2, 2 }, { 2, 2 }, { 2, 2 } }); test.testIterateOverMDFloatArrayInNaturalBlocks(new int[] { 2, 2 }, new long[] { 4, 5 }, new float[] { 0f, 2f, 4f, 10f, 12f, 14f }, new int[][] { { 2, 2 }, { 2, 2 }, { 2, 1 }, { 2, 2 }, { 2, 2 }, { 2, 1 } }); test.testIterateOverMDFloatArrayInNaturalBlocks(new int[] { 3, 2 }, new long[] { 5, 4 }, new float[] { 0f, 2f, 12f, 14f }, new int[][] { { 3, 2 }, { 3, 2 }, { 2, 2 }, { 2, 2 } }); test.testIterateOverMDFloatArrayInNaturalBlocks(new int[] { 2, 2 }, new long[] { 5, 4 }, new float[] { 0f, 2f, 8f, 10f, 16f, 18f }, new int[][] { { 2, 2 }, { 2, 2 }, { 2, 2 }, { 2, 2 }, { 1, 2 }, { 1, 2 } }); test.testSetExtentBug(); test.testMDFloatArrayBlockWise(); test.testMDFloatArraySliced(); test.testMDFloatArrayBlockWiseWithMemoryOffset(); test.testDoubleArrayAsByteArray(); test.testCompressedDataSet(); test.testCreateEmptyFloatMatrix(); test.testFloatVectorLength1(); test.testFloatMatrixLength1(); test.testOneRowFloatMatrix(); test.testEmptyVectorDataSets(); test.testEmptyVectorDataSetsContiguous(); test.testEmptyVectorDataSetsCompact(); test.testEmptyMatrixDataSets(); test.testEmptyMatrixDataSetsContiguous(); test.testOverwriteVectorIncreaseSize(); test.testOverwriteMatrixIncreaseSize(); test.testOverwriteStringVectorDecreaseSize(); test.testAttributes(); test.testSimpleDataspaceAttributes(); test.testTimeStampAttributes(); test.testTimeDurationAttributes(); test.testTimeStampArrayAttributes(); test.testTimeDurationArrayAttributes(); test.testAttributeDimensionArray(); test.testAttributeDimensionArrayOverwrite(); test.testCreateDataTypes(); test.testGroups(); test.testDefaultHousekeepingFile(); test.testNonDefaultHousekeepingFile(); test.testHousekeepingFileSuffixNonPrintable(); test.testSoftLink(); test.testBrokenSoftLink(); test.testDeleteSoftLink(); test.testRenameLink(); try { test.testRenameLinkOverwriteFails(); } catch (HDF5SymbolTableException ex) { // Expected. } try { test.testRenameLinkSrcNonExistentFails(); } catch (HDF5SymbolTableException ex) { // Expected. } test.testOverwriteKeepWithEmptyString(); test.testOverwriteKeepWithShorterString(); test.testOverwriteKeepWithLongerString(); test.testReplaceWithLongerString(); test.testNullOnGetSymbolicLinkTargetForNoLink(); test.testUpdateSoftLink(); test.testExternalLink(); test.testEnum(); test.testAnonymousEnum(); test.testJavaEnum(); test.testEnum16(); try { test.testConfusedEnum(); System.err.println("testConfusedEnum(): failure not detected."); } catch (HDF5JavaException ex) { assertEquals("Enum member index 0 of enum testEnum is 'ONE', but should be 'THREE'", ex.getMessage()); } test.testReplaceConfusedEnum(); test.testEnumArray(); test.testEnumMDArray(); test.testEnumMDArrayBlockWise(); test.testJavaEnumArray(); test.testEnumArrayBlock(); test.testEnumArrayBlockScalingCompression(); test.testEnumArrayFromIntArray(); test.testEnumArray16BitFromIntArray(); test.testEnumArray16BitFromIntArrayScaled(); test.testEnumArray16BitFromIntArrayLarge(); test.testEnumArrayBlock16Bit(); test.testEnumArrayScaleCompression(); test.testOpaqueType(); test.testCompound(); test.testCompoundInferStringLength(); test.testCompoundVariableLengthString(); test.testCompoundVariableLengthStringUsingHints(); test.testCompoundReference(); test.testCompoundHintVLString(); test.testClosedCompoundType(); test.testAnonCompound(); test.testOverwriteCompound(); test.testOverwriteCompoundKeepType(); test.testCompoundJavaEnum(); test.testEnumFromCompoundJavaEnum(); test.testCompoundJavaEnumArray(); test.testCompoundJavaEnumMap(); test.testCompoundAttribute(); test.testCompoundAttributeMemoryAlignment(); test.testCompoundIncompleteJavaPojo(); test.testCompoundManualMapping(); test.testInferredCompoundType(); test.testInferredIncompletelyMappedCompoundType(); test.testNameChangeInCompoundMapping(); test.testInferredCompoundTypedWithEnum(); test.testInferredCompoundTypeWithEnumArray(); test.testCompoundMap(); test.testCompoundMapManualMapping(); test.testCompoundMapManualMappingWithConversion(); test.testDateCompound(); test.testMatrixCompound(); try { test.testMatrixCompoundSizeMismatch(); System.err.println("testMatrixCompoundSizeMismatch(): failure not detected."); } catch (IllegalArgumentException ex) { // Expected } try { test.testMatrixCompoundDifferentNumberOfColumnsPerRow(); System.err .println("testMatrixCompoundDifferentNumberOfColumnsPerRow(): failure not detected."); } catch (IllegalArgumentException ex) { // Expected } test.testCompoundOverflow(); test.testBitFieldCompound(); test.testCompoundMapArray(); test.testCompoundArray(); test.testCompoundArrayBlockWise(); test.testCompoundMapMDArray(); test.testCompoundMDArray(); test.testCompoundMDArrayManualMapping(); test.testCompoundMDArrayBlockWise(); test.testIterateOverMDCompoundArrayInNaturalBlocks(); test.testConfusedCompound(); test.testMDArrayCompound(); test.testMDArrayCompoundArray(); test.testGetGroupMemberInformation(); try { test.testGetLinkInformationFailed(); System.err.println("testGetObjectTypeFailed(): failure not detected."); } catch (HDF5JavaException ex) { // Expected } test.testGetObjectType(); test.testHardLink(); test.testNullOnGetSymbolicLinkTargetForNoLink(); test.testReadByteArrayDataSetBlockWise(); test.testWriteByteArrayDataSetBlockWise(); test.testCreateByteArrayDataSetBlockSize0(); test.testCreateFloatArrayWithDifferentStorageLayouts(); test.testWriteByteArrayDataSetBlockWiseExtend(); test.testWriteByteMatrixDataSetBlockWise(); test.testWriteByteArrayDataSetBlockWiseMismatch(); test.testWriteByteMatrixDataSetBlockWiseMismatch(); test.testReadFloatMatrixDataSetBlockWise(); test.testWriteFloatMatrixDataSetBlockWise(); test.testWriteFloatMatrixDataSetBlockWiseWithOffset(); test.testReadMDFloatArrayAsByteArray(); test.testExtendContiguousDataset(); test.testAutomaticDeletionOfDataSetOnWrite(); test.testAutomaticDeletionOfDataSetOnCreate(); test.testTimestamps(); test.testTimestampArray(); test.testTimestampArrayChunked(); test.testTimeDurations(); test.testSmallTimeDurations(); test.testTimeDurationArray(); test.testTimeDurationMDArray(); test.testTimeDurationArrayChunked(); test.testNumericConversion(); test.testNumericConversionWithNumericConversionsSwitchedOff(); test.testSetDataSetSize(); test.testObjectReference(); test.testObjectReferenceArray(); test.testObjectReferenceOverwriteWithKeep(); test.testObjectReferenceOverwriteWithKeepOverridden(); test.testObjectReferenceArrayBlockWise(); test.testObjectReferenceAttribute(); test.testObjectReferenceArrayAttribute(); test.testObjectReferenceMDArrayAttribute(); test.testObjectReferenceMDArray(); test.testObjectReferenceMDArrayBlockWise(); test.testHDFJavaLowLevel(); test.finalize(); } @Test public void testStrangeDataSetName() { final File file = new File(workingDirectory, "testStrangeDataSetName.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.configure(file).noAutoDereference().writer(); writer.int32().write("\0\255", 15); writer.int32().write("\0\254", 13); writer.close(); final IHDF5Reader reader = HDF5Factory.configureForReading(file).noAutoDereference().reader(); assertEquals(15, reader.int32().read("\0\255")); assertEquals(13, reader.int32().read("\0\254")); reader.close(); } @Test public void testCreateSomeDeepGroup() { final File datasetFile = new File(workingDirectory, "deepGroup.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().configure(datasetFile).useUTF8CharacterEncoding() .writer(); final String groupName = "/some/deep/and/non/existing/group"; writer.object().createGroup(groupName); assertTrue(writer.isGroup(groupName)); writer.close(); } @Test public void testGetGroupMembersIteratively() { final File datasetFile = new File(workingDirectory, "writereadwriteread.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String groupName = "/test/group/"; final String dset1Name = "dset1"; final String dset1Path = groupName + dset1Name; final float[] dset1 = new float[] { 1.3f, 2.4f, 3.6f }; writer.float32().writeArray(dset1Path, dset1); final List members1 = writer.getGroupMembers(groupName); assertEquals(1, members1.size()); assertEquals(dset1Name, members1.get(0)); final String dset2Name = "dset2"; final String dset2Path = groupName + dset2Name; final int[] dset2 = new int[] { 1, 2, 3 }; writer.int32().writeArray(dset2Path, dset2); final Set members2 = new HashSet(writer.getGroupMembers(groupName)); assertEquals(2, members2.size()); assertTrue(members2.contains(dset1Name)); assertTrue(members2.contains(dset2Name)); writer.close(); } @Test public void testOverwriteScalar() { final File datasetFile = new File(workingDirectory, "overwriteScalar.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.open(datasetFile); writer.int32().write("a", 4); assertEquals(HDF5DataClass.INTEGER, writer.getDataSetInformation("a").getTypeInformation() .getDataClass()); assertTrue(writer.getDataSetInformation("a").isSigned()); writer.float32().write("a", 1e6f); assertEquals(HDF5DataClass.FLOAT, writer.getDataSetInformation("a").getTypeInformation() .getDataClass()); assertTrue(writer.getDataSetInformation("a").isSigned()); assertEquals(1e6f, writer.float32().read("a")); writer.close(); } @Test public void testOverwriteScalarKeepDataSet() { final File datasetFile = new File(workingDirectory, "overwriteScalarKeepDataSet.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.configure(datasetFile).keepDataSetsIfTheyExist().writer(); writer.int32().write("a", 4); assertEquals(HDF5DataClass.INTEGER, writer.getDataSetInformation("a").getTypeInformation() .getDataClass()); writer.float32().write("a", 5.1f); assertEquals(HDF5DataClass.INTEGER, writer.getDataSetInformation("a").getTypeInformation() .getDataClass()); assertEquals(5, writer.int32().read("a")); writer.close(); } @Test public void testScalarValues() { final File datasetFile = new File(workingDirectory, "values.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String booleanDatasetName = "/boolean"; writer.writeBoolean(booleanDatasetName, true); final String byteDatasetName = "/byte"; writer.int8().write(byteDatasetName, toInt8(17)); final String unsignedByteOverflowDatasetName = "/ubyteOverflow"; writer.uint8().write(unsignedByteOverflowDatasetName, (byte) 1024); final String shortDatasetName = "/short"; writer.int16().write(shortDatasetName, (short) 1000); final String intDatasetName = "/int"; writer.int32().write(intDatasetName, 1000000); final String longDatasetName = "/long"; writer.int64().write(longDatasetName, 10000000000L); final String floatDatasetName = "/float"; writer.float32().write(floatDatasetName, 0.001f); final String doubleDatasetName = "/double"; writer.float64().write(doubleDatasetName, 1.0E100); final String stringDatasetName = "/string"; writer.string().write(stringDatasetName, "some string"); final String stringWithZeroDatasetName = "/stringWithZero"; writer.string().write(stringWithZeroDatasetName, "some string\0with zero"); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); assertTrue(reader.readBoolean(booleanDatasetName)); assertEquals(0, reader.object().getRank(booleanDatasetName)); assertTrue(Arrays.equals(new long[0], reader.object().getDimensions(booleanDatasetName))); assertEquals(17, reader.int8().read(byteDatasetName)); assertEquals(0, reader.object().getRank(byteDatasetName)); assertTrue(Arrays.equals(new long[0], reader.object().getDimensions(byteDatasetName))); assertTrue(reader.getDataSetInformation(byteDatasetName).isSigned()); assertEquals(0, reader.int16().read(unsignedByteOverflowDatasetName)); assertFalse(reader.getDataSetInformation(unsignedByteOverflowDatasetName).isSigned()); assertEquals(1000, reader.int16().read(shortDatasetName)); assertEquals(1000000, reader.int32().read(intDatasetName)); assertEquals(10000000000L, reader.int64().read(longDatasetName)); assertEquals(0.001f, reader.float32().read(floatDatasetName)); assertEquals(0, reader.object().getRank(floatDatasetName)); assertTrue(Arrays.equals(new long[0], reader.object().getDimensions(floatDatasetName))); assertEquals(1.0E100, reader.float64().read(doubleDatasetName)); assertEquals("some string", reader.string().read(stringDatasetName)); assertEquals("some string", reader.string().read(stringWithZeroDatasetName)); assertEquals("some string\0with zero", reader.string().readRaw(stringWithZeroDatasetName)); reader.close(); } @Test public void testUnsignedInt8ValuesArray() { final String byteDatasetName = "/byte"; final File datasetFile = new File(workingDirectory, "unsignedInt8Values.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final byte[] valuesWritten = new byte[] { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, (byte) 128, (byte) 255 }; writer.uint8().writeArray(byteDatasetName, valuesWritten); writer.uint8().setAttr(byteDatasetName, "attr", (byte) 224); final byte[] valuesRead1 = writer.uint8().readArray(byteDatasetName); assertTrue(Arrays.equals(valuesWritten, valuesRead1)); assertEquals(224, UnsignedIntUtils.toUint8(writer.uint8().getAttr(byteDatasetName, "attr"))); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); assertFalse(reader.getDataSetInformation(byteDatasetName).isSigned()); final byte[] valuesRead2 = reader.uint8().readArray(byteDatasetName); assertTrue(Arrays.equals(valuesWritten, valuesRead2)); assertEquals(224, UnsignedIntUtils.toUint8(reader.uint8().getAttr(byteDatasetName, "attr"))); reader.close(); } @Test public void testUnsignedInt16ValuesArray() { final String byteDatasetName = "/byte"; final File datasetFile = new File(workingDirectory, "unsignedInt16Values.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final short[] valuesWritten = new short[] { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 256, 1024 }; writer.uint16().writeArray(byteDatasetName, valuesWritten); writer.uint16().setAttr(byteDatasetName, "attr", (short) 60000); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); assertFalse(reader.getDataSetInformation(byteDatasetName).isSigned()); final short[] valuesRead = reader.uint16().readArray(byteDatasetName); assertTrue(Arrays.equals(valuesWritten, valuesRead)); assertEquals(60000, UnsignedIntUtils.toUint16(reader.uint16().getAttr(byteDatasetName, "attr"))); reader.close(); } @Test public void testReadMDFloatArrayWithSlicing() { final File datasetFile = new File(workingDirectory, "mdArray.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String floatDatasetName = "/floatMatrix"; final MDFloatArray arrayWritten = new MDFloatArray(new int[] { 3, 2, 4 }); int count = 0; for (int i = 0; i < arrayWritten.size(0); ++i) { for (int j = 0; j < arrayWritten.size(1); ++j) { for (int k = 0; k < arrayWritten.size(2); ++k) { arrayWritten.set(++count, new int[] { i, j, k }); } } } writer.float32().writeMDArray(floatDatasetName, arrayWritten); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final MDFloatArray arrayRead = reader.float32().readMDArray(floatDatasetName); assertEquals(arrayWritten, arrayRead); final IndexMap boundIndex1 = new IndexMap().bind(1, 0); final long[] boundIndex1Arr = new long[] { -1, 0, -1 }; final MDFloatArray slice1 = new MDFloatArray(new float[] { 1f, 2f, 3f, 4f, 9f, 10f, 11f, 12f, 17f, 18f, 19f, 20f }, new int[] { 3, 4 }); final MDFloatArray slice1BlockOfs00 = new MDFloatArray(new float[] { 1f, 2f, 9f, 10f }, new int[] { 2, 2 }); final MDFloatArray slice1BlockOfs01 = new MDFloatArray(new float[] { 2f, 3f, 10f, 11f }, new int[] { 2, 2 }); final MDFloatArray slice1BlockOfs10 = new MDFloatArray(new float[] { 9f, 10f, 17f, 18f }, new int[] { 2, 2 }); final MDFloatArray slice1BlockOfs11 = new MDFloatArray(new float[] { 10f, 11f, 18f, 19f }, new int[] { 2, 2 }); final IndexMap boundIndex2 = new IndexMap().bind(2, 3).bind(0, 1); final long[] boundIndex2Arr = new long[] { 1, -1, 3 }; final MDFloatArray slice2 = new MDFloatArray(new float[] { 12f, 16f }, new int[] { 2 }); assertEquals(slice1, reader.float32().readMDArraySlice(floatDatasetName, boundIndex1)); assertEquals(slice1, reader.float32().readMDArraySlice(floatDatasetName, boundIndex1Arr)); assertEquals(slice1BlockOfs00, reader.float32().readSlicedMDArrayBlockWithOffset(floatDatasetName, new int[] { 2, 2 }, new long[] { 0, 0 }, boundIndex1)); assertEquals(slice1BlockOfs00, reader.float32().readSlicedMDArrayBlockWithOffset(floatDatasetName, new int[] { 2, 2 }, new long[] { 0, 0 }, boundIndex1Arr)); assertEquals(slice1BlockOfs01, reader.float32().readSlicedMDArrayBlockWithOffset(floatDatasetName, new int[] { 2, 2 }, new long[] { 0, 1 }, boundIndex1)); assertEquals(slice1BlockOfs01, reader.float32().readSlicedMDArrayBlockWithOffset(floatDatasetName, new int[] { 2, 2 }, new long[] { 0, 1 }, boundIndex1Arr)); assertEquals(slice1BlockOfs10, reader.float32().readSlicedMDArrayBlockWithOffset(floatDatasetName, new int[] { 2, 2 }, new long[] { 1, 0 }, boundIndex1)); assertEquals(slice1BlockOfs10, reader.float32().readSlicedMDArrayBlockWithOffset(floatDatasetName, new int[] { 2, 2 }, new long[] { 1, 0 }, boundIndex1Arr)); assertEquals(slice1BlockOfs11, reader.float32().readSlicedMDArrayBlockWithOffset(floatDatasetName, new int[] { 2, 2 }, new long[] { 1, 1 }, boundIndex1)); assertEquals(slice1BlockOfs11, reader.float32().readSlicedMDArrayBlockWithOffset(floatDatasetName, new int[] { 2, 2 }, new long[] { 1, 1 }, boundIndex1Arr)); assertEquals(slice2, reader.float32().readMDArraySlice(floatDatasetName, boundIndex2)); assertEquals(slice2, reader.float32().readMDArraySlice(floatDatasetName, boundIndex2Arr)); reader.close(); } @Test public void testBooleanArray() { final File datasetFile = new File(workingDirectory, "booleanArray.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String booleanDatasetName = "/booleanArray"; final String longArrayDataSetName = "/longArray"; final BitSet arrayWritten = new BitSet(); arrayWritten.set(32); writer.writeBitField(booleanDatasetName, arrayWritten); writer.int64().writeArray(longArrayDataSetName, BitSetConversionUtils.toStorageForm(arrayWritten)); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final BitSet arrayRead = reader.readBitField(booleanDatasetName); try { reader.readBitField(longArrayDataSetName); fail("Failed to detect type mismatch."); } catch (HDF5DatatypeInterfaceException ex) { // Expected, as the types do not match. } assertEquals(arrayWritten, arrayRead); final HDF5DataSetInformation info = reader.getDataSetInformation(booleanDatasetName); assertEquals(HDF5DataClass.BITFIELD, info.getTypeInformation().getDataClass()); assertChunkSizes(info, HDF5Utils.MIN_CHUNK_SIZE); reader.close(); } @Test public void testBooleanArrayBlock() { final File datasetFile = new File(workingDirectory, "booleanArrayBlock.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String booleanDatasetName = "/booleanArray"; final BitSet arrayWritten = new BitSet(); writer.bool().createBitField(booleanDatasetName, 4L, 2); arrayWritten.set(32); arrayWritten.set(40); writer.bool().writeBitFieldBlock(booleanDatasetName, arrayWritten, 2, 0); arrayWritten.clear(); arrayWritten.set(0); writer.bool().writeBitFieldBlock(booleanDatasetName, arrayWritten, 2, 1); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final BitSet arrayBlockRead = reader.bool().readBitFieldBlock(booleanDatasetName, 2, 1); assertEquals(1, arrayBlockRead.cardinality()); assertTrue(arrayBlockRead.get(0)); assertTrue(reader.bool().isBitSet(booleanDatasetName, 32)); assertTrue(reader.bool().isBitSet(booleanDatasetName, 40)); assertTrue(reader.bool().isBitSet(booleanDatasetName, 128)); assertFalse(reader.bool().isBitSet(booleanDatasetName, 33)); assertFalse(reader.bool().isBitSet(booleanDatasetName, 64)); assertFalse(reader.bool().isBitSet(booleanDatasetName, 256)); assertFalse(reader.bool().isBitSet(booleanDatasetName, 512)); reader.close(); } @Test public void testBitFieldArray() { final File datasetFile = new File(workingDirectory, "bitFieldArray.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String booleanDatasetName = "/bitFieldArray"; final BitSet[] arrayWritten = new BitSet[] { new BitSet(), new BitSet(), new BitSet() }; arrayWritten[0].set(32); arrayWritten[1].set(40); arrayWritten[2].set(17); writer.bool().writeBitFieldArray(booleanDatasetName, arrayWritten, INT_AUTO_SCALING); final String bigBooleanDatasetName = "/bigBitFieldArray"; final BitSet[] bigAarrayWritten = new BitSet[] { new BitSet(), new BitSet(), new BitSet() }; bigAarrayWritten[0].set(32); bigAarrayWritten[1].set(126); bigAarrayWritten[2].set(17); bigAarrayWritten[2].set(190); writer.bool().writeBitFieldArray(bigBooleanDatasetName, bigAarrayWritten, INT_AUTO_SCALING); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); assertTrue( Arrays.toString(reader.object().getDataSetInformation(booleanDatasetName) .getDimensions()), Arrays.equals(new long[] { 1, 3 }, reader.object().getDataSetInformation(booleanDatasetName) .getDimensions())); assertEquals(HDF5DataClass.BITFIELD, reader.object().getDataSetInformation(booleanDatasetName).getTypeInformation() .getDataClass()); final BitSet[] arrayRead = reader.bool().readBitFieldArray(booleanDatasetName); assertEquals(3, arrayRead.length); assertEquals(1, arrayRead[0].cardinality()); assertTrue(arrayRead[0].get(32)); assertEquals(1, arrayRead[1].cardinality()); assertTrue(arrayRead[1].get(40)); assertEquals(1, arrayRead[2].cardinality()); assertTrue(arrayRead[2].get(17)); assertEquals(HDF5DataClass.BITFIELD, reader.object().getDataSetInformation(bigBooleanDatasetName).getTypeInformation() .getDataClass()); final BitSet[] bigArrayRead = reader.bool().readBitFieldArray(bigBooleanDatasetName); assertEquals(3, arrayRead.length); assertEquals(1, bigArrayRead[0].cardinality()); assertTrue(bigArrayRead[0].get(32)); assertEquals(1, bigArrayRead[1].cardinality()); assertTrue(bigArrayRead[1].get(126)); assertEquals(2, bigArrayRead[2].cardinality()); assertTrue(bigArrayRead[2].get(17)); assertTrue(bigArrayRead[2].get(190)); reader.close(); } @Test public void testBitFieldArrayBlockWise() { final File datasetFile = new File(workingDirectory, "bitFieldArrayBlockWise.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String booleanDatasetName = "/bitFieldArray"; final BitSet[] arrayWritten = new BitSet[] { new BitSet(), new BitSet(), new BitSet(), new BitSet() }; arrayWritten[0].set(0); arrayWritten[1].set(1); arrayWritten[2].set(2); arrayWritten[3].set(3); final int count = 100; writer.bool().createBitFieldArray(booleanDatasetName, 4, count * arrayWritten.length, INT_AUTO_SCALING); for (int i = 0; i < count; ++i) { writer.bool().writeBitFieldArrayBlock(booleanDatasetName, arrayWritten, i); } writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final HDF5DataSetInformation info = reader.object().getDataSetInformation(booleanDatasetName); assertEquals(HDF5DataClass.BITFIELD, info.getTypeInformation().getDataClass()); assertEquals(2, info.getDimensions().length); assertEquals(1, info.getDimensions()[0]); assertEquals(count * arrayWritten.length, info.getDimensions()[1]); for (int i = 0; i < count; ++i) { assertTrue( "Block " + i, Arrays.equals(arrayWritten, reader.bool().readBitFieldArrayBlock(booleanDatasetName, 4, i))); } reader.close(); } private void assertChunkSizes(final HDF5DataSetInformation info, final long... expectedChunkSize) { assertEquals(HDF5StorageLayout.CHUNKED, info.getStorageLayout()); final int[] chunkSize = info.tryGetChunkSizes(); assertNotNull(chunkSize); assertEquals(expectedChunkSize.length, chunkSize.length); for (int i = 0; i < expectedChunkSize.length; ++i) { assertEquals(Integer.toString(i), expectedChunkSize[i], chunkSize[i]); } } @Test public void testMDFloatArrayBlockWise() { final File datasetFile = new File(workingDirectory, "mdArrayBlockWise.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String floatDatasetName = "/floatMatrix"; final String floatDatasetName2 = "/floatMatrix2"; final long[] shape = new long[] { 10, 10, 10 }; final int[] blockShape = new int[] { 5, 5, 5 }; writer.float32().createMDArray(floatDatasetName, shape, blockShape); writer.float32().createMDArray(floatDatasetName2, shape, blockShape); final float[] flatArray = new float[MDArray.getLength(blockShape)]; for (int i = 0; i < flatArray.length; ++i) { flatArray[i] = i; } final MDFloatArray arrayBlockWritten = new MDFloatArray(flatArray, blockShape); for (int i = 0; i < 2; ++i) { for (int j = 0; j < 2; ++j) { for (int k = 0; k < 2; ++k) { final long[] blockIndex = new long[] { i, j, k }; writer.float32().writeMDArrayBlock(floatDatasetName, arrayBlockWritten, blockIndex); writer.float32().writeMDArrayBlock(floatDatasetName2, arrayBlockWritten, blockIndex); } } } final MDFloatArray arraySliceWritten1 = new MDFloatArray(new float[] { 1000f, 2000f, 3000f, 4000f, 5000f }, new int[] { 1, 5 }); final long[] slicedBlock1 = new long[] { 4, 1 }; final IndexMap imap1 = new IndexMap().bind(1, 7); writer.float32().writeSlicedMDArrayBlock(floatDatasetName2, arraySliceWritten1, slicedBlock1, imap1); final MDFloatArray arraySliceWritten2 = new MDFloatArray(new float[] { -1f, -2f, -3f, -4f, -5f, -6f }, new int[] { 3, 2 }); final long[] slicedBlockOffs2 = new long[] { 2, 6 }; final IndexMap imap2 = new IndexMap().bind(0, 9); writer.float32().writeSlicedMDArrayBlockWithOffset(floatDatasetName2, arraySliceWritten2, slicedBlockOffs2, imap2); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); for (int i = 0; i < 2; ++i) { for (int j = 0; j < 2; ++j) { for (int k = 0; k < 2; ++k) { final long[] blockIndex = new long[] { i, j, k }; final MDFloatArray arrayRead = reader.float32().readMDArrayBlock(floatDatasetName, blockShape, blockIndex); assertEquals(Arrays.toString(blockIndex), arrayBlockWritten, arrayRead); // {0, 1, 1} is the first block we overwrote, { 1, 0, 1} the second block. if (false == Arrays.equals(new long[] { 0, 1, 1 }, blockIndex) && false == Arrays.equals(new long[] { 1, 0, 1 }, blockIndex)) { assertEquals( Arrays.toString(blockIndex), arrayBlockWritten, reader.float32().readMDArrayBlock(floatDatasetName2, blockShape, blockIndex)); } } } } final MDFloatArray arraySliceRead1 = reader.float32().readSlicedMDArrayBlock(floatDatasetName2, arraySliceWritten1.dimensions(), slicedBlock1, imap1); assertEquals(arraySliceWritten1, arraySliceRead1); final MDFloatArray arraySliceRead2 = reader.float32().readSlicedMDArrayBlockWithOffset(floatDatasetName2, arraySliceWritten2.dimensions(), slicedBlockOffs2, imap2); assertEquals(arraySliceWritten2, arraySliceRead2); reader.close(); } @Test public void testMDFloatArraySliced() { final File datasetFile = new File(workingDirectory, "mdArraySliced.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String floatDatasetName = "/floatMatrix"; final long[] shape = new long[] { 10, 10, 10 }; final int[] sliceShape = new int[] { 10, 10 }; final int[] sliceBlockShape = new int[] { 1, 10, 10 }; writer.float32().createMDArray(floatDatasetName, shape, sliceBlockShape); final float[] baseArray = new float[MDArray.getLength(sliceShape)]; for (int i = 0; i < baseArray.length; ++i) { baseArray[i] = i; } float[] floatArrayWritten = baseArray.clone(); for (int i = 0; i < 10; ++i) { writer.float32().writeMDArraySlice(floatDatasetName, new MDFloatArray(timesTwo(floatArrayWritten), sliceShape), new long[] { i, -1, -1 }); } writer.close(); floatArrayWritten = baseArray.clone(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); for (int i = 0; i < 10; ++i) { final MDFloatArray arrayRead = reader.float32().readMDArraySlice(floatDatasetName, new long[] { i, -1, -1 }); assertEquals(Integer.toString(i), new MDFloatArray(timesTwo(floatArrayWritten), sliceShape), arrayRead); } reader.close(); } private static float[] timesTwo(float[] array) { for (int i = 0; i < array.length; ++i) { array[i] *= 2; } return array; } @Test public void testMDFloatArrayBlockWiseWithMemoryOffset() { final File datasetFile = new File(workingDirectory, "mdArrayBlockWiseWithMemoryOffset.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String floatDatasetName = "/floatMatrix"; final long[] shape = new long[] { 10, 10 }; writer.float32().createMDArray(floatDatasetName, shape, MDArray.toInt(shape)); final float[] flatArray = new float[MDArray.getLength(shape)]; for (int i = 0; i < flatArray.length; ++i) { flatArray[i] = i; } final MDFloatArray arrayBlockWritten = new MDFloatArray(flatArray, shape); writer.float32().writeMDArrayBlockWithOffset(floatDatasetName, arrayBlockWritten, new int[] { 2, 2 }, new long[] { 0, 0 }, new int[] { 1, 3 }); writer.float32().writeMDArrayBlockWithOffset(floatDatasetName, arrayBlockWritten, new int[] { 2, 2 }, new long[] { 2, 2 }, new int[] { 5, 1 }); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final float[][] matrixRead = reader.float32().readMatrix(floatDatasetName); reader.close(); assertEquals(13f, matrixRead[0][0]); assertEquals(14f, matrixRead[0][1]); assertEquals(23f, matrixRead[1][0]); assertEquals(24f, matrixRead[1][1]); assertEquals(51f, matrixRead[2][2]); assertEquals(52f, matrixRead[2][3]); assertEquals(61f, matrixRead[3][2]); assertEquals(62f, matrixRead[3][3]); for (int i = 0; i < 10; ++i) { for (int j = 0; j < 10; ++j) { if ((i < 2 && j < 2) || (i > 1 && i < 4 && j > 1 && j < 4)) { continue; } assertEquals("(" + i + "," + j + "}", 0f, matrixRead[i][j]); } } } @Test public void testStringVariableLength() { final File datasetFile = new File(workingDirectory, "stringVariableLength.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); writer.string().writeVL("a", ""); writer.string().writeVL("b", "\0"); writer.string().writeVL("c", "\0ABC\0"); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); assertEquals("", reader.readString("a")); assertEquals("\0", reader.readString("b")); assertEquals("\0ABC\0", reader.readString("c")); reader.close(); } @Test public void testDataSets() { final File datasetFile = new File(workingDirectory, "datasets.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String floatDatasetName = "/Group1/floats"; final float[] floatDataWritten = new float[] { 2.8f, 8.2f, -3.1f, 0.0f, 10000.0f }; writer.float32().writeArray(floatDatasetName, floatDataWritten); final long[] longDataWritten = new long[] { 10, -1000000, 1, 0, 100000000000L }; final String longDatasetName = "/Group2/longs"; writer.int64().writeArray(longDatasetName, longDataWritten); final byte[] byteDataWritten = new byte[] { 0, -1, 1, -128, 127 }; final String byteDatasetName = "/Group2/bytes"; writer.int8().writeArray(byteDatasetName, byteDataWritten, INT_DEFLATE); final short[] shortDataWritten = new short[] { 0, -1, 1, -128, 127 }; final String shortDatasetName = "/Group2/shorts"; writer.int16().writeArray(shortDatasetName, shortDataWritten, INT_DEFLATE); final String intDatasetName1 = "/Group2/ints1"; final int[] intDataWritten = new int[] { 0, 1, 2, 3, 4 }; final String intDatasetName2 = "/Group2/ints2"; writer.int32().writeArray(intDatasetName1, intDataWritten, INT_DEFLATE); writer.int32().writeArray(intDatasetName2, intDataWritten, INT_SHUFFLE_DEFLATE); writer.file().flush(); final String stringDataWritten1 = "Some Random String"; final String stringDataWritten2 = "Another Random String"; final String stringDatasetName = "/Group3/strings"; final String stringDatasetName2 = "/Group4/strings"; writer.string().write(stringDatasetName, stringDataWritten1); writer.string().writeVL(stringDatasetName2, stringDataWritten1); writer.string().writeVL(stringDatasetName2, stringDataWritten2); final String stringDatasetName3 = "/Group4/stringArray"; writer.string().writeArrayVL(stringDatasetName3, new String[] { stringDataWritten1, stringDataWritten2 }); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final float[] floatDataRead = reader.float32().readArray(floatDatasetName); assertTrue(Arrays.equals(floatDataWritten, floatDataRead)); assertEquals(1, reader.object().getRank(floatDatasetName)); assertTrue(Arrays.equals(new long[] { floatDataWritten.length }, reader.object().getDimensions(floatDatasetName))); final long[] longDataRead = reader.int64().readArray(longDatasetName); assertTrue(Arrays.equals(longDataWritten, longDataRead)); final byte[] byteDataRead = reader.int8().readArray(byteDatasetName); assertTrue(Arrays.equals(byteDataWritten, byteDataRead)); final short[] shortDataRead = reader.int16().readArray(shortDatasetName); assertTrue(Arrays.equals(shortDataWritten, shortDataRead)); final String stringDataRead1 = reader.string().read(stringDatasetName); final int[] intDataRead1 = reader.int32().readArray(intDatasetName1); assertTrue(Arrays.equals(intDataWritten, intDataRead1)); final int[] intDataRead2 = reader.int32().readArray(intDatasetName2); assertTrue(Arrays.equals(intDataWritten, intDataRead2)); assertEquals(stringDataWritten1, stringDataRead1); final String stringDataRead2 = reader.string().read(stringDatasetName2); assertEquals(stringDataWritten2, stringDataRead2); final String[] vlStringArrayRead = reader.string().readArray(stringDatasetName3); assertEquals(stringDataWritten1, vlStringArrayRead[0]); assertEquals(stringDataWritten2, vlStringArrayRead[1]); reader.close(); } @Test public void testScaleOffsetFilterInt() { final File datasetFile = new File(workingDirectory, "scaleoffsetfilterint.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final int[] intWritten = new int[1000000]; for (int i = 0; i < intWritten.length; ++i) { intWritten[i] = (i % 4); } writer.int32().writeArray("ds", intWritten, INT_AUTO_SCALING_DEFLATE); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final int[] intRead = reader.int32().readArray("ds"); assertTrue(Arrays.equals(intRead, intWritten)); reader.close(); // Shouldn't work in strict HDF5 1.6 mode. final File file2 = new File(workingDirectory, "scaleoffsetfilterintfailed.h5"); file2.delete(); assertFalse(file2.exists()); file2.deleteOnExit(); final IHDF5Writer writer2 = HDF5FactoryProvider.get().configure(file2).fileFormat(FileFormat.STRICTLY_1_6) .writer(); try { writer2.int32().writeArray("ds", intWritten, INT_AUTO_SCALING_DEFLATE); fail("Usage of scaling compression in strict HDF5 1.6 mode not detected"); } catch (IllegalStateException ex) { assertTrue(ex.getMessage().indexOf("not allowed") >= 0); } writer2.close(); } @Test public void testScaleOffsetFilterFloat() { final File datasetFile = new File(workingDirectory, "scaleoffsetfilterfloat.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final float[] floatWritten = new float[1000000]; for (int i = 0; i < floatWritten.length; ++i) { floatWritten[i] = (i % 10) / 10f; } writer.float32().writeArray("ds", floatWritten, FLOAT_SCALING1_DEFLATE); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final float[] floatRead = reader.float32().readArray("ds"); assertTrue(Arrays.equals(floatRead, floatWritten)); reader.close(); } @Test public void testMaxPathLength() { final File datasetFile = new File(workingDirectory, "maxpathlength.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String madnessOverwhelmesUs1 = StringUtils.repeat("a", 16384); final String madnessOverwhelmesUs2 = StringUtils.repeat("/b", 8192); writer.int32().write(madnessOverwhelmesUs1, 17); writer.float32().write(madnessOverwhelmesUs2, 0.0f); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); assertEquals(17, reader.int32().read(madnessOverwhelmesUs1)); assertEquals(0.0f, reader.float32().read(madnessOverwhelmesUs2)); reader.close(); } @Test public void testExceedMaxPathLength() { final File datasetFile = new File(workingDirectory, "exceedmaxpathlength.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String madnessOverwhelmesUs = StringUtils.repeat("a", 16385); try { writer.int32().write(madnessOverwhelmesUs, 17); fail("path overflow not detected"); } catch (HDF5JavaException ex) { assertEquals(0, ex.getMessage().indexOf("Path too long")); } finally { writer.close(); } } @Test public void testAccessClosedReaderWriter() { final File datasetFile = new File(workingDirectory, "datasetsNonExtendable.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); writer.close(); try { writer.writeBoolean("dataSet", true); } catch (HDF5JavaException ex) { assertEquals(String.format("HDF5 file '%s' is closed.", datasetFile.getAbsolutePath()), ex.getMessage()); } final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); reader.close(); try { reader.readBoolean("dataSet"); } catch (HDF5JavaException ex) { assertEquals(String.format("HDF5 file '%s' is closed.", datasetFile.getAbsolutePath()), ex.getMessage()); } } @Test public void testDataSetsNonExtendable() { final File datasetFile = new File(workingDirectory, "datasetsNonExtendable.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().configure(datasetFile).dontUseExtendableDataTypes() .syncMode(SyncMode.SYNC_BLOCK).writer(); final String floatDatasetName = "/Group1/floats"; final float[] floatDataWritten = new float[] { 2.8f, 8.2f, -3.1f, 0.0f, 10000.0f }; writer.float32().writeArray(floatDatasetName, floatDataWritten); final String compressedFloatDatasetName = "/Group1/floatsCompressed"; writer.float32().writeArray(compressedFloatDatasetName, floatDataWritten, FLOAT_DEFLATE); final long[] longDataWritten = new long[] { 10, -1000000, 1, 0, 100000000000L }; final String longDatasetName = "/Group2/longs"; writer.int64().writeArray(longDatasetName, longDataWritten); final long[] longDataWrittenAboveCompactThreshold = new long[128]; for (int i = 0; i < longDataWrittenAboveCompactThreshold.length; ++i) { longDataWrittenAboveCompactThreshold[i] = i; } final String longDatasetNameAboveCompactThreshold = "/Group2/longsContiguous"; writer.int64().writeArray(longDatasetNameAboveCompactThreshold, longDataWrittenAboveCompactThreshold); final String longDatasetNameAboveCompactThresholdCompress = "/Group2/longsChunked"; writer.int64().writeArray(longDatasetNameAboveCompactThresholdCompress, longDataWrittenAboveCompactThreshold, INT_DEFLATE); final byte[] byteDataWritten = new byte[] { 0, -1, 1, -128, 127 }; final String byteDatasetName = "/Group2/bytes"; writer.int8().writeArray(byteDatasetName, byteDataWritten, INT_DEFLATE); final String stringDataWritten = "Some Random String"; final String stringDatasetName = "/Group3/strings"; final String stringDatasetName2 = "/Group4/strings"; writer.string().write(stringDatasetName, stringDataWritten); writer.string().writeVL(stringDatasetName2, stringDataWritten); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final float[] floatDataRead = reader.float32().readArray(floatDatasetName); HDF5DataSetInformation info = reader.getDataSetInformation(floatDatasetName); assertEquals(HDF5StorageLayout.COMPACT, info.getStorageLayout()); assertNull(info.tryGetChunkSizes()); assertTrue(info.isSigned()); assertTrue(Arrays.equals(floatDataWritten, floatDataRead)); final long[] compressedLongDataRead = reader.int64().readArray(longDatasetNameAboveCompactThresholdCompress); info = reader.getDataSetInformation(longDatasetNameAboveCompactThresholdCompress); assertChunkSizes(info, longDataWrittenAboveCompactThreshold.length); assertTrue(Arrays.equals(longDataWrittenAboveCompactThreshold, compressedLongDataRead)); final long[] longDataRead = reader.int64().readArray(longDatasetName); info = reader.getDataSetInformation(longDatasetName); assertEquals(HDF5StorageLayout.COMPACT, info.getStorageLayout()); assertNull(info.tryGetChunkSizes()); assertTrue(Arrays.equals(longDataWritten, longDataRead)); final long[] longDataReadAboveCompactThreshold = reader.int64().readArray(longDatasetNameAboveCompactThreshold); info = reader.getDataSetInformation(longDatasetNameAboveCompactThreshold); assertEquals(HDF5StorageLayout.CONTIGUOUS, info.getStorageLayout()); assertNull(info.tryGetChunkSizes()); assertTrue(Arrays.equals(longDataWrittenAboveCompactThreshold, longDataReadAboveCompactThreshold)); final byte[] byteDataRead = reader.int8().readArray(byteDatasetName); assertTrue(Arrays.equals(byteDataWritten, byteDataRead)); final String stringDataRead = reader.readString(stringDatasetName); assertEquals(stringDataWritten, stringDataRead); reader.close(); } @Test public void testOverwriteContiguousDataSet() { // Test for a bug in 1.8.1 and 1.8.2 when overwriting contiguous data sets and thereby // changing its size. // We have some workaround code in IHDF5Writer.getDataSetId(), this is why this test runs // green. As new versions of HDF5 become available, one can try to comment out the // workaround code and see whether this test still runs red. final File datasetFile = new File(workingDirectory, "overwriteContiguousDataSet.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final String dsName = "longArray"; IHDF5Writer writer = HDF5FactoryProvider.get().configure(datasetFile).dontUseExtendableDataTypes() .writer(); // Creating the group is part of the "bug magic". writer.object().createGroup("group"); final long[] arrayWritten1 = new long[1000]; for (int i = 0; i < arrayWritten1.length; ++i) { arrayWritten1[i] = i; } writer.int64().writeArray(dsName, arrayWritten1); writer.close(); writer = HDF5FactoryProvider.get().open(datasetFile); final long[] arrayWritten2 = new long[5]; for (int i = 0; i < arrayWritten1.length; ++i) { arrayWritten1[i] = i * i; } writer.int64().writeArray(dsName, arrayWritten2); writer.close(); IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final long[] arrayRead = reader.int64().readArray(dsName); assertTrue(Arrays.equals(arrayWritten2, arrayRead)); reader.close(); } @Test public void testCompactDataset() { final File datasetFile = new File(workingDirectory, "compactDS.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final String dsName = "ds"; long[] data = new long[] { 1, 2, 3 }; IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); writer.int64().writeArray(dsName, data, HDF5IntStorageFeatures.INT_COMPACT); assertEquals(HDF5StorageLayout.COMPACT, writer.getDataSetInformation(dsName) .getStorageLayout()); writer.close(); IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); assertTrue(Arrays.equals(data, reader.int64().readArray(dsName))); reader.close(); } @Test public void testCreateEmptyFixedSizeDataSets() { final File datasetFile = new File(workingDirectory, "createEmptyFixedSizeDataSets.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); IHDF5Writer writer = HDF5Factory.open(datasetFile); writer.int64().createArray("longArr", 5, HDF5IntStorageFeatures.INT_COMPACT); writer.int64().createMDArray("longMDArr", new int[] { 5, 5 }, HDF5IntStorageFeatures.INT_COMPACT); writer.bool() .createBitFieldArray("bitfieldArr", 128, 5, HDF5IntStorageFeatures.INT_COMPACT); writer.enumeration().createArray("enumArr", writer.enumeration().getAnonType(new String[] { "a", "b", "c" }), 5, HDF5IntStorageFeatures.INT_COMPACT); writer.enumeration().createMDArray("enumMDArr", writer.enumeration().getAnonType(new String[] { "a", "b", "c" }), new int[] { 5, 5 }, HDF5IntStorageFeatures.INT_COMPACT); writer.close(); IHDF5Reader reader = HDF5Factory.openForReading(datasetFile); HDF5DataSetInformation info = reader.getDataSetInformation("longArr"); assertTrue(Arrays.equals(new long[] { 5 }, info.getDimensions())); assertNull(info.tryGetChunkSizes()); assertEquals(HDF5StorageLayout.COMPACT, info.getStorageLayout()); info = reader.getDataSetInformation("longMDArr"); assertTrue(Arrays.equals(new long[] { 5, 5 }, info.getDimensions())); assertNull(info.tryGetChunkSizes()); assertEquals(HDF5StorageLayout.COMPACT, info.getStorageLayout()); info = reader.getDataSetInformation("enumArr"); assertTrue(Arrays.equals(new long[] { 5 }, info.getDimensions())); assertNull(info.tryGetChunkSizes()); assertEquals(HDF5StorageLayout.COMPACT, info.getStorageLayout()); info = reader.getDataSetInformation("enumMDArr"); assertTrue(Arrays.equals(new long[] { 5, 5 }, info.getDimensions())); assertNull(info.tryGetChunkSizes()); assertEquals(HDF5StorageLayout.COMPACT, info.getStorageLayout()); info = reader.getDataSetInformation("bitfieldArr"); assertTrue(Arrays.equals(new long[] { 2, 5 }, info.getDimensions())); assertNull(info.tryGetChunkSizes()); assertEquals(HDF5StorageLayout.COMPACT, info.getStorageLayout()); reader.close(); } @Test public void testCreateEmptyGrowableDataSets() { final File datasetFile = new File(workingDirectory, "createEmptyGrowableDataSets.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); IHDF5Writer writer = HDF5Factory.open(datasetFile); writer.int64().createArray("longArr", 5); writer.int64().createMDArray("longMDArr", new int[] { 5, 5 }); writer.bool().createBitFieldArray("bitfieldArr", 128, 5); writer.enumeration().createArray("enumArr", writer.enumeration().getAnonType(new String[] { "a", "b", "c" }), 5); writer.enumeration().createMDArray("enumMDArr", writer.enumeration().getAnonType(new String[] { "a", "b", "c" }), new int[] { 5, 5 }); writer.close(); IHDF5Reader reader = HDF5Factory.openForReading(datasetFile); HDF5DataSetInformation info = reader.object().getDataSetInformation("longArr"); assertTrue(Arrays.equals(new long[] { 5 }, info.getDimensions())); assertTrue(Arrays.equals(new int[] { 5 }, info.tryGetChunkSizes())); assertEquals(HDF5StorageLayout.CHUNKED, info.getStorageLayout()); info = reader.object().getDataSetInformation("longMDArr"); assertTrue(Arrays.equals(new long[] { 5, 5 }, info.getDimensions())); assertTrue(Arrays.equals(new int[] { 5, 5 }, info.tryGetChunkSizes())); assertEquals(HDF5StorageLayout.CHUNKED, info.getStorageLayout()); info = reader.object().getDataSetInformation("enumArr"); assertTrue(Arrays.equals(new long[] { 5 }, info.getDimensions())); assertTrue(Arrays.equals(new int[] { 5 }, info.tryGetChunkSizes())); assertEquals(HDF5StorageLayout.CHUNKED, info.getStorageLayout()); info = reader.object().getDataSetInformation("enumMDArr"); assertTrue(Arrays.equals(new long[] { 5, 5 }, info.getDimensions())); assertTrue(Arrays.equals(new int[] { 5, 5 }, info.tryGetChunkSizes())); assertEquals(HDF5StorageLayout.CHUNKED, info.getStorageLayout()); info = reader.object().getDataSetInformation("bitfieldArr"); assertTrue(Arrays.equals(new long[] { 2, 5 }, info.getDimensions())); assertTrue(Arrays.equals(new int[] { 2, 5 }, info.tryGetChunkSizes())); assertEquals(HDF5StorageLayout.CHUNKED, info.getStorageLayout()); reader.close(); } @Test public void testCreateZeroLengthGrowableDataSets() { final File datasetFile = new File(workingDirectory, "createZeroLengthGrowableDataSets.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); IHDF5Writer writer = HDF5Factory.open(datasetFile); writer.int64().createArray("longArr", 5, INT_CHUNKED); writer.int64().createMDArray("longMDArr", new int[] { 5, 5 }, INT_CHUNKED); writer.bool().createBitFieldArray("bitfieldArr", 128, 5, INT_CHUNKED); writer.enumeration().createArray("enumArr", writer.enumeration().getAnonType(new String[] { "a", "b", "c" }), 5, INT_CHUNKED); writer.enumeration().createMDArray("enumMDArr", writer.enumeration().getAnonType(new String[] { "a", "b", "c" }), new int[] { 5, 5 }, INT_CHUNKED); writer.close(); IHDF5Reader reader = HDF5Factory.openForReading(datasetFile); HDF5DataSetInformation info = reader.object().getDataSetInformation("longArr"); assertTrue(Arrays.equals(new long[] { 0 }, info.getDimensions())); assertTrue(Arrays.equals(new int[] { 5 }, info.tryGetChunkSizes())); assertEquals(HDF5StorageLayout.CHUNKED, info.getStorageLayout()); info = reader.object().getDataSetInformation("longMDArr"); assertTrue(Arrays.equals(new long[] { 0, 0 }, info.getDimensions())); assertTrue(Arrays.equals(new int[] { 5, 5 }, info.tryGetChunkSizes())); assertEquals(HDF5StorageLayout.CHUNKED, info.getStorageLayout()); info = reader.object().getDataSetInformation("enumArr"); assertTrue(Arrays.equals(new long[] { 0 }, info.getDimensions())); assertTrue(Arrays.equals(new int[] { 5 }, info.tryGetChunkSizes())); assertEquals(HDF5StorageLayout.CHUNKED, info.getStorageLayout()); info = reader.object().getDataSetInformation("enumMDArr"); assertTrue(Arrays.equals(new long[] { 0, 0 }, info.getDimensions())); assertTrue(Arrays.equals(new int[] { 5, 5 }, info.tryGetChunkSizes())); assertEquals(HDF5StorageLayout.CHUNKED, info.getStorageLayout()); info = reader.object().getDataSetInformation("bitfieldArr"); assertTrue(Arrays.equals(new long[] { 2, 0 }, info.getDimensions())); assertTrue(Arrays.equals(new int[] { 2, 5 }, info.tryGetChunkSizes())); assertEquals(HDF5StorageLayout.CHUNKED, info.getStorageLayout()); reader.close(); } @Test public void testCreateEmptyDefaultFixedSizeDataSets() { final File datasetFile = new File(workingDirectory, "createEmptyDefaultFixedSizeDataSets.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); IHDF5Writer writer = HDF5Factory.configure(datasetFile).dontUseExtendableDataTypes().writer(); writer.int64().createArray("longArr", 5); writer.int64().createMDArray("longMDArr", new int[] { 5, 5 }); writer.bool().createBitFieldArray("bitfieldArr", 128, 5); writer.enumeration().createArray("enumArr", writer.enumeration().getAnonType(new String[] { "a", "b", "c" }), 5); writer.close(); IHDF5Reader reader = HDF5Factory.openForReading(datasetFile); HDF5DataSetInformation info = reader.getDataSetInformation("longArr"); assertTrue(Arrays.equals(new long[] { 5 }, info.getDimensions())); assertEquals(HDF5StorageLayout.COMPACT, info.getStorageLayout()); info = reader.getDataSetInformation("longMDArr"); assertTrue(Arrays.equals(new long[] { 5, 5 }, info.getDimensions())); assertEquals(HDF5StorageLayout.COMPACT, info.getStorageLayout()); info = reader.getDataSetInformation("enumArr"); assertTrue(Arrays.equals(new long[] { 5 }, info.getDimensions())); assertEquals(HDF5StorageLayout.COMPACT, info.getStorageLayout()); info = reader.getDataSetInformation("bitfieldArr"); assertTrue(Arrays.equals(new long[] { 2, 5 }, info.getDimensions())); assertEquals(HDF5StorageLayout.COMPACT, info.getStorageLayout()); reader.close(); } @Test public void testExtendChunkedDataset() { final File datasetFile = new File(workingDirectory, "extendChunked.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final String dsName = "ds"; long[] data = new long[] { 1, 2, 3, 4 }; IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); writer.int64().createArray(dsName, 5, 3); writer.int64().writeArray(dsName, data, HDF5IntStorageFeatures.INT_NO_COMPRESSION_KEEP); writer.close(); IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); long[] dataRead = reader.int64().readArray(dsName); assertTrue(Arrays.equals(data, dataRead)); reader.close(); // Now write a larger data set and see whether the data set is correctly extended. writer = HDF5FactoryProvider.get().open(datasetFile); data = new long[] { 17, 42, 1, 2, 3, 101, -5 }; writer.int64().writeArray(dsName, data); writer.close(); reader = HDF5FactoryProvider.get().openForReading(datasetFile); dataRead = reader.int64().readArray(dsName); assertTrue(Arrays.equals(data, dataRead)); reader.close(); } @Test public void testExtendContiguousDataset() { final File datasetFile = new File(workingDirectory, "extendContiguous.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final String dsName = "ds"; long[] longArrayWritten = new long[] { 1, 2, 3 }; IHDF5Writer writer = HDF5FactoryProvider.get().configure(datasetFile).dontUseExtendableDataTypes() .writer(); // Set maxdims such that COMPACT_LAYOUT_THRESHOLD (int bytes!) is exceeded so that we get a // contiguous data set. writer.int64().createArray(dsName, 128, 1); writer.int64().writeArray(dsName, longArrayWritten); writer.close(); IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final long[] longArrayRead = reader.int64().readArray(dsName); assertTrue(Arrays.equals(longArrayWritten, longArrayRead)); reader.close(); // Now write a larger data set and see whether the data set is correctly extended. writer = HDF5FactoryProvider.get().open(datasetFile); longArrayWritten = new long[] { 17, 42, 1, 2, 3 }; writer.int64().writeArray(dsName, longArrayWritten); writer.close(); reader = HDF5FactoryProvider.get().openForReading(datasetFile); assertTrue(Arrays.equals(longArrayWritten, reader.int64().readArray(dsName))); reader.close(); } @Test public void testAutomaticDeletionOfDataSetOnWrite() { final File datasetFile = new File(workingDirectory, "automaticDeletionOfDataSetOnWrite.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = new HDF5WriterConfigurator(datasetFile).writer(); writer.float32().createArray("f", 12, HDF5FloatStorageFeatures.FLOAT_COMPACT); writer.float32().writeArray("f", new float[] { 1f, 2f, 3f, 4f, 5f }); writer.close(); final IHDF5Reader reader = new HDF5ReaderConfigurator(datasetFile).reader(); HDF5DataSetInformation info = reader.getDataSetInformation("f"); assertEquals(HDF5StorageLayout.CHUNKED, info.getStorageLayout()); assertEquals(5, info.tryGetChunkSizes()[0]); reader.close(); } @Test public void testAutomaticDeletionOfDataSetOnCreate() { final File datasetFile = new File(workingDirectory, "automaticDeletionOfDataSetOnCreate.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = new HDF5WriterConfigurator(datasetFile).writer(); writer.float32().createArray("f", 12, 6, HDF5FloatStorageFeatures.FLOAT_COMPACT); writer.float32().createArray("f", 10, HDF5FloatStorageFeatures.FLOAT_CONTIGUOUS); // This won't overwrite the data set as it is a block write command. writer.float32().writeArrayBlock("f", new float[] { 1f, 2f, 3f, 4f, 5f }, 0); writer.close(); final IHDF5Reader reader = new HDF5ReaderConfigurator(datasetFile).reader(); HDF5DataSetInformation info = reader.getDataSetInformation("f"); assertEquals(HDF5StorageLayout.CONTIGUOUS, info.getStorageLayout()); assertEquals(10, info.getDimensions()[0]); assertNull(info.tryGetChunkSizes()); reader.close(); } @Test public void testSpacesInDataSetName() { final File datasetFile = new File(workingDirectory, "datasetsWithSpaces.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String floatDatasetName = "Float Dataset"; final float[] floatDataWritten = new float[] { 2.8f, 8.2f, -3.1f, 0.0f, 10000.0f }; writer.float32().writeArray(floatDatasetName, floatDataWritten); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final float[] floatDataRead = reader.float32().readArray(floatDatasetName); assertTrue(Arrays.equals(floatDataWritten, floatDataRead)); reader.close(); } @Test public void testFloatArrayTypeDataSet() { final File datasetFile = new File(workingDirectory, "floatArrayTypeDataSet.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final HDF5ArrayTypeFloatWriter efWriter = new HDF5ArrayTypeFloatWriter((HDF5Writer) writer); final float[] floatDataWritten = new float[] { 2.8f, 8.2f, -3.1f, 0.0f, 10000.0f }; efWriter.writeFloatArrayArrayType("f", floatDataWritten); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); assertEquals("FLOAT(4, #5):{}", reader.getDataSetInformation("f").toString()); final float[] floatDataRead = reader.float32().readArray("f"); assertTrue(Arrays.equals(floatDataWritten, floatDataRead)); reader.close(); } @Test public void testDoubleArrayAsByteArray() { final File datasetFile = new File(workingDirectory, "doubleArrayTypeDataSetAsByteArray.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final HDF5ArrayTypeFloatWriter efWriter = new HDF5ArrayTypeFloatWriter((HDF5Writer) writer); writer.float64().createArray("f", 6, 3); final double[] floatDataWritten = new double[] { 2.8, 8.2, -3.1, 0.0, 10000.0 }; efWriter.writeDoubleArrayBigEndian("f", floatDataWritten, HDF5FloatStorageFeatures.FLOAT_NO_COMPRESSION_KEEP); final double[] floatDataWritten2 = new double[] { 2.8, 8.2, -3.1, 0.0 }; writer.float64().writeMDArray("f2", new MDDoubleArray(floatDataWritten2, new int[] { 2, 2 })); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); assertEquals("FLOAT(8):{5}", reader.getDataSetInformation("f").toString()); final byte[] byteDataRead = reader.readAsByteArray("f"); final double[] floatDataRead = NativeData.byteToDouble(byteDataRead, ByteOrder.NATIVE); assertTrue(Arrays.equals(floatDataWritten, floatDataRead)); final byte[] byteDataRead2 = reader.readAsByteArray("f2"); final double[] floatDataRead2 = NativeData.byteToDouble(byteDataRead2, ByteOrder.NATIVE); assertTrue(Arrays.equals(floatDataWritten2, floatDataRead2)); byte[] byteDataBlockRead = reader.opaque().readArrayBlock("f", 2, 1); assertEquals(16, byteDataBlockRead.length); assertEquals(floatDataWritten[2], NativeData.byteToDouble(byteDataBlockRead, ByteOrder.NATIVE, 0, 1)[0]); assertEquals(floatDataWritten[3], NativeData.byteToDouble(byteDataBlockRead, ByteOrder.NATIVE, 8, 1)[0]); byteDataBlockRead = reader.opaque().readArrayBlockWithOffset("f", 2, 1); assertEquals(16, byteDataBlockRead.length); assertEquals(floatDataWritten[1], NativeData.byteToDouble(byteDataBlockRead, ByteOrder.NATIVE, 0, 1)[0]); assertEquals(floatDataWritten[2], NativeData.byteToDouble(byteDataBlockRead, ByteOrder.NATIVE, 8, 1)[0]); final double[][] values = { { 2.8, 8.2, -3.1 }, { 0.0, 10000.0 } }; int i = 0; for (HDF5DataBlock block : reader.opaque().getArrayNaturalBlocks("f")) { assertEquals(i, block.getIndex()); assertEquals(i * 3, block.getOffset()); assertTrue(Arrays.equals(values[i], NativeData.byteToDouble(block.getData(), ByteOrder.NATIVE))); ++i; } reader.close(); } @Test public void testFloatArrayTypeDataSetOverwrite() { final File datasetFile = new File(workingDirectory, "floatArrayTypeDataSetOverwrite.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final HDF5ArrayTypeFloatWriter efWriter = new HDF5ArrayTypeFloatWriter((HDF5Writer) writer); final float[] floatDataWritten = new float[] { 2.8f, 8.2f, -3.1f, 0.0f, 10000.0f }; efWriter.writeFloatArrayArrayType("f", floatDataWritten); final float[] floatDataWritten2 = new float[] { 0.1f, 8.2f, -3.1f, 0.0f, 20000.0f }; writer.float32().writeArray("f", floatDataWritten2); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); assertEquals("FLOAT(4):{5}", reader.getDataSetInformation("f").toString()); final float[] floatDataRead = reader.float32().readArray("f"); assertTrue(Arrays.equals(floatDataWritten2, floatDataRead)); reader.close(); } @Test public void testFloatMDArrayTypeDataSet() { final File datasetFile = new File(workingDirectory, "floatMDArrayTypeDataSet.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final HDF5ArrayTypeFloatWriter efWriter = new HDF5ArrayTypeFloatWriter((HDF5Writer) writer); final MDFloatArray floatDataWritten = new MDFloatArray(new float[] { 2.8f, 8.2f, -3.1f, -0.1f, 10000.0f, 1.111f }, new int[] { 3, 2 }); efWriter.writeFloatArrayArrayType("fa", floatDataWritten); efWriter.writeFloat2DArrayArrayType1DSpace1d("fas", floatDataWritten); writer.float32().writeMDArray("f", floatDataWritten); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); assertEquals("FLOAT(4, [3,2]):{}", reader.getDataSetInformation("fa").toString()); final MDFloatArray floatDataReadFa = reader.float32().readMDArray("fa"); assertEquals(floatDataWritten, floatDataReadFa); final MDFloatArray floatDataReadFas = reader.float32().readMDArray("fas"); assertEquals(floatDataWritten, floatDataReadFas); final MDFloatArray floatBlock = new MDFloatArray(new float[] { -3.1f, -0.1f }, new int[] { 1, 2 }); assertEquals(floatBlock, reader.float32().readMDArrayBlock("f", new int[] { 1, -1 }, new long[] { 1, 0 })); assertEquals(floatBlock, reader.float32().readMDArrayBlock("fas", new int[] { 1, -1 }, new long[] { 1, 0 })); try { reader.float32().readMDArrayBlock("fa", new int[] { 1, -1 }, new long[] { 1, 0 }); fail("Illegal block-wise reading of array-type not detected."); } catch (HDF5JavaException ex) { // Expected } assertEquals(2, reader.object().getRank("f")); assertTrue(Arrays.equals(new long[] { 3, 2 }, reader.object().getDimensions("f"))); assertEquals(2, reader.object().getRank("fa")); assertTrue(Arrays.equals(new long[] { 3, 2 }, reader.object().getDimensions("fa"))); assertEquals(2, reader.object().getRank("fas")); assertTrue(Arrays.equals(new long[] { 3, 2 }, reader.object().getDimensions("fas"))); reader.close(); } @Test public void testFloatArrayCreateCompactOverwriteBlock() { final File datasetFile = new File(workingDirectory, "testFloatArrayCreateCompactOverwroteBlock.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); writer.float32().writeArray("f", new float[] { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 }, HDF5FloatStorageFeatures.FLOAT_COMPACT); writer.float32().writeArrayBlockWithOffset("f", new float[] { 400, 500, 600 }, 3, 3); float[] arrayWritten = new float[] { 1, 2, 3, 400, 500, 600, 7, 8, 9, 10 }; writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); assertTrue(Arrays.equals(arrayWritten, reader.float32().readArray("f"))); reader.close(); } @Test public void testReadFloatMatrixDataSetBlockWise() { final File datasetFile = new File(workingDirectory, "readFloatMatrixBlockWise.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String dsName = "ds"; final float[][] floatMatrix = new float[10][10]; for (int i = 0; i < floatMatrix.length; ++i) { for (int j = 0; j < floatMatrix[i].length; ++j) { floatMatrix[i][j] = i * j; } } writer.float32().writeMatrix(dsName, floatMatrix); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final int blockSize = 5; for (int i = 0; i < 2; ++i) { for (int j = 0; j < 2; ++j) { final float[][] floatMatrixBlockRead = reader.float32().readMatrixBlock(dsName, blockSize, blockSize, i, j); assertEquals(blockSize, floatMatrixBlockRead.length); assertEquals(blockSize, floatMatrixBlockRead[0].length); final float[][] floatMatrixBlockExpected = new float[blockSize][]; for (int k = 0; k < blockSize; ++k) { final float[] rowExpected = new float[blockSize]; System.arraycopy(floatMatrix[i * blockSize + k], blockSize * j, rowExpected, 0, blockSize); floatMatrixBlockExpected[k] = rowExpected; } assertMatrixEquals(floatMatrixBlockExpected, floatMatrixBlockRead); } } reader.close(); } @Test public void testMDIntArrayDifferentSizesElementType() { final File datasetFile = new File(workingDirectory, "testMDIntArrayDifferentSizesElementType.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final MDIntArray arr = new MDIntArray(new int[] { 2, 2 }); arr.set(1, 0, 0); arr.set(2, 0, 1); arr.set(3, 1, 0); arr.set(4, 1, 1); arr.incNumberOfHyperRows(1); arr.set(5, 2, 0); arr.set(6, 2, 1); writer.int16().createMDArray("array", new int[] { 3, 2 }); writer.int32().writeMDArrayBlock("array", arr, new long[] { 0, 0 }); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); assertEquals(arr, reader.int32().readMDArray("array")); reader.close(); } @Test public void testMDIntArrayDifferentSizesElementTypeUnsignedByte() { final File datasetFile = new File(workingDirectory, "testMDIntArrayDifferentSizesElementTypeUnsignedByte.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final MDIntArray arr = new MDIntArray(new int[] { 2, 2 }); arr.set(1, 0, 0); arr.set(2, 0, 1); arr.set(3, 1, 0); arr.set(4, 1, 1); arr.incNumberOfHyperRows(1); arr.set(5, 2, 0); arr.set(255, 2, 1); writer.uint8().createMDArray("array", new int[] { 3, 2 }); writer.int32().writeMDArrayBlock("array", arr, new long[] { 0, 0 }); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); assertEquals(arr, reader.int32().readMDArray("array")); } @Test public void testSetExtentBug() { final File datasetFile = new File(workingDirectory, "setExtentBug.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String dsName = "ds"; final float[][] floatMatrixBlockWritten = new float[][] { { 1, 2 }, { 3, 4 } }; final int blockSize = 2; writer.float32().createMatrix(dsName, 0, 0, blockSize, blockSize); writer.float32().writeMatrixBlock(dsName, floatMatrixBlockWritten, 0, 0); writer.float32().writeMatrixBlock(dsName, floatMatrixBlockWritten, 0, 1); // The next line will make the the block (0,1) disappear if the bug is present. writer.float32().writeMatrixBlock(dsName, floatMatrixBlockWritten, 1, 0); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final float[][] floatMatrixBlockRead = reader.float32().readMatrixBlock(dsName, blockSize, blockSize, 0, 1); assertMatrixEquals(floatMatrixBlockWritten, floatMatrixBlockRead); reader.close(); } @Test public void testWriteFloatMatrixDataSetBlockWise() { final File datasetFile = new File(workingDirectory, "writeFloatMatrixBlockWise.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String dsName = "ds"; final float[][] floatMatrixBlockWritten = new float[5][5]; for (int i = 0; i < floatMatrixBlockWritten.length; ++i) { for (int j = 0; j < floatMatrixBlockWritten[i].length; ++j) { floatMatrixBlockWritten[i][j] = i * j; } } final int blockSize = 5; writer.float32().createMatrix(dsName, 2 * blockSize, 2 * blockSize, blockSize, blockSize); for (int i = 0; i < 2; ++i) { for (int j = 0; j < 2; ++j) { writer.float32().writeMatrixBlock(dsName, floatMatrixBlockWritten, i, j); } } writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); for (int i = 0; i < 2; ++i) { for (int j = 0; j < 2; ++j) { final float[][] floatMatrixBlockRead = reader.float32().readMatrixBlock(dsName, blockSize, blockSize, i, j); assertMatrixEquals(floatMatrixBlockWritten, floatMatrixBlockRead); } } reader.close(); } @Test public void testWriteFloatMatrixDataSetBlockWiseWithOffset() { final File datasetFile = new File(workingDirectory, "writeFloatMatrixBlockWiseWithOffset.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String dsName = "ds"; final float[][] floatMatrixBlockWritten = new float[5][5]; int count = 0; for (int i = 0; i < floatMatrixBlockWritten.length; ++i) { for (int j = 0; j < floatMatrixBlockWritten[i].length; ++j) { floatMatrixBlockWritten[i][j] = ++count; } } final int blockSize = 5; final int offsetX = 2; final int offsetY = 3; writer.float32().createMatrix(dsName, 2 * blockSize, 2 * blockSize, blockSize, blockSize); writer.float32().writeMatrixBlockWithOffset(dsName, floatMatrixBlockWritten, 5, 5, offsetX, offsetY); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final float[][] floatMatrixBlockRead = reader.float32().readMatrixBlockWithOffset(dsName, blockSize, blockSize, offsetX, offsetY); assertMatrixEquals(floatMatrixBlockWritten, floatMatrixBlockRead); final float[][] floatMatrixRead = reader.float32().readMatrix(dsName); // Subtract the non-zero block. for (int i = 0; i < floatMatrixBlockWritten.length; ++i) { for (int j = 0; j < floatMatrixBlockWritten[i].length; ++j) { floatMatrixRead[offsetX + i][offsetY + j] -= floatMatrixBlockWritten[i][j]; } } for (int i = 0; i < floatMatrixRead.length; ++i) { for (int j = 0; j < floatMatrixRead[i].length; ++j) { assertEquals(i + ":" + j, 0.0f, floatMatrixRead[i][j]); } } reader.close(); } @Test public void testReadMDFloatArrayAsByteArray() { final File datasetFile = new File(workingDirectory, "readMDFloatArrayAsByteArray.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); writer.float32().writeMatrix("fm", new float[][] { { 1f, 2f }, { 3f, 4f } }); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final byte[] arr = reader.readAsByteArray("fm"); assertEquals(1f, NativeData.byteToFloat(arr, ByteOrder.NATIVE, 0, 1)[0]); assertEquals(2f, NativeData.byteToFloat(arr, ByteOrder.NATIVE, 4, 1)[0]); assertEquals(3f, NativeData.byteToFloat(arr, ByteOrder.NATIVE, 8, 1)[0]); assertEquals(4f, NativeData.byteToFloat(arr, ByteOrder.NATIVE, 12, 1)[0]); try { reader.opaque().readArrayBlock("fm", 2, 0); fail("readAsByteArrayBlock() is expected to fail on datasets of rank > 1"); } catch (HDF5JavaException ex) { assertEquals("Data Set is expected to be of rank 1 (rank=2)", ex.getMessage()); } reader.close(); } @Test public void testReadByteArrayDataSetBlockWise() { final File datasetFile = new File(workingDirectory, "readByteArrayBlockWise.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String dsName = "ds"; final byte[] byteArray = new byte[100]; for (int i = 0; i < byteArray.length; ++i) { byteArray[i] = (byte) (100 + i); } writer.int8().writeArray(dsName, byteArray); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final int blockSize = 10; for (int i = 0; i < 10; ++i) { final byte[] byteArrayBlockRead = reader.int8().readArrayBlock(dsName, blockSize, i); assertEquals(blockSize, byteArrayBlockRead.length); final byte[] byteArrayBlockExpected = new byte[blockSize]; System.arraycopy(byteArray, blockSize * i, byteArrayBlockExpected, 0, blockSize); assertTrue("Block " + i, Arrays.equals(byteArrayBlockExpected, byteArrayBlockRead)); } reader.close(); } @Test public void testWriteByteArrayDataSetBlockWise() { final File datasetFile = new File(workingDirectory, "writeByteArrayBlockWise.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String dsName = "ds"; final int size = 100; final int blockSize = 10; final int numberOfBlocks = 10; writer.int8().createArray(dsName, size, blockSize, INT_DEFLATE); final byte[] block = new byte[blockSize]; for (int i = 0; i < numberOfBlocks; ++i) { Arrays.fill(block, (byte) i); writer.int8().writeArrayBlock(dsName, block, i); } writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final byte[] byteArrayRead = reader.readAsByteArray(dsName); reader.close(); assertEquals(size, byteArrayRead.length); for (int i = 0; i < byteArrayRead.length; ++i) { assertEquals("Byte " + i, (i / blockSize), byteArrayRead[i]); } } @Test public void testCreateByteArrayDataSetBlockSize0() { final File datasetFile = new File(workingDirectory, "testCreateByteArrayDataSetBlockSize0"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String dsName = "ds"; final int size = 100; final int blockSize = 10; final int numberOfBlocks = 10; final int nominalBlockSize = 0; writer.int8().createArray(dsName, size, nominalBlockSize, INT_DEFLATE); final byte[] block = new byte[blockSize]; for (int i = 0; i < numberOfBlocks; ++i) { Arrays.fill(block, (byte) i); writer.int8().writeArrayBlock(dsName, block, i); } writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final byte[] byteArrayRead = reader.readAsByteArray(dsName); reader.close(); assertEquals(size, byteArrayRead.length); for (int i = 0; i < byteArrayRead.length; ++i) { assertEquals("Byte " + i, (i / blockSize), byteArrayRead[i]); } } @Test public void testCreateFloatArrayWithDifferentStorageLayouts() { final File datasetFile = new File(workingDirectory, "testCreateFloatArrayWithDifferentStorageLayouts"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String dsName1 = "ds1"; final String dsName2 = "ds2"; final int size = 100; writer.float32().createArray(dsName1, size, HDF5FloatStorageFeatures.FLOAT_CONTIGUOUS); writer.float32().createArray(dsName2, size, HDF5FloatStorageFeatures.FLOAT_CHUNKED); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final HDF5DataSetInformation info1 = reader.getDataSetInformation(dsName1); final HDF5DataSetInformation info2 = reader.getDataSetInformation(dsName2); reader.close(); assertEquals(HDF5StorageLayout.CONTIGUOUS, info1.getStorageLayout()); assertEquals(size, info1.getDimensions()[0]); assertNull(info1.tryGetChunkSizes()); assertEquals(HDF5StorageLayout.CHUNKED, info2.getStorageLayout()); assertEquals(0, info2.getDimensions()[0]); assertEquals(size, info2.tryGetChunkSizes()[0]); } @Test public void testWriteByteArrayDataSetBlockWiseExtend() { final File datasetFile = new File(workingDirectory, "writeByteArrayBlockWiseExtend.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String dsName = "ds"; final int size = 100; final int blockSize = 10; final int numberOfBlocks = 10; writer.int8().createArray(dsName, 0, blockSize, INT_DEFLATE); final byte[] block = new byte[blockSize]; for (int i = 0; i < numberOfBlocks; ++i) { Arrays.fill(block, (byte) i); writer.int8().writeArrayBlock(dsName, block, i); } writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final byte[] byteArrayRead = reader.readAsByteArray(dsName); reader.close(); assertEquals(size, byteArrayRead.length); for (int i = 0; i < byteArrayRead.length; ++i) { assertEquals("Byte " + i, (i / blockSize), byteArrayRead[i]); } } @Test public void testWriteByteArrayDataSetBlockWiseMismatch() { final File datasetFile = new File(workingDirectory, "writeByteArrayBlockWise.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String dsName = "ds"; final int size = 99; final int blockSize = 10; final int numberOfBlocks = 10; writer.int8().createArray(dsName, size, blockSize, INT_DEFLATE); final byte[] block = new byte[blockSize]; for (int i = 0; i < numberOfBlocks; ++i) { Arrays.fill(block, (byte) i); if (blockSize * (i + 1) > size) { final int ofs = blockSize * i; writer.int8().writeArrayBlockWithOffset(dsName, block, size - ofs, ofs); } else { writer.int8().writeArrayBlock(dsName, block, i); } } writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final byte[] byteArrayRead = reader.int8().readArray(dsName); reader.close(); assertEquals(size, byteArrayRead.length); for (int i = 0; i < byteArrayRead.length; ++i) { assertEquals("Byte " + i, (i / blockSize), byteArrayRead[i]); } } @Test public void testWriteOpaqueByteArrayDataSetBlockWise() { final File datasetFile = new File(workingDirectory, "writeOpaqueByteArrayBlockWise.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String dsName = "ds"; final int size = 100; final int blockSize = 10; final int numberOfBlocks = 10; final HDF5OpaqueType opaqueDataType = writer.opaque() .createArray(dsName, "TAG", size / 2, blockSize, GENERIC_DEFLATE_MAX); final byte[] block = new byte[blockSize]; for (int i = 0; i < numberOfBlocks; ++i) { Arrays.fill(block, (byte) i); writer.opaque().writeArrayBlock(dsName, opaqueDataType, block, i); } writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final byte[] byteArrayRead = reader.readAsByteArray(dsName); reader.close(); assertEquals(size, byteArrayRead.length); for (int i = 0; i < byteArrayRead.length; ++i) { assertEquals("Byte " + i, (i / blockSize), byteArrayRead[i]); } } @Test public void testWriteOpaqueByteArrayDataSetBlockWiseMismatch() { final File datasetFile = new File(workingDirectory, "writeOpaqueByteArrayBlockWise.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String dsName = "ds"; final int size = 99; final int blockSize = 10; final int numberOfBlocks = 10; final HDF5OpaqueType opaqueDataType = writer.opaque().createArray(dsName, "TAG", size, blockSize, GENERIC_DEFLATE); final byte[] block = new byte[blockSize]; for (int i = 0; i < numberOfBlocks; ++i) { Arrays.fill(block, (byte) i); if (blockSize * (i + 1) > size) { final int ofs = blockSize * i; writer.opaque().writeArrayBlockWithOffset(dsName, opaqueDataType, block, size - ofs, ofs); } else { writer.opaque().writeArrayBlock(dsName, opaqueDataType, block, i); } } writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final byte[] byteArrayRead = reader.readAsByteArray(dsName); reader.close(); assertEquals(size, byteArrayRead.length); for (int i = 0; i < byteArrayRead.length; ++i) { assertEquals("Byte " + i, (i / blockSize), byteArrayRead[i]); } } @Test public void testWriteByteMatrixDataSetBlockWise() { final File datasetFile = new File(workingDirectory, "writeByteMatrixBlockWise.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String dsName = "ds"; final int sizeX = 100; final int sizeY = 10; final int blockSizeX = 10; final int blockSizeY = 5; final int numberOfBlocksX = 10; final int numberOfBlocksY = 2; writer.int8().createMatrix(dsName, sizeX, sizeY, blockSizeX, blockSizeY, INT_DEFLATE); final byte[][] block = new byte[blockSizeX][blockSizeY]; for (int i = 0; i < numberOfBlocksX; ++i) { for (int j = 0; j < numberOfBlocksY; ++j) { for (int k = 0; k < blockSizeX; ++k) { Arrays.fill(block[k], (byte) (i + j)); } writer.int8().writeMatrixBlock(dsName, block, i, j); } } writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final byte[][] byteMatrixRead = reader.int8().readMatrix(dsName); reader.close(); assertEquals(sizeX, byteMatrixRead.length); for (int i = 0; i < byteMatrixRead.length; ++i) { for (int j = 0; j < byteMatrixRead[i].length; ++j) { assertEquals("Byte (" + i + "," + j + ")", (i / blockSizeX + j / blockSizeY), byteMatrixRead[i][j]); } } } @Test public void testWriteByteMatrixDataSetBlockWiseMismatch() { final File datasetFile = new File(workingDirectory, "writeByteMatrixBlockWiseMismatch.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String dsName = "ds"; final int sizeX = 99; final int sizeY = 12; final int blockSizeX = 10; final int blockSizeY = 5; final int numberOfBlocksX = 10; final int numberOfBlocksY = 3; writer.int8().createMatrix(dsName, sizeX, sizeY, blockSizeX, blockSizeY, INT_DEFLATE); final byte[][] block = new byte[blockSizeX][blockSizeY]; for (int i = 0; i < numberOfBlocksX; ++i) { for (int j = 0; j < numberOfBlocksY; ++j) { for (int k = 0; k < blockSizeX; ++k) { Arrays.fill(block[k], (byte) (i + j)); } writer.int8().writeMatrixBlockWithOffset(dsName, block, Math.min(blockSizeX, sizeX - i * blockSizeX), Math.min(blockSizeY, sizeY - j * blockSizeY), i * blockSizeX, j * blockSizeY); } } writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final byte[][] byteMatrixRead = reader.int8().readMatrix(dsName); reader.close(); assertEquals(sizeX, byteMatrixRead.length); for (int i = 0; i < byteMatrixRead.length; ++i) { for (int j = 0; j < byteMatrixRead[i].length; ++j) { assertEquals("Byte (" + i + "," + j + ")", (i / blockSizeX + j / blockSizeY), byteMatrixRead[i][j]); } } } @Test public void testReadToFloatMDArray() { final File datasetFile = new File(workingDirectory, "readToFloatMDArray.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String dsName = "ds"; final MDFloatArray arrayWritten = new MDFloatArray(new float[] { 1, 2, 3, 4, 5, 6, 7, 8, 9 }, new int[] { 3, 3 }); writer.float32().writeMDArray(dsName, arrayWritten); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final MDFloatArray arrayRead = new MDFloatArray(new int[] { 10, 10 }); final int memOfsX = 2; final int memOfsY = 3; reader.float32().readToMDArrayWithOffset(dsName, arrayRead, new int[] { memOfsX, memOfsY }); reader.close(); final boolean[][] isSet = new boolean[10][10]; for (int i = 0; i < arrayWritten.size(0); ++i) { for (int j = 0; j < arrayWritten.size(1); ++j) { isSet[memOfsX + i][memOfsY + j] = true; assertEquals("(" + i + "," + j + ")", arrayWritten.get(i, j), arrayRead.get(memOfsX + i, memOfsY + j)); } } for (int i = 0; i < arrayRead.size(0); ++i) { for (int j = 0; j < arrayRead.size(1); ++j) { if (isSet[i][j] == false) { assertEquals("(" + i + "," + j + ")", 0f, arrayRead.get(i, j)); } } } } @DataProvider private Object[][] provideSizes() { return new Object[][] { { 10, 99 }, { 10, 100 }, { 10, 101 } }; } @Test(dataProvider = "provideSizes") public void testIterateOverFloatArrayInNaturalBlocks(int blockSize, int dataSetSize) { final File datasetFile = new File(workingDirectory, "iterateOverFloatArrayInNaturalBlocks.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String dsName = "ds"; final float[] arrayWritten = new float[dataSetSize]; for (int i = 0; i < dataSetSize; ++i) { arrayWritten[i] = i; } writer.float32().createArray(dsName, dataSetSize, blockSize); writer.float32().writeArrayBlock(dsName, arrayWritten, 0); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); int i = 0; for (HDF5DataBlock block : reader.float32().getArrayNaturalBlocks(dsName)) { assertEquals(i, block.getIndex()); assertEquals(blockSize * i, block.getOffset()); final float[] arrayReadBlock = block.getData(); if (blockSize * (i + 1) > dataSetSize) { assertEquals(dataSetSize - i * blockSize, arrayReadBlock.length); } else { assertEquals(blockSize, arrayReadBlock.length); } final float[] arrayWrittenBlock = new float[arrayReadBlock.length]; System.arraycopy(arrayWritten, (int) block.getOffset(), arrayWrittenBlock, 0, arrayWrittenBlock.length); assertTrue(Arrays.equals(arrayWrittenBlock, arrayReadBlock)); ++i; } assertEquals(dataSetSize / blockSize + (dataSetSize % blockSize != 0 ? 1 : 0), i); reader.close(); } @Test public void testReadToFloatMDArrayBlockWithOffset() { final File datasetFile = new File(workingDirectory, "readToFloatMDArrayBlockWithOffset.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String dsName = "ds"; final MDFloatArray arrayWritten = new MDFloatArray(new float[] { 1, 2, 3, 4, 5, 6, 7, 8, 9 }, new int[] { 3, 3 }); writer.float32().writeMDArray(dsName, arrayWritten); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final MDFloatArray arrayRead = new MDFloatArray(new int[] { 10, 10 }); final int memOfsX = 2; final int memOfsY = 3; final int diskOfsX = 1; final int diskOfsY = 0; final int blockSizeX = 3; final int blockSizeY = 2; final int[] effectiveDimensions = reader.float32().readToMDArrayBlockWithOffset(dsName, arrayRead, new int[] { blockSizeX, blockSizeY }, new long[] { diskOfsX, diskOfsY }, new int[] { memOfsX, memOfsY }); reader.close(); assertEquals(blockSizeX - 1, effectiveDimensions[0]); assertEquals(blockSizeY, effectiveDimensions[1]); final boolean[][] isSet = new boolean[10][10]; for (int i = 0; i < effectiveDimensions[0]; ++i) { for (int j = 0; j < effectiveDimensions[1]; ++j) { isSet[memOfsX + i][memOfsY + j] = true; assertEquals("(" + i + "," + j + ")", arrayWritten.get(diskOfsX + i, diskOfsY + j), arrayRead.get(memOfsX + i, memOfsY + j)); } } for (int i = 0; i < arrayRead.size(0); ++i) { for (int j = 0; j < arrayRead.size(1); ++j) { if (isSet[i][j] == false) { assertEquals("(" + i + "," + j + ")", 0f, arrayRead.get(i, j)); } } } } @Test public void testReadToTimeDurationMDArrayBlockWithOffset() { final File datasetFile = new File(workingDirectory, "readToTimeDurationMDArrayBlockWithOffset.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String dsName = "ds"; final HDF5TimeDurationMDArray arrayWritten = new HDF5TimeDurationMDArray(new long[] { 1, 1, 1, 1, 1, 1, 1, 1, 1 }, new int[] { 3, 3 }, HDF5TimeUnit.MINUTES); writer.duration().writeMDArray(dsName, arrayWritten); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final HDF5TimeDurationMDArray arrayRead = new HDF5TimeDurationMDArray(new int[] { 10, 10 }, HDF5TimeUnit.SECONDS); final int memOfsX = 2; final int memOfsY = 3; final int diskOfsX = 1; final int diskOfsY = 0; final int blockSizeX = 3; final int blockSizeY = 2; final int[] effectiveDimensions = reader.duration().readToMDArrayBlockWithOffset(dsName, arrayRead, new int[] { blockSizeX, blockSizeY }, new long[] { diskOfsX, diskOfsY }, new int[] { memOfsX, memOfsY }); reader.close(); assertEquals(blockSizeX - 1, effectiveDimensions[0]); assertEquals(blockSizeY, effectiveDimensions[1]); final boolean[][] isSet = new boolean[10][10]; for (int i = 0; i < effectiveDimensions[0]; ++i) { for (int j = 0; j < effectiveDimensions[1]; ++j) { isSet[memOfsX + i][memOfsY + j] = true; assertEquals("(" + i + "," + j + ")", 60 * arrayWritten.get(diskOfsX + i, diskOfsY + j), arrayRead.get(memOfsX + i, memOfsY + j)); } } for (int i = 0; i < arrayRead.size(0); ++i) { for (int j = 0; j < arrayRead.size(1); ++j) { if (isSet[i][j] == false) { assertEquals("(" + i + "," + j + ")", 0, arrayRead.get(i, j)); } } } } @Test(dataProvider = "provideSizes") public void testIterateOverStringArrayInNaturalBlocks(int blockSize, int dataSetSize) { final File datasetFile = new File(workingDirectory, "testIterateOverStringArrayInNaturalBlocks.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String dsName = "ds"; final String[] arrayWritten = new String[dataSetSize]; for (int i = 0; i < dataSetSize; ++i) { arrayWritten[i] = "" + i; } writer.string().createArray(dsName, dataSetSize, blockSize); writer.string().writeArrayBlock(dsName, arrayWritten, 0); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); int i = 0; for (HDF5DataBlock block : reader.string().getArrayNaturalBlocks(dsName)) { assertEquals(i, block.getIndex()); assertEquals(blockSize * i, block.getOffset()); final String[] arrayReadBlock = block.getData(); if (blockSize * (i + 1) > dataSetSize) { assertEquals(dataSetSize - i * blockSize, arrayReadBlock.length); } else { assertEquals(blockSize, arrayReadBlock.length); } final String[] arrayWrittenBlock = new String[arrayReadBlock.length]; System.arraycopy(arrayWritten, (int) block.getOffset(), arrayWrittenBlock, 0, arrayWrittenBlock.length); assertTrue(Arrays.equals(arrayWrittenBlock, arrayReadBlock)); ++i; } assertEquals(dataSetSize / blockSize + (dataSetSize % blockSize != 0 ? 1 : 0), i); reader.close(); } @DataProvider private Object[][] provideMDSizes() { return new Object[][] { { new int[] { 2, 2 }, new long[] { 4, 3 }, new float[] { 0f, 2f, 6f, 8f }, new int[][] { { 2, 2 }, { 2, 1 }, { 2, 2 }, { 2, 1 } } }, { new int[] { 2, 2 }, new long[] { 4, 4 }, new float[] { 0f, 2f, 8f, 10f }, new int[][] { { 2, 2 }, { 2, 2 }, { 2, 2 }, { 2, 2 } } }, { new int[] { 2, 2 }, new long[] { 4, 5 }, new float[] { 0f, 2f, 4f, 10f, 12f, 14f }, new int[][] { { 2, 2 }, { 2, 2 }, { 2, 1 }, { 2, 2 }, { 2, 2 }, { 2, 1 } } }, { new int[] { 3, 2 }, new long[] { 5, 4 }, new float[] { 0f, 2f, 12f, 14f }, new int[][] { { 3, 2 }, { 3, 2 }, { 2, 2 }, { 2, 2 } } }, { new int[] { 2, 2 }, new long[] { 5, 4 }, new float[] { 0f, 2f, 8f, 10f, 16f, 18f }, new int[][] { { 2, 2 }, { 2, 2 }, { 2, 2 }, { 2, 2 }, { 1, 2 }, { 1, 2 } } }, }; } @Test(dataProvider = "provideMDSizes") public void testIterateOverMDFloatArrayInNaturalBlocks(int[] blockSize, long[] dataSetSize, float[] firstNumberPerIteration, int[][] blockSizePerIteration) { final File datasetFile = new File(workingDirectory, "iterateOverMDFloatArrayInNaturalBlocks.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String dsName = "ds"; final float[] flattenedArray = new float[getNumberOfElements(dataSetSize)]; for (int i = 0; i < flattenedArray.length; ++i) { flattenedArray[i] = i; } final MDFloatArray arrayWritten = new MDFloatArray(flattenedArray, dataSetSize); writer.float32().createMDArray(dsName, dataSetSize, blockSize); writer.float32().writeMDArrayBlock(dsName, arrayWritten, new long[blockSize.length]); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); int i = 0; for (HDF5MDDataBlock block : reader.float32().getMDArrayNaturalBlocks(dsName)) { assertEquals(firstNumberPerIteration[i], block.getData().get(0, 0)); assertTrue(Arrays.equals(block.getData().dimensions(), blockSizePerIteration[i])); ++i; } assertEquals(firstNumberPerIteration.length, i); reader.close(); } private static int getNumberOfElements(long[] size) { int elements = 1; for (long dim : size) { elements *= dim; } return elements; } @Test public void testStringArray() { final File stringArrayFile = new File(workingDirectory, "stringArray.h5"); stringArrayFile.delete(); assertFalse(stringArrayFile.exists()); stringArrayFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(stringArrayFile); final String[] data = new String[] { "abc", "ABCxxx", "xyz" }; final String dataSetName = "/aStringArray"; writer.writeStringArray(dataSetName, data); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(stringArrayFile); final String[] dataStored = reader.readStringArray(dataSetName); assertTrue(Arrays.equals(data, dataStored)); reader.close(); } @Test public void testStringArrayUTF8() { final File stringArrayFile = new File(workingDirectory, "stringArrayUTF8.h5"); stringArrayFile.delete(); assertFalse(stringArrayFile.exists()); stringArrayFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().configure(stringArrayFile).useUTF8CharacterEncoding() .writer(); final String[] data = new String[] { "abc", "ABCxxx", "\u00b6\u00bc\u09ab" }; final String dataSetName = "/aStringArray"; writer.writeStringArray(dataSetName, data); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(stringArrayFile); final String[] dataStored = reader.readStringArray(dataSetName); assertTrue(Arrays.equals(data, dataStored)); reader.close(); } @Test public void testStringArrayUTF8WithZeroChar() { final File stringArrayFile = new File(workingDirectory, "stringArrayUTF8WithZeroChar.h5"); stringArrayFile.delete(); assertFalse(stringArrayFile.exists()); stringArrayFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().configure(stringArrayFile).useUTF8CharacterEncoding() .writer(); final String[] data = new String[] { "abc", "ABCxxx", "\u00b6\000\u00bc\u09ab" }; final String dataSetName = "/aStringArray"; writer.writeStringArray(dataSetName, data); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(stringArrayFile); final String[] dataStored = reader.string().readArrayRaw(dataSetName); assertEquals(3, dataStored.length); assertEquals(StringUtils.rightPad("abc", 8, "\0"), dataStored[0]); assertEquals(StringUtils.rightPad("ABCxxx", 8, "\0"), dataStored[1]); assertEquals("\u00b6\000\u00bc\u09ab", dataStored[2]); reader.close(); } @Test public void testStringArrayBlock() { final File stringArrayFile = new File(workingDirectory, "stringArrayBlock.h5"); stringArrayFile.delete(); assertFalse(stringArrayFile.exists()); stringArrayFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(stringArrayFile); final String[] data = new String[] { "abc\0A", "ABCxxx\0" + "1", "xyz\0;" }; final String[] dataZeroTerm = zeroTerm(data); final String[] dataPadded = pad(data, 8); final String emptyPadded = StringUtils.rightPad("", 8, '\0'); final String dataSetName = "/aStringArray"; writer.string().createArray(dataSetName, 8, 5, 3); writer.string().writeArrayBlock(dataSetName, data, 1); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(stringArrayFile); String[] dataStored = reader.string().readArray(dataSetName); assertTrue(Arrays.equals(new String[] { "", "", "", dataZeroTerm[0], dataZeroTerm[1], dataZeroTerm[2] }, dataStored)); dataStored = reader.string().readArrayRaw(dataSetName); assertTrue(Arrays.equals(new String[] { emptyPadded, emptyPadded, emptyPadded, dataPadded[0], dataPadded[1], dataPadded[2] }, dataStored)); dataStored = reader.string().readArrayBlock(dataSetName, 3, 0); assertTrue(Arrays.equals(new String[] { "", "", "" }, dataStored)); dataStored = reader.string().readArrayBlockRaw(dataSetName, 3, 0); assertTrue(Arrays.equals(new String[] { emptyPadded, emptyPadded, emptyPadded }, dataStored)); dataStored = reader.string().readArrayBlock(dataSetName, 3, 1); assertTrue(Arrays.equals(dataZeroTerm, dataStored)); dataStored = reader.string().readArrayBlockRaw(dataSetName, 3, 1); assertTrue(Arrays.equals(dataPadded, dataStored)); dataStored = reader.string().readArrayBlockWithOffset(dataSetName, 3, 2); assertTrue(Arrays.equals(new String[] { "", dataZeroTerm[0], dataZeroTerm[1] }, dataStored)); dataStored = reader.string().readArrayBlockWithOffsetRaw(dataSetName, 3, 2); assertTrue(Arrays.equals(new String[] { emptyPadded, dataPadded[0], dataPadded[1] }, dataStored)); reader.close(); } @Test public void testStringArrayBlockCompact() { final File stringArrayFile = new File(workingDirectory, "stringArrayBlockCompact.h5"); stringArrayFile.delete(); assertFalse(stringArrayFile.exists()); stringArrayFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(stringArrayFile); final String[] data = new String[] { "abc", "ABCxxx", "xyz" }; final String dataSetName = "/aStringArray"; writer.string().createArray(dataSetName, 6, 6, HDF5GenericStorageFeatures.GENERIC_COMPACT); writer.string().writeArrayBlock(dataSetName, data, 1); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(stringArrayFile); String[] dataStored = reader.readStringArray(dataSetName); assertTrue(Arrays.equals(new String[] { "", "", "", data[0], data[1], data[2] }, dataStored)); dataStored = reader.string().readArrayBlock(dataSetName, 3, 0); assertTrue(Arrays.equals(new String[] { "", "", "" }, dataStored)); dataStored = reader.string().readArrayBlock(dataSetName, 3, 1); assertTrue(Arrays.equals(data, dataStored)); dataStored = reader.string().readArrayBlockWithOffset(dataSetName, 3, 2); assertTrue(Arrays.equals(new String[] { "", data[0], data[1] }, dataStored)); reader.close(); } @Test public void testStringArrayBlockVL() { final File stringArrayFile = new File(workingDirectory, "stringArrayBlockVL.h5"); stringArrayFile.delete(); assertFalse(stringArrayFile.exists()); stringArrayFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(stringArrayFile); final String[] data1 = new String[] { "abc", "ABCxxx", "xyz" }; final String[] data2 = new String[] { "abd", "ABDxxx", "xyw" }; final String[] data = new String[] { "", "", "", "abc", "ABCxxx", "xyz", "abd", "ABDxxx", "xyw" }; final String dataSetName = "/aStringArray"; writer.string().createArrayVL(dataSetName, 0, 5); writer.string().writeArrayBlock(dataSetName, data1, 1); writer.string().writeArrayBlock(dataSetName, data2, 2); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(stringArrayFile); String[] dataRead = reader.readStringArray(dataSetName); assertTrue(Arrays.equals(data, dataRead)); dataRead = reader.string().readArrayBlock(dataSetName, 3, 1); assertTrue(Arrays.equals(data1, dataRead)); dataRead = reader.string().readArrayBlock(dataSetName, 3, 2); assertTrue(Arrays.equals(data2, dataRead)); dataRead = reader.string().readArrayBlockWithOffset(dataSetName, 3, 5); assertTrue(Arrays.equals(new String[] { "xyz", "abd", "ABDxxx" }, dataRead)); reader.close(); } @Test public void testStringArrayMD() { final File stringArrayFile = new File(workingDirectory, "stringMDArray.h5"); stringArrayFile.delete(); assertFalse(stringArrayFile.exists()); stringArrayFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(stringArrayFile); final MDArray data = new MDArray(new String[] { "abc", "ABCxxx", "xyz", "DEF" }, new long[] { 2, 2 }); final String dataSetName = "/aStringArray"; writer.string().writeMDArray(dataSetName, data); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(stringArrayFile); final MDArray dataStored = reader.string().readMDArray(dataSetName); assertTrue(Arrays.equals(data.getAsFlatArray(), dataStored.getAsFlatArray())); assertTrue(Arrays.equals(data.dimensions(), dataStored.dimensions())); reader.close(); } @Test public void testStringArrayMDBlocks() { final File stringArrayFile = new File(workingDirectory, "stringMDArrayBlocks.h5"); stringArrayFile.delete(); assertFalse(stringArrayFile.exists()); stringArrayFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(stringArrayFile); final String dataSetName = "/aStringArray"; writer.string().createMDArray(dataSetName, 8, new long[] { 4, 4 }, new int[] { 2, 2 }); final MDArray data = new MDArray(new String[] { "abc", "ABCxxx\0" + 1, "xyz\0;", "DEF\0" + 8 }, new long[] { 2, 2 }); final MDArray dataZeroTerm = new MDArray(zeroTerm(data.getAsFlatArray()), data.dimensions()); final MDArray dataPadded = new MDArray(pad(data.getAsFlatArray(), 8), data.dimensions()); for (int i = 0; i < 2; ++i) { for (int j = 0; j < 2; ++j) { writer.string().writeMDArrayBlock(dataSetName, data, new long[] { i, j }); } } writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(stringArrayFile); int i = 0; int j = 0; for (HDF5MDDataBlock> block : reader.string().getMDArrayNaturalBlocks( dataSetName)) { assertTrue(Arrays.equals(dataZeroTerm.getAsFlatArray(), block.getData() .getAsFlatArray())); assertTrue(Arrays.equals(dataZeroTerm.dimensions(), block.getData().dimensions())); assertTrue(Arrays.equals(new long[] { i, j }, block.getIndex())); if (++j > 1) { j = 0; ++i; } } i = 0; j = 0; for (HDF5MDDataBlock> block : reader.string().getMDArrayNaturalBlocksRaw( dataSetName)) { assertTrue(Arrays.equals(dataPadded.getAsFlatArray(), block.getData().getAsFlatArray())); assertTrue(Arrays.equals(dataPadded.dimensions(), block.getData().dimensions())); assertTrue(Arrays.equals(new long[] { i, j }, block.getIndex())); if (++j > 1) { j = 0; ++i; } } reader.close(); } private String[] pad(String[] data, int len) { final String[] result = new String[data.length]; for (int i = 0; i < result.length; ++i) { result[i] = StringUtils.rightPad(data[i], len, '\0'); } return result; } private String[] zeroTerm(String[] data) { final String[] result = new String[data.length]; for (int i = 0; i < result.length; ++i) { result[i] = zeroTerm(data[i]); } return result; } private String zeroTerm(String s) { int idx = s.indexOf('\0'); if (idx < 0) { return s; } else { return s.substring(0, idx); } } @Test public void testStringMDArrayVL() { final File stringArrayFile = new File(workingDirectory, "stringMDArrayVL.h5"); stringArrayFile.delete(); assertFalse(stringArrayFile.exists()); stringArrayFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(stringArrayFile); final MDArray data = new MDArray(new String[] { "abc", "ABCxxx", "xyz", "DEF" }, new long[] { 2, 2 }); final String dataSetName = "/aStringArray"; writer.string().writeMDArrayVL(dataSetName, data); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(stringArrayFile); final MDArray dataStored = reader.string().readMDArray(dataSetName); assertTrue(Arrays.equals(data.getAsFlatArray(), dataStored.getAsFlatArray())); assertTrue(Arrays.equals(data.dimensions(), dataStored.dimensions())); final HDF5DataSetInformation info = reader.getDataSetInformation(dataSetName); reader.close(); assertTrue(info.getTypeInformation().isVariableLengthString()); assertEquals("STRING(-1)", info.getTypeInformation().toString()); assertEquals(HDF5StorageLayout.CHUNKED, info.getStorageLayout()); assertTrue(Arrays.toString(info.getDimensions()), Arrays.equals(new long[] { 2, 2 }, info.getDimensions())); assertTrue(Arrays.toString(info.getMaxDimensions()), Arrays.equals(new long[] { -1, -1 }, info.getMaxDimensions())); assertTrue(Arrays.toString(info.tryGetChunkSizes()), Arrays.equals(MDArray.toInt(info.getDimensions()), info.tryGetChunkSizes())); } @Test public void testStringMDArrayVLBlocks() { final File stringArrayFile = new File(workingDirectory, "stringMDArrayVLBlocks.h5"); stringArrayFile.delete(); assertFalse(stringArrayFile.exists()); stringArrayFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(stringArrayFile); final long[] dims = new long[] { 8, 8 }; final int[] blockSize = new int[] { 2, 2 }; final MDArray data = new MDArray(new String[] { "abc", "ABCxxx", "xyz", "DEF" }, blockSize); final String dataSetName = "/aStringArray"; writer.string().createMDArrayVL(dataSetName, dims, blockSize); writer.string().writeMDArrayBlock(dataSetName, data, new long[] { 1, 1 }); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(stringArrayFile); final MDArray dataStored = reader.string().readMDArrayBlock(dataSetName, blockSize, new long[] { 1, 1 }); assertTrue(Arrays.equals(data.getAsFlatArray(), dataStored.getAsFlatArray())); assertTrue(Arrays.equals(data.dimensions(), dataStored.dimensions())); assertTrue(Arrays.equals(new String[] { "", "", "", "" }, reader.string().readMDArrayBlock(dataSetName, blockSize, new long[] { 1, 0 }).getAsFlatArray())); assertTrue(Arrays.equals(new String[] { "", "", "", "" }, reader.string().readMDArrayBlock(dataSetName, blockSize, new long[] { 0, 1 }).getAsFlatArray())); assertTrue(Arrays.equals(new String[] { "", "", "", "" }, reader.string().readMDArrayBlock(dataSetName, blockSize, new long[] { 2, 2 }).getAsFlatArray())); final HDF5DataSetInformation info = reader.getDataSetInformation(dataSetName); reader.close(); assertTrue(info.getTypeInformation().isVariableLengthString()); assertEquals("STRING(-1)", info.getTypeInformation().toString()); assertEquals(HDF5StorageLayout.CHUNKED, info.getStorageLayout()); assertTrue(Arrays.equals(dims, info.getDimensions())); assertTrue(Arrays.equals(new long[] { -1, -1 }, info.getMaxDimensions())); assertTrue(Arrays.equals(blockSize, info.tryGetChunkSizes())); } @Test public void testOverwriteString() { final File stringOverwriteFile = new File(workingDirectory, "overwriteString.h5"); stringOverwriteFile.delete(); assertFalse(stringOverwriteFile.exists()); stringOverwriteFile.deleteOnExit(); IHDF5Writer writer = HDF5FactoryProvider.get().configure(stringOverwriteFile) .dontUseExtendableDataTypes().writer(); final String largeData = StringUtils.repeat("a", 12); final String smallData = "abc1234"; final String dataSetName = "/aString"; writer.string().write(dataSetName, smallData); writer.string().write(dataSetName, largeData); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(stringOverwriteFile); final String dataRead = reader.readString(dataSetName); assertEquals(largeData, dataRead); reader.close(); } @Test public void testOverwriteStringWithLarge() { final File stringOverwriteFile = new File(workingDirectory, "overwriteStringWithLarge.h5"); stringOverwriteFile.delete(); assertFalse(stringOverwriteFile.exists()); stringOverwriteFile.deleteOnExit(); IHDF5Writer writer = HDF5FactoryProvider.get().configure(stringOverwriteFile).writer(); final String largeData = StringUtils.repeat("a", 64 * 1024); final String smallData = "abc1234"; final String dataSetName = "/aString"; writer.string().write(dataSetName, smallData); writer.string().write(dataSetName, largeData); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(stringOverwriteFile); final String dataRead = reader.readString(dataSetName); assertEquals(largeData, dataRead); reader.close(); } @Test public void testOverwriteStringWithLargeKeepCompact() { final File stringOverwriteFile = new File(workingDirectory, "overwriteStringWithLargeKeepCompact.h5"); stringOverwriteFile.delete(); assertFalse(stringOverwriteFile.exists()); stringOverwriteFile.deleteOnExit(); IHDF5Writer writer = HDF5FactoryProvider.get().configure(stringOverwriteFile).writer(); final String largeData = StringUtils.repeat("a", 64 * 1024); final String smallData = "abc1234"; final String dataSetName = "/aString"; writer.string().write(dataSetName, smallData); writer.string().write(dataSetName, largeData, HDF5GenericStorageFeatures.GENERIC_CONTIGUOUS_KEEP); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(stringOverwriteFile); final String dataRead = reader.readString(dataSetName); assertEquals(largeData.substring(0, smallData.length()), dataRead); assertEquals(HDF5StorageLayout.COMPACT, reader.getDataSetInformation(dataSetName) .getStorageLayout()); reader.close(); } @Test public void testSmallString() { final File smallStringFile = new File(workingDirectory, "smallString.h5"); smallStringFile.delete(); assertFalse(smallStringFile.exists()); smallStringFile.deleteOnExit(); IHDF5Writer writer = HDF5FactoryProvider.get().configure(smallStringFile).writer(); final String dataSetName = "/aString"; writer.string().write(dataSetName, "abc"); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(smallStringFile); final String dataRead = reader.readString(dataSetName); assertEquals("abc", dataRead); assertEquals(HDF5StorageLayout.COMPACT, reader.getDataSetInformation(dataSetName) .getStorageLayout()); reader.close(); } @Test public void testVeryLargeString() { final File veryLargeStringFile = new File(workingDirectory, "veryLargeString.h5"); veryLargeStringFile.delete(); assertFalse(veryLargeStringFile.exists()); veryLargeStringFile.deleteOnExit(); IHDF5Writer writer = HDF5FactoryProvider.get().configure(veryLargeStringFile).writer(); final String largeData = StringUtils.repeat("a", 64 * 1024); final String dataSetName = "/aString"; writer.string().write(dataSetName, largeData); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(veryLargeStringFile); final String dataRead = reader.readString(dataSetName); assertEquals(largeData, dataRead); assertEquals(HDF5StorageLayout.CONTIGUOUS, reader.getDataSetInformation(dataSetName) .getStorageLayout()); reader.close(); } @Test public void testReadStringAsByteArray() { final File file = new File(workingDirectory, "readStringAsByteArray.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer w = HDF5Factory.open(file); w.string().write("a", "abc"); w.close(); final IHDF5Reader r = HDF5Factory.openForReading(file); final byte[] b = r.readAsByteArray("a"); assertEquals("abc", new String(b)); r.close(); } @Test public void testReadStringVLAsByteArray() { final File file = new File(workingDirectory, "readStringVLAsByteArray.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer w = HDF5Factory.open(file); w.string().writeVL("a", "abc"); w.close(); final IHDF5Reader r = HDF5Factory.openForReading(file); final byte[] b = r.readAsByteArray("a"); assertEquals("abc", new String(b)); r.close(); } @Test public void testReadStringAttributeAsByteArray() { final File file = new File(workingDirectory, "readStringAttributeAsByteArray.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer w = HDF5Factory.open(file); w.string().setAttr("/", "a", "abc"); w.close(); final IHDF5Reader r = HDF5Factory.openForReading(file); final byte[] b = r.opaque().getArrayAttr("/", "a"); assertEquals("abc", new String(b)); r.close(); } @Test public void testStringAttributeFixedLength() { final File file = new File(workingDirectory, "stringAttributeFixedLength.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer w = HDF5Factory.open(file); w.string().setAttr("/", "a", "a\0c"); w.close(); final IHDF5Reader r = HDF5Factory.openForReading(file); final String b = r.string().getAttrRaw("/", "a"); assertEquals("a\0c", b); r.close(); } @Test public void testStringAttributeLength0() { final File file = new File(workingDirectory, "stringAttributeLength0.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer w = HDF5Factory.open(file); w.string().setAttr("/", "a", ""); w.close(); final IHDF5Reader r = HDF5Factory.openForReading(file); final String b = r.string().getAttr("/", "a"); assertEquals("", b); r.close(); } @Test public void testStringAttributeFixedLengthExplicitlySaveLength() { final File file = new File(workingDirectory, "stringAttributeFixedLengthExplicitlySaveLength.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer w = HDF5Factory.open(file); w.string().setAttr("/", "a", "a\0c"); w.close(); final IHDF5Reader r = HDF5Factory.openForReading(file); assertEquals("a\0c", r.string().getAttrRaw("/", "a")); assertEquals("a", r.string().getAttr("/", "a")); r.close(); } @Test public void testStringAttributeFixedLengthOverwriteWithShorter() { final File file = new File(workingDirectory, "stringAttributeFixedLengthOverwriteWithShorter.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer w = HDF5Factory.open(file); w.string().setAttr("/", "a", "abcdef"); // This will delete the old attribute and write a new one with length 3. w.string().setAttr("/", "a", "ghi"); w.string().setAttr("/", "b", "abcdef", 6); // This will keep the old attribute (of length 6) and just overwrite its value. w.string().setAttr("/", "b", "jkl", 6); w.close(); final IHDF5Reader r = HDF5Factory.openForReading(file); assertEquals("ghi", r.string().getAttrRaw("/", "a")); assertEquals("jkl\0\0\0", r.string().getAttrRaw("/", "b")); r.close(); } @Test public void testStringAttributeUTF8FixedLength() { final File file = new File(workingDirectory, "stringAttributeUTF8FixedLength.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer w = HDF5Factory.configure(file).useUTF8CharacterEncoding().writer(); w.string().setAttr("/", "a", "a\0c"); w.close(); final IHDF5Reader r = HDF5Factory.openForReading(file); assertEquals("a\0c", r.string().getAttrRaw("/", "a")); r.close(); } @Test public void testStringArrayAttributeLengthFitsValue() { final File file = new File(workingDirectory, "stringArrayAttributeLengthFitsValue.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer w = HDF5Factory.open(file); w.string().setArrayAttr("/", "a", new String[] { "12", "a\0c", "QWERTY" }); w.close(); final IHDF5Reader r = HDF5Factory.openForReading(file); final String[] s0Term = r.string().getArrayAttr("/", "a"); final String[] sFixed = r.string().getArrayAttrRaw("/", "a"); assertTrue(Arrays.equals(new String[] { "12", "a", "QWERTY" }, s0Term)); assertTrue(Arrays.equals(new String[] { "12\0\0\0\0", "a\0c\0\0\0", "QWERTY" }, sFixed)); r.close(); } @Test public void testStringArrayAttributeFixedLength() { final File file = new File(workingDirectory, "stringArrayAttributeFixedLength.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer w = HDF5Factory.open(file); w.string().setArrayAttr("/", "a", new String[] { "12", "a\0c", "QWERTY" }, 7); w.close(); final IHDF5Reader r = HDF5Factory.openForReading(file); final String[] s0Term = r.string().getArrayAttr("/", "a"); final String[] sFixed = r.string().getArrayAttrRaw("/", "a"); assertTrue(Arrays.equals(new String[] { "12", "a", "QWERTY" }, s0Term)); assertTrue(Arrays.equals(new String[] { "12\0\0\0\0\0", "a\0c\0\0\0\0", "QWERTY\0" }, sFixed)); r.close(); } @Test public void testStringArrayAttributeUTF8LengthFitsValue() { final File file = new File(workingDirectory, "stringArrayAttributeUTF8LengthFitsValue.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer w = HDF5Factory.configure(file).useUTF8CharacterEncoding().writer(); w.string().setArrayAttr("/", "a", new String[] { "12", "a\0c", "QWERTY" }); w.close(); final IHDF5Reader r = HDF5Factory.openForReading(file); final String[] b = r.string().getArrayAttrRaw("/", "a"); assertTrue(Arrays.equals(new String[] { "12\0\0\0\0", "a\0c\0\0\0", "QWERTY" }, b)); r.close(); } @Test public void testStringArrayAttributeUTF8FixedLength() { final File file = new File(workingDirectory, "stringArrayAttributeUTF8FixedLength.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer w = HDF5Factory.configure(file).useUTF8CharacterEncoding().writer(); w.string().setArrayAttr("/", "a", new String[] { "12", "a\0c", "QWERTY" }, 7); w.close(); final IHDF5Reader r = HDF5Factory.openForReading(file); final String[] sFixed = r.string().getArrayAttrRaw("/", "a"); final String[] s0Term = r.string().getArrayAttr("/", "a"); assertTrue(Arrays.equals(new String[] { StringUtils.rightPad("12", 7 * 4, '\0'), StringUtils.rightPad("a\0c", 7 * 4, '\0'), StringUtils.rightPad("QWERTY", 7 * 4, '\0') }, sFixed)); assertTrue(Arrays.equals(new String[] { "12", "a", "QWERTY" }, s0Term)); r.close(); } @Test public void testStringMDArrayAttributeFixedLength() { final File file = new File(workingDirectory, "stringMDArrayAttributeFixedLength.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer w = HDF5Factory.open(file); final MDArray array = new MDArray(new String[] { "12", "a\0c", "QWERTY", "" }, new int[] { 2, 2 }); w.string().setMDArrayAttr("/", "a", array, 7); w.close(); final IHDF5Reader r = HDF5Factory.openForReading(file); final MDArray s0Term = r.string().getMDArrayAttr("/", "a"); final MDArray sFixed = r.string().getMDArrayAttrRaw("/", "a"); assertEquals(new MDArray(new String[] { "12", "a", "QWERTY", "" }, new int[] { 2, 2 }), s0Term); assertEquals(new MDArray(new String[] { "12\0\0\0\0\0", "a\0c\0\0\0\0", "QWERTY\0", "\0\0\0\0\0\0\0" }, new int[] { 2, 2 }), sFixed); r.close(); } @Test public void testStringMDArrayAttributeUTF8LengthFitsValue() { final File file = new File(workingDirectory, "stringMDArrayAttributeUTF8LengthFitsValue.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer w = HDF5Factory.configure(file).useUTF8CharacterEncoding().writer(); final MDArray array = new MDArray(new String[] { "\u00b6\u00bc\u09ab", "a\0c", "QWERTY", "" }, new int[] { 2, 2 }); w.string().setMDArrayAttr("/", "a", array); w.close(); final IHDF5Reader r = HDF5Factory.openForReading(file); final MDArray b1 = r.string().getMDArrayAttr("/", "a"); assertEquals(new MDArray(new String[] { "\u00b6\u00bc\u09ab", "a", "QWERTY", "" }, new int[] { 2, 2 }), b1); final MDArray b2 = r.string().getMDArrayAttrRaw("/", "a"); assertEquals(new MDArray(new String[] { "\u00b6\u00bc\u09ab", "a\0c\0\0\0\0", "QWERTY\0", "\0\0\0\0\0\0\0" }, new int[] { 2, 2 }), b2); r.close(); } @Test public void testStringMDArrayAttributeUTF8FixedLength() { final File file = new File(workingDirectory, "stringMDArrayAttributeUTF8FixedLength.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer w = HDF5Factory.configure(file).useUTF8CharacterEncoding().writer(); final MDArray array = new MDArray(new String[] { "\u00b6\u00bc\u09ab", "a\0c", "QWERTY", "" }, new int[] { 2, 2 }); w.string().setMDArrayAttr("/", "a", array, 7); w.close(); final IHDF5Reader r = HDF5Factory.openForReading(file); final MDArray b1 = r.string().getMDArrayAttr("/", "a"); assertEquals(new MDArray(new String[] { "\u00b6\u00bc\u09ab", "a", "QWERTY", "" }, new int[] { 2, 2 }), b1); final MDArray b2 = r.string().getMDArrayAttrRaw("/", "a"); // Note: the first string contains 28 bytes, but uses 7 bytes to encode 3 characters, thus // it has only 28 - (7-3) = 24 characters. assertEquals( new MDArray(new String[] { StringUtils.rightPad("\u00b6\u00bc\u09ab", 7 * 4 - 4, '\0'), StringUtils.rightPad("a\0c", 7 * 4, '\0'), StringUtils.rightPad("QWERTY", 7 * 4, '\0'), StringUtils.rightPad("", 7 * 4, '\0') }, new int[] { 2, 2 }), b2); r.close(); } @Test public void testStringCompact() { final File stringCompactFile = new File(workingDirectory, "stringCompact.h5"); stringCompactFile.delete(); assertFalse(stringCompactFile.exists()); stringCompactFile.deleteOnExit(); IHDF5Writer writer = HDF5FactoryProvider.get().configure(stringCompactFile).writer(); final String smallData = "abc1234"; final String dataSetName1 = "/aString"; writer.string().write(dataSetName1, smallData, HDF5GenericStorageFeatures.GENERIC_COMPACT); final String dataSetName2 = "/anotherString"; final String largeData = StringUtils.repeat("a", 64 * 1024 - 13); writer.string().write(dataSetName2, largeData, HDF5GenericStorageFeatures.GENERIC_COMPACT); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(stringCompactFile); final String dataRead1 = reader.readString(dataSetName1); assertEquals(HDF5StorageLayout.COMPACT, reader.getDataSetInformation(dataSetName1) .getStorageLayout()); assertEquals(smallData, dataRead1); final String dataRead2 = reader.readString(dataSetName2); assertEquals(HDF5StorageLayout.COMPACT, reader.getDataSetInformation(dataSetName2) .getStorageLayout()); assertEquals(largeData, dataRead2); reader.close(); } @Test public void testStringContiguous() { final File stringCompactFile = new File(workingDirectory, "stringContiguous.h5"); stringCompactFile.delete(); assertFalse(stringCompactFile.exists()); stringCompactFile.deleteOnExit(); IHDF5Writer writer = HDF5FactoryProvider.get().configure(stringCompactFile).writer(); final String smallData = "abc1234"; final String dataSetName1 = "/aString"; writer.string().write(dataSetName1, smallData, HDF5GenericStorageFeatures.GENERIC_CONTIGUOUS); final String dataSetName2 = "/anotherString"; final String largeData = StringUtils.repeat("a", 64 * 1024 - 13); writer.string().write(dataSetName2, largeData, HDF5GenericStorageFeatures.GENERIC_CONTIGUOUS); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(stringCompactFile); final String dataRead1 = reader.readString(dataSetName1); assertEquals(HDF5StorageLayout.CONTIGUOUS, reader.getDataSetInformation(dataSetName1) .getStorageLayout()); assertEquals(smallData, dataRead1); final String dataRead2 = reader.readString(dataSetName2); assertEquals(HDF5StorageLayout.CONTIGUOUS, reader.getDataSetInformation(dataSetName2) .getStorageLayout()); assertEquals(largeData, dataRead2); reader.close(); } @Test public void testStringUnicode() throws Exception { final File stringUnicodeFile = new File(workingDirectory, "stringUnicode.h5"); stringUnicodeFile.delete(); assertFalse(stringUnicodeFile.exists()); stringUnicodeFile.deleteOnExit(); IHDF5Writer writer = HDF5FactoryProvider.get().configure(stringUnicodeFile).dontUseExtendableDataTypes() .useUTF8CharacterEncoding().writer(); final String uniCodeData = "\u00b6\u00bc\u09ab"; final String dataSetName = "/aString"; final String attributeName = "attr1"; final String uniCodeAttributeData = "\u09bb"; writer.string().write(dataSetName, uniCodeData); writer.string().setAttr(dataSetName, attributeName, uniCodeAttributeData); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(stringUnicodeFile); final String dataRead = reader.readString(dataSetName); final String attributeDataRead = reader.string().getAttr(dataSetName, attributeName); assertEquals(uniCodeData, dataRead); assertEquals(uniCodeAttributeData, attributeDataRead); reader.close(); } @Test public void testStringArrayCompact() { final File stringArrayFile = new File(workingDirectory, "stringArrayCompact.h5"); stringArrayFile.delete(); assertFalse(stringArrayFile.exists()); stringArrayFile.deleteOnExit(); IHDF5Writer writer = HDF5FactoryProvider.get().configure(stringArrayFile).dontUseExtendableDataTypes() .writer(); final String[] data = new String[] { "abc1234", "ABCxxxX", "xyzUVWX" }; final String dataSetName = "/aStringArray"; writer.writeStringArray(dataSetName, data); writer.close(); writer = HDF5FactoryProvider.get().open(stringArrayFile); writer.writeStringArray(dataSetName, new String[] { data[0], data[1] }); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(stringArrayFile); String[] dataStored = reader.readStringArray(dataSetName); assertTrue(Arrays.equals(new String[] { data[0], data[1] }, dataStored)); reader.close(); } @Test public void testStringCompression() { final File compressedStringFile = new File(workingDirectory, "compressedStrings.h5"); compressedStringFile.delete(); assertFalse(compressedStringFile.exists()); compressedStringFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(compressedStringFile); final int size = 100000; final String dataSetName = "/hopefullyCompressedString"; final String longMonotonousString = StringUtils.repeat("a", size); writer.string().write(dataSetName, longMonotonousString, GENERIC_DEFLATE); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(compressedStringFile); final String longMonotonousStringStored = reader.readString(dataSetName); assertEquals(longMonotonousString, longMonotonousStringStored); reader.close(); assertTrue(Long.toString(compressedStringFile.length()), compressedStringFile.length() < size / 10); } @Test public void testStringArrayCompression() { final File compressedStringArrayFile = new File(workingDirectory, "compressedStringArray.h5"); compressedStringArrayFile.delete(); assertFalse(compressedStringArrayFile.exists()); compressedStringArrayFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(compressedStringArrayFile); final int size = 100000; final String longMonotonousString = StringUtils.repeat("a", size); final String[] data = new String[] { longMonotonousString, longMonotonousString, longMonotonousString }; final String dataSetName = "/aHopeFullyCompressedStringArray"; writer.string().writeArray(dataSetName, data, size, GENERIC_DEFLATE); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(compressedStringArrayFile); final String[] dataStored = reader.readStringArray(dataSetName); assertTrue(Arrays.equals(data, dataStored)); reader.close(); assertTrue(Long.toString(compressedStringArrayFile.length()), compressedStringArrayFile.length() < 3 * size / 10); } @Test public void testStringVLArray() { final File compressedStringArrayFile = new File(workingDirectory, "StringVLArray.h5"); compressedStringArrayFile.delete(); assertFalse(compressedStringArrayFile.exists()); compressedStringArrayFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(compressedStringArrayFile); final int size = 100000; final String longMonotonousString = StringUtils.repeat("a", size); final String[] data = new String[] { longMonotonousString, longMonotonousString, longMonotonousString }; final String dataSetName = "/aHopeFullyCompressedStringArray"; writer.string().writeArrayVL(dataSetName, data); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(compressedStringArrayFile); final String[] dataStored = reader.readStringArray(dataSetName); assertTrue(Arrays.equals(data, dataStored)); assertTrue(reader.getDataSetInformation(dataSetName).getTypeInformation() .isVariableLengthString()); reader.close(); } private void assertMatrixEquals(final float[][] floatMatrixWritten, final float[][] floatMatrixRead) { assertEquals(floatMatrixWritten.length, floatMatrixRead.length); for (int i = 0; i < floatMatrixWritten.length; ++i) { assertEquals(floatMatrixWritten[i].length, floatMatrixRead[i].length); for (int j = 0; j < floatMatrixWritten[i].length; ++j) { assertEquals(i + ":" + j, floatMatrixWritten[i][j], floatMatrixRead[i][j]); } } } @Test public void testCompressedDataSet() { final File datasetFile = new File(workingDirectory, "compressed.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String stringDatasetName = "/compressed"; final StringBuilder b = new StringBuilder(); for (int i = 0; i < 10000; ++i) { b.append("easyToCompress"); } writer.int8().writeArray(stringDatasetName, b.toString().getBytes(), INT_DEFLATE); writer.close(); } @Test public void testCreateEmptyFloatMatrix() { final File datasetFile = new File(workingDirectory, "initiallyEmptyFloatMatrix.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String floatDatasetName = "/emptyMatrix"; writer.float32().createMatrix(floatDatasetName, 2, 2, FLOAT_CHUNKED); writer.close(); writer = HDF5FactoryProvider.get().open(datasetFile); float[][] floatMatrixRead = writer.float32().readMatrix(floatDatasetName); assertEquals(0, floatMatrixRead.length); // No write a non-empty matrix float[][] floatMatrixWritten = new float[][] { { 1f, 2f, 3f }, { 4f, 5f, 6f }, { 7f, 8f, 9f } }; writer.float32().writeMatrix(floatDatasetName, floatMatrixWritten); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); floatMatrixRead = reader.float32().readMatrix(floatDatasetName); assertTrue(equals(floatMatrixWritten, floatMatrixRead)); reader.close(); } @Test public void testFloatVectorLength1() { final File datasetFile = new File(workingDirectory, "singleFloatVector.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String floatDatasetName = "/singleFloat"; final float[] floatDataWritten = new float[] { 1.0f }; writer.float32().writeArray(floatDatasetName, floatDataWritten); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); reader.object().hasAttribute(floatDatasetName, "flag"); final float[] floatDataRead = reader.float32().readArray(floatDatasetName); assertTrue(Arrays.equals(floatDataWritten, floatDataRead)); reader.close(); } @Test public void testFloatMatrixLength1() { final File datasetFile = new File(workingDirectory, "singleFloatMatrix.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String floatDatasetName = "/singleFloat"; final float[][] floatDataWritten = new float[][] { { 1.0f } }; writer.float32().writeMatrix(floatDatasetName, floatDataWritten); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final float[][] floatDataRead = reader.float32().readMatrix(floatDatasetName); assertTrue(equals(floatDataWritten, floatDataRead)); reader.close(); } @Test public void testOneRowFloatMatrix() { final File datasetFile = new File(workingDirectory, "oneRowFloatMatrix.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String floatDatasetName = "/singleFloat"; final float[][] floatDataWritten = new float[][] { { 1.0f, 2.0f } }; writer.float32().writeMatrix(floatDatasetName, floatDataWritten); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final float[][] floatDataRead = reader.float32().readMatrix(floatDatasetName); assertTrue(equals(floatDataWritten, floatDataRead)); reader.close(); } private static boolean equals(float[][] a, float[][] a2) { if (a == a2) { return true; } if (a == null || a2 == null) { return false; } int rows = a.length; if (a2.length != rows) { return false; } for (int i = 0; i < rows; i++) { int columns = a[i].length; if (a2[i].length != columns) { return false; } for (int j = 0; j < columns; j++) { if (Float.floatToIntBits(a[i][j]) != Float.floatToIntBits(a2[i][j])) { return false; } } } return true; } @Test public void testEmptyVectorDataSets() { final File datasetFile = new File(workingDirectory, "emptyVectorDatasets.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String floatDatasetName = "/float"; writer.float32().writeArray(floatDatasetName, new float[0]); final String doubleDatasetName = "/double"; writer.float64().writeArray(doubleDatasetName, new double[0]); final String byteDatasetName = "byte"; writer.int8().writeArray(byteDatasetName, new byte[0]); final String shortDatasetName = "/short"; writer.int16().writeArray(shortDatasetName, new short[0]); final String intDatasetName = "/int"; writer.int32().writeArray(intDatasetName, new int[0]); final String longDatasetName = "/long"; writer.int64().writeArray(longDatasetName, new long[0]); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); assertEquals(HDF5ObjectType.DATASET, reader.object().getObjectType(floatDatasetName)); assertTrue(reader.float32().readArray(floatDatasetName).length == 0); assertTrue(reader.float64().readArray(doubleDatasetName).length == 0); assertTrue(reader.int8().readArray(byteDatasetName).length == 0); assertTrue(reader.int16().readArray(shortDatasetName).length == 0); assertTrue(reader.int32().readArray(intDatasetName).length == 0); assertTrue(reader.int64().readArray(longDatasetName).length == 0); reader.close(); } @Test public void testEmptyVectorDataSetsContiguous() { final File datasetFile = new File(workingDirectory, "emptyVectorDatasetsContiguous.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().configure(datasetFile).dontUseExtendableDataTypes() .writer(); final String floatDatasetName = "/float"; writer.float32().writeArray(floatDatasetName, new float[0]); final String doubleDatasetName = "/double"; writer.float64().writeArray(doubleDatasetName, new double[0]); final String byteDatasetName = "byte"; writer.int8().writeArray(byteDatasetName, new byte[0]); final String shortDatasetName = "/short"; writer.int16().writeArray(shortDatasetName, new short[0]); final String intDatasetName = "/int"; writer.int32().writeArray(intDatasetName, new int[0]); final String longDatasetName = "/long"; writer.int64().writeArray(longDatasetName, new long[0]); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); assertEquals(HDF5ObjectType.DATASET, reader.object().getObjectType(floatDatasetName)); assertTrue(reader.float32().readArray(floatDatasetName).length == 0); assertTrue(reader.float64().readArray(doubleDatasetName).length == 0); assertTrue(reader.int8().readArray(byteDatasetName).length == 0); assertTrue(reader.int16().readArray(shortDatasetName).length == 0); assertTrue(reader.int32().readArray(intDatasetName).length == 0); assertTrue(reader.int64().readArray(longDatasetName).length == 0); reader.close(); } @Test public void testEmptyVectorDataSetsCompact() { final File datasetFile = new File(workingDirectory, "emptyVectorDatasetsCompact.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String floatDatasetName = "/float"; writer.float32().writeArray(floatDatasetName, new float[0], HDF5FloatStorageFeatures.FLOAT_COMPACT); final String doubleDatasetName = "/double"; writer.float64().writeArray(doubleDatasetName, new double[0], HDF5FloatStorageFeatures.FLOAT_COMPACT); final String byteDatasetName = "byte"; writer.int8().writeArray(byteDatasetName, new byte[0], HDF5IntStorageFeatures.INT_COMPACT); final String shortDatasetName = "/short"; writer.int16().writeArray(shortDatasetName, new short[0], HDF5IntStorageFeatures.INT_COMPACT); final String intDatasetName = "/int"; writer.int32().writeArray(intDatasetName, new int[0], HDF5IntStorageFeatures.INT_COMPACT); final String longDatasetName = "/long"; writer.int64().writeArray(longDatasetName, new long[0], HDF5IntStorageFeatures.INT_COMPACT); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); assertEquals(HDF5ObjectType.DATASET, reader.object().getObjectType(floatDatasetName)); assertTrue(reader.float32().readArray(floatDatasetName).length == 0); assertTrue(reader.float64().readArray(doubleDatasetName).length == 0); assertTrue(reader.int8().readArray(byteDatasetName).length == 0); assertTrue(reader.int16().readArray(shortDatasetName).length == 0); assertTrue(reader.int32().readArray(intDatasetName).length == 0); assertTrue(reader.int64().readArray(longDatasetName).length == 0); reader.close(); } @Test public void testEmptyMatrixDataSets() { final File datasetFile = new File(workingDirectory, "emptyMatrixDatasets.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String floatDatasetName = "/float"; writer.float32().writeMatrix(floatDatasetName, new float[0][0]); final String doubleDatasetName = "/double"; writer.float64().writeMatrix(doubleDatasetName, new double[1][0]); final String byteDatasetName = "byte"; writer.int8().writeMatrix(byteDatasetName, new byte[2][0]); final String shortDatasetName = "/short"; writer.int16().writeMatrix(shortDatasetName, new short[3][0]); final String intDatasetName = "/int"; writer.int32().writeMatrix(intDatasetName, new int[4][0]); final String longDatasetName = "/long"; writer.int64().writeMatrix(longDatasetName, new long[5][0]); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); assertTrue(isEmpty(reader.float32().readMatrix(floatDatasetName))); assertTrue(isEmpty(reader.float64().readMatrix(doubleDatasetName))); assertTrue(isEmpty(reader.int8().readMatrix(byteDatasetName))); assertTrue(isEmpty(reader.int16().readMatrix(shortDatasetName))); assertTrue(isEmpty(reader.int32().readMatrix(intDatasetName))); assertTrue(isEmpty(reader.int64().readMatrix(longDatasetName))); reader.close(); } @Test public void testEmptyMatrixDataSetsContiguous() { final File datasetFile = new File(workingDirectory, "emptyMatrixDatasetsContiguous.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().configure(datasetFile).dontUseExtendableDataTypes() .writer(); final String floatDatasetName = "/float"; writer.float32().writeMatrix(floatDatasetName, new float[0][0]); final String doubleDatasetName = "/double"; writer.float64().writeMatrix(doubleDatasetName, new double[1][0]); final String byteDatasetName = "byte"; writer.int8().writeMatrix(byteDatasetName, new byte[2][0]); final String shortDatasetName = "/short"; writer.int16().writeMatrix(shortDatasetName, new short[3][0]); final String intDatasetName = "/int"; writer.int32().writeMatrix(intDatasetName, new int[4][0]); final String longDatasetName = "/long"; writer.int64().writeMatrix(longDatasetName, new long[5][0]); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); assertTrue(isEmpty(reader.float32().readMatrix(floatDatasetName))); assertTrue(isEmpty(reader.float64().readMatrix(doubleDatasetName))); assertTrue(isEmpty(reader.int8().readMatrix(byteDatasetName))); assertTrue(isEmpty(reader.int16().readMatrix(shortDatasetName))); assertTrue(isEmpty(reader.int32().readMatrix(intDatasetName))); assertTrue(isEmpty(reader.int64().readMatrix(longDatasetName))); reader.close(); } @Test public void testOverwriteVectorIncreaseSize() { final File datasetFile = new File(workingDirectory, "resizableVector.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String dsName = "/vector"; final float[] firstVector = new float[] { 1f, 2f, 3f }; writer.float32().writeArray(dsName, firstVector); writer.close(); writer = HDF5FactoryProvider.get().open(datasetFile); final float[] secondVector = new float[] { 1f, 2f, 3f, 4f }; writer.float32().writeArray(dsName, secondVector); writer.close(); IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final float[] vectorRead = reader.float32().readArray(dsName); reader.close(); assertTrue(Arrays.equals(secondVector, vectorRead)); } @Test public void testOverwriteWithEmptyVector() { final File datasetFile = new File(workingDirectory, "overwriteVector1.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String dsName = "/vector"; final byte[] firstVector = new byte[] { 1, 2, 3 }; writer.int8().writeArray(dsName, firstVector); writer.close(); writer = HDF5FactoryProvider.get().open(datasetFile); final byte[] emptyVector = new byte[0]; writer.int8().writeArray(dsName, emptyVector); writer.close(); IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final byte[] vectorRead = reader.int8().readArray(dsName); reader.close(); assertTrue(Arrays.equals(emptyVector, vectorRead)); } @Test public void testOverwriteEmptyVectorWithNonEmptyVector() { final File datasetFile = new File(workingDirectory, "overwriteVector2.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String dsName = "/vector"; final byte[] emptyVector = new byte[0]; writer.int8().writeArray(dsName, emptyVector); writer.close(); writer = HDF5FactoryProvider.get().open(datasetFile); final byte[] nonEmptyVector = new byte[] { 1 }; writer.int8().writeArray(dsName, nonEmptyVector); writer.close(); IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final byte[] vectorRead = reader.int8().readArray(dsName); reader.close(); assertTrue(Arrays.equals(nonEmptyVector, vectorRead)); } @Test public void testDeleteVector() { final File datasetFile = new File(workingDirectory, "deleteVector.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); try { final String dsName = "/vector"; final byte[] firstVector = new byte[] { 1, 2, 3 }; writer.int8().writeArray(dsName, firstVector); writer.close(); writer = HDF5FactoryProvider.get().open(datasetFile); writer.delete(dsName.substring(1)); } finally { writer.close(); } IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); try { final List members = reader.object().getAllGroupMembers("/"); assertEquals(1, members.size()); assertEquals(HDF5Utils.getDataTypeGroup("").substring(1), members.get(0)); } finally { reader.close(); } } @Test public void testDeleteGroup() { final File datasetFile = new File(workingDirectory, "deleteGroup.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); try { final String groupName = "/group"; final String dsName = groupName + "/vector"; final byte[] firstVector = new byte[] { 1, 2, 3 }; writer.int8().writeArray(dsName, firstVector); writer.close(); writer = HDF5FactoryProvider.get().open(datasetFile); writer.delete(groupName); } finally { writer.close(); } final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); try { final List members = reader.object().getAllGroupMembers("/"); assertEquals(1, members.size()); assertEquals(HDF5Utils.getDataTypeGroup("").substring(1), members.get(0)); assertEquals(0, reader.getGroupMembers("/").size()); } finally { reader.close(); } } @Test public void testRenameLink() { final File file = new File(workingDirectory, "renameLink.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); writer.writeBoolean("/some/boolean/value", true); writer.object().move("/some/boolean/value", "/a/new/home"); assertFalse(writer.exists("/home/boolean/value")); assertTrue(writer.exists("/a/new/home")); writer.close(); } @Test(expectedExceptions = HDF5SymbolTableException.class) public void testRenameLinkOverwriteFails() { final File file = new File(workingDirectory, "renameLinkOverwriteFails.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); writer.writeBoolean("/some/boolean/value", true); writer.int32().write("/a/new/home", 4); writer.object().move("/some/boolean/value", "/a/new/home"); writer.close(); } @Test(expectedExceptions = HDF5SymbolTableException.class) public void testRenameLinkSrcNonExistentFails() { final File file = new File(workingDirectory, "renameLinkSrcNonExistentFails.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); writer.object().move("/some/boolean/value", "/a/new/home"); writer.close(); } @Test public void testOverwriteKeepWithEmptyString() { final File datasetFile = new File(workingDirectory, "overwriteWithEmtpyString.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String dsName = "/string"; writer.string().write(dsName, "non-empty"); writer.close(); writer = HDF5FactoryProvider.get().configure(datasetFile).keepDataSetsIfTheyExist().writer(); writer.string().write(dsName, ""); writer.close(); IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final String stringRead = reader.readString(dsName); reader.close(); assertEquals("", stringRead); } @Test public void testOverwriteKeepWithShorterString() { final File datasetFile = new File(workingDirectory, "overwriteWithShorterString.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String dsName = "/string"; writer.string().write(dsName, "non-empty"); writer.close(); writer = HDF5FactoryProvider.get().configure(datasetFile).keepDataSetsIfTheyExist().writer(); writer.string().write(dsName, "non"); writer.close(); IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final String stringRead = reader.readString(dsName); reader.close(); assertEquals("non", stringRead); } @Test public void testOverwriteKeepWithLongerString() { final File datasetFile = new File(workingDirectory, "overwriteWithLongerString.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String dsName = "/string"; writer.string().write(dsName, "non-empty"); writer.close(); writer = HDF5FactoryProvider.get().configure(datasetFile).keepDataSetsIfTheyExist().writer(); writer.string().write(dsName, "0123456789"); writer.close(); IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final String stringRead = reader.readString(dsName); reader.close(); assertEquals("012345678", stringRead); } @Test public void testReplaceWithLongerString() { final File datasetFile = new File(workingDirectory, "replaceWithLongerString.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String dsName = "/string"; writer.string().write(dsName, "non-empty"); writer.close(); writer = HDF5FactoryProvider.get().open(datasetFile); writer.string().write(dsName, "0123456789"); writer.close(); IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final String stringRead = reader.readString(dsName); reader.close(); assertEquals("0123456789", stringRead); } @Test public void testOverwriteMatrixIncreaseSize() { final File datasetFile = new File(workingDirectory, "resizableMatrix.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String dsName = "/matrix"; final float[][] firstMatrix = new float[][] { { 1f, 2f, 3f }, { 4f, 5f, 6f } }; writer.float32().writeMatrix(dsName, firstMatrix); writer.close(); writer = HDF5FactoryProvider.get().open(datasetFile); final float[][] secondMatrix = new float[][] { { 1f, 2f, 3f, 4f }, { 5f, 6f, 7f, 8f }, { 9f, 10f, 11f, 12f } }; writer.float32().writeMatrix(dsName, secondMatrix); writer.close(); IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final float[][] matrixRead = reader.float32().readMatrix(dsName); reader.close(); assertMatrixEquals(secondMatrix, matrixRead); } @Test public void testOverwriteStringVectorDecreaseSize() { final File datasetFile = new File(workingDirectory, "resizableStringVector.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String dsName = "/vector"; final String[] firstVector = new String[] { "a", "b", "c" }; writer.writeStringArray(dsName, firstVector); writer.close(); writer = HDF5FactoryProvider.get().open(datasetFile); final String[] secondVector = new String[] { "a", "b" }; writer.writeStringArray(dsName, secondVector); writer.close(); IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final String[] vectorRead = reader.readStringArray(dsName); reader.close(); assertTrue(Arrays.equals(secondVector, vectorRead)); } private static boolean isEmpty(Object matrix) { Object maybeAnArray = matrix; do { if (Array.getLength(maybeAnArray) == 0) { return true; } maybeAnArray = Array.get(maybeAnArray, 0); } while (maybeAnArray.getClass().isArray()); return false; } @Test public void testStringArrayWithNullStrings() { final File datasetFile = new File(workingDirectory, "stringArrayWithNullStrings.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String dsName = "/vector"; final String[] array = new String[] { "a\0c", "b", "" }; writer.writeStringArray(dsName, array); writer.close(); IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final String[] arrayRead = reader.string().readArrayRaw(dsName); reader.close(); assertEquals(array.length, arrayRead.length); assertEquals("a\0c", arrayRead[0]); assertEquals(StringUtils.rightPad("b", 3, '\0'), arrayRead[1]); assertEquals(StringUtils.rightPad("", 3, '\0'), arrayRead[2]); } @Test public void testStringMDArrayWithNullStrings() { final File datasetFile = new File(workingDirectory, "stringMDArrayWithNullStrings.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String dsName = "/vector"; final String[] array = new String[] { "a\0c", "b", "", "\000123456" }; final MDArray mdArray = new MDArray(array, new int[] { 2, 2 }); writer.string().writeMDArray(dsName, mdArray); writer.close(); IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final MDArray arrayRead = reader.string().readMDArrayRaw(dsName); assertTrue(Arrays.equals(mdArray.dimensions(), arrayRead.dimensions())); assertEquals(StringUtils.rightPad(mdArray.get(0, 0), 7, '\0'), arrayRead.get(0, 0)); assertEquals(StringUtils.rightPad(mdArray.get(0, 1), 7, '\0'), arrayRead.get(0, 1)); assertEquals(StringUtils.rightPad(mdArray.get(1, 0), 7, '\0'), arrayRead.get(1, 0)); assertEquals(StringUtils.rightPad(mdArray.get(1, 1), 7, '\0'), arrayRead.get(1, 1)); assertEquals(2, reader.object().getRank(dsName)); assertTrue(Arrays.equals(new long[] { 2, 2 }, reader.object().getDimensions(dsName))); reader.close(); } @Test public void testTimestamps() { final File datasetFile = new File(workingDirectory, "timestamps.h5"); final String timeStampDS = "prehistoric"; final long timestampValue = 10000L; final String noTimestampDS = "notatimestamp"; final long someLong = 173756123L; datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); writer.time().write(timeStampDS, timestampValue); writer.int64().write(noTimestampDS, someLong); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); assertEquals(HDF5DataTypeVariant.TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH, reader .object().tryGetTypeVariant(timeStampDS)); final HDF5DataSetInformation info = reader.getDataSetInformation(timeStampDS); assertTrue(info.isScalar()); assertEquals(HDF5StorageLayout.COMPACT, info.getStorageLayout()); assertNull(info.tryGetChunkSizes()); assertEquals(HDF5DataClass.INTEGER, info.getTypeInformation().getDataClass()); assertTrue(info.isTimeStamp()); assertFalse(info.isTimeDuration()); assertEquals(HDF5DataTypeVariant.TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH, info.tryGetTypeVariant()); assertEquals(HDF5DataTypeVariant.TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH, info .getTypeInformation().tryGetTypeVariant()); assertEquals(timestampValue, reader.time().readTimeStamp(timeStampDS)); assertEquals(timestampValue, reader.time().readDate(timeStampDS).getTime()); try { reader.time().readTimeStamp(noTimestampDS); fail("Failed to detect non-timestamp value."); } catch (HDF5JavaException ex) { if (ex.getMessage().contains("not a time stamp") == false) { throw ex; } // That is what we expect. } reader.close(); } @Test public void testTimestampArray() { final File datasetFile = new File(workingDirectory, "timestampArray.h5"); final String timeSeriesDS = "/some/timeseries"; final long[] timeSeries = new long[10]; for (int i = 0; i < timeSeries.length; ++i) { timeSeries[i] = i * 10000L; } final long[] notATimeSeries = new long[100]; final String noTimeseriesDS = "nota/timeseries"; datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); writer.time().writeArray(timeSeriesDS, timeSeries); writer.int64().writeArray(noTimeseriesDS, notATimeSeries); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final HDF5DataSetInformation info = reader.getDataSetInformation(timeSeriesDS); assertEquals(HDF5DataTypeVariant.TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH, info.tryGetTypeVariant()); assertChunkSizes(info, 10); assertTrue(Arrays.equals(timeSeries, reader.time().readTimeStampArray(timeSeriesDS))); final Date[] datesRead = reader.readDateArray(timeSeriesDS); final long[] timeStampsRead = new long[datesRead.length]; for (int i = 0; i < timeStampsRead.length; ++i) { timeStampsRead[i] = datesRead[i].getTime(); } assertTrue(Arrays.equals(timeSeries, timeStampsRead)); try { reader.time().readTimeStampArray(noTimeseriesDS); fail("Failed to detect non-timestamp array."); } catch (HDF5JavaException ex) { if (ex.getMessage().contains("not a time stamp") == false) { throw ex; } // That is what we expect. } reader.close(); } @Test public void testTimestampArrayChunked() { final File datasetFile = new File(workingDirectory, "timestampArrayChunked.h5"); final String timeSeriesDS = "/some/timeseries"; final long[] timeSeries = new long[10]; for (int i = 0; i < timeSeries.length; ++i) { timeSeries[i] = i * 10000L; } datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); writer.time().createArray(timeSeriesDS, 0, 10, GENERIC_DEFLATE); for (int i = 0; i < 10; ++i) { writer.time().writeArrayBlock(timeSeriesDS, timeSeries, i); } writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final HDF5DataSetInformation info = reader.getDataSetInformation(timeSeriesDS); assertEquals(HDF5DataTypeVariant.TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH, info.tryGetTypeVariant()); assertChunkSizes(info, 10); for (int i = 0; i < 10; ++i) { assertTrue(Arrays.equals(timeSeries, reader.time().readTimeStampArrayBlock(timeSeriesDS, 10, i))); } reader.close(); } @Test public void testTimeDurations() { final File datasetFile = new File(workingDirectory, "timedurations.h5"); final String timeDurationDS = "someDuration"; final String timeDurationDS2 = "someOtherDuration"; final long timeDurationInSeconds = 10000L; final long timeDurationInMilliSeconds = 10000L * 1000L; final long timeDurationInHoursRounded = 3L; final String noTimestampDS = "notatimeduration"; final long someLong = 173756123L; datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); writer.duration().write(timeDurationDS, timeDurationInSeconds, HDF5TimeUnit.SECONDS); final HDF5TimeDuration timeDurationWithUnit = new HDF5TimeDuration(timeDurationInHoursRounded, HDF5TimeUnit.HOURS); writer.writeTimeDuration(timeDurationDS2, timeDurationWithUnit); writer.int64().write(noTimestampDS, someLong); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final HDF5DataSetInformation info = reader.getDataSetInformation(timeDurationDS); assertTrue(info.isScalar()); assertEquals(HDF5StorageLayout.COMPACT, info.getStorageLayout()); assertNull(info.tryGetChunkSizes()); assertEquals(HDF5DataClass.INTEGER, info.getTypeInformation().getDataClass()); assertTrue(info.isTimeDuration()); assertFalse(info.isTimeStamp()); assertEquals(HDF5TimeUnit.SECONDS, reader.duration().tryGetTimeUnit(timeDurationDS)); assertEquals(HDF5DataTypeVariant.TIME_DURATION_SECONDS, info.tryGetTypeVariant()); assertEquals(HDF5TimeUnit.SECONDS, info.tryGetTimeUnit()); assertEquals(timeDurationInSeconds, HDF5TimeUnit.SECONDS.convert(reader.readTimeDuration(timeDurationDS))); assertEquals(timeDurationInMilliSeconds, HDF5TimeUnit.MILLISECONDS.convert(reader.readTimeDuration(timeDurationDS))); assertEquals(timeDurationInHoursRounded, HDF5TimeUnit.HOURS.convert(reader.readTimeDuration(timeDurationDS))); assertEquals(new HDF5TimeDuration(timeDurationInSeconds, HDF5TimeUnit.SECONDS), reader.readTimeDuration(timeDurationDS)); assertEquals(timeDurationWithUnit, reader.readTimeDuration(timeDurationDS2)); try { reader.readTimeDuration(noTimestampDS); fail("Failed to detect non-timeduration value."); } catch (HDF5JavaException ex) { if (ex.getMessage().contains("not a time duration") == false) { throw ex; } // That is what we expect. } reader.close(); } @Test public void testSmallTimeDurations() { final File datasetFile = new File(workingDirectory, "smalltimedurations.h5"); final String timeDurationDS = "someDuration"; final short timeDurationInSeconds = 10000; final long timeDurationInMilliSeconds = 10000L * 1000L; final long timeDurationInHoursRounded = 3L; datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); writer.int16().write(timeDurationDS, timeDurationInSeconds); writer.object().setTypeVariant(timeDurationDS, HDF5TimeUnit.SECONDS.getTypeVariant()); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final HDF5DataSetInformation info = reader.getDataSetInformation(timeDurationDS); assertTrue(info.isScalar()); assertEquals(HDF5StorageLayout.COMPACT, info.getStorageLayout()); assertNull(info.tryGetChunkSizes()); assertEquals(HDF5DataClass.INTEGER, info.getTypeInformation().getDataClass()); assertEquals(NativeData.SHORT_SIZE, info.getTypeInformation().getElementSize()); assertTrue(info.isTimeDuration()); assertFalse(info.isTimeStamp()); assertEquals(HDF5TimeUnit.SECONDS, reader.duration().tryGetTimeUnit(timeDurationDS)); assertEquals(HDF5DataTypeVariant.TIME_DURATION_SECONDS, info.tryGetTypeVariant()); assertEquals(HDF5TimeUnit.SECONDS, info.tryGetTimeUnit()); assertEquals(timeDurationInSeconds, HDF5TimeUnit.SECONDS.convert(reader.duration().read(timeDurationDS))); assertEquals(timeDurationInMilliSeconds, HDF5TimeUnit.MILLISECONDS.convert(reader.duration().read(timeDurationDS))); assertEquals(timeDurationInHoursRounded, HDF5TimeUnit.HOURS.convert(reader.readTimeDuration(timeDurationDS))); reader.close(); } @Test public void testTimeDurationArray() { final File datasetFile = new File(workingDirectory, "timedurationarray.h5"); final String timeDurationDS = "someDuration"; final HDF5TimeDuration[] durationsWritten = new HDF5TimeDuration[] { new HDF5TimeDuration(2, HDF5TimeUnit.SECONDS), new HDF5TimeDuration(5, HDF5TimeUnit.HOURS), new HDF5TimeDuration(1, HDF5TimeUnit.DAYS) }; datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); writer.writeTimeDurationArray(timeDurationDS, HDF5TimeDurationArray.create(durationsWritten)); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final HDF5DataSetInformation info = reader.getDataSetInformation(timeDurationDS); assertTrue(info.isTimeDuration()); assertFalse(info.isTimeStamp()); assertEquals(HDF5TimeUnit.SECONDS, info.tryGetTimeUnit()); final HDF5TimeDurationArray durationsRead = reader.readTimeDurationArray(timeDurationDS); assertEquals(durationsWritten.length, durationsRead.getLength()); for (int i = 0; i < durationsWritten.length; ++i) { assertTrue(durationsRead.get(i).isEquivalent(durationsWritten[i])); } assertEquals(new HDF5TimeDurationMDArray(new long[] { 2, 18000, 86400 }, new int[] { 3 }, HDF5TimeUnit.SECONDS), reader.duration().readMDArray(timeDurationDS)); reader.close(); } @Test public void testTimeDurationMDArray() { final File datasetFile = new File(workingDirectory, "timedurationarray.h5"); final String timeDurationDS = "someDuration"; final HDF5TimeDurationMDArray durationsWritten = new HDF5TimeDurationMDArray(new HDF5TimeDuration[] { new HDF5TimeDuration(2, HDF5TimeUnit.SECONDS), new HDF5TimeDuration(4, HDF5TimeUnit.SECONDS), new HDF5TimeDuration(8, HDF5TimeUnit.SECONDS), new HDF5TimeDuration(16, HDF5TimeUnit.SECONDS), new HDF5TimeDuration(1, HDF5TimeUnit.MINUTES), new HDF5TimeDuration(17, HDF5TimeUnit.MINUTES), new HDF5TimeDuration(42, HDF5TimeUnit.MINUTES), new HDF5TimeDuration(111, HDF5TimeUnit.MINUTES), new HDF5TimeDuration(5, HDF5TimeUnit.HOURS), new HDF5TimeDuration(10, HDF5TimeUnit.HOURS), new HDF5TimeDuration(20, HDF5TimeUnit.HOURS), new HDF5TimeDuration(40, HDF5TimeUnit.HOURS), new HDF5TimeDuration(1, HDF5TimeUnit.DAYS), new HDF5TimeDuration(2, HDF5TimeUnit.DAYS), new HDF5TimeDuration(4, HDF5TimeUnit.DAYS), new HDF5TimeDuration(8, HDF5TimeUnit.DAYS), }, new int[] { 4, 4 }); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); writer.duration().writeMDArray(timeDurationDS, durationsWritten); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final HDF5DataSetInformation info = reader.getDataSetInformation(timeDurationDS); assertTrue(info.isTimeDuration()); assertFalse(info.isTimeStamp()); assertEquals(HDF5TimeUnit.SECONDS, info.tryGetTimeUnit()); final HDF5TimeDurationMDArray durationsRead = reader.duration().readMDArray(timeDurationDS); assertEquals(durationsWritten, durationsRead); assertEquals(new HDF5TimeDurationMDArray(new long[] { 2, 4, 8, 16 }, new int[] { 1, 4 }, HDF5TimeUnit.SECONDS), reader.duration().readMDArrayBlock(timeDurationDS, new int[] { 1, 4 }, new long[] { 0, 0 })); assertEquals( new HDF5TimeDurationMDArray(new long[] { 1, 17, 42, 111 }, new int[] { 1, 4 }, HDF5TimeUnit.MINUTES), HDF5TimeUnit.MINUTES.convert(reader.duration().readMDArrayBlock(timeDurationDS, new int[] { 1, 4 }, new long[] { 1, 0 }))); assertEquals( new HDF5TimeDurationMDArray(new long[] { 5, 10, 20, 40 }, new int[] { 1, 4 }, HDF5TimeUnit.HOURS), HDF5TimeUnit.HOURS.convert(reader.duration().readMDArrayBlock(timeDurationDS, new int[] { 1, 4 }, new long[] { 2, 0 }))); assertEquals( new HDF5TimeDurationMDArray(new long[] { 1, 2, 4, 8 }, new int[] { 1, 4 }, HDF5TimeUnit.DAYS), HDF5TimeUnit.DAYS.convert(reader.duration().readMDArrayBlock(timeDurationDS, new int[] { 1, 4 }, new long[] { 3, 0 }))); reader.close(); } @Test public void testTimeDurationArrayChunked() { final File datasetFile = new File(workingDirectory, "timeDurationArrayChunked.h5"); final String timeDurationSeriesDS = "/some/timeseries"; final String timeDurationSeriesDS2 = "/some/timeseries2"; final long[] timeDurationSeriesMillis = new long[10]; final long[] timeDurationSeriesMicros = new long[10]; for (int i = 0; i < timeDurationSeriesMillis.length; ++i) { timeDurationSeriesMillis[i] = i * 10000L; timeDurationSeriesMicros[i] = timeDurationSeriesMillis[i] * 1000L; } datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); writer.duration().createArray(timeDurationSeriesDS, 100, 10, HDF5TimeUnit.MILLISECONDS, GENERIC_DEFLATE); for (int i = 0; i < 10; ++i) { writer.duration().writeArrayBlock(timeDurationSeriesDS, new HDF5TimeDurationArray(timeDurationSeriesMicros, HDF5TimeUnit.MICROSECONDS), i); } writer.duration().createArray(timeDurationSeriesDS2, 100, 10, HDF5TimeUnit.SECONDS, GENERIC_DEFLATE); final HDF5TimeDuration[] timeDurationSeries = new HDF5TimeDuration[] { new HDF5TimeDuration(timeDurationSeriesMicros[0], HDF5TimeUnit.MICROSECONDS), new HDF5TimeDuration(timeDurationSeriesMicros[1], HDF5TimeUnit.MICROSECONDS), new HDF5TimeDuration(timeDurationSeriesMillis[2], HDF5TimeUnit.MILLISECONDS), new HDF5TimeDuration(timeDurationSeriesMillis[3], HDF5TimeUnit.MILLISECONDS), new HDF5TimeDuration(timeDurationSeriesMillis[4] / 1000L, HDF5TimeUnit.SECONDS), new HDF5TimeDuration(timeDurationSeriesMillis[5] / 1000L, HDF5TimeUnit.SECONDS), new HDF5TimeDuration(6, HDF5TimeUnit.HOURS), new HDF5TimeDuration(7, HDF5TimeUnit.HOURS), new HDF5TimeDuration(8, HDF5TimeUnit.DAYS), new HDF5TimeDuration(9, HDF5TimeUnit.DAYS) }; for (int i = 0; i < 10; ++i) { writer.duration().writeArrayBlock(timeDurationSeriesDS2, HDF5TimeDurationArray.create(timeDurationSeries), i); } writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); final HDF5DataSetInformation info = reader.getDataSetInformation(timeDurationSeriesDS); assertEquals(HDF5DataTypeVariant.TIME_DURATION_MILLISECONDS, info.tryGetTypeVariant()); assertChunkSizes(info, 10); for (int i = 0; i < 10; ++i) { assertTrue(Arrays.equals( timeDurationSeriesMicros, HDF5TimeUnit.MICROSECONDS.convert(reader.duration().readArrayBlock( timeDurationSeriesDS, 10, i)))); } final HDF5DataSetInformation info2 = reader.getDataSetInformation(timeDurationSeriesDS2); assertEquals(HDF5DataTypeVariant.TIME_DURATION_SECONDS, info2.tryGetTypeVariant()); assertChunkSizes(info2, 10); for (int i = 0; i < 10; ++i) { final long[] block = HDF5TimeUnit.MICROSECONDS.convert(reader.duration().readArrayBlock( timeDurationSeriesDS2, 10, i)); for (int j = 0; j < block.length; ++j) { assertEquals(HDF5TimeUnit.MICROSECONDS.convert(timeDurationSeries[j]), block[j]); } } for (int i = 0; i < 10; ++i) { final HDF5TimeDurationArray block = reader.duration().readArrayBlock(timeDurationSeriesDS2, 10, i); for (int j = 0; j < block.getLength(); ++j) { assertTrue(block.get(j).isEquivalent(timeDurationSeries[j])); } } for (HDF5DataBlock block : reader.duration().getArrayNaturalBlocks( timeDurationSeriesDS2)) { final HDF5TimeDurationArray data = block.getData(); for (int j = 0; j < data.getLength(); ++j) { assertTrue(data.get(j) + "<>" + timeDurationSeries[j], data.get(j).isEquivalent(timeDurationSeries[j])); } } reader.close(); } @Test public void testAttributes() { final File attributeFile = new File(workingDirectory, "attributes.h5"); attributeFile.delete(); assertFalse(attributeFile.exists()); attributeFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(attributeFile); final String datasetName = "SomeDataSet"; writer.int32().writeArray(datasetName, new int[0]); final String booleanAttributeName = "Boolean Attribute"; final boolean booleanAttributeValueWritten = true; writer.bool().setAttr(datasetName, booleanAttributeName, booleanAttributeValueWritten); assertTrue(writer.object().hasAttribute(datasetName, booleanAttributeName)); final String integerAttributeName = "Integer Attribute"; final int integerAttributeValueWritten = 17; writer.int32().setAttr(datasetName, integerAttributeName, integerAttributeValueWritten); final String byteAttributeName = "Byte Attribute"; final byte byteAttributeValueWritten = 17; writer.int8().setAttr(datasetName, byteAttributeName, byteAttributeValueWritten); final String unsignedByteAttributeName = "Unsigned Byte Attribute"; final short unsignedByteAttributeValueWritten = 128; writer.uint8().setAttr(datasetName, unsignedByteAttributeName, (byte) unsignedByteAttributeValueWritten); final String stringAttributeName = "String Attribute"; final String stringAttributeValueWritten = "Some String Value"; writer.string().setAttr(datasetName, stringAttributeName, stringAttributeValueWritten); final String stringAttributeNameVL = "String Attribute VL"; final String stringAttributeValueVLWritten1 = "Some String Value"; writer.string().setAttrVL(datasetName, stringAttributeNameVL, stringAttributeValueVLWritten1); final String stringAttributeValueVLWritten2 = "Some Other String Value"; writer.string().setAttrVL(datasetName, stringAttributeNameVL, stringAttributeValueVLWritten2); final String integerArrayAttributeName = "Integer Array Attribute"; final int[] integerArrayAttributeValueWritten = new int[] { 17, 23, 42 }; writer.int32().setArrayAttr(datasetName, integerArrayAttributeName, integerArrayAttributeValueWritten); final String stringArrayAttributeName = "String Array Attribute"; final String[] stringArrayAttributeValueWritten = new String[] { "Some String Value I", "Some String Value II", "Some String Value III" }; writer.string().setArrayAttr(datasetName, stringArrayAttributeName, stringArrayAttributeValueWritten); final String string2DArrayAttributeName = "String 2D Array Attribute"; final MDArray string2DArrayAttributeValueWritten = new MDArray( new String[] { "Some String Value I", "Some String Value II", "Some String Value III", "IV" }, new int[] { 2, 2 }); writer.string().setMDArrayAttr(datasetName, string2DArrayAttributeName, string2DArrayAttributeValueWritten); final HDF5EnumerationType enumType = writer.enumeration().getType("MyEnum", new String[] { "ONE", "TWO", "THREE" }, false); final String enumAttributeName = "Enum Attribute"; final HDF5EnumerationValue enumAttributeValueWritten = new HDF5EnumerationValue(enumType, "TWO"); writer.enumeration().setAttr(datasetName, enumAttributeName, enumAttributeValueWritten); assertEquals(enumAttributeValueWritten.getType(), writer.enumeration().getAttributeType(datasetName, enumAttributeName)); final String enumArrayAttributeName = "Enum Array Attribute"; final HDF5EnumerationValueArray enumArrayAttributeValueWritten = new HDF5EnumerationValueArray(enumType, new String[] { "TWO", "THREE", "ONE" }); writer.enumeration().setArrayAttr(datasetName, enumArrayAttributeName, enumArrayAttributeValueWritten); final String enumMDArrayAttributeName = "Enum Array MD Attribute"; final HDF5EnumerationValueMDArray enumMDArrayAttributeValueWritten = new HDF5EnumerationValueMDArray(enumType, new MDArray(new String[] { "TWO", "THREE", "ONE", "ONE" }, new int[] { 2, 2 })); writer.enumeration().setMDArrayAttr(datasetName, enumMDArrayAttributeName, enumMDArrayAttributeValueWritten); final String volatileAttributeName = "Some Volatile Attribute"; writer.int32().setAttr(datasetName, volatileAttributeName, 21); writer.object().deleteAttribute(datasetName, volatileAttributeName); final String floatArrayAttributeName = "Float Array Attribute"; final float[] floatArrayAttribute = new float[] { 3f, 3.1f, 3.14f, 3.142f, 3.1416f }; writer.float32().setArrayAttr(datasetName, floatArrayAttributeName, floatArrayAttribute); final String floatArrayMDAttributeName = "Float Array Multi-dimensional Attribute"; final MDFloatArray floatMatrixAttribute = new MDFloatArray(new float[][] { { 1, 2, 3 }, { 4, 5, 6 } }); writer.float32().setMDArrayAttr(datasetName, floatArrayMDAttributeName, floatMatrixAttribute); final MDFloatArray floatMatrixAttribute2 = new MDFloatArray(new float[][] { { 2, 3, 4 }, { 7, 8, 9 } }); writer.float32().setMatrixAttr(datasetName, floatArrayMDAttributeName, floatMatrixAttribute2.toMatrix()); final String byteArrayAttributeName = "Byte Array Attribute"; final byte[] byteArrayAttribute = new byte[] { 1, 2, 3 }; writer.int8().setArrayAttr(datasetName, byteArrayAttributeName, byteArrayAttribute); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(attributeFile); assertTrue(reader.object().hasAttribute(datasetName, booleanAttributeName)); final boolean booleanAttributeValueRead = reader.bool().getAttr(datasetName, booleanAttributeName); assertEquals(booleanAttributeValueWritten, booleanAttributeValueRead); final int integerAttributeValueRead = reader.int32().getAttr(datasetName, integerAttributeName); assertEquals(integerAttributeValueWritten, integerAttributeValueRead); final byte byteAttributeValueRead = reader.int8().getAttr(datasetName, byteAttributeName); assertEquals(byteAttributeValueWritten, byteAttributeValueRead); final short unsignedByteAttributeValueRead = reader.int16().getAttr(datasetName, unsignedByteAttributeName); assertEquals(unsignedByteAttributeValueWritten, unsignedByteAttributeValueRead); HDF5DataTypeInformation info = reader.object().getAttributeInformation(datasetName, integerAttributeName); assertEquals(HDF5DataClass.INTEGER, info.getDataClass()); assertEquals(4, info.getElementSize()); final String stringAttributeValueRead = reader.string().getAttr(datasetName, stringAttributeName); assertEquals(stringAttributeValueWritten, stringAttributeValueRead); final int[] intArrayAttributeValueRead = reader.int32().getArrayAttr(datasetName, integerArrayAttributeName); assertTrue(Arrays.equals(integerArrayAttributeValueWritten, intArrayAttributeValueRead)); final String[] stringArrayAttributeValueRead = reader.string().getArrayAttr(datasetName, stringArrayAttributeName); assertTrue(Arrays.equals(stringArrayAttributeValueWritten, stringArrayAttributeValueRead)); info = reader.object().getAttributeInformation(datasetName, stringArrayAttributeName); assertTrue(info.isArrayType()); assertEquals(HDF5DataClass.STRING, info.getDataClass()); assertEquals(21, info.getElementSize()); // longest string in the string array assertEquals(3, info.getNumberOfElements()); assertEquals(1, info.getDimensions().length); final MDArray string2DArrayAttributeValueRead = reader.string().getMDArrayAttr(datasetName, string2DArrayAttributeName); assertEquals(string2DArrayAttributeValueWritten, string2DArrayAttributeValueRead); final String stringAttributeValueVLRead = reader.string().getAttr(datasetName, stringAttributeNameVL); assertEquals(stringAttributeValueVLWritten2, stringAttributeValueVLRead); final HDF5EnumerationValue enumAttributeValueRead = reader.enumeration().getAttr(datasetName, enumAttributeName); final String enumAttributeStringValueRead = reader.enumeration().getAttrAsString(datasetName, enumAttributeName); assertEquals(enumAttributeValueWritten.getValue(), enumAttributeValueRead.getValue()); assertEquals(enumAttributeValueWritten.getValue(), enumAttributeStringValueRead); final HDF5EnumerationType enumAttributeType = reader.enumeration().getAttributeType(datasetName, enumAttributeName); assertEquals(enumAttributeValueWritten.getType(), enumAttributeType); assertEquals("MyEnum", enumAttributeType.getName()); final String[] enumArrayAttributeReadAsString = reader.enumeration().getArrayAttr(datasetName, enumArrayAttributeName) .toStringArray(); assertEquals(enumArrayAttributeValueWritten.getLength(), enumArrayAttributeReadAsString.length); for (int i = 0; i < enumArrayAttributeReadAsString.length; ++i) { assertEquals(enumArrayAttributeValueWritten.getValue(i), enumArrayAttributeReadAsString[i]); } final HDF5EnumerationValueArray enumArrayAttributeRead = reader.enumeration().getArrayAttr(datasetName, enumArrayAttributeName); final HDF5EnumerationType enumAttributeArrayType = reader.enumeration().getAttributeType(datasetName, enumArrayAttributeName); assertEquals(enumArrayAttributeRead.getType(), enumAttributeArrayType); assertEquals("MyEnum", enumAttributeArrayType.getName()); assertEquals(enumArrayAttributeValueWritten.getLength(), enumArrayAttributeRead.getLength()); for (int i = 0; i < enumArrayAttributeRead.getLength(); ++i) { assertEquals(enumArrayAttributeValueWritten.getValue(i), enumArrayAttributeRead.getValue(i)); } // Let's try to read the first element of the array using getEnumAttributeAsString assertEquals(enumArrayAttributeValueWritten.getValue(0), reader.enumeration() .getAttrAsString(datasetName, enumArrayAttributeName)); // Let's try to read the first element of the array using getEnumAttribute assertEquals(enumArrayAttributeValueWritten.getValue(0), reader.enumeration().getAttr(datasetName, enumArrayAttributeName).getValue()); assertFalse(reader.object().hasAttribute(datasetName, volatileAttributeName)); final HDF5EnumerationValueMDArray enumMDArrayAttributeRead = reader.enumeration().getMDArrayAttr(datasetName, enumMDArrayAttributeName); assertEquals(enumMDArrayAttributeValueWritten.toStringArray(), enumMDArrayAttributeRead.toStringArray()); assertEquals(enumArrayAttributeValueWritten.getLength(), enumArrayAttributeRead.getLength()); for (int i = 0; i < enumArrayAttributeRead.getLength(); ++i) { assertEquals(enumArrayAttributeValueWritten.getValue(i), enumArrayAttributeRead.getValue(i)); } assertTrue(Arrays.equals(floatArrayAttribute, reader.float32().getArrayAttr(datasetName, floatArrayAttributeName))); assertTrue(floatMatrixAttribute2.equals(reader.float32().getMDArrayAttr(datasetName, floatArrayMDAttributeName))); assertTrue(floatMatrixAttribute2.equals(new MDFloatArray(reader.float32().getMatrixAttr( datasetName, floatArrayMDAttributeName)))); assertTrue(Arrays.equals(byteArrayAttribute, reader.int8().getArrayAttr(datasetName, byteArrayAttributeName))); reader.close(); } @Test public void testSimpleDataspaceAttributes() { final File attributeFile = new File(workingDirectory, "simpleDataspaceAttributes.h5"); attributeFile.delete(); assertFalse(attributeFile.exists()); attributeFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().configure(attributeFile) .useSimpleDataSpaceForAttributes().writer(); final String datasetName = "SomeDataSet"; final String floatAttrName = "SomeFloatAttr"; final String floatAttrArrayName = "SomeFloatArrayAttr"; final String floatAttrMDArrayName = "SomeFloatMDArrayAttr"; final String unsignedIntAttrName = "SomeUnsignedIntAttr"; final String unsignedIntAttrArrayName = "SomeUnsignedIntArrayAttr"; final String unsignedIntAttrMDArrayName = "SomeUnsignedIntMDArrayAttr"; final String referenceAttrArrayName = "SomeRefAttr"; final String dateTimeAttrName = "SomeDateTimeAttr"; final String dateTimeAttrArrayName = "SomeDateTimeArrayAttr"; final String timeDurationAttrName = "SomeTimeDurationAttr"; final String timeDurationAttrArrayName = "SomeTimeDurationArrayAttr"; writer.float32().writeArray(datasetName, new float[0]); writer.float32().setAttr(datasetName, floatAttrName, 17.0f); final float[] floatArrayValueWritten = new float[] { 1, 2, 3, }; writer.float32().setArrayAttr(datasetName, floatAttrArrayName, floatArrayValueWritten); final MDFloatArray floatMDArrayWritten = new MDFloatArray(new float[] { 1, 2, 3, 4 }, new int[] { 2, 2 }); writer.float32().setMDArrayAttr(datasetName, floatAttrMDArrayName, floatMDArrayWritten); writer.uint32().setAttr(datasetName, unsignedIntAttrName, toInt32(4000000000L)); final int[] uintArrayValueWritten = new int[] { toInt32(4000000001L), toInt32(4000000002L), toInt32(4000000003L) }; writer.uint32().setArrayAttr(datasetName, unsignedIntAttrArrayName, uintArrayValueWritten); final MDIntArray uintMDArrayValueWritten = new MDIntArray(new int[] { toInt32(4000000000L), toInt32(4000000002L), toInt32(4000000003L), toInt32(4000000003L) }, new int[] { 2, 2 }); writer.uint32().setMDArrayAttr(datasetName, unsignedIntAttrMDArrayName, uintMDArrayValueWritten); writer.reference().setArrayAttr(datasetName, referenceAttrArrayName, new String[] { datasetName, datasetName }); writer.time().setAttr(datasetName, dateTimeAttrName, 1000L); writer.time().setArrayAttr(datasetName, dateTimeAttrArrayName, new long[] { 1000L, 2000L }); writer.duration().setAttr(datasetName, timeDurationAttrName, new HDF5TimeDuration(100L, HDF5TimeUnit.SECONDS)); writer.duration().setArrayAttr(datasetName, timeDurationAttrArrayName, new HDF5TimeDurationArray(new long[] { 100L, 150L }, HDF5TimeUnit.SECONDS)); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(attributeFile); assertTrue(reader.object().hasAttribute(datasetName, floatAttrName)); final float attributeValue = reader.float32().getAttr(datasetName, floatAttrName); assertEquals(17.0f, attributeValue); final HDF5BaseReader baseReader = ((HDF5FloatReader) reader.float32()).getBaseReader(); final int objectId = baseReader.h5.openObject(baseReader.fileId, datasetName, baseReader.fileRegistry); int attributeId = baseReader.h5.openAttribute(objectId, floatAttrName, baseReader.fileRegistry); int attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, baseReader.fileRegistry); assertEquals(H5T_FLOAT, baseReader.h5.getClassType(attributeTypeId)); assertTrue(reader.object().hasAttribute(datasetName, floatAttrArrayName)); final float[] attributeArrayValueRead = reader.float32().getArrayAttr(datasetName, floatAttrArrayName); assertTrue(Arrays.equals(floatArrayValueWritten, attributeArrayValueRead)); attributeId = baseReader.h5.openAttribute(objectId, floatAttrArrayName, baseReader.fileRegistry); attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, baseReader.fileRegistry); assertEquals(H5T_FLOAT, baseReader.h5.getClassType(attributeTypeId)); assertTrue(reader.object().hasAttribute(datasetName, floatAttrMDArrayName)); final MDFloatArray attributeMDArrayValueRead = reader.float32().getMDArrayAttr(datasetName, floatAttrMDArrayName); assertEquals(floatMDArrayWritten, attributeMDArrayValueRead); assertEquals(toInt32(4000000000L), reader.uint32() .getAttr(datasetName, unsignedIntAttrName)); attributeId = baseReader.h5.openAttribute(objectId, unsignedIntAttrName, baseReader.fileRegistry); attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, baseReader.fileRegistry); assertEquals(H5T_INTEGER, baseReader.h5.getClassType(attributeTypeId)); assertTrue(Arrays.equals(uintArrayValueWritten, reader.uint32().getArrayAttr(datasetName, unsignedIntAttrArrayName))); attributeId = baseReader.h5.openAttribute(objectId, unsignedIntAttrArrayName, baseReader.fileRegistry); attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, baseReader.fileRegistry); assertEquals(H5T_INTEGER, baseReader.h5.getClassType(attributeTypeId)); assertEquals(uintMDArrayValueWritten, reader.uint32().getMDArrayAttr(datasetName, unsignedIntAttrMDArrayName)); attributeId = baseReader.h5.openAttribute(objectId, unsignedIntAttrMDArrayName, baseReader.fileRegistry); attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, baseReader.fileRegistry); assertEquals(H5T_INTEGER, baseReader.h5.getClassType(attributeTypeId)); attributeId = baseReader.h5.openAttribute(objectId, referenceAttrArrayName, baseReader.fileRegistry); attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, baseReader.fileRegistry); assertEquals(H5T_REFERENCE, baseReader.h5.getClassType(attributeTypeId)); final String[] referenceValues = reader.reference().getArrayAttr(datasetName, referenceAttrArrayName); assertEquals(2, referenceValues.length); assertEquals("/" + datasetName, referenceValues[0]); assertEquals("/" + datasetName, referenceValues[1]); assertEquals(1000L, reader.time().getAttrAsLong(datasetName, dateTimeAttrName)); assertTrue(Arrays.equals(new long[] { 1000L, 2000L }, reader.time().getArrayAttrAsLong(datasetName, dateTimeAttrArrayName))); attributeId = baseReader.h5.openAttribute(objectId, dateTimeAttrName, baseReader.fileRegistry); attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, baseReader.fileRegistry); assertEquals(H5T_INTEGER, baseReader.h5.getClassType(attributeTypeId)); attributeId = baseReader.h5.openAttribute(objectId, "__TYPE_VARIANT__" + dateTimeAttrName + "__", baseReader.fileRegistry); attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, baseReader.fileRegistry); assertEquals(H5T_ENUM, baseReader.h5.getClassType(attributeTypeId)); assertEquals(new HDF5TimeDuration(100L, HDF5TimeUnit.SECONDS), reader.duration().getAttr(datasetName, timeDurationAttrName)); assertEquals(new HDF5TimeDurationArray(new long[] { 100L, 150L }, HDF5TimeUnit.SECONDS), reader.duration().getArrayAttr(datasetName, timeDurationAttrArrayName)); attributeId = baseReader.h5 .openAttribute(objectId, timeDurationAttrName, baseReader.fileRegistry); attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, baseReader.fileRegistry); assertEquals(H5T_INTEGER, baseReader.h5.getClassType(attributeTypeId)); attributeId = baseReader.h5.openAttribute(objectId, "__TYPE_VARIANT__" + timeDurationAttrName + "__", baseReader.fileRegistry); attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, baseReader.fileRegistry); assertEquals(H5T_ENUM, baseReader.h5.getClassType(attributeTypeId)); reader.close(); } @Test public void testTimeStampAttributes() { final File attributeFile = new File(workingDirectory, "timeStampAttributes.h5"); attributeFile.delete(); assertFalse(attributeFile.exists()); attributeFile.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.open(attributeFile); final String datasetName = "SomeDataSet"; final String lastChangedAttr = "lastChanged"; final String someLongAttr = "someLong"; final Date now = new Date(); writer.int32().writeArray(datasetName, new int[0]); writer.int64().setAttr(datasetName, someLongAttr, 115L); writer.time().setAttr(datasetName, lastChangedAttr, now); writer.close(); final IHDF5Reader reader = HDF5Factory.openForReading(attributeFile); assertEquals(HDF5DataTypeVariant.TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH, reader .object().tryGetTypeVariant(datasetName, lastChangedAttr)); assertFalse(reader.time().isTimeStamp(datasetName)); assertTrue(reader.time().isTimeStamp(datasetName, lastChangedAttr)); assertFalse(reader.duration().isTimeDuration(datasetName, lastChangedAttr)); assertEquals(now, reader.time().getAttr(datasetName, lastChangedAttr)); assertFalse(reader.time().isTimeStamp(datasetName, someLongAttr)); try { reader.time().getAttrAsLong(datasetName, someLongAttr); fail("Did not detect non-time-stamp attribute."); } catch (HDF5JavaException ex) { assertEquals("Attribute 'someLong' of data set 'SomeDataSet' is not a time stamp.", ex.getMessage()); } reader.close(); } @Test public void testTimeDurationAttributes() { final File attributeFile = new File(workingDirectory, "timeDurationAttributes.h5"); attributeFile.delete(); assertFalse(attributeFile.exists()); attributeFile.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.open(attributeFile); final String datasetName = "SomeDataSet"; final String validUntilAttr = "validUtil"; final String someLongAttr = "someLong"; writer.int32().writeArray(datasetName, new int[0]); writer.duration().setAttr(datasetName, validUntilAttr, 10, HDF5TimeUnit.MINUTES); writer.int64().setAttr(datasetName, someLongAttr, 115L); writer.close(); final IHDF5Reader reader = HDF5Factory.openForReading(attributeFile); assertEquals(HDF5DataTypeVariant.TIME_DURATION_MINUTES, reader.object().tryGetTypeVariant(datasetName, validUntilAttr)); assertFalse(reader.time().isTimeStamp(datasetName)); assertFalse(reader.time().isTimeStamp(datasetName, validUntilAttr)); assertTrue(reader.duration().isTimeDuration(datasetName, validUntilAttr)); assertEquals(HDF5TimeUnit.MINUTES, reader.duration().tryGetTimeUnit(datasetName, validUntilAttr)); assertEquals(new HDF5TimeDuration(10, HDF5TimeUnit.MINUTES), reader.duration().getAttr(datasetName, validUntilAttr)); assertEquals( 10 * 60, reader.duration().getAttr(datasetName, validUntilAttr) .getValue(HDF5TimeUnit.SECONDS)); assertFalse(reader.duration().isTimeDuration(datasetName, someLongAttr)); try { reader.duration().getAttr(datasetName, someLongAttr); fail("Did not detect non-time-duration attribute."); } catch (HDF5JavaException ex) { assertEquals("Attribute 'someLong' of data set 'SomeDataSet' is not a time duration.", ex.getMessage()); } reader.close(); } @Test public void testTimeStampArrayAttributes() { final File attributeFile = new File(workingDirectory, "timeStampArrayAttributes.h5"); attributeFile.delete(); assertFalse(attributeFile.exists()); attributeFile.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.open(attributeFile); final String datasetName = "SomeDataSet"; final String lastChangedAttr = "lastChanged"; final String someDates = "someDates"; final String someLongAttr = "someLong"; final Date now = new Date(); writer.int32().writeArray(datasetName, new int[0]); writer.int64().setArrayAttr(datasetName, someLongAttr, new long[] { 115L }); writer.time().setArrayAttr(datasetName, lastChangedAttr, new Date[] { now }); writer.time().setMDArrayAttr( datasetName, someDates, new MDArray(new Date[] { now, new Date(now.getTime() - 1000L), new Date(now.getTime() - 2000L), new Date(now.getTime() - 3000L) }, new int[] { 2, 2 })); writer.close(); final IHDF5Reader reader = HDF5Factory.openForReading(attributeFile); assertEquals(HDF5DataTypeVariant.TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH, reader .object().tryGetTypeVariant(datasetName, lastChangedAttr)); assertFalse(reader.time().isTimeStamp(datasetName)); assertTrue(reader.time().isTimeStamp(datasetName, lastChangedAttr)); assertFalse(reader.duration().isTimeDuration(datasetName, lastChangedAttr)); assertEquals(1, reader.time().getArrayAttr(datasetName, lastChangedAttr).length); assertEquals(now, reader.time().getArrayAttr(datasetName, lastChangedAttr)[0]); assertFalse(reader.time().isTimeStamp(datasetName, someLongAttr)); assertTrue(reader.time().isTimeStamp(datasetName, someDates)); assertEquals(now.getTime(), reader.time().getMDArrayAttrAsLong(datasetName, someDates).get(0, 0)); assertEquals(now.getTime() - 1000L, reader.time().getMDArrayAttrAsLong(datasetName, someDates).get(0, 1)); assertEquals(now.getTime() - 2000L, reader.time().getMDArrayAttrAsLong(datasetName, someDates).get(1, 0)); assertEquals(now.getTime() - 3000L, reader.time().getMDArrayAttrAsLong(datasetName, someDates).get(1, 1)); try { reader.time().getArrayAttrAsLong(datasetName, someLongAttr); fail("Did not detect non-time-stamp attribute."); } catch (HDF5JavaException ex) { assertEquals("Attribute 'someLong' of data set 'SomeDataSet' is not a time stamp.", ex.getMessage()); } reader.close(); } @Test public void testTimeDurationArrayAttributes() { final File attributeFile = new File(workingDirectory, "timeDurationArrayAttributes.h5"); attributeFile.delete(); assertFalse(attributeFile.exists()); attributeFile.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.open(attributeFile); final String datasetName = "SomeDataSet"; final String validUntilAttr = "validUtil"; final String someDurations = "someDurations"; final String someLongAttr = "someLong"; writer.int32().writeArray(datasetName, new int[0]); writer.duration().setArrayAttr(datasetName, validUntilAttr, HDF5TimeDurationArray.create(HDF5TimeUnit.MINUTES, 10)); final HDF5TimeDurationMDArray someDurationValues = new HDF5TimeDurationMDArray(new long[] { 1, 2, 3, 4 }, new int[] { 2, 2 }, HDF5TimeUnit.MINUTES); writer.duration().setMDArrayAttr(datasetName, someDurations, someDurationValues); writer.int64().setArrayAttr(datasetName, someLongAttr, new long[] { 115L }); writer.close(); final IHDF5Reader reader = HDF5Factory.openForReading(attributeFile); assertEquals(HDF5DataTypeVariant.TIME_DURATION_MINUTES, reader.object().tryGetTypeVariant(datasetName, validUntilAttr)); assertFalse(reader.time().isTimeStamp(datasetName)); assertFalse(reader.time().isTimeStamp(datasetName, validUntilAttr)); assertTrue(reader.duration().isTimeDuration(datasetName, validUntilAttr)); assertEquals(HDF5TimeUnit.MINUTES, reader.duration().tryGetTimeUnit(datasetName, validUntilAttr)); assertEquals(1, reader.duration().getArrayAttr(datasetName, validUntilAttr).getLength()); assertEquals(new HDF5TimeDuration(10, HDF5TimeUnit.MINUTES), reader.duration() .getArrayAttr(datasetName, validUntilAttr).get(0)); assertEquals( 10 * 60, reader.duration().getArrayAttr(datasetName, validUntilAttr) .getValue(0, HDF5TimeUnit.SECONDS)); assertFalse(reader.duration().isTimeDuration(datasetName, someLongAttr)); assertTrue(reader.duration().isTimeDuration(datasetName, someDurations)); assertEquals(someDurationValues, reader.duration().getMDArrayAttr(datasetName, someDurations)); try { reader.duration().getArrayAttr(datasetName, someLongAttr); fail("Did not detect non-time-duration attribute."); } catch (HDF5JavaException ex) { assertEquals("Attribute 'someLong' of data set 'SomeDataSet' is not a time duration.", ex.getMessage()); } reader.close(); } @Test public void testAttributeDimensionArray() { final File attributeFile = new File(workingDirectory, "attributeDimensionalArray.h5"); attributeFile.delete(); assertFalse(attributeFile.exists()); attributeFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(attributeFile); final HDF5ArrayTypeFloatWriter efWriter = new HDF5ArrayTypeFloatWriter((HDF5Writer) writer); final String datasetName = "SomeDataSet"; final String attributeName = "farray"; final float[] farray = new float[] { 0, 10, 100 }; writer.int32().writeArray(datasetName, new int[0]); efWriter.setFloatArrayAttributeDimensional(datasetName, attributeName, farray); final HDF5DataTypeInformation info = writer.object().getAttributeInformation(datasetName, attributeName); assertEquals("FLOAT(4, #3)", info.toString()); assertFalse(info.isArrayType()); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(attributeFile); assertTrue(Arrays.equals(farray, reader.float32().getArrayAttr(datasetName, attributeName))); } @Test public void testAttributeDimensionArrayOverwrite() { final File attributeFile = new File(workingDirectory, "attributeDimensionalArrayOverwrite.h5"); attributeFile.delete(); assertFalse(attributeFile.exists()); attributeFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(attributeFile); final HDF5ArrayTypeFloatWriter efWriter = new HDF5ArrayTypeFloatWriter((HDF5Writer) writer); final String datasetName = "SomeDataSet"; final String attributeName = "farray"; final float[] farray = new float[] { 0, 10, 100 }; writer.int32().writeArray(datasetName, new int[0]); efWriter.setFloatArrayAttributeDimensional(datasetName, attributeName, farray); writer.float32().setArrayAttr(datasetName, attributeName, farray); final HDF5DataTypeInformation info = writer.object().getAttributeInformation(datasetName, attributeName); assertEquals("FLOAT(4, #3)", info.toString()); assertTrue(info.isArrayType()); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(attributeFile); assertTrue(Arrays.equals(farray, reader.float32().getArrayAttr(datasetName, attributeName))); } @Test public void testCreateDataTypes() { final File file = new File(workingDirectory, "types.h5"); final String enumName = "TestEnum"; file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); try { final List initialDataTypes = writer.getGroupMembers(HDF5Utils.getDataTypeGroup("")); writer.enumeration().getType(enumName, new String[] { "ONE", "TWO", "THREE" }, false); final Set dataTypes = new HashSet(writer.getGroupMembers(HDF5Utils.getDataTypeGroup(""))); assertEquals(initialDataTypes.size() + 1, dataTypes.size()); assertTrue(dataTypes.contains(HDF5Utils.ENUM_PREFIX + enumName)); } finally { writer.close(); } } @Test public void testGroups() { final File groupFile = new File(workingDirectory, "groups.h5"); groupFile.delete(); assertFalse(groupFile.exists()); groupFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(groupFile); final String groupName1 = "/group"; final String groupName2 = "/group2"; final String groupName4 = "/dataSetGroup"; final String groupName5 = "/group5"; final String dataSetName = groupName4 + "/dataset"; writer.object().createGroup(groupName1); writer.object().createGroup(groupName2); writer.int8().writeArray(dataSetName, new byte[] { 1 }); assertTrue(writer.isGroup(groupName1)); assertTrue(writer.isGroup(groupName2)); assertTrue(writer.isGroup(groupName4)); assertFalse(writer.isGroup(dataSetName)); assertFalse(writer.isGroup(groupName5)); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(groupFile); assertTrue(reader.isGroup(groupName1)); assertEquals(HDF5ObjectType.GROUP, reader.object().getObjectType(groupName1)); assertTrue(reader.isGroup(groupName4)); assertEquals(HDF5ObjectType.GROUP, reader.object().getObjectType(groupName4)); assertFalse(reader.isGroup(dataSetName)); reader.close(); } @Test public void testDefaultHousekeepingFile() { final File file = new File(workingDirectory, "defaultHousekeepingFile.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); assertEquals("", writer.file().getHouseKeepingNameSuffix()); assertEquals("__abc__", writer.object().toHouseKeepingPath("abc")); writer.string().write(writer.object().toHouseKeepingPath("abc"), "ABC"); assertTrue(writer.exists("__abc__")); assertTrue(writer.object().getGroupMemberPaths("/").isEmpty()); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); assertTrue(reader.object().getAttributeNames("/").isEmpty()); assertEquals("", reader.file().getHouseKeepingNameSuffix()); assertEquals("__abc__", reader.object().toHouseKeepingPath("abc")); assertTrue(reader.exists("__abc__")); assertEquals("ABC", reader.readString("__abc__")); assertTrue(reader.object().getGroupMemberPaths("/").isEmpty()); reader.close(); } @Test public void testNonDefaultHousekeepingFile() { final File file = new File(workingDirectory, "nonDefaultHousekeepingFile.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.configure(file).houseKeepingNameSuffix("XXX").writer(); assertEquals("XXX", writer.file().getHouseKeepingNameSuffix()); assertEquals("abcXXX", writer.object().toHouseKeepingPath("abc")); writer.string().write(writer.object().toHouseKeepingPath("abc"), "ABC"); assertTrue(writer.exists("abcXXX")); assertFalse(writer.exists("__abc__")); assertTrue(writer.object().getGroupMemberPaths("/").isEmpty()); writer.close(); // The house keeping index is only considered when creating a new file. // If the file exists, the one saved in the file takes precedence. final IHDF5Writer writer2 = HDF5Factory.configure(file).houseKeepingNameSuffix("YYY").writer(); assertEquals("XXX", writer2.file().getHouseKeepingNameSuffix()); assertEquals("abcXXX", writer2.object().toHouseKeepingPath("abc")); assertTrue(writer2.exists("abcXXX")); writer2.string().write(writer2.object().toHouseKeepingPath("abc"), "CAB"); assertFalse(writer2.exists("__abc__")); assertFalse(writer2.exists("abcYYY")); assertEquals("CAB", writer2.readString("abcXXX")); assertTrue(writer2.object().getGroupMemberPaths("/").isEmpty()); writer2.close(); final IHDF5Reader reader = HDF5Factory.openForReading(file); assertTrue(reader.object().getAttributeNames("/").isEmpty()); assertEquals("XXX", reader.file().getHouseKeepingNameSuffix()); assertEquals("abcXXX", reader.object().toHouseKeepingPath("abc")); assertTrue(reader.exists("abcXXX")); assertFalse(reader.exists("__abc__")); assertEquals("CAB", reader.readString("abcXXX")); assertTrue(reader.object().getGroupMemberPaths("/").isEmpty()); reader.close(); } @Test public void testHousekeepingFileSuffixNonPrintable() { final File file = new File(workingDirectory, "housekeepingFileSuffixNonPrintable.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.configure(file).houseKeepingNameSuffix("\1\0").writer(); assertEquals("\1\0", writer.file().getHouseKeepingNameSuffix()); assertEquals("abc\1\0", writer.object().toHouseKeepingPath("abc")); writer.string().write(writer.object().toHouseKeepingPath("abc"), "ABC"); assertTrue(writer.exists("abc\1\0")); assertFalse(writer.exists("__abc__")); assertTrue(writer.object().getGroupMemberPaths("/").isEmpty()); writer.close(); final IHDF5Reader reader = HDF5Factory.openForReading(file); assertEquals("\1\0", reader.file().getHouseKeepingNameSuffix()); assertEquals("abc\1\0", reader.object().toHouseKeepingPath("abc")); assertTrue(reader.exists("abc\1\0")); assertFalse(reader.exists("__abc__")); assertEquals("ABC", reader.readString("abc\1\0")); assertTrue(reader.object().getGroupMemberPaths("/").isEmpty()); reader.close(); } @Test public void testGetObjectType() { final File file = new File(workingDirectory, "typeInfo.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); writer.writeBoolean("/some/flag", false); writer.object().createSoftLink("/some", "/linkToSome"); writer.object().createSoftLink("/some/flag", "/linkToFlag"); writer.object().createHardLink("/some/flag", "/some/flag2"); writer.bool().setAttr("/some/flag2", "test", true); assertEquals(HDF5ObjectType.GROUP, writer.object().getObjectType("/some")); assertEquals(HDF5ObjectType.SOFT_LINK, writer.object().getObjectType("/linkToSome", false)); assertEquals(HDF5ObjectType.GROUP, writer.object().getObjectType("/some")); assertEquals(HDF5ObjectType.GROUP, writer.object().getObjectType("/linkToSome")); assertEquals(HDF5ObjectType.DATASET, writer.object().getObjectType("/some/flag", false)); assertEquals(HDF5ObjectType.DATASET, writer.object().getObjectType("/some/flag")); assertEquals(HDF5ObjectType.SOFT_LINK, writer.object().getObjectType("/linkToFlag", false)); assertEquals(HDF5ObjectType.DATASET, writer.object().getObjectType("/linkToFlag")); assertFalse(writer.exists("non_existent")); assertEquals(HDF5ObjectType.NONEXISTENT, writer.object().getObjectType("non_existent")); writer.close(); } @Test(expectedExceptions = HDF5JavaException.class) public void testGetLinkInformationFailed() { final File file = new File(workingDirectory, "linkInfo.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); try { assertFalse(writer.exists("non_existent")); writer.object().getLinkInformation("non_existent").checkExists(); } finally { writer.close(); } } @Test public void testGetDataSetInformation() { final File file = new File(workingDirectory, "dsInfo.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); writer.int32().write("dsScalar", 12); writer.int16().writeMatrix("ds", new short[][] { { (short) 1, (short) 2, (short) 3 }, { (short) 4, (short) 5, (short) 6 } }); final String s = "this is a string"; writer.string().write("stringDS", s); writer.string().writeVL("stringDSVL", s); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); final HDF5DataSetInformation scalarInfo = reader.getDataSetInformation("dsScalar"); assertEquals(HDF5DataClass.INTEGER, scalarInfo.getTypeInformation().getDataClass()); assertEquals(4, scalarInfo.getTypeInformation().getElementSize()); assertEquals(0, scalarInfo.getRank()); assertTrue(scalarInfo.isScalar()); assertEquals(0, scalarInfo.getDimensions().length); assertNull(scalarInfo.tryGetChunkSizes()); final HDF5DataSetInformation info = reader.getDataSetInformation("ds"); assertEquals(HDF5DataClass.INTEGER, info.getTypeInformation().getDataClass()); assertEquals(2, info.getTypeInformation().getElementSize()); assertEquals(2, info.getRank()); assertFalse(info.isScalar()); assertEquals(2, info.getDimensions()[0]); assertEquals(3, info.getDimensions()[1]); assertChunkSizes(info, 2, 3); final HDF5DataSetInformation stringInfo = reader.getDataSetInformation("stringDS"); assertEquals(HDF5DataClass.STRING, stringInfo.getTypeInformation().getDataClass()); assertEquals(s.length(), stringInfo.getTypeInformation().getElementSize()); assertEquals(0, stringInfo.getDimensions().length); assertEquals(0, stringInfo.getMaxDimensions().length); assertEquals(HDF5StorageLayout.COMPACT, stringInfo.getStorageLayout()); assertNull(stringInfo.tryGetChunkSizes()); final HDF5DataSetInformation stringInfoVL = reader.getDataSetInformation("stringDSVL"); assertEquals(HDF5DataClass.STRING, stringInfoVL.getTypeInformation().getDataClass()); assertTrue(stringInfoVL.getTypeInformation().isVariableLengthString()); assertEquals(-1, stringInfoVL.getTypeInformation().getElementSize()); assertEquals(0, stringInfoVL.getDimensions().length); assertEquals(HDF5StorageLayout.COMPACT, stringInfoVL.getStorageLayout()); assertNull(stringInfoVL.tryGetChunkSizes()); assertEquals(0, stringInfoVL.getDimensions().length); assertEquals(0, stringInfoVL.getMaxDimensions().length); reader.close(); } @Test(expectedExceptions = HDF5SymbolTableException.class) public void testGetDataSetInformationFailed() { final File file = new File(workingDirectory, "dsInfo.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); try { assertFalse(writer.exists("non_existent")); writer.getDataSetInformation("non_existent"); } finally { writer.close(); } } @Test public void testGetGroupMemberInformation() { final File groupFile = new File(workingDirectory, "groupMemberInformation.h5"); groupFile.delete(); assertFalse(groupFile.exists()); groupFile.deleteOnExit(); final String groupName1 = "/group"; final String groupName2 = "/dataSetGroup"; final String dataSetName = groupName2 + "/dataset"; final String dataSetName2 = "ds2"; final String linkName = "/link"; final IHDF5Writer writer = HDF5FactoryProvider.get().open(groupFile); try { writer.object().createGroup(groupName1); writer.int8().writeArray(dataSetName, new byte[] { 1 }); writer.string().write(dataSetName2, "abc"); writer.object().createSoftLink(dataSetName2, linkName); } finally { writer.close(); } final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(groupFile); final Map map = new HashMap(); for (HDF5LinkInformation info : reader.object().getAllGroupMemberInformation("/", false)) { map.put(info.getPath(), info); } HDF5LinkInformation info; assertEquals(5, map.size()); info = map.get(groupName1); assertNotNull(info); assertTrue(info.exists()); assertEquals(HDF5ObjectType.GROUP, info.getType()); assertNull(info.tryGetSymbolicLinkTarget()); info = map.get(groupName2); assertNotNull(info); assertTrue(info.exists()); assertEquals(HDF5ObjectType.GROUP, info.getType()); assertNull(info.tryGetSymbolicLinkTarget()); info = map.get("/" + dataSetName2); assertNotNull(info); assertTrue(info.exists()); assertEquals(HDF5ObjectType.DATASET, info.getType()); assertNull(info.tryGetSymbolicLinkTarget()); info = map.get(linkName); assertNotNull(info); assertTrue(info.exists()); assertEquals(HDF5ObjectType.SOFT_LINK, info.getType()); assertNull(info.tryGetSymbolicLinkTarget()); map.clear(); for (HDF5LinkInformation info2 : reader.object().getGroupMemberInformation("/", true)) { map.put(info2.getPath(), info2); } assertEquals(4, map.size()); info = map.get(groupName1); assertNotNull(info); assertTrue(info.exists()); assertEquals(HDF5ObjectType.GROUP, info.getType()); assertNull(info.tryGetSymbolicLinkTarget()); info = map.get(groupName2); assertNotNull(info); assertTrue(info.exists()); assertEquals(HDF5ObjectType.GROUP, info.getType()); assertNull(info.tryGetSymbolicLinkTarget()); info = map.get("/" + dataSetName2); assertNotNull(info); assertTrue(info.exists()); assertEquals(HDF5ObjectType.DATASET, info.getType()); assertNull(info.tryGetSymbolicLinkTarget()); info = map.get(linkName); assertNotNull(info); assertTrue(info.exists()); assertEquals(HDF5ObjectType.SOFT_LINK, info.getType()); assertEquals(dataSetName2, info.tryGetSymbolicLinkTarget()); reader.close(); } @Test public void testHardLink() { final File linkFile = new File(workingDirectory, "hardLink.h5"); linkFile.delete(); assertFalse(linkFile.exists()); linkFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(linkFile); final String str = "BlaBlub"; writer.string().write("/data/set", str); writer.object().createHardLink("/data/set", "/data/link"); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(linkFile); assertEquals(HDF5ObjectType.DATASET, reader.object().getObjectType("/data/link")); assertEquals(str, reader.readString("/data/link")); reader.close(); } @Test public void testSoftLink() { final File linkFile = new File(workingDirectory, "softLink.h5"); linkFile.delete(); assertFalse(linkFile.exists()); linkFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(linkFile); writer.writeBoolean("/data/set", true); writer.object().createSoftLink("/data/set", "/data/link"); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(linkFile); assertEquals(HDF5ObjectType.SOFT_LINK, reader.object().getObjectType("/data/link", false)); assertEquals("/data/set", reader.object().getLinkInformation("/data/link") .tryGetSymbolicLinkTarget()); reader.close(); } @Test public void testUpdateSoftLink() { final File file = new File(workingDirectory, "updateSoftLink.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); final long now = System.currentTimeMillis(); final String dataSetName1 = "creationTime1"; final String dataSetName2 = "creationTime2"; final String linkName = "time"; writer.time().write(dataSetName1, now); writer.time().write(dataSetName2, now); writer.object().createSoftLink(dataSetName1, linkName); writer.object().createOrUpdateSoftLink(dataSetName2, linkName); try { writer.object().createOrUpdateSoftLink(dataSetName1, dataSetName2); } catch (HDF5LibraryException ex) { assertEquals(HDF5Constants.H5E_EXISTS, ex.getMinorErrorNumber()); } writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); assertEquals(dataSetName2, reader.object().getLinkInformation(linkName) .tryGetSymbolicLinkTarget()); reader.close(); } @Test public void testBrokenSoftLink() { final File linkFile = new File(workingDirectory, "brokenSoftLink.h5"); linkFile.delete(); assertFalse(linkFile.exists()); linkFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(linkFile); writer.object().createSoftLink("/does/not/exist", "/linkToNowhere"); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(linkFile); assertFalse(reader.exists("/linkToNowhere")); assertTrue(reader.object().exists("/linkToNowhere", false)); assertEquals(HDF5ObjectType.SOFT_LINK, reader.object().getObjectType("/linkToNowhere", false)); assertEquals("/does/not/exist", reader.object().getLinkInformation("/linkToNowhere") .tryGetSymbolicLinkTarget()); reader.close(); } @Test public void testDeleteSoftLink() { final File linkFile = new File(workingDirectory, "deleteSoftLink.h5"); linkFile.delete(); assertFalse(linkFile.exists()); linkFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(linkFile); writer.writeBoolean("/group/boolean", true); writer.object().createSoftLink("/group", "/link"); writer.delete("/link"); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(linkFile); assertFalse(reader.object().exists("/link", false)); assertTrue(reader.exists("/group")); assertTrue(reader.exists("/group/boolean")); reader.close(); } @Test public void testNullOnGetSymbolicLinkTargetForNoLink() { final File noLinkFile = new File(workingDirectory, "noLink.h5"); noLinkFile.delete(); assertFalse(noLinkFile.exists()); noLinkFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(noLinkFile); writer.writeBoolean("/data/set", true); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(noLinkFile); try { assertNull(reader.object().getLinkInformation("/data/set").tryGetSymbolicLinkTarget()); } finally { reader.close(); } } @Test public void testExternalLink() { final File fileToLinkTo = new File(workingDirectory, "fileToLinkTo.h5"); fileToLinkTo.delete(); assertFalse(fileToLinkTo.exists()); fileToLinkTo.deleteOnExit(); final IHDF5Writer writer1 = HDF5FactoryProvider.get().open(fileToLinkTo); final String dataSetName = "/data/set"; final String dataSetValue = "Some data set value..."; writer1.string().write(dataSetName, dataSetValue); writer1.close(); final File linkFile = new File(workingDirectory, "externalLink.h5"); linkFile.delete(); assertFalse(linkFile.exists()); linkFile.deleteOnExit(); final IHDF5Writer writer2 = HDF5FactoryProvider.get().open(linkFile); final String linkName = "/data/link"; writer2.object().createExternalLink(fileToLinkTo.getPath(), dataSetName, linkName); writer2.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(linkFile); assertEquals(HDF5ObjectType.EXTERNAL_LINK, reader.object().getObjectType(linkName, false)); assertEquals(dataSetValue, reader.readString(linkName)); final String expectedLink = OSUtilities.isWindows() ? "EXTERNAL::targets\\unit-test-wd\\hdf5-roundtrip-wd\\fileToLinkTo.h5::/data/set" : "EXTERNAL::targets/unit-test-wd/hdf5-roundtrip-wd/fileToLinkTo.h5::/data/set"; assertEquals(expectedLink, reader.object().getLinkInformation(linkName) .tryGetSymbolicLinkTarget()); reader.close(); } @Test public void testDataTypeInfoOptions() { final File file = new File(workingDirectory, "dataTypeInfoOptions.h5"); final String enumDsName = "/testEnum"; final String dateDsName = "/testDate"; file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.configure(file).writer(); writer.enumeration().write(enumDsName, JavaEnum.TWO); writer.time().write(dateDsName, new Date(10000L)); writer.close(); final IHDF5Reader reader = HDF5Factory.openForReading(file); final HDF5DataTypeInformation minimalEnumInfo = reader.object().getDataSetInformation(enumDsName, DataTypeInfoOptions.MINIMAL) .getTypeInformation(); assertFalse(minimalEnumInfo.knowsDataTypePath()); assertFalse(minimalEnumInfo.knowsDataTypeVariant()); assertNull(minimalEnumInfo.tryGetName()); assertNull(minimalEnumInfo.tryGetTypeVariant()); final HDF5DataTypeInformation defaultInfo = reader.getDataSetInformation(enumDsName).getTypeInformation(); assertFalse(defaultInfo.knowsDataTypePath()); assertTrue(defaultInfo.knowsDataTypeVariant()); assertNull(defaultInfo.tryGetName()); assertEquals(HDF5DataTypeVariant.NONE, defaultInfo.tryGetTypeVariant()); final HDF5DataTypeInformation allInfo = reader.object().getDataSetInformation(enumDsName, DataTypeInfoOptions.ALL) .getTypeInformation(); assertTrue(allInfo.knowsDataTypePath()); assertTrue(allInfo.knowsDataTypeVariant()); assertEquals(JavaEnum.class.getSimpleName(), allInfo.tryGetName()); final HDF5DataTypeInformation minimalDateInfo = reader.object().getDataSetInformation(dateDsName, DataTypeInfoOptions.MINIMAL) .getTypeInformation(); assertFalse(minimalDateInfo.knowsDataTypePath()); assertFalse(minimalDateInfo.knowsDataTypeVariant()); assertNull(minimalDateInfo.tryGetName()); assertNull(minimalDateInfo.tryGetTypeVariant()); final HDF5DataTypeInformation defaultDateInfo = reader.object().getDataSetInformation(dateDsName, DataTypeInfoOptions.DEFAULT) .getTypeInformation(); assertFalse(defaultDateInfo.knowsDataTypePath()); assertTrue(defaultDateInfo.knowsDataTypeVariant()); assertNull(defaultDateInfo.tryGetName()); assertEquals(HDF5DataTypeVariant.TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH, defaultDateInfo.tryGetTypeVariant()); final HDF5DataTypeInformation allDateInfo = reader.object().getDataSetInformation(dateDsName, DataTypeInfoOptions.ALL) .getTypeInformation(); assertTrue(allDateInfo.knowsDataTypePath()); assertTrue(allDateInfo.knowsDataTypeVariant()); assertNull(allDateInfo.tryGetName()); assertEquals(HDF5DataTypeVariant.TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH, allDateInfo.tryGetTypeVariant()); reader.close(); } enum JavaEnum { ONE, TWO, THREE } @Test public void testJavaEnum() { final File file = new File(workingDirectory, "javaEnum.h5"); final String dsName = "/testEnum"; file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.configure(file).keepDataSetsIfTheyExist().writer(); writer.enumeration().write(dsName, JavaEnum.THREE); writer.enumeration().setAttr(dsName, "attr", JavaEnum.TWO); writer.close(); final IHDF5Reader reader = HDF5Factory.openForReading(file); assertEquals(JavaEnum.THREE, reader.enumeration().read(dsName, JavaEnum.class)); assertEquals(JavaEnum.TWO, reader.enumeration().getAttr(dsName, "attr").getValue(JavaEnum.class)); final String valueStr = reader.readEnumAsString(dsName); assertEquals("THREE", valueStr); final HDF5EnumerationValue value = reader.enumeration().read(dsName); assertEquals("THREE", value.getValue()); final String expectedDataTypePath = HDF5Utils.createDataTypePath(HDF5Utils.ENUM_PREFIX, "", JavaEnum.class.getSimpleName()); assertEquals(expectedDataTypePath, reader.object().tryGetDataTypePath(value.getType())); assertEquals(expectedDataTypePath, reader.object().tryGetDataTypePath(dsName)); final HDF5EnumerationType type = reader.enumeration().getDataSetType(dsName); assertEquals(3, type.getValues().size()); assertEquals("ONE", type.getValues().get(0)); assertEquals("TWO", type.getValues().get(1)); assertEquals("THREE", type.getValues().get(2)); reader.close(); } @Test public void testEnum() { final File file = new File(workingDirectory, "enum.h5"); final String enumTypeName = "testEnumType"; final String dsName = "/testEnum"; file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.configure(file).keepDataSetsIfTheyExist().writer(); HDF5EnumerationType type = writer.enumeration().getType(enumTypeName, new String[] { "ONE", "TWO", "THREE" }, false); writer.enumeration().write(dsName, new HDF5EnumerationValue(type, "THREE")); // That is wrong, but we disable the check, so no exception should be thrown. writer.enumeration().getType(enumTypeName, new String[] { "THREE", "ONE", "TWO" }, false); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); type = reader.enumeration().getType(enumTypeName); assertEquals(enumTypeName, type.tryGetName()); final HDF5DataTypeInformation typeInfo = reader.object().getDataSetInformation(dsName, DataTypeInfoOptions.ALL) .getTypeInformation(); assertEquals(enumTypeName, typeInfo.tryGetName()); assertEquals(HDF5Utils.createDataTypePath(HDF5Utils.ENUM_PREFIX, "", enumTypeName), typeInfo.tryGetDataTypePath()); final String valueStr = reader.readEnumAsString(dsName); assertEquals("THREE", valueStr); final HDF5EnumerationValue value = reader.enumeration().read(dsName); assertEquals("THREE", value.getValue()); final String expectedDataTypePath = HDF5Utils.createDataTypePath(HDF5Utils.ENUM_PREFIX, "", enumTypeName); assertEquals(expectedDataTypePath, reader.object().tryGetDataTypePath(value.getType())); assertEquals(expectedDataTypePath, reader.object().tryGetDataTypePath(dsName)); type = reader.enumeration().getDataSetType(dsName); assertEquals("THREE", reader.enumeration().read(dsName, type).getValue()); reader.close(); final IHDF5Writer writer2 = HDF5FactoryProvider.get().open(file); type = writer2.enumeration().getType(enumTypeName, new String[] { "ONE", "TWO", "THREE" }, true); assertEquals("THREE", writer2.enumeration().read(dsName, type).getValue()); writer2.close(); } enum NumberEnum { ONE, TWO, THREE, FOUR, FIVE } @Test public void testAnonymousEnum() { final File file = new File(workingDirectory, "anonymousEnum.h5"); final String dsName = "/testEnum"; final String dsName2 = "/testEnum2"; file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.configure(file).keepDataSetsIfTheyExist().writer(); HDF5EnumerationType type = writer.enumeration().getAnonType(new String[] { "ONE", "TWO", "THREE", "FOUR", "INFINITY" }); writer.enumeration().write(dsName, new HDF5EnumerationValue(type, "INFINITY")); HDF5EnumerationType type2 = writer.enumeration().getAnonType(NumberEnum.class); writer.enumeration().write(dsName2, new HDF5EnumerationValue(type2, NumberEnum.FIVE)); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); assertEquals("INFINITY", reader.readEnumAsString(dsName)); assertEquals("INFINITY", reader.enumeration().read(dsName).getValue()); assertEquals("FIVE", reader.readEnumAsString(dsName2)); assertEquals(NumberEnum.FIVE, reader.enumeration().read(dsName2).getValue(NumberEnum.class)); reader.close(); } @Test public void testEnum16() { final File file = new File(workingDirectory, "enum16bit.h5"); final String enumTypeName = "testEnumType16"; final String dsName = "/testEnum"; file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.configure(file).keepDataSetsIfTheyExist().writer(); HDF5EnumerationType type = createEnum16Bit(writer, enumTypeName); writer.enumeration().write(dsName, new HDF5EnumerationValue(type, "17")); final String[] confusedValues = new String[type.getEnumType().getValueArray().length]; System.arraycopy(confusedValues, 0, confusedValues, 1, confusedValues.length - 1); confusedValues[0] = "XXX"; // This is wrong, but we disabled the check. writer.enumeration().getType(enumTypeName, confusedValues, false); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); type = reader.enumeration().getType(enumTypeName); final String valueStr = reader.readEnumAsString(dsName); assertEquals("17", valueStr); final HDF5EnumerationValue value = reader.enumeration().read(dsName); assertEquals("17", value.getValue()); type = reader.enumeration().getDataSetType(dsName); assertEquals("17", reader.enumeration().read(dsName, type).getValue()); reader.close(); final IHDF5Writer writer2 = HDF5FactoryProvider.get().open(file); type = writer2.enumeration().getType(enumTypeName, type.getEnumType().getValueArray(), true); assertEquals("17", writer2.enumeration().read(dsName, type).getValue()); // That is wrong, but we disable the check, so no exception should be thrown. writer2.close(); } @Test(expectedExceptions = HDF5JavaException.class) public void testConfusedEnum() { final File file = new File(workingDirectory, "confusedEnum.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); IHDF5Writer writer = HDF5Factory.open(file); HDF5EnumerationType type = writer.enumeration().getType("testEnum", new String[] { "ONE", "TWO", "THREE" }, false); writer.enumeration().write("/testEnum", new HDF5EnumerationValue(type, 2)); writer.close(); try { writer = HDF5Factory.configure(file).keepDataSetsIfTheyExist().writer(); writer.enumeration().getType("testEnum", new String[] { "THREE", "ONE", "TWO" }, true); } finally { writer.close(); } } @Test public void testReplaceConfusedEnum() { final File file = new File(workingDirectory, "replaceConfusedEnum.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); IHDF5Writer writer = HDF5Factory.open(file); HDF5EnumerationType type = writer.enumeration().getType("testEnum", new String[] { "ONE", "TWO", "THREE" }, false); writer.enumeration().write("/testEnum", new HDF5EnumerationValue(type, 2)); writer.close(); writer = HDF5Factory.open(file); final HDF5EnumerationType type2 = writer.enumeration().getType("testEnum", new String[] { "THREE", "ONE", "TWO" }, true); assertEquals("testEnum", type2.getName()); assertEquals("testEnum__REPLACED_1", writer.enumeration().getDataSetType("/testEnum") .getName()); writer.close(); } @Test public void testEnumArray() { final File file = new File(workingDirectory, "enumArray.h5"); final String enumTypeName = "testEnum"; file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); HDF5EnumerationType enumType = writer.enumeration().getType(enumTypeName, new String[] { "ONE", "TWO", "THREE" }, false); HDF5EnumerationValueArray arrayWritten = new HDF5EnumerationValueArray(enumType, new String[] { "TWO", "ONE", "THREE" }); writer.enumeration().writeArray("/testEnum", arrayWritten); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); final HDF5EnumerationValueArray arrayRead = reader.enumeration().readArray("/testEnum"); enumType = reader.enumeration().getDataSetType("/testEnum"); final HDF5EnumerationValueArray arrayRead2 = reader.enumeration().readArray("/testEnum", enumType); final String[] stringArrayRead = reader.enumeration().readArray("/testEnum").toStringArray(); assertEquals(arrayWritten.getLength(), stringArrayRead.length); assertEquals(arrayWritten.getLength(), arrayRead.getLength()); assertEquals(arrayWritten.getLength(), arrayRead2.getLength()); for (int i = 0; i < stringArrayRead.length; ++i) { assertEquals("Index " + i, arrayWritten.getValue(i), arrayRead.getValue(i)); assertEquals("Index " + i, arrayWritten.getValue(i), arrayRead2.getValue(i)); assertEquals("Index " + i, arrayWritten.getValue(i), stringArrayRead[i]); } reader.close(); } @Test public void testEnumMDArray() { final File file = new File(workingDirectory, "enumMDArray.h5"); final String enumTypeName = "testEnum"; file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); HDF5EnumerationValueMDArray arrayWritten = writer.enumeration().newMDArray( enumTypeName, new String[] { "ONE", "TWO", "THREE" }, new MDArray(new String[] { "TWO", "ONE", "THREE", "TWO", "ONE", "THREE", "TWO", "ONE", "THREE", "TWO", "ONE", "THREE", "TWO", "ONE", "THREE", "TWO", "ONE", "THREE", "TWO", "ONE", "THREE", "TWO", "ONE", "THREE" }, new int[] { 2, 3, 4 })); writer.enumeration().writeMDArray("/testEnum", arrayWritten); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); final HDF5EnumerationValueMDArray arrayRead = reader.enumeration().readMDArray("/testEnum"); final HDF5EnumerationType enumType = reader.enumeration().getDataSetType("/testEnum"); final HDF5EnumerationValueMDArray arrayRead2 = reader.enumeration().readMDArray("/testEnum", enumType); final MDArray stringArrayRead = arrayRead2.toStringArray(); assertTrue(Arrays.equals(arrayWritten.dimensions(), stringArrayRead.dimensions())); assertTrue(Arrays.equals(arrayWritten.dimensions(), arrayRead.dimensions())); assertTrue(Arrays.equals(arrayWritten.dimensions(), arrayRead2.dimensions())); for (int i = 0; i < stringArrayRead.size(); ++i) { assertEquals("Index " + i, arrayWritten.getValue(i), arrayRead.getValue(i)); assertEquals("Index " + i, arrayWritten.getValue(i), arrayRead2.getValue(i)); assertEquals("Index " + i, arrayWritten.getValue(i), stringArrayRead.get(i)); } reader.close(); } @Test public void testEnumMDArrayBlockWise() { final File file = new File(workingDirectory, "enumMDArrayBlockWise.h5"); final String enumTypeName = "testEnum"; file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); HDF5EnumerationType enumType = writer.enumeration().getType(enumTypeName, new String[] { "ONE", "TWO", "THREE" }, false); HDF5EnumerationValueMDArray arrayBlockWritten1 = new HDF5EnumerationValueMDArray(enumType, new MDArray(new String[] { "TWO", "ONE", "THREE", "THREE", "TWO", "ONE", }, new int[] { 2, 3, 1 })); HDF5EnumerationValueMDArray arrayBlockWritten2 = new HDF5EnumerationValueMDArray(enumType, new MDArray(new String[] { "ONE", "TWO", "THREE", "THREE", "TWO", "ONE", }, new int[] { 2, 3, 1 })); HDF5EnumerationValueMDArray arrayBlockWritten3 = new HDF5EnumerationValueMDArray(enumType, new MDArray(new String[] { "THREE", "TWO", "ONE", "ONE", "TWO", "THREE", }, new int[] { 2, 3, 1 })); writer.enumeration().createMDArray("/testEnum", enumType, new int[] { 2, 3, 1 }); for (int i = 0; i < 4; ++i) { writer.enumeration().writeMDArrayBlock("/testEnum", arrayBlockWritten1, new long[] { 0, 0, i }); writer.enumeration().writeMDArrayBlock("/testEnum", arrayBlockWritten2, new long[] { 1, 0, i }); writer.enumeration().writeMDArrayBlock("/testEnum", arrayBlockWritten3, new long[] { 0, 1, i }); } writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); assertTrue(Arrays.equals(new long[] { 4, 6, 4 }, reader.getDataSetInformation("/testEnum").getDimensions())); for (int i = 0; i < 4; ++i) { assertEquals(arrayBlockWritten1, reader.enumeration().readMDArrayBlock("/testEnum", new int[] { 2, 3, 1 }, new long[] { 0, 0, i })); assertEquals(arrayBlockWritten2, reader.enumeration().readMDArrayBlock("/testEnum", new int[] { 2, 3, 1 }, new long[] { 1, 0, i })); assertEquals(arrayBlockWritten3, reader.enumeration().readMDArrayBlock("/testEnum", new int[] { 2, 3, 1 }, new long[] { 0, 1, i })); } enumType = reader.enumeration().getDataSetType("/testEnum"); for (int i = 0; i < 4; ++i) { assertEquals(arrayBlockWritten1, reader.enumeration().readMDArrayBlock("/testEnum", enumType, new int[] { 2, 3, 1 }, new long[] { 0, 0, i })); assertEquals(arrayBlockWritten2, reader.enumeration().readMDArrayBlock("/testEnum", enumType, new int[] { 2, 3, 1 }, new long[] { 1, 0, i })); assertEquals(arrayBlockWritten3, reader.enumeration().readMDArrayBlock("/testEnum", enumType, new int[] { 2, 3, 1 }, new long[] { 0, 1, i })); } for (HDF5MDEnumBlock block : reader.enumeration().getMDArrayBlocks("/testEnum", enumType)) { assertTrue(Long.toString(block.getIndex()[2]), block.getIndex()[2] >= 0 && block.getIndex()[2] < 4); if (block.getIndex()[0] == 0 && block.getIndex()[1] == 0) { assertEquals(arrayBlockWritten1, block.getData()); } else if (block.getIndex()[0] == 0 && block.getIndex()[1] == 1) { assertEquals(arrayBlockWritten3, block.getData()); } else if (block.getIndex()[0] == 1 && block.getIndex()[1] == 0) { assertEquals(arrayBlockWritten2, block.getData()); } else if (block.getIndex()[0] == 1 && block.getIndex()[1] == 1) { assertTrue(Arrays.equals(new int[] { 2, 3, 1 }, block.getData().dimensions())); assertTrue(Arrays.equals(new byte[6], ((MDByteArray) block.getData() .getOrdinalValues()).getAsFlatArray())); } else { fail("Unexpected index " + Arrays.toString(block.getIndex())); } } reader.close(); } @Test public void testJavaEnumArray() { final File file = new File(workingDirectory, "javaEnumArray.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); final JavaEnum[] arrayWritten = new JavaEnum[] { JavaEnum.TWO, JavaEnum.ONE, JavaEnum.THREE, JavaEnum.ONE }; final JavaEnum[] arrayBlockTwoWritten = new JavaEnum[] { JavaEnum.THREE, JavaEnum.ONE, JavaEnum.TWO, JavaEnum.THREE }; writer.enumeration().writeArray("/testEnum", writer.enumeration().newArray(arrayWritten)); final HDF5EnumerationType type = writer.enumeration().createArray("/testEnumBlockwise", writer.enumeration().getType(JavaEnum.class), 16); writer.enumeration().writeArrayBlock("/testEnumBlockwise", new HDF5EnumerationValueArray(type, arrayWritten), 0); writer.enumeration().writeArrayBlock("/testEnumBlockwise", writer.enumeration().newArray(arrayBlockTwoWritten), 1); writer.enumeration().writeArrayBlockWithOffset("/testEnumBlockwise", new HDF5EnumerationValueArray(type, arrayBlockTwoWritten), arrayBlockTwoWritten.length, 8); writer.enumeration().writeArrayBlockWithOffset("/testEnumBlockwise", writer.enumeration().newArray(arrayWritten), arrayWritten.length, 12); final JavaEnum[] attributeArrayWritten = new JavaEnum[] { JavaEnum.THREE, JavaEnum.ONE, JavaEnum.TWO }; writer.enumeration().setArrayAttr("/testEnum", "attr", writer.enumeration().newArray(attributeArrayWritten)); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); final JavaEnum[] arrayRead = reader.enumeration().readArray("/testEnum").toEnumArray(JavaEnum.class); final JavaEnum[] attributeArrayRead = reader.enumeration().getArrayAttr("/testEnum", "attr").toEnumArray(JavaEnum.class); final JavaEnum[] arrayBlockRead0 = reader.enumeration().readArrayBlock("/testEnumBlockwise", 4, 0) .toEnumArray(JavaEnum.class); final JavaEnum[] arrayBlockRead1 = reader.enumeration().readArrayBlock("/testEnumBlockwise", 4, 1) .toEnumArray(JavaEnum.class); final JavaEnum[] arrayBlockRead2 = reader.enumeration().readArrayBlock("/testEnumBlockwise", 4, 2) .toEnumArray(JavaEnum.class); final JavaEnum[] arrayBlockRead3 = reader.enumeration().readArrayBlock("/testEnumBlockwise", 4, 3) .toEnumArray(JavaEnum.class); reader.close(); assertEquals(arrayWritten.length, arrayRead.length); for (int i = 0; i < arrayWritten.length; ++i) { assertEquals(arrayWritten[i], arrayRead[i]); } assertEquals(attributeArrayWritten.length, attributeArrayRead.length); for (int i = 0; i < attributeArrayWritten.length; ++i) { assertEquals(attributeArrayWritten[i], attributeArrayRead[i]); } assertEquals(arrayWritten.length, arrayBlockRead0.length); assertEquals(arrayWritten.length, arrayBlockRead1.length); assertEquals(arrayWritten.length, arrayBlockRead2.length); assertEquals(arrayWritten.length, arrayBlockRead3.length); for (int i = 0; i < arrayWritten.length; ++i) { assertEquals(arrayWritten[i], arrayBlockRead0[i]); assertEquals(arrayBlockTwoWritten[i], arrayBlockRead1[i]); assertEquals(arrayBlockTwoWritten[i], arrayBlockRead2[i]); assertEquals(arrayWritten[i], arrayBlockRead3[i]); } } @Test public void testEnumArrayBlock() { final File file = new File(workingDirectory, "enumArrayBlock.h5"); final String enumTypeName = "testEnum"; final int chunkSize = 4; file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); HDF5EnumerationType enumType = writer.enumeration().getType(enumTypeName, new String[] { "ONE", "TWO", "THREE" }, false); writer.enumeration().createArray("/testEnum", enumType, chunkSize); HDF5EnumerationValueArray arrayWritten = new HDF5EnumerationValueArray(enumType, new String[] { "TWO", "ONE", "THREE", "TWO" }); writer.enumeration().writeArrayBlock("/testEnum", arrayWritten, 1); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); final HDF5EnumerationValueArray arrayReadBlock0 = reader.enumeration().readArrayBlock(enumTypeName, chunkSize, 0); enumType = reader.enumeration().getDataSetType(enumTypeName); final HDF5EnumerationValueArray arrayReadBlock1 = reader.enumeration().readArrayBlock(enumTypeName, enumType, chunkSize, 1); final String[] stringArrayRead = reader.enumeration().readArray(enumTypeName).toStringArray(); assertEquals(arrayWritten.getLength() * 2, stringArrayRead.length); assertEquals(arrayWritten.getLength(), arrayReadBlock0.getLength()); assertEquals(arrayWritten.getLength(), arrayReadBlock1.getLength()); for (int i = 0; i < arrayReadBlock0.getLength(); ++i) { assertEquals("Index " + i, "ONE", arrayReadBlock0.getValue(i)); assertEquals("Index " + i, "ONE", stringArrayRead[i]); } for (int i = 0; i < arrayReadBlock0.getLength(); ++i) { assertEquals("Index " + i, arrayWritten.getValue(i), arrayReadBlock1.getValue(i)); assertEquals("Index " + i, arrayWritten.getValue(i), stringArrayRead[chunkSize + i]); } final HDF5EnumerationValueArray[] dataBlocksExpected = new HDF5EnumerationValueArray[] { arrayReadBlock0, arrayReadBlock1 }; int blockIndex = 0; for (HDF5DataBlock block : reader.enumeration().getArrayBlocks( enumTypeName, enumType)) { final HDF5EnumerationValueArray blockExpected = dataBlocksExpected[blockIndex++]; final HDF5EnumerationValueArray blockRead = block.getData(); assertEquals(chunkSize, blockRead.getLength()); for (int i = 0; i < blockExpected.getLength(); ++i) { assertEquals("Index " + i, blockExpected.getValue(i), blockRead.getValue(i)); } } reader.close(); } @Test public void testEnumArrayBlockScalingCompression() { final File file = new File(workingDirectory, "enumArrayBlockScalingCompression.h5"); final String enumTypeName = "testEnum"; final int chunkSize = 4; file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); HDF5EnumerationType enumType = writer.enumeration().getType(enumTypeName, new String[] { "ONE", "TWO", "THREE" }, false); writer.enumeration().createArray("/testEnum", enumType, 0, chunkSize, HDF5IntStorageFeatures.INT_AUTO_SCALING); HDF5EnumerationValueArray arrayWritten = new HDF5EnumerationValueArray(enumType, new String[] { "TWO", "ONE", "THREE", "ONE" }); writer.enumeration().writeArrayBlock("/testEnum", arrayWritten, 1); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); final HDF5EnumerationValueArray arrayReadBlock0 = reader.enumeration().readArrayBlock(enumTypeName, chunkSize, 0); enumType = reader.enumeration().getDataSetType(enumTypeName); final HDF5EnumerationValueArray arrayReadBlock1 = reader.enumeration().readArrayBlock(enumTypeName, enumType, chunkSize, 1); final String[] stringArrayRead = reader.enumeration().readArray(enumTypeName).toStringArray(); assertEquals(arrayWritten.getLength() * 2, stringArrayRead.length); assertEquals(arrayWritten.getLength(), arrayReadBlock0.getLength()); assertEquals(arrayWritten.getLength(), arrayReadBlock1.getLength()); for (int i = 0; i < arrayReadBlock0.getLength(); ++i) { assertEquals("Index " + i, "ONE", arrayReadBlock0.getValue(i)); assertEquals("Index " + i, "ONE", stringArrayRead[i]); } for (int i = 0; i < arrayReadBlock0.getLength(); ++i) { assertEquals("Index " + i, arrayWritten.getValue(i), arrayReadBlock1.getValue(i)); assertEquals("Index " + i, arrayWritten.getValue(i), stringArrayRead[chunkSize + i]); } final HDF5EnumerationValueArray[] dataBlocksExpected = new HDF5EnumerationValueArray[] { arrayReadBlock0, arrayReadBlock1 }; int blockIndex = 0; for (HDF5DataBlock block : reader.enumeration().getArrayBlocks( enumTypeName, enumType)) { final HDF5EnumerationValueArray blockExpected = dataBlocksExpected[blockIndex++]; final HDF5EnumerationValueArray blockRead = block.getData(); assertEquals(chunkSize, blockRead.getLength()); for (int i = 0; i < blockExpected.getLength(); ++i) { assertEquals("Index " + i, blockExpected.getValue(i), blockRead.getValue(i)); } } reader.close(); } @Test public void testEnumArray16BitFromIntArray() { final File file = new File(workingDirectory, "enumArray16BitFromIntArray.h5"); final String enumTypeName = "testEnum"; file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); final HDF5EnumerationType enumType = createEnum16Bit(writer, enumTypeName); final int[] arrayWritten = new int[] { 8, 16, 722, 913, 333 }; writer.enumeration().writeArray("/testEnum", new HDF5EnumerationValueArray(enumType, arrayWritten)); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); final String[] stringArrayRead = reader.enumeration().readArray("/testEnum").toStringArray(); assertEquals(arrayWritten.length, stringArrayRead.length); for (int i = 0; i < stringArrayRead.length; ++i) { assertEquals("Index " + i, enumType.getValues().get(arrayWritten[i]), stringArrayRead[i]); } final HDF5EnumerationValueArray arrayRead = reader.enumeration().readArray("/testEnum"); assertEquals(arrayWritten.length, arrayRead.getLength()); for (int i = 0; i < arrayRead.getLength(); ++i) { assertEquals("Index " + i, enumType.getValues().get(arrayWritten[i]), arrayRead.getValue(i)); } reader.close(); } @Test public void testEnumArray16BitFromIntArrayScaled() { final File file = new File(workingDirectory, "testEnumArray16BitFromIntArrayScaled.h5"); final String enumTypeName = "testEnum"; file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); final HDF5EnumerationType enumType = createEnum16Bit(writer, enumTypeName); final int[] arrayWritten = new int[] { 8, 16, 722, 913, 333 }; writer.enumeration().writeArray("/testEnum", new HDF5EnumerationValueArray(enumType, arrayWritten), HDF5IntStorageFeatures.INT_AUTO_SCALING); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); final String[] stringArrayRead = reader.enumeration().readArray("/testEnum").toStringArray(); assertEquals(arrayWritten.length, stringArrayRead.length); for (int i = 0; i < stringArrayRead.length; ++i) { assertEquals("Index " + i, enumType.getValues().get(arrayWritten[i]), stringArrayRead[i]); } final HDF5EnumerationValueArray arrayRead = reader.enumeration().readArray("/testEnum"); assertEquals(arrayWritten.length, arrayRead.getLength()); for (int i = 0; i < arrayRead.getLength(); ++i) { assertEquals("Index " + i, enumType.getValues().get(arrayWritten[i]), arrayRead.getValue(i)); } reader.close(); } @Test public void testEnumArray16BitFromIntArrayLarge() { final File file = new File(workingDirectory, "enumArray16BitFromIntArrayLarge.h5"); final String enumTypeName = "testEnum"; file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); final HDF5EnumerationType enumType = createEnum16Bit(writer, enumTypeName); final int[] arrayWritten = new int[100]; for (int i = 0; i < arrayWritten.length; ++i) { arrayWritten[i] = 10 * i; } writer.enumeration().writeArray("/testEnum", new HDF5EnumerationValueArray(enumType, arrayWritten)); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); final String[] stringArrayRead = reader.enumeration().readArray("/testEnum").toStringArray(); assertEquals(arrayWritten.length, stringArrayRead.length); for (int i = 0; i < stringArrayRead.length; ++i) { assertEquals("Index " + i, enumType.getValues().get(arrayWritten[i]), stringArrayRead[i]); } reader.close(); } @Test public void testEnumArrayBlock16Bit() { final File file = new File(workingDirectory, "enumArrayBlock16Bit.h5"); final String enumTypeName = "testEnum"; final int chunkSize = 4; file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); HDF5EnumerationType enumType = createEnum16Bit(writer, enumTypeName); writer.enumeration().createArray("/testEnum", enumType, chunkSize); final HDF5EnumerationValueArray arrayWritten = new HDF5EnumerationValueArray(enumType, new int[] { 8, 16, 722, 913 }); writer.enumeration().writeArrayBlock("/testEnum", arrayWritten, 1); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); final HDF5EnumerationValueArray arrayReadBlock0 = reader.enumeration().readArrayBlock(enumTypeName, chunkSize, 0); enumType = reader.enumeration().getDataSetType(enumTypeName); final HDF5EnumerationValueArray arrayReadBlock1 = reader.enumeration().readArrayBlock(enumTypeName, enumType, chunkSize, 1); final String[] stringArrayRead = reader.enumeration().readArray(enumTypeName).toStringArray(); assertEquals(arrayWritten.getLength() * 2, stringArrayRead.length); assertEquals(arrayWritten.getLength(), arrayReadBlock0.getLength()); assertEquals(arrayWritten.getLength(), arrayReadBlock1.getLength()); for (int i = 0; i < arrayReadBlock0.getLength(); ++i) { assertEquals("Index " + i, "0", arrayReadBlock0.getValue(i)); assertEquals("Index " + i, "0", stringArrayRead[i]); } for (int i = 0; i < arrayReadBlock0.getLength(); ++i) { assertEquals("Index " + i, arrayWritten.getValue(i), arrayReadBlock1.getValue(i)); assertEquals("Index " + i, arrayWritten.getValue(i), stringArrayRead[chunkSize + i]); } final HDF5EnumerationValueArray[] dataBlocksExpected = new HDF5EnumerationValueArray[] { arrayReadBlock0, arrayReadBlock1 }; int blockIndex = 0; for (HDF5DataBlock block : reader.enumeration().getArrayBlocks( enumTypeName, enumType)) { final HDF5EnumerationValueArray blockExpected = dataBlocksExpected[blockIndex++]; final HDF5EnumerationValueArray blockRead = block.getData(); assertEquals(chunkSize, blockRead.getLength()); for (int i = 0; i < blockExpected.getLength(); ++i) { assertEquals("Index " + i, blockExpected.getValue(i), blockRead.getValue(i)); } } reader.close(); } @Test public void testEnumArrayScaleCompression() { final File file = new File(workingDirectory, "enumArrayScaleCompression.h5"); final String enumTypeName = "testEnum"; file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); HDF5EnumerationType enumType = writer.enumeration().getType(enumTypeName, new String[] { "A", "C", "G", "T" }, false); final Random rng = new Random(); final String[] arrayWrittenString = new String[100000]; for (int i = 0; i < arrayWrittenString.length; ++i) { arrayWrittenString[i] = enumType.getValues().get(rng.nextInt(4)); } final HDF5EnumerationValueArray arrayWritten = new HDF5EnumerationValueArray(enumType, arrayWrittenString); writer.enumeration().writeArray("/testEnum", arrayWritten, INT_AUTO_SCALING); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); assertEquals(HDF5DataClass.ENUM, reader.object().getDataSetInformation("/testEnum") .getTypeInformation().getDataClass()); final HDF5EnumerationValueArray arrayRead = reader.enumeration().readArray("/testEnum"); enumType = reader.enumeration().getDataSetType("/testEnum"); final HDF5EnumerationValueArray arrayRead2 = reader.enumeration().readArray("/testEnum", enumType); final String[] stringArrayRead = reader.enumeration().readArray("/testEnum").toStringArray(); assertEquals(arrayWritten.getLength(), stringArrayRead.length); assertEquals(arrayWritten.getLength(), arrayRead.getLength()); assertEquals(arrayWritten.getLength(), arrayRead2.getLength()); for (int i = 0; i < stringArrayRead.length; ++i) { assertEquals("Index " + i, arrayWritten.getValue(i), arrayRead.getValue(i)); assertEquals("Index " + i, arrayWritten.getValue(i), arrayRead2.getValue(i)); assertEquals("Index " + i, arrayWritten.getValue(i), stringArrayRead[i]); } reader.close(); // Shouldn't work in strict HDF5 1.6 mode. final File file2 = new File(workingDirectory, "scaleoffsetfilterenumfailed.h5"); file2.delete(); assertFalse(file2.exists()); file2.deleteOnExit(); final IHDF5Writer writer2 = HDF5FactoryProvider.get().configure(file2).fileFormat(FileFormat.STRICTLY_1_6) .writer(); HDF5EnumerationType enumType2 = writer2.enumeration().getType(enumTypeName, new String[] { "A", "C", "G", "T" }, false); final HDF5EnumerationValueArray arrayWritten2 = new HDF5EnumerationValueArray(enumType2, arrayWrittenString); try { writer2.enumeration().writeArray("/testEnum", arrayWritten2, INT_AUTO_SCALING); fail("Usage of scaling compression in strict HDF5 1.6 mode not detected"); } catch (IllegalStateException ex) { assertTrue(ex.getMessage().indexOf("not allowed") >= 0); } writer2.close(); } @Test public void testOpaqueType() { final File file = new File(workingDirectory, "opaqueType.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final String opaqueDataSetName = "/opaque/ds"; final String byteArrayDataSetName = "/bytearr/ds"; final String opaqueTag = "my opaque type"; final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); final byte[] byteArrayWritten = new byte[] { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 }; writer.int8().writeArray(byteArrayDataSetName, byteArrayWritten); writer.opaque().writeArray(opaqueDataSetName, opaqueTag, byteArrayWritten); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); HDF5DataSetInformation info = reader.getDataSetInformation(byteArrayDataSetName); assertEquals(HDF5DataClass.INTEGER, info.getTypeInformation().getDataClass()); assertChunkSizes(info, byteArrayWritten.length); info = reader.getDataSetInformation(opaqueDataSetName); assertEquals(HDF5DataClass.OPAQUE, info.getTypeInformation().getDataClass()); assertEquals(opaqueTag, info.getTypeInformation().tryGetOpaqueTag()); assertChunkSizes(info, byteArrayWritten.length); assertEquals(opaqueTag, reader.opaque().tryGetOpaqueTag(opaqueDataSetName)); assertEquals(opaqueTag, reader.opaque().tryGetOpaqueType(opaqueDataSetName).getTag()); assertNull(reader.opaque().tryGetOpaqueTag(byteArrayDataSetName)); assertNull(reader.opaque().tryGetOpaqueType(byteArrayDataSetName)); final byte[] byteArrayRead = reader.readAsByteArray(byteArrayDataSetName); assertTrue(Arrays.equals(byteArrayWritten, byteArrayRead)); final byte[] byteArrayReadOpaque = reader.readAsByteArray(opaqueDataSetName); assertTrue(Arrays.equals(byteArrayWritten, byteArrayReadOpaque)); reader.close(); } private HDF5EnumerationType createEnum16Bit(final IHDF5Writer writer, final String enumTypeName) { final String[] enumValues = new String[1024]; for (int i = 0; i < enumValues.length; ++i) { enumValues[i] = Integer.toString(i); } final HDF5EnumerationType enumType = writer.enumeration().getType(enumTypeName, enumValues, false); return enumType; } @Test public void testEnumArrayFromIntArray() { final File file = new File(workingDirectory, "enumArrayFromIntArray.h5"); final String enumTypeName = "testEnum"; file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); final HDF5EnumerationType enumType = writer.enumeration().getType(enumTypeName, new String[] { "ONE", "TWO", "THREE" }, false); final int[] arrayWritten = new int[] { enumType.tryGetIndexForValue("TWO").byteValue(), enumType.tryGetIndexForValue("ONE").byteValue(), enumType.tryGetIndexForValue("THREE").byteValue() }; writer.enumeration().writeArray("/testEnum", new HDF5EnumerationValueArray(enumType, arrayWritten)); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); final String[] stringArrayRead = reader.enumeration().readArray("/testEnum").toStringArray(); assertEquals(arrayWritten.length, stringArrayRead.length); for (int i = 0; i < stringArrayRead.length; ++i) { assertEquals("Index " + i, enumType.getValues().get(arrayWritten[i]), stringArrayRead[i]); } reader.close(); } static class Record { int a; float b; long l; double c; @CompoundElement(unsigned = true) short d; boolean e; String f; HDF5EnumerationValue g; int[] ar; float[] br; long[] lr; double[] cr; short[] dr; @CompoundElement(unsigned = true) byte[] er; MDIntArray fr; char[] gr; Record(int a, float b, long l, double c, short d, boolean e, String f, HDF5EnumerationValue g, int[] ar, float[] br, long[] lr, double[] cr, short[] dr, byte[] er, MDIntArray fr, char[] gr) { this.a = a; this.b = b; this.l = l; this.c = c; this.d = d; this.e = e; this.f = f; this.g = g; this.ar = ar; this.br = br; this.lr = lr; this.cr = cr; this.dr = dr; this.er = er; this.fr = fr; this.gr = gr; } Record() { } static HDF5CompoundMemberInformation[] getMemberInfo(HDF5EnumerationType enumType) { return HDF5CompoundMemberInformation.create(Record.class, "", getShuffledMapping(enumType)); } static HDF5CompoundType getHDF5Type(IHDF5Reader reader) { final HDF5EnumerationType enumType = reader.enumeration().getType("someEnumType", new String[] { "1", "Two", "THREE" }); return reader.compound().getType(null, Record.class, getMapping(enumType)); } private static HDF5CompoundMemberMapping[] getMapping(HDF5EnumerationType enumType) { return new HDF5CompoundMemberMapping[] { mapping("a"), mapping("b"), mapping("l"), mapping("c"), mapping("d").unsigned(), mapping("e"), mapping("f").length(3), mapping("g").enumType(enumType), mapping("ar").length(3), mapping("br").length(2), mapping("lr").length(3), mapping("cr").length(1), mapping("dr").length(2), mapping("er").length(4).unsigned(), mapping("fr").dimensions(2, 2), mapping("gr").length(5) }; } private static HDF5CompoundMemberMapping[] getShuffledMapping(HDF5EnumerationType enumType) { return new HDF5CompoundMemberMapping[] { mapping("er").length(4), mapping("e"), mapping("b"), mapping("br").length(2), mapping("g").enumType(enumType), mapping("lr").length(3), mapping("gr").length(5), mapping("c"), mapping("ar").length(3), mapping("a"), mapping("d"), mapping("cr").length(1), mapping("f").length(3), mapping("fr").dimensions(2, 2), mapping("dr").length(2), mapping("l") }; } // // Object // @Override public int hashCode() { final HashCodeBuilder builder = new HashCodeBuilder(); builder.append(a); builder.append(b); builder.append(c); builder.append(d); builder.append(e); builder.append(f); builder.append(g); builder.append(ar); builder.append(br); builder.append(cr); builder.append(dr); builder.append(er); return builder.toHashCode(); } @Override public boolean equals(Object obj) { if (obj == null || obj instanceof Record == false) { return false; } final Record that = (Record) obj; final EqualsBuilder builder = new EqualsBuilder(); builder.append(a, that.a); builder.append(b, that.b); builder.append(c, that.c); builder.append(d, that.d); builder.append(e, that.e); builder.append(f, that.f); builder.append(g, that.g); builder.append(ar, that.ar); builder.append(br, that.br); builder.append(cr, that.cr); builder.append(dr, that.dr); builder.append(er, that.er); builder.append(fr, that.fr); return builder.isEquals(); } @Override public String toString() { final ToStringBuilder builder = new ToStringBuilder(this); builder.append(a); builder.append(b); builder.append(c); builder.append(d); builder.append(e); builder.append(f); builder.append(g); builder.append(ar); builder.append(br); builder.append(cr); builder.append(dr); builder.append(er); builder.append(fr); return builder.toString(); } } @Test public void testCompoundAttribute() { final File file = new File(workingDirectory, "compoundAttribute.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.open(file); final SimpleInheretingRecord recordWritten = new SimpleInheretingRecord(3.14159f, 42, (short) 17, "xzy", new long[][] { { 1, 2, 3 }, { 4, 5, 6 } }); writer.compound().setAttr("/", "cpd", recordWritten); final SimpleInheretingRecord[] recordArrWritten = new SimpleInheretingRecord[] { new SimpleInheretingRecord(3.14159f, 100, (short) 1, "abc", new long[][] { { 10, 20, 30 }, { 40, 50, 60 } }), new SimpleInheretingRecord(3.14159f, 1000, (short) 2, "def", new long[][] { { 70, 80, 90 }, { 100, 110, 120 } }), }; writer.compound().setArrayAttr("/", "cpdArray", recordArrWritten); writer.compound().setArrayAttr("/", "cpdArray", recordArrWritten); final MDArray recordMDArrWritten = new MDArray(new SimpleInheretingRecord[] { new SimpleInheretingRecord(3.14159f, 100, (short) 1, "abc", new long[][] { { 10, 20, 30 }, { 40, 50, 60 } }), new SimpleInheretingRecord(3.14159f, 1000, (short) 2, "def", new long[][] { { 70, 80, 90 }, { 100, 110, 120 } }), new SimpleInheretingRecord(-1f, 10000, (short) 1, "ghi", new long[][] { { 10, 20, 30 }, { 40, 50, 60 } }), new SimpleInheretingRecord(11.111111f, 100000, (short) 2, "jkl", new long[][] { { 70, 80, 90 }, { 100, 110, 120 } }), }, new int[] { 2, 2 }); writer.compound().setMDArrayAttr("/", "cpdMDArray", recordMDArrWritten); writer.close(); final IHDF5Reader reader = HDF5Factory.openForReading(file); final HDF5CompoundType type = reader.compound().getAttributeType("/", "cpd", SimpleInheretingRecord.class); assertFalse(type.isMappingIncomplete()); assertFalse(type.isDiskRepresentationIncomplete()); assertFalse(type.isMemoryRepresentationIncomplete()); type.checkMappingComplete(); final SimpleInheretingRecord recordRead = reader.compound().getAttr("/", "cpd", SimpleInheretingRecord.class); assertEquals(recordWritten, recordRead); final SimpleInheretingRecord[] recordArrRead = reader.compound().getArrayAttr("/", "cpdArray", SimpleInheretingRecord.class); assertTrue(Arrays.equals(recordArrWritten, recordArrRead)); final MDArray recordMDArrRead = reader.compound().getMDArrayAttr("/", "cpdMDArray", SimpleInheretingRecord.class); assertEquals(recordMDArrWritten, recordMDArrRead); reader.close(); } static class RecordRequiringMemAlignment { byte b1; short s; byte b2; int i; byte b3; long l; public RecordRequiringMemAlignment() { } RecordRequiringMemAlignment(byte b1, short s, byte b2, int i, byte b3, long l) { super(); this.b1 = b1; this.s = s; this.b2 = b2; this.i = i; this.b3 = b3; this.l = l; } @Override public int hashCode() { final int prime = 31; int result = 1; result = prime * result + b1; result = prime * result + b2; result = prime * result + b3; result = prime * result + i; result = prime * result + (int) (l ^ (l >>> 32)); result = prime * result + s; return result; } @Override public boolean equals(Object obj) { if (this == obj) { return true; } if (obj == null) { return false; } if (getClass() != obj.getClass()) { return false; } RecordRequiringMemAlignment other = (RecordRequiringMemAlignment) obj; if (b1 != other.b1) { return false; } if (b2 != other.b2) { return false; } if (b3 != other.b3) { return false; } if (i != other.i) { return false; } if (l != other.l) { return false; } if (s != other.s) { return false; } return true; } @Override public String toString() { return "RecordRequringMemAlignment [b1=" + b1 + ", s=" + s + ", b2=" + b2 + ", i=" + i + ", b3=" + b3 + ", l=" + l + "]"; } } @Test public void testCompoundAttributeMemoryAlignment() { final File file = new File(workingDirectory, "compoundAttributeMemoryAlignment.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.open(file); final RecordRequiringMemAlignment recordWritten = new RecordRequiringMemAlignment((byte) 1, (short) 2, (byte) 3, 4, (byte) 5, 6L); writer.int32().write("val", 0); writer.compound().setAttr("val", "attr0d", recordWritten); final RecordRequiringMemAlignment[] recordArrayWritten = new RecordRequiringMemAlignment[] { new RecordRequiringMemAlignment((byte) 7, (short) 8, (byte) 9, 10, (byte) 11, 12L), new RecordRequiringMemAlignment((byte) 13, (short) 14, (byte) 15, 16, (byte) 17, 18L) }; writer.compound().setArrayAttr("val", "attr1d", recordArrayWritten); final MDArray recordMDArrayWritten = new MDArray(new RecordRequiringMemAlignment[] { new RecordRequiringMemAlignment((byte) 19, (short) 20, (byte) 21, 22, (byte) 23, 24L), new RecordRequiringMemAlignment((byte) 25, (short) 26, (byte) 27, 28, (byte) 29, 30L), new RecordRequiringMemAlignment((byte) 31, (short) 32, (byte) 33, 34, (byte) 35, 36L), new RecordRequiringMemAlignment((byte) 37, (short) 38, (byte) 39, 40, (byte) 41, 42L), }, new long[] { 2, 2 }); writer.compound().setMDArrayAttr("val", "attr2d", recordMDArrayWritten); writer.close(); final IHDF5Reader reader = HDF5Factory.openForReading(file); final HDF5CompoundType type = reader.compound().getInferredType(RecordRequiringMemAlignment.class); final HDF5CompoundMemberInformation[] infos = type.getCompoundMemberInformation(); for (int i = 0; i < infos.length; ++i) { assertEquals(infos[i].getName() + "(" + i + ")", type.getObjectByteifyer() .getByteifyers()[i].getOffsetOnDisk(), infos[i].getOffsetOnDisk()); assertEquals(infos[i].getName() + "(" + i + ")", type.getObjectByteifyer() .getByteifyers()[i].getOffsetInMemory(), infos[i].getOffsetInMemory()); assertEquals(infos[i].getName() + "(" + i + ")", type.getObjectByteifyer() .getByteifyers()[i].getSize(), infos[i].getType().getElementSize()); } final RecordRequiringMemAlignment recordRead = reader.compound().getAttr("val", "attr0d", RecordRequiringMemAlignment.class); assertEquals(recordWritten, recordRead); final RecordRequiringMemAlignment[] recordArrayRead = reader.compound().getArrayAttr("val", "attr1d", RecordRequiringMemAlignment.class); assertTrue(Arrays.equals(recordArrayWritten, recordArrayRead)); final MDArray recordMDArrayRead = reader.compound() .getMDArrayAttr("val", "attr2d", RecordRequiringMemAlignment.class); assertTrue(recordMDArrayWritten.equals(recordMDArrayRead)); reader.close(); } @Test public void testCompound() { final File file = new File(workingDirectory, "compound.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.open(file); final SimpleInheretingRecord recordWritten = new SimpleInheretingRecord(3.14159f, 42, (short) 17, "xzy", new long[][] { { 1, 2, 3 }, { 4, 5, 6 } }); writer.compound().write("cpd", recordWritten); final SimpleInheretingRecord2 recordWritten2 = new SimpleInheretingRecord2(3.14159f, 42, (short) 17, "xzy", new long[][] { { 1, 2, 3 }, { 4, 5, 6 }, { 7, 8, 9 } }); writer.compound().write("cpd2", recordWritten2); final SimpleInheretingRecord3 recordWritten3 = new SimpleInheretingRecord3(3.14159f, 42, (short) 17, "xzy", new long[][] { { 1, 2, 3 }, { 4, 5, 6 }, { 7, 8, 11 } }); writer.compound().write("cpd3", recordWritten3); final File file2 = new File(workingDirectory, "compound2.h5"); file2.delete(); assertFalse(file2.exists()); file2.deleteOnExit(); final IHDF5Writer writer2 = HDF5Factory.open(file2); final HDF5CompoundType clonedType = writer2.compound().getClonedType( writer.compound().getDataSetType("cpd", HDF5CompoundDataMap.class)); writer2.compound().write("cpd", clonedType, writer.compound().read("cpd", HDF5CompoundDataMap.class)); writer.close(); writer2.close(); final IHDF5Reader reader = HDF5Factory.openForReading(file); final HDF5CompoundType type = reader.compound().getDataSetType("cpd", SimpleInheretingRecord.class); assertFalse(type.isMappingIncomplete()); assertFalse(type.isDiskRepresentationIncomplete()); assertFalse(type.isMemoryRepresentationIncomplete()); type.checkMappingComplete(); final SimpleInheretingRecord recordRead = reader.compound().read("cpd", type); assertEquals(recordWritten, recordRead); final SimpleInheretingRecord2 recordRead2 = reader.compound().read("cpd2", SimpleInheretingRecord2.class); assertEquals(recordWritten2, recordRead2); final SimpleInheretingRecord3 recordRead3 = reader.compound().read("cpd3", SimpleInheretingRecord3.class); assertEquals(recordWritten3, recordRead3); HDF5CompoundMemberInformation[] infos = type.getCompoundMemberInformation(); for (int i = 0; i < infos.length; ++i) { assertEquals("" + i, type.getObjectByteifyer().getByteifyers()[i].getOffsetOnDisk(), infos[i].getOffsetOnDisk()); assertEquals("" + i, type.getObjectByteifyer().getByteifyers()[i].getOffsetInMemory(), infos[i].getOffsetInMemory()); } reader.close(); final IHDF5Reader reader2 = HDF5Factory.openForReading(file2); final HDF5CompoundType type2 = reader2.compound().getDataSetType("cpd", SimpleInheretingRecord.class); assertFalse(type2.isMappingIncomplete()); assertFalse(type2.isDiskRepresentationIncomplete()); assertFalse(type2.isMemoryRepresentationIncomplete()); assertEquals("SimpleInheretingRecord", type2.getName()); type2.checkMappingComplete(); final SimpleInheretingRecord recordReadFile2 = reader2.compound().read("cpd", type2); assertEquals(recordWritten, recordReadFile2); reader2.close(); } static class SimpleStringRecord { String s1; String s2; SimpleStringRecord() { } SimpleStringRecord(String s, String s2) { this.s1 = s; this.s2 = s2; } @Override public int hashCode() { final int prime = 31; int result = 1; result = prime * result + ((s1 == null) ? 0 : s1.hashCode()); result = prime * result + ((s2 == null) ? 0 : s2.hashCode()); return result; } @Override public boolean equals(Object obj) { if (this == obj) { return true; } if (obj == null) { return false; } if (getClass() != obj.getClass()) { return false; } SimpleStringRecord other = (SimpleStringRecord) obj; if (s1 == null) { if (other.s1 != null) { return false; } } else if (!s1.equals(other.s1)) { return false; } if (s2 == null) { if (other.s2 != null) { return false; } } else if (!s2.equals(other.s2)) { return false; } return true; } } @Test public void testCompoundInferStringLength() { final File file = new File(workingDirectory, "stringsInCompound.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.open(file); final SimpleStringRecord recordWritten = new SimpleStringRecord("hello", "X"); writer.compound().write("strings", recordWritten); final SimpleStringRecord[] recordArrayWritten = new SimpleStringRecord[] { new SimpleStringRecord("hello", "X"), new SimpleStringRecord("Y2", "0123456789") }; writer.compound().writeArray("stringsArray", recordArrayWritten); writer.close(); final IHDF5Reader reader = HDF5Factory.openForReading(file); final HDF5CompoundType type = reader.compound().getInferredType(recordWritten); assertEquals(2, type.getCompoundMemberInformation().length); assertEquals("s1", type.getCompoundMemberInformation()[0].getName()); assertEquals(HDF5DataClass.STRING, type.getCompoundMemberInformation()[0].getType() .getDataClass()); assertEquals(recordWritten.s1.length(), type.getCompoundMemberInformation()[0].getType() .getSize()); assertEquals("s2", type.getCompoundMemberInformation()[1].getName()); assertEquals(HDF5DataClass.STRING, type.getCompoundMemberInformation()[1].getType() .getDataClass()); assertEquals(recordWritten.s2.length(), type.getCompoundMemberInformation()[1].getType() .getSize()); final SimpleStringRecord recordRead = reader.compound().read("strings", type); assertEquals(recordWritten, recordRead); final HDF5CompoundType arrayType = reader.compound().getInferredType(recordArrayWritten); assertEquals("s1", arrayType.getCompoundMemberInformation()[0].getName()); assertEquals(HDF5DataClass.STRING, arrayType.getCompoundMemberInformation()[0].getType() .getDataClass()); assertEquals(recordArrayWritten[0].s1.length(), arrayType.getCompoundMemberInformation()[0] .getType().getSize()); assertEquals("s2", arrayType.getCompoundMemberInformation()[1].getName()); assertEquals(HDF5DataClass.STRING, arrayType.getCompoundMemberInformation()[1].getType() .getDataClass()); assertEquals(recordArrayWritten[1].s2.length(), arrayType.getCompoundMemberInformation()[1] .getType().getSize()); final SimpleStringRecord[] recordArrayRead = reader.compound().readArray("stringsArray", SimpleStringRecord.class); assertEquals(2, recordArrayRead.length); assertEquals(recordArrayWritten[0], recordArrayRead[0]); assertEquals(recordArrayWritten[1], recordArrayRead[1]); reader.close(); } static class SimpleRecordWithStringsAndIntsAnnoted { @CompoundElement(variableLength = true) String s1; int i1; @CompoundElement(variableLength = true) String s2; int i2; SimpleRecordWithStringsAndIntsAnnoted() { } SimpleRecordWithStringsAndIntsAnnoted(String s1, int i1, String s2, int i2) { this.s1 = s1; this.i1 = i1; this.s2 = s2; this.i2 = i2; } @Override public int hashCode() { final int prime = 31; int result = 1; result = prime * result + i1; result = prime * result + i2; result = prime * result + ((s1 == null) ? 0 : s1.hashCode()); result = prime * result + ((s2 == null) ? 0 : s2.hashCode()); return result; } @Override public boolean equals(Object obj) { if (this == obj) { return true; } if (obj == null) { return false; } if (getClass() != obj.getClass()) { return false; } SimpleRecordWithStringsAndIntsAnnoted other = (SimpleRecordWithStringsAndIntsAnnoted) obj; if (i1 != other.i1) { return false; } if (i2 != other.i2) { return false; } if (s1 == null) { if (other.s1 != null) { return false; } } else if (!s1.equals(other.s1)) { return false; } if (s2 == null) { if (other.s2 != null) { return false; } } else if (!s2.equals(other.s2)) { return false; } return true; } @Override public String toString() { return "SimpleRecordWithStringsAndIntsAnnotated [s1=" + s1 + ", i1=" + i1 + ", s2=" + s2 + ", i2=" + i2 + "]"; } } static class SimpleRecordWithStringsAndInts { String s1; int i1; @CompoundElement(dimensions = { 10 }) String s2; int i2; SimpleRecordWithStringsAndInts() { } SimpleRecordWithStringsAndInts(String s1, int i1, String s2, int i2) { this.s1 = s1; this.i1 = i1; this.s2 = s2; this.i2 = i2; } @Override public int hashCode() { final int prime = 31; int result = 1; result = prime * result + i1; result = prime * result + i2; result = prime * result + ((s1 == null) ? 0 : s1.hashCode()); result = prime * result + ((s2 == null) ? 0 : s2.hashCode()); return result; } @Override public boolean equals(Object obj) { if (this == obj) { return true; } if (obj == null) { return false; } if (getClass() != obj.getClass()) { return false; } SimpleRecordWithStringsAndInts other = (SimpleRecordWithStringsAndInts) obj; if (i1 != other.i1) { return false; } if (i2 != other.i2) { return false; } if (s1 == null) { if (other.s1 != null) { return false; } } else if (!s1.equals(other.s1)) { return false; } if (s2 == null) { if (other.s2 != null) { return false; } } else if (!s2.equals(other.s2)) { return false; } return true; } @Override public String toString() { return "SimpleRecordWithStringsAndInts [s1=" + s1 + ", i1=" + i1 + ", s2=" + s2 + ", i2=" + i2 + "]"; } } @Test public void testCompoundVariableLengthString() { final File file = new File(workingDirectory, "variableLengthStringsInCompound.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.open(file); final HDF5CompoundType typeWritten = writer.compound().getInferredType(SimpleRecordWithStringsAndIntsAnnoted.class); final SimpleRecordWithStringsAndIntsAnnoted recordWritten = new SimpleRecordWithStringsAndIntsAnnoted("hello", 17, "world", 1); writer.compound().write("stringAntInt", typeWritten, recordWritten); final SimpleRecordWithStringsAndIntsAnnoted[] recordArrayWritten = new SimpleRecordWithStringsAndIntsAnnoted[] { new SimpleRecordWithStringsAndIntsAnnoted("hello", 3, "0123456789", 100000), new SimpleRecordWithStringsAndIntsAnnoted("Y2", -1, "What?", -100000) }; writer.compound().writeArray("stringsArray", typeWritten, recordArrayWritten); writer.close(); final IHDF5Reader reader = HDF5Factory.openForReading(file); final HDF5CompoundType typeRead = reader.compound().getDataSetType("stringAntInt", SimpleRecordWithStringsAndIntsAnnoted.class); assertEquals(4, typeRead.getCompoundMemberInformation().length); assertEquals("s1", typeRead.getCompoundMemberInformation()[0].getName()); assertEquals(HDF5DataClass.STRING, typeRead.getCompoundMemberInformation()[0].getType() .getDataClass()); assertTrue(typeRead.getCompoundMemberInformation()[0].getType().isVariableLengthString()); assertEquals(HDFNativeData.getMachineWordSize(), typeRead.getCompoundMemberInformation()[0] .getType().getSize()); assertEquals("i1", typeRead.getCompoundMemberInformation()[1].getName()); assertEquals(HDF5DataClass.INTEGER, typeRead.getCompoundMemberInformation()[1].getType() .getDataClass()); assertEquals("s2", typeRead.getCompoundMemberInformation()[2].getName()); assertEquals(HDF5DataClass.STRING, typeRead.getCompoundMemberInformation()[2].getType() .getDataClass()); assertTrue(typeRead.getCompoundMemberInformation()[2].getType().isVariableLengthString()); assertEquals(HDFNativeData.getMachineWordSize(), typeRead.getCompoundMemberInformation()[2] .getType().getSize()); assertEquals("i2", typeRead.getCompoundMemberInformation()[3].getName()); assertEquals(HDF5DataClass.INTEGER, typeRead.getCompoundMemberInformation()[3].getType() .getDataClass()); assertFalse(typeRead.getCompoundMemberInformation()[3].getType().isVariableLengthString()); final SimpleRecordWithStringsAndIntsAnnoted recordRead = reader.compound().read("stringAntInt", typeRead); assertEquals(recordWritten, recordRead); final HDF5CompoundType arrayTypeRead = reader.compound().getDataSetType("stringsArray", SimpleRecordWithStringsAndIntsAnnoted.class); assertEquals(4, arrayTypeRead.getCompoundMemberInformation().length); assertEquals("s1", arrayTypeRead.getCompoundMemberInformation()[0].getName()); assertEquals(HDF5DataClass.STRING, arrayTypeRead.getCompoundMemberInformation()[0] .getType().getDataClass()); assertTrue(arrayTypeRead.getCompoundMemberInformation()[0].getType() .isVariableLengthString()); assertEquals(HDFNativeData.getMachineWordSize(), arrayTypeRead.getCompoundMemberInformation()[0].getType().getSize()); assertEquals("i1", arrayTypeRead.getCompoundMemberInformation()[1].getName()); assertEquals(HDF5DataClass.INTEGER, arrayTypeRead.getCompoundMemberInformation()[1] .getType().getDataClass()); assertEquals("s2", arrayTypeRead.getCompoundMemberInformation()[2].getName()); assertEquals(HDF5DataClass.STRING, arrayTypeRead.getCompoundMemberInformation()[2] .getType().getDataClass()); assertTrue(arrayTypeRead.getCompoundMemberInformation()[2].getType() .isVariableLengthString()); assertEquals(HDFNativeData.getMachineWordSize(), arrayTypeRead.getCompoundMemberInformation()[2].getType().getSize()); assertEquals("i2", arrayTypeRead.getCompoundMemberInformation()[3].getName()); assertEquals(HDF5DataClass.INTEGER, arrayTypeRead.getCompoundMemberInformation()[3] .getType().getDataClass()); assertFalse(arrayTypeRead.getCompoundMemberInformation()[3].getType() .isVariableLengthString()); final SimpleRecordWithStringsAndIntsAnnoted[] recordArrayRead = reader.compound().readArray("stringsArray", arrayTypeRead); assertEquals(recordArrayWritten.length, recordArrayRead.length); assertEquals(recordArrayWritten[0], recordArrayRead[0]); assertEquals(recordArrayWritten[1], recordArrayRead[1]); reader.close(); } @Test public void testCompoundVariableLengthStringUsingHints() { final File file = new File(workingDirectory, "variableLengthStringsInCompoundUsingHints.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.open(file); final HDF5CompoundType typeWritten = writer.compound().getInferredType(SimpleRecordWithStringsAndInts.class, new HDF5CompoundMappingHints().useVariableLengthStrings()); final SimpleRecordWithStringsAndInts recordWritten = new SimpleRecordWithStringsAndInts("hello", 17, "world", 1); writer.compound().write("stringAntInt", typeWritten, recordWritten); final SimpleRecordWithStringsAndInts[] recordArrayWritten = new SimpleRecordWithStringsAndInts[] { new SimpleRecordWithStringsAndInts("hello", 3, "0123456789", 100000), new SimpleRecordWithStringsAndInts("Y2", -1, "What?", -100000) }; writer.compound().writeArray("stringsArray", typeWritten, recordArrayWritten); writer.close(); final IHDF5Reader reader = HDF5Factory.openForReading(file); final HDF5CompoundType typeRead = reader.compound().getDataSetType("stringAntInt", SimpleRecordWithStringsAndInts.class); assertEquals(4, typeRead.getCompoundMemberInformation().length); assertEquals("s1", typeRead.getCompoundMemberInformation()[0].getName()); assertEquals(HDF5DataClass.STRING, typeRead.getCompoundMemberInformation()[0].getType() .getDataClass()); assertTrue(typeRead.getCompoundMemberInformation()[0].getType().isVariableLengthString()); assertEquals(HDFNativeData.getMachineWordSize(), typeRead.getCompoundMemberInformation()[0] .getType().getSize()); assertEquals("i1", typeRead.getCompoundMemberInformation()[1].getName()); assertEquals(HDF5DataClass.INTEGER, typeRead.getCompoundMemberInformation()[1].getType() .getDataClass()); assertEquals("s2", typeRead.getCompoundMemberInformation()[2].getName()); assertEquals(HDF5DataClass.STRING, typeRead.getCompoundMemberInformation()[2].getType() .getDataClass()); assertFalse(typeRead.getCompoundMemberInformation()[2].getType().isVariableLengthString()); assertEquals(10, typeRead.getCompoundMemberInformation()[2].getType().getElementSize()); assertEquals(10, typeRead.getCompoundMemberInformation()[2].getType().getSize()); assertEquals("i2", typeRead.getCompoundMemberInformation()[3].getName()); assertEquals(HDF5DataClass.INTEGER, typeRead.getCompoundMemberInformation()[3].getType() .getDataClass()); assertFalse(typeRead.getCompoundMemberInformation()[3].getType().isVariableLengthString()); final SimpleRecordWithStringsAndInts recordRead = reader.compound().read("stringAntInt", typeRead); assertEquals(recordWritten, recordRead); final HDF5CompoundType arrayTypeRead = reader.compound().getDataSetType("stringsArray", SimpleRecordWithStringsAndInts.class); assertEquals(4, arrayTypeRead.getCompoundMemberInformation().length); assertEquals("s1", arrayTypeRead.getCompoundMemberInformation()[0].getName()); assertEquals(HDF5DataClass.STRING, arrayTypeRead.getCompoundMemberInformation()[0] .getType().getDataClass()); assertTrue(arrayTypeRead.getCompoundMemberInformation()[0].getType() .isVariableLengthString()); assertEquals(HDFNativeData.getMachineWordSize(), arrayTypeRead.getCompoundMemberInformation()[0].getType().getSize()); assertEquals("i1", arrayTypeRead.getCompoundMemberInformation()[1].getName()); assertEquals(HDF5DataClass.INTEGER, arrayTypeRead.getCompoundMemberInformation()[1] .getType().getDataClass()); assertEquals("s2", arrayTypeRead.getCompoundMemberInformation()[2].getName()); assertEquals(HDF5DataClass.STRING, arrayTypeRead.getCompoundMemberInformation()[2] .getType().getDataClass()); assertFalse(arrayTypeRead.getCompoundMemberInformation()[2].getType() .isVariableLengthString()); assertEquals(10, arrayTypeRead.getCompoundMemberInformation()[2].getType().getElementSize()); assertEquals(10, arrayTypeRead.getCompoundMemberInformation()[2].getType().getSize()); assertEquals("i2", arrayTypeRead.getCompoundMemberInformation()[3].getName()); assertEquals(HDF5DataClass.INTEGER, arrayTypeRead.getCompoundMemberInformation()[3] .getType().getDataClass()); assertFalse(arrayTypeRead.getCompoundMemberInformation()[3].getType() .isVariableLengthString()); final SimpleRecordWithStringsAndInts[] recordArrayRead = reader.compound().readArray("stringsArray", arrayTypeRead); assertEquals(recordArrayWritten.length, recordArrayRead.length); assertEquals(recordArrayWritten[0], recordArrayRead[0]); assertEquals(recordArrayWritten[1], recordArrayRead[1]); reader.close(); } static class SimpleRecordWithReference { @CompoundElement(reference = true) String ref; SimpleRecordWithReference() { } SimpleRecordWithReference(String ref) { this.ref = ref; } @Override public int hashCode() { final int prime = 31; int result = 1; result = prime * result + ((ref == null) ? 0 : ref.hashCode()); return result; } @Override public boolean equals(Object obj) { if (this == obj) { return true; } if (obj == null) { return false; } if (getClass() != obj.getClass()) { return false; } SimpleRecordWithReference other = (SimpleRecordWithReference) obj; if (ref == null) { if (other.ref != null) { return false; } } else if (!ref.equals(other.ref)) { return false; } return true; } @Override public String toString() { return "SimpleRecordWithReference [ref=" + ref + "]"; } } @Test public void testCompoundReference() { final File file = new File(workingDirectory, "compoundReference.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.open(file); writer.int32().write("a", 17); writer.float64().write("b", 0.001); writer.compound().write("cpd1", new SimpleRecordWithReference("a")); writer.compound().write("cpd2", new SimpleRecordWithReference("b")); writer.close(); final IHDF5Reader reader = HDF5Factory.openForReading(file); final HDF5CompoundMemberInformation[] infoFromJavaObjs = HDF5CompoundMemberInformation.create(SimpleRecordWithReference.class, "", HDF5CompoundMemberMapping.inferMapping(SimpleRecordWithReference.class)); assertEquals(1, infoFromJavaObjs.length); assertEquals("ref:REFERENCE(8)", infoFromJavaObjs[0].toString()); final HDF5CompoundMemberInformation[] infoFromHDF5Objs = reader.compound().getDataSetInfo("cpd1"); assertEquals(1, infoFromHDF5Objs.length); assertEquals("ref:REFERENCE(8)", infoFromHDF5Objs[0].toString()); final SimpleRecordWithReference recordRead1 = reader.compound().read("cpd1", SimpleRecordWithReference.class); assertEquals("/a", reader.reference().resolvePath(recordRead1.ref)); assertEquals("INTEGER(4):{}", reader.object().getDataSetInformation(recordRead1.ref) .toString()); assertEquals(17, reader.int32().read(recordRead1.ref)); final HDF5CompoundMemberInformation[] info2 = reader.compound().getDataSetInfo("cpd2"); assertEquals(1, info2.length); assertEquals("ref:REFERENCE(8)", info2[0].toString()); final SimpleRecordWithReference recordRead2 = reader.compound().read("cpd2", SimpleRecordWithReference.class); assertEquals("/b", reader.reference().resolvePath(recordRead2.ref)); assertEquals("FLOAT(8):{}", reader.object().getDataSetInformation(recordRead2.ref) .toString()); assertEquals(0.001, reader.float64().read(recordRead2.ref)); reader.close(); } @Test public void testClosedCompoundType() { final File file = new File(workingDirectory, "closedCompoundType.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.open(file); final SimpleInheretingRecord recordWritten = new SimpleInheretingRecord(3.14159f, 42, (short) 17, "xzy", new long[][] { { 1, 2, 3 }, { 4, 5, 6 } }); final HDF5CompoundType type = writer.compound().getInferredType(SimpleInheretingRecord.class); writer.compound().write("cpd", recordWritten); writer.close(); final File file2 = new File(workingDirectory, "closedCompoundType2.h5"); file2.delete(); assertFalse(file2.exists()); file2.deleteOnExit(); final IHDF5Writer writer2 = HDF5Factory.open(file2); try { writer2.compound().write("cpd", type, recordWritten); fail("Failed to detect closed type."); } catch (HDF5JavaException ex) { assertEquals("Type SimpleInheretingRecord is closed.", ex.getMessage()); } try { writer2.compound().getClonedType(type); fail("Failed to detect closed type."); } catch (HDF5JavaException ex) { assertEquals("Type SimpleInheretingRecord is closed.", ex.getMessage()); } writer2.close(); } @Test public void testAnonCompound() { final File file = new File(workingDirectory, "anonCompound.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.open(file); final HDF5CompoundType anonType1 = writer.compound().getInferredAnonType(SimpleInheretingRecord.class); assertEquals("UNKNOWN", anonType1.getName()); final SimpleInheretingRecord recordWritten = new SimpleInheretingRecord(3.14159f, 42, (short) 17, "xzy", new long[][] { { 1, 2, 3 }, { 4, 5, 6 } }); writer.compound().write("cpd", anonType1, recordWritten); final SimpleInheretingRecord2 recordWritten2 = new SimpleInheretingRecord2(3.14159f, 42, (short) 17, "xzy", new long[][] { { 1, 2, 3 }, { 4, 5, 6 }, { 7, 8, 9 } }); final HDF5CompoundType anonType2 = writer.compound().getInferredAnonType(recordWritten2); assertEquals("UNKNOWN", anonType2.getName()); writer.compound().write("cpd2", anonType2, recordWritten2); final SimpleInheretingRecord3 recordWritten3 = new SimpleInheretingRecord3(3.14159f, 42, (short) 17, "xzy", new long[][] { { 1, 2, 3 }, { 4, 5, 6 }, { 7, 8, 11 } }); final HDF5CompoundType anonType3 = writer.compound().getInferredAnonType(recordWritten3); assertEquals("UNKNOWN", anonType3.getName()); writer.compound().write("cpd3", anonType3, recordWritten3); final File file2 = new File(workingDirectory, "anonCompound2.h5"); file2.delete(); assertFalse(file2.exists()); file2.deleteOnExit(); final IHDF5Writer writer2 = HDF5Factory.open(file2); final HDF5CompoundType clonedType = writer2.compound().getClonedType( writer.compound().getDataSetType("cpd", HDF5CompoundDataMap.class)); writer2.compound().write("cpd", clonedType, writer.compound().read("cpd", HDF5CompoundDataMap.class)); writer.close(); writer2.close(); final IHDF5Reader reader = HDF5Factory.openForReading(file); final HDF5CompoundType type = reader.compound().getDataSetType("cpd", SimpleInheretingRecord.class); assertFalse(type.isMappingIncomplete()); assertFalse(type.isDiskRepresentationIncomplete()); assertFalse(type.isMemoryRepresentationIncomplete()); type.checkMappingComplete(); final SimpleInheretingRecord recordRead = reader.compound().read("cpd", type); assertEquals(recordWritten, recordRead); final SimpleInheretingRecord2 recordRead2 = reader.compound().read("cpd2", SimpleInheretingRecord2.class); assertEquals(recordWritten2, recordRead2); final SimpleInheretingRecord3 recordRead3 = reader.compound().read("cpd3", SimpleInheretingRecord3.class); assertEquals(recordWritten3, recordRead3); reader.close(); final IHDF5Reader reader2 = HDF5Factory.openForReading(file2); final HDF5CompoundType type2 = reader2.compound().getDataSetType("cpd", SimpleInheretingRecord.class); assertFalse(type2.isMappingIncomplete()); assertFalse(type2.isDiskRepresentationIncomplete()); assertFalse(type2.isMemoryRepresentationIncomplete()); assertEquals("UNKNOWN", type2.getName()); type2.checkMappingComplete(); final SimpleInheretingRecord recordReadFile2 = reader2.compound().read("cpd", type2); assertEquals(recordWritten, recordReadFile2); reader2.close(); } static class StringEnumCompoundType { String fruit; StringEnumCompoundType() { } StringEnumCompoundType(String fruit) { this.fruit = fruit; } } static class OrdinalEnumCompoundType { int fruit; OrdinalEnumCompoundType() { } OrdinalEnumCompoundType(int fruit) { this.fruit = fruit; } } @Test public void testCompoundJavaEnum() { final File file = new File(workingDirectory, "compoundJavaEnum.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.open(file); final JavaEnumCompoundType recordWritten = new JavaEnumCompoundType(FruitEnum.CHERRY); writer.compound().write("cpd", recordWritten); writer.close(); final IHDF5Reader reader = HDF5Factory.openForReading(file); final HDF5CompoundType type = reader.compound().getDataSetType("cpd", JavaEnumCompoundType.class); assertFalse(type.isMappingIncomplete()); assertFalse(type.isDiskRepresentationIncomplete()); assertFalse(type.isMemoryRepresentationIncomplete()); type.checkMappingComplete(); final JavaEnumCompoundType recordRead = reader.compound().read("cpd", type); assertEquals(recordWritten, recordRead); final StringEnumCompoundType stringRecordRead = reader.readCompound("cpd", StringEnumCompoundType.class); assertEquals(FruitEnum.CHERRY.name(), stringRecordRead.fruit); final OrdinalEnumCompoundType ordinalRecordRead = reader.readCompound("cpd", OrdinalEnumCompoundType.class); assertEquals(FruitEnum.CHERRY.ordinal(), ordinalRecordRead.fruit); reader.close(); } @Test public void testEnumFromCompoundJavaEnum() { final File file = new File(workingDirectory, "enumsFromCompoundJavaEnum.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.open(file); final JavaMultipleEnumsCompoundType recordWritten = new JavaMultipleEnumsCompoundType(FruitEnum.APPLE, ColorEnum.BLUE, StateEnum.ONGOING); HDF5CompoundType type = writer.compound().getInferredAnonType(JavaMultipleEnumsCompoundType.class); writer.compound().write("cpd", type, recordWritten); Map enumMap = type.getEnumTypeMap(); assertEquals("[fruit, color, state]", enumMap.keySet().toString()); writer.enumeration().write("fruit", new HDF5EnumerationValue(enumMap.get("fruit"), "ORANGE")); writer.enumeration() .write("color", new HDF5EnumerationValue(enumMap.get("color"), "BLACK")); writer.enumeration() .write("state", new HDF5EnumerationValue(enumMap.get("state"), "READY")); writer.close(); final IHDF5Reader reader = HDF5Factory.openForReading(file); type = reader.compound().getDataSetType("cpd", JavaMultipleEnumsCompoundType.class); assertFalse(type.isMappingIncomplete()); assertFalse(type.isDiskRepresentationIncomplete()); assertFalse(type.isMemoryRepresentationIncomplete()); type.checkMappingComplete(); final JavaMultipleEnumsCompoundType recordRead = reader.compound().read("cpd", type); enumMap = type.getEnumTypeMap(); assertEquals(recordWritten, recordRead); assertEquals(FruitEnum.APPLE, recordRead.fruit); assertEquals(ColorEnum.BLUE, recordRead.color); assertEquals(StateEnum.ONGOING, recordRead.state); assertEquals(reader.enumeration().getDataSetType("fruit"), enumMap.get("fruit")); assertEquals(reader.enumeration().getDataSetType("color"), enumMap.get("color")); assertEquals(reader.enumeration().getDataSetType("state"), enumMap.get("state")); assertEquals("ORANGE", reader.enumeration().read("fruit").getValue()); assertEquals("BLACK", reader.enumeration().read("color").getValue()); assertEquals("READY", reader.enumeration().read("state").getValue()); reader.close(); } static class JavaEnumArrayCompoundType { FruitEnum[] fruits; JavaEnumArrayCompoundType() { } JavaEnumArrayCompoundType(FruitEnum[] fruits) { this.fruits = fruits; } @Override public int hashCode() { final int prime = 31; int result = 1; result = prime * result + Arrays.hashCode(fruits); return result; } @Override public boolean equals(Object obj) { if (this == obj) { return true; } if (obj == null) { return false; } if (getClass() != obj.getClass()) { return false; } JavaEnumArrayCompoundType other = (JavaEnumArrayCompoundType) obj; if (!Arrays.equals(fruits, other.fruits)) { return false; } return true; } @Override public String toString() { return "JavaEnumArrayCompoundType [fruits=" + Arrays.toString(fruits) + "]"; } } static class StringEnumArrayCompoundType { String[] fruits; StringEnumArrayCompoundType() { } StringEnumArrayCompoundType(String[] fruits) { this.fruits = fruits; } } static class OrdinalEnumArrayCompoundType { int[] fruits; OrdinalEnumArrayCompoundType() { } OrdinalEnumArrayCompoundType(int[] fruits) { this.fruits = fruits; } } @Test public void testCompoundJavaEnumArray() { final File file = new File(workingDirectory, "compoundJavaEnumArray.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.open(file); final JavaEnumArrayCompoundType recordWritten = new JavaEnumArrayCompoundType(new FruitEnum[] { FruitEnum.CHERRY, FruitEnum.APPLE, FruitEnum.ORANGE }); writer.compound().write("cpd", recordWritten); writer.close(); final IHDF5Reader reader = HDF5Factory.openForReading(file); final HDF5CompoundType type = reader.compound().getDataSetType("cpd", JavaEnumArrayCompoundType.class); assertFalse(type.isMappingIncomplete()); assertFalse(type.isDiskRepresentationIncomplete()); assertFalse(type.isMemoryRepresentationIncomplete()); type.checkMappingComplete(); final JavaEnumArrayCompoundType recordRead = reader.compound().read("cpd", type); assertEquals(recordWritten, recordRead); final StringEnumArrayCompoundType stringRecordRead = reader.readCompound("cpd", StringEnumArrayCompoundType.class); assertTrue(Arrays.toString(stringRecordRead.fruits), Arrays.equals(new String[] { "CHERRY", "APPLE", "ORANGE" }, stringRecordRead.fruits)); final OrdinalEnumArrayCompoundType ordinalRecordRead = reader.readCompound("cpd", OrdinalEnumArrayCompoundType.class); assertTrue(Arrays.toString(ordinalRecordRead.fruits), Arrays.equals(new int[] { 2, 0, 1 }, ordinalRecordRead.fruits)); reader.close(); } @Test public void testCompoundJavaEnumMap() { final File file = new File(workingDirectory, "compoundJavaEnumMap.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.open(file); final HDF5CompoundDataMap recordWritten = new HDF5CompoundDataMap(); recordWritten.put("fruit", FruitEnum.ORANGE); writer.compound().write("cpd", recordWritten); writer.close(); final IHDF5Reader reader = HDF5Factory.openForReading(file); final HDF5CompoundType type = reader.compound().getDataSetType("cpd", HDF5CompoundDataMap.class); assertFalse(type.isMappingIncomplete()); assertFalse(type.isDiskRepresentationIncomplete()); assertFalse(type.isMemoryRepresentationIncomplete()); type.checkMappingComplete(); final Map recordRead = reader.compound().read("cpd", type); assertEquals(1, recordRead.size()); assertEquals("ORANGE", recordRead.get("fruit").toString()); reader.close(); } @Test public void testCompoundIncompleteJavaPojo() { final File file = new File(workingDirectory, "compoundIncompleteJavaPojo.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.open(file); final SimpleInheretingRecord recordWritten = new SimpleInheretingRecord(3.14159f, 42, (short) 17, "xzy", new long[][] { { 1, 2, 3 }, { 4, 5, 6 } }); writer.compound().write("cpd", recordWritten); writer.close(); final IHDF5Reader reader = HDF5Factory.openForReading(file); final HDF5CompoundType type = reader.compound().getDataSetType("cpd", SimpleRecord.class); assertTrue(type.isMappingIncomplete()); assertFalse(type.isDiskRepresentationIncomplete()); assertTrue(type.isMemoryRepresentationIncomplete()); try { type.checkMappingComplete(); fail("Uncomplete mapping not detected."); } catch (HDF5JavaException ex) { assertEquals( "Incomplete mapping for compound type 'SimpleInheretingRecord': unmapped members: {ll}", ex.getMessage()); } final SimpleRecord recordRead = reader.compound().read("cpd", type); assertEquals(recordWritten.getF(), recordRead.getF()); assertEquals(recordWritten.getI(), recordRead.getI()); assertEquals(recordWritten.getD(), recordRead.getD()); assertEquals(recordWritten.getS(), recordRead.getS()); final HDF5CompoundType type2 = reader.compound().getInferredType("cpd", SimpleRecord.class, null, false); assertFalse(type2.isMappingIncomplete()); assertFalse(type2.isDiskRepresentationIncomplete()); assertFalse(type2.isMemoryRepresentationIncomplete()); type2.checkMappingComplete(); final SimpleRecord recordRead2 = reader.compound().read("cpd", type2); assertEquals(recordWritten.getF(), recordRead2.getF()); assertEquals(recordWritten.getI(), recordRead2.getI()); assertEquals(recordWritten.getD(), recordRead2.getD()); assertEquals(recordWritten.getS(), recordRead2.getS()); reader.close(); } @Test public void testCompoundHintVLString() { final File file = new File(workingDirectory, "testCompoundHintVLString.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.configure(file).useUTF8CharacterEncoding().writer(); writer.compound().getInferredType(SimpleStringRecord.class, new HDF5CompoundMappingHints().useVariableLengthStrings()); final HDF5CompoundType typeWritten = writer.compound().getInferredType("SimpleStringRecordByTemplate", new SimpleStringRecord("aaa", "bb"), new HDF5CompoundMappingHints().useVariableLengthStrings()); final SimpleStringRecord recordWritten = new SimpleStringRecord("aaa", "\u3453"); writer.compound().write("cpd", typeWritten, recordWritten); writer.close(); final IHDF5Reader reader = HDF5Factory.openForReading(file); final HDF5CompoundType typeRead = reader.compound().getNamedType(SimpleStringRecord.class); final HDF5CompoundType type2Read = reader.compound().getNamedType("SimpleStringRecordByTemplate", SimpleStringRecord.class); assertEquals(2, typeRead.getCompoundMemberInformation().length); assertTrue(typeRead.getCompoundMemberInformation()[0].getType().isVariableLengthString()); assertTrue(typeRead.getCompoundMemberInformation()[1].getType().isVariableLengthString()); assertTrue(type2Read.getCompoundMemberInformation()[0].getType().isVariableLengthString()); assertTrue(type2Read.getCompoundMemberInformation()[1].getType().isVariableLengthString()); final SimpleStringRecord recordRead = reader.compound().read("cpd", type2Read); assertEquals(recordWritten, recordRead); reader.close(); } @Test public void testCompoundMap() { final File file = new File(workingDirectory, "testCompoundMap.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.configure(file).useUTF8CharacterEncoding().writer(); final HDF5EnumerationType enumType = writer.enumeration().getType("someEnumType", new String[] { "1", "Two", "THREE" }); final HDF5CompoundDataMap map = new HDF5CompoundDataMap(); final float a = 3.14159f; map.put("a", a); final int[] b = new int[] { 17, -1 }; map.put("b", b); final String c = "Teststring\u3453"; map.put("c", c); final HDF5EnumerationValueArray d = new HDF5EnumerationValueArray(enumType, new String[] { "Two", "1" }); map.put("d", d); final BitSet e = new BitSet(); e.set(15); map.put("e", e); final float[][] f = new float[][] { { 1.0f, -1.0f }, { 1e6f, -1e6f } }; map.put("f", f); final MDLongArray g = new MDLongArray(new long[] { 1, 2, 3, 4, 5, 6, 7, 8 }, new int[] { 2, 2, 2 }); map.put("g", g); final HDF5TimeDuration h = new HDF5TimeDuration(17, HDF5TimeUnit.HOURS); map.put("h", h); final Date ii = new Date(10000); map.put("i", ii); writer.compound().write("cpd", map); writer.close(); final IHDF5Reader reader = HDF5Factory.openForReading(file); final HDF5CompoundType typeRead = reader.compound().getDataSetType("cpd", HDF5CompoundDataMap.class); assertEquals("a:b:c:d:e:f:g:h:i", typeRead.getName()); final HDF5CompoundDataMap mapRead = reader.compound().read("cpd", typeRead); assertEquals(9, mapRead.size()); assertEquals(a, mapRead.get("a")); assertTrue(ArrayUtils.toString(mapRead.get("b")), ArrayUtils.isEquals(b, mapRead.get("b"))); assertEquals(c, mapRead.get("c")); final HDF5EnumerationValueArray dRead = (HDF5EnumerationValueArray) mapRead.get("d"); assertEquals("someEnumType", dRead.getType().getName()); assertEquals(d.getLength(), dRead.getLength()); for (int i = 0; i < d.getLength(); ++i) { assertEquals("enum array idx=" + i, d.getValue(i), dRead.getValue(i)); } assertEquals(e, mapRead.get("e")); assertTrue(ArrayUtils.toString(mapRead.get("f")), ArrayUtils.isEquals(f, mapRead.get("f"))); assertEquals(g, mapRead.get("g")); assertEquals(h, mapRead.get("h")); assertEquals(ii, mapRead.get("i")); final HDF5CompoundType typeRead2 = reader.compound().getDataSetType("cpd", HDF5CompoundDataMap.class, new HDF5CompoundMappingHints().enumReturnType(EnumReturnType.STRING)); final HDF5CompoundDataMap mapRead2 = reader.compound().read("cpd", typeRead2); final String[] dRead2 = (String[]) mapRead2.get("d"); assertEquals(dRead.getLength(), dRead2.length); for (int i = 0; i < dRead2.length; ++i) { assertEquals(dRead.getValue(i), dRead2[i]); } final HDF5CompoundType typeRead3 = reader.compound().getDataSetType("cpd", HDF5CompoundDataMap.class, new HDF5CompoundMappingHints().enumReturnType(EnumReturnType.ORDINAL)); final HDF5CompoundDataMap mapRead3 = reader.compound().read("cpd", typeRead3); final int[] dRead3 = (int[]) mapRead3.get("d"); assertEquals(dRead.getLength(), dRead3.length); for (int i = 0; i < dRead3.length; ++i) { assertEquals(dRead.getOrdinal(i), dRead3[i]); } reader.close(); } @Test public void testCompoundMapManualMapping() { final File file = new File(workingDirectory, "testCompoundMapManualMapping.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); final HDF5EnumerationType enumType = writer.enumeration().getType("someEnumType", new String[] { "1", "Two", "THREE" }); final HDF5CompoundType type = writer.compound() .getType( "MapCompoundA", HDF5CompoundDataMap.class, new HDF5CompoundMemberMapping[] { HDF5CompoundMemberMapping.mapping("a").memberClass( float.class), mapping("b").memberClass(int[].class).length(2), mapping("c").memberClass(char[].class).length(12), mapping("d").enumType(enumType).length(2), mapping("e").memberClass(BitSet.class).length(2), mapping("f").memberClass(float[][].class).dimensions(2, 2), mapping("g").memberClass(MDLongArray.class).dimensions( new int[] { 2, 2, 2 }), mapping("h") .memberClass(HDF5TimeDuration.class) .typeVariant( HDF5DataTypeVariant.TIME_DURATION_HOURS), mapping("i").memberClass(Date.class) }); final HDF5CompoundDataMap map = new HDF5CompoundDataMap(); final float a = 3.14159f; map.put("a", a); final int[] b = new int[] { 17, -1 }; map.put("b", b); final String c = "Teststring"; map.put("c", c); final HDF5EnumerationValueArray d = new HDF5EnumerationValueArray(enumType, new String[] { "Two", "1" }); map.put("d", d); final BitSet e = new BitSet(); e.set(15); map.put("e", e); final float[][] f = new float[][] { { 1.0f, -1.0f }, { 1e6f, -1e6f } }; map.put("f", f); final MDLongArray g = new MDLongArray(new long[] { 1, 2, 3, 4, 5, 6, 7, 8 }, new int[] { 2, 2, 2 }); map.put("g", g); final HDF5TimeDuration h = new HDF5TimeDuration(17, HDF5TimeUnit.HOURS); map.put("h", h); final Date ii = new Date(10000); map.put("i", ii); writer.compound().write("cpd", type, map); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); final HDF5CompoundType typeRead = reader.compound().getDataSetType("cpd", HDF5CompoundDataMap.class); assertEquals("MapCompoundA", typeRead.getName()); final HDF5CompoundDataMap mapRead = reader.compound().read("cpd", typeRead); assertEquals(9, mapRead.size()); assertEquals(a, mapRead.get("a")); assertTrue(ArrayUtils.toString(mapRead.get("b")), ArrayUtils.isEquals(b, mapRead.get("b"))); assertEquals(c, mapRead.get("c")); final HDF5EnumerationValueArray dRead = (HDF5EnumerationValueArray) mapRead.get("d"); assertEquals("someEnumType", dRead.getType().getName()); assertEquals(d.getLength(), dRead.getLength()); for (int i = 0; i < d.getLength(); ++i) { assertEquals("enum array idx=" + i, d.getValue(i), dRead.getValue(i)); } assertEquals(e, mapRead.get("e")); assertTrue(ArrayUtils.toString(mapRead.get("f")), ArrayUtils.isEquals(f, mapRead.get("f"))); assertEquals(g, mapRead.get("g")); assertEquals(h, mapRead.get("h")); assertEquals(ii, mapRead.get("i")); reader.close(); } @Test public void testCompoundMapManualMappingWithConversion() { final File file = new File(workingDirectory, "testCompoundMapManualMappingWithConversion.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); final HDF5EnumerationType enumType = writer.enumeration().getType("someEnumType", new String[] { "1", "Two", "THREE" }); final HDF5CompoundType type = writer.compound() .getType( "MapCompoundA", HDF5CompoundDataMap.class, new HDF5CompoundMemberMapping[] { HDF5CompoundMemberMapping.mapping("a").memberClass( float.class), mapping("b").memberClass(short.class), mapping("c").memberClass(Date.class), mapping("d").enumType(enumType).length(2), mapping("e").memberClass(double.class), mapping("f") .memberClass(HDF5TimeDuration.class) .typeVariant( HDF5DataTypeVariant.TIME_DURATION_HOURS) }); final HDF5CompoundDataMap map = new HDF5CompoundDataMap(); final double a = 3.14159; map.put("a", a); final int b = 17; map.put("b", b); final long c = System.currentTimeMillis(); map.put("c", c); final int[] d = new int[] { 1, 0 }; map.put("d", d); final long e = 187493613; map.put("e", e); final short f = 12; map.put("f", f); writer.compound().write("cpd", type, map); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); final HDF5CompoundType typeRead = reader.compound().getDataSetType("cpd", HDF5CompoundDataMap.class); assertEquals("MapCompoundA", typeRead.getName()); final HDF5CompoundDataMap mapRead = reader.compound().read("cpd", typeRead); assertEquals(map.size(), mapRead.size()); assertEquals((float) a, mapRead.get("a")); assertEquals((short) b, mapRead.get("b")); assertEquals(new Date(c), mapRead.get("c")); final HDF5EnumerationValueArray dRead = (HDF5EnumerationValueArray) mapRead.get("d"); assertEquals("someEnumType", dRead.getType().getName()); assertEquals(d.length, dRead.getLength()); for (int i = 0; i < d.length; ++i) { assertEquals("enum array idx=" + i, d[i], dRead.getOrdinal(i)); } assertEquals((double) e, mapRead.get("e")); assertEquals(new HDF5TimeDuration(f, HDF5TimeUnit.HOURS), mapRead.get("f")); reader.close(); } @Test public void testCompoundManualMapping() { final File file = new File(workingDirectory, "compoundManualMapping.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); HDF5CompoundType compoundType = Record.getHDF5Type(writer); HDF5EnumerationType enumType = writer.enumeration().getType("someEnumType"); final Record recordWritten = new Record(1, 2.0f, 100000000L, 3.0, (short) 4, true, "one", new HDF5EnumerationValue(enumType, "THREE"), new int[] { 1, 2, 3 }, new float[] { 8.0f, -17.0f }, new long[] { -10, -11, -12 }, new double[] { 3.14159 }, new short[] { 1000, 2000 }, new byte[] { 11, 12, 13, 14 }, new MDIntArray(new int[][] { { 1, 2 }, { 3, 4 } }), new char[] { 'A', 'b', 'C' }); writer.compound().write("/testCompound", compoundType, recordWritten); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); final HDF5CompoundMemberInformation[] memMemberInfo = Record.getMemberInfo(reader.enumeration().getType("someEnumType")); final HDF5CompoundMemberInformation[] diskMemberInfo = reader.compound().getDataSetInfo("/testCompound", DataTypeInfoOptions.ALL); assertEquals(memMemberInfo.length, diskMemberInfo.length); Arrays.sort(memMemberInfo); Arrays.sort(diskMemberInfo); for (int i = 0; i < memMemberInfo.length; ++i) { assertEquals(memMemberInfo[i], diskMemberInfo[i]); } compoundType = Record.getHDF5Type(reader); final Record recordRead = reader.compound().read("/testCompound", Record.getHDF5Type(reader)); assertEquals(recordWritten, recordRead); reader.close(); } @Test public void testCompoundMapArray() { final File file = new File(workingDirectory, "testCompoundMapArray.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.open(file); final HDF5CompoundDataMap map1 = new HDF5CompoundDataMap(); final float a1 = 3.14159f; map1.put("a", a1); final HDF5CompoundDataMap map2 = new HDF5CompoundDataMap(); final float a2 = 18.32f; map2.put("a", a2); final HDF5CompoundDataMap map3 = new HDF5CompoundDataMap(); final float a3 = 1.546e5f; map3.put("a", a3); writer.writeCompoundArray("cpd", new HDF5CompoundDataMap[] { map1, map2, map3 }); writer.close(); final IHDF5Reader reader = HDF5Factory.openForReading(file); final HDF5CompoundDataMap[] maps = reader.compound().readArray("cpd", HDF5CompoundDataMap.class); assertEquals(3, maps.length); assertEquals(map1, maps[0]); assertEquals(map2, maps[1]); assertEquals(map3, maps[2]); reader.close(); } @Test public void testCompoundMapMDArray() { final File file = new File(workingDirectory, "testCompoundMapMDArray.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.open(file); final HDF5CompoundDataMap map1 = new HDF5CompoundDataMap(); final float a1 = 3.14159f; map1.put("a", a1); final HDF5CompoundDataMap map2 = new HDF5CompoundDataMap(); final float a2 = 18.32f; map2.put("a", a2); final HDF5CompoundDataMap map3 = new HDF5CompoundDataMap(); final float a3 = 1.546e5f; map3.put("a", a3); final HDF5CompoundDataMap map4 = new HDF5CompoundDataMap(); final float a4 = -3.2f; map4.put("a", a4); writer.compound().writeMDArray("cpd", new MDArray(new HDF5CompoundDataMap[] { map1, map2, map3, map4 }, new int[] { 2, 2 })); writer.close(); final IHDF5Reader reader = HDF5Factory.openForReading(file); final MDArray maps = reader.compound().readMDArray("cpd", HDF5CompoundDataMap.class); assertTrue(ArrayUtils.isEquals(new int[] { 2, 2 }, maps.dimensions())); assertEquals(map1, maps.get(0, 0)); assertEquals(map2, maps.get(0, 1)); assertEquals(map3, maps.get(1, 0)); assertEquals(map4, maps.get(1, 1)); reader.close(); } static class DateRecord { Date d; DateRecord() { } DateRecord(Date d) { this.d = d; } @Override public int hashCode() { final int prime = 31; int result = 1; result = prime * result + ((d == null) ? 0 : d.hashCode()); return result; } @Override public boolean equals(Object obj) { if (this == obj) return true; if (obj == null) return false; if (getClass() != obj.getClass()) return false; DateRecord other = (DateRecord) obj; if (d == null) { if (other.d != null) return false; } else if (!d.equals(other.d)) return false; return true; } } @Test public void testDateCompound() { final File file = new File(workingDirectory, "compoundWithDate.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); HDF5CompoundType compoundType = writer.compound().getType(DateRecord.class, new HDF5CompoundMemberMapping[] { mapping("d") }); final DateRecord recordWritten = new DateRecord(new Date()); final String objectPath = "/testDateCompound"; writer.compound().write(objectPath, compoundType, recordWritten); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); final HDF5CompoundMemberInformation[] memMemberInfo = HDF5CompoundMemberInformation.create(DateRecord.class, "", mapping("d")); final HDF5CompoundMemberInformation[] diskMemberInfo = HDF5CompoundMemberInformation.create(DateRecord.class, "", new HDF5CompoundMemberMapping[] { mapping("d") }); assertEquals(memMemberInfo.length, diskMemberInfo.length); for (int i = 0; i < memMemberInfo.length; ++i) { assertEquals(memMemberInfo[i], diskMemberInfo[i]); } compoundType = reader.compound().getType(DateRecord.class, new HDF5CompoundMemberMapping[] { mapping("d") }); assertEquals(HDF5DataTypeVariant.TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH, compoundType.getObjectByteifyer().getByteifyers()[0].getTypeVariant()); final DateRecord recordRead = reader.compound().read(objectPath, reader.compound().getType(DateRecord.class, mapping("d"))); assertEquals(recordWritten, recordRead); HDF5CompoundType mapCompoundType = reader.compound().getDataSetType(objectPath, HDF5CompoundDataMap.class); assertEquals(HDF5DataTypeVariant.TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH, mapCompoundType.getObjectByteifyer().getByteifyers()[0].getTypeVariant()); final HDF5CompoundDataMap mapRead = reader.compound().read(objectPath, mapCompoundType); assertEquals(recordWritten.d, mapRead.get("d")); reader.close(); } static class MatrixRecord { byte[][] b; short[][] s; int[][] i; long[][] l; float[][] f; double[][] d; MatrixRecord() { } MatrixRecord(byte[][] b, short[][] s, int[][] i, long[][] l, float[][] f, double[][] d) { this.b = b; this.s = s; this.i = i; this.l = l; this.f = f; this.d = d; } static HDF5CompoundMemberMapping[] getMapping() { return new HDF5CompoundMemberMapping[] { mapping("b").dimensions(1, 2), mapping("s").dimensions(2, 1), mapping("i").dimensions(2, 2), mapping("l").dimensions(3, 2), mapping("f").dimensions(2, 2), mapping("d").dimensions(2, 3) }; } @Override public boolean equals(Object obj) { if (this == obj) return true; if (obj == null) return false; if (getClass() != obj.getClass()) return false; MatrixRecord other = (MatrixRecord) obj; if (!HDF5RoundtripTest.equals(b, other.b)) return false; if (!HDF5RoundtripTest.equals(d, other.d)) return false; if (!HDF5RoundtripTest.equals(f, other.f)) return false; if (!HDF5RoundtripTest.equals(i, other.i)) return false; if (!HDF5RoundtripTest.equals(l, other.l)) return false; if (!HDF5RoundtripTest.equals(s, other.s)) return false; return true; } } @Test public void testMatrixCompound() { final File file = new File(workingDirectory, "compoundWithMatrix.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); HDF5CompoundType compoundType = writer.compound().getType(MatrixRecord.class, MatrixRecord.getMapping()); final MatrixRecord recordWritten = new MatrixRecord(new byte[][] { { 1, 2 } }, new short[][] { { 1 }, { 2 } }, new int[][] { { 1, 2 }, { 3, 4 } }, new long[][] { { 1, 2 }, { 3, 4 }, { 5, 6 } }, new float[][] { { 1, 2 }, { 3, 4 } }, new double[][] { { 1, 2, 3 }, { 4, 5, 6 } }); String name = "/testMatrixCompound"; writer.compound().write(name, compoundType, recordWritten); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); final HDF5CompoundMemberInformation[] memMemberInfo = HDF5CompoundMemberInformation.create(MatrixRecord.class, "", MatrixRecord.getMapping()); final HDF5CompoundMemberInformation[] diskMemberInfo = HDF5CompoundMemberInformation.create(MatrixRecord.class, "", MatrixRecord.getMapping()); assertEquals(memMemberInfo.length, diskMemberInfo.length); for (int i = 0; i < memMemberInfo.length; ++i) { assertEquals(memMemberInfo[i], diskMemberInfo[i]); } compoundType = reader.compound().getType(MatrixRecord.class, MatrixRecord.getMapping()); final MatrixRecord recordRead = reader.compound().read(name, reader.compound().getType(MatrixRecord.class, MatrixRecord.getMapping())); assertEquals(recordWritten, recordRead); reader.close(); } @Test(expectedExceptions = IllegalArgumentException.class) public void testMatrixCompoundSizeMismatch() { final File file = new File(workingDirectory, "compoundWithSizeMismatchMatrix.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); HDF5CompoundType compoundType = writer.compound().getType(MatrixRecord.class, MatrixRecord.getMapping()); final MatrixRecord recordWritten = new MatrixRecord(new byte[][] { { 1, 2 } }, new short[][] { { 1 }, { 2 } }, new int[][] { { 1, 2 }, { 3, 4 } }, new long[][] { { 1, 2 }, { 3, 4 }, { 5, 6 } }, new float[][] { { 1, 2 }, { 3, 4 } }, new double[][] { { 1, 2, 3, 4 }, { 5, 6, 7, 8 }, { 9, 10, 11, 12, 13 } }); String name = "/testMatrixCompound"; writer.compound().write(name, compoundType, recordWritten); } @Test(expectedExceptions = IllegalArgumentException.class) public void testMatrixCompoundDifferentNumberOfColumnsPerRow() { final File file = new File(workingDirectory, "compoundWithMatrixDifferentNumberOfColumnsPerRow.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); HDF5CompoundType compoundType = writer.compound().getType(MatrixRecord.class, MatrixRecord.getMapping()); final MatrixRecord recordWritten = new MatrixRecord(new byte[][] { { 1, 2 } }, new short[][] { { 1 }, { 2 } }, new int[][] { { 1, 2 }, { 3, 4 } }, new long[][] { { 1, 2 }, { 3, 4 }, { 5, 6 } }, new float[][] { { 1, 2 }, { 3, 4 } }, new double[][] { { 1, 2, 3 }, { 4, 5 } }); String name = "/testMatrixCompound"; writer.compound().write(name, compoundType, recordWritten); } private static boolean equals(double[][] a, double[][] a2) { if (a == a2) { return true; } if (a == null || a2 == null) { return false; } int rows = a.length; if (a2.length != rows) { return false; } for (int i = 0; i < rows; i++) { int columns = a[i].length; if (a2[i].length != columns) { return false; } for (int j = 0; j < columns; j++) { if (Double.doubleToLongBits(a[i][j]) != Double.doubleToLongBits(a2[i][j])) { return false; } } } return true; } private static boolean equals(byte[][] a, byte[][] a2) { if (a == a2) { return true; } if (a == null || a2 == null) { return false; } int rows = a.length; if (a2.length != rows) { return false; } for (int i = 0; i < rows; i++) { int columns = a[i].length; if (a2[i].length != columns) { return false; } for (int j = 0; j < columns; j++) { if (a[i][j] != a2[i][j]) { return false; } } } return true; } private static boolean equals(short[][] a, short[][] a2) { if (a == a2) { return true; } if (a == null || a2 == null) { return false; } int rows = a.length; if (a2.length != rows) { return false; } for (int i = 0; i < rows; i++) { int columns = a[i].length; if (a2[i].length != columns) { return false; } for (int j = 0; j < columns; j++) { if (a[i][j] != a2[i][j]) { return false; } } } return true; } private static boolean equals(int[][] a, int[][] a2) { if (a == a2) { return true; } if (a == null || a2 == null) { return false; } int rows = a.length; if (a2.length != rows) { return false; } for (int i = 0; i < rows; i++) { int columns = a[i].length; if (a2[i].length != columns) { return false; } for (int j = 0; j < columns; j++) { if (a[i][j] != a2[i][j]) { return false; } } } return true; } private static boolean equals(long[][] a, long[][] a2) { if (a == a2) { return true; } if (a == null || a2 == null) { return false; } int rows = a.length; if (a2.length != rows) { return false; } for (int i = 0; i < rows; i++) { int columns = a[i].length; if (a2[i].length != columns) { return false; } for (int j = 0; j < columns; j++) { if (a[i][j] != a2[i][j]) { return false; } } } return true; } @Test public void testCompoundOverflow() { final File file = new File(workingDirectory, "compoundOverflow.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); HDF5CompoundType compoundType = Record.getHDF5Type(writer); HDF5EnumerationType enumType = writer.enumeration().getType("someEnumType"); final Record recordWritten = new Record(1, 2.0f, 100000000L, 3.0, (short) 4, true, "one", new HDF5EnumerationValue(enumType, "THREE"), new int[] { 1, 2, 3 }, new float[] { 8.0f, -17.0f }, new long[] { -10, -11, -12 }, new double[] { 3.14159 }, new short[] { 1000, 2000 }, new byte[] { 11, 12, 13, 14, 0, 0, 0 }, new MDIntArray(new int[][] { { 5, 6 }, { 7, 8 } }), new char[] { 'A', 'b', 'C' }); try { writer.compound().write("/testCompound", compoundType, recordWritten); fail("Failed to detect overflow."); } catch (HDF5JavaException ex) { if (ex.getMessage().contains("must not exceed 4 bytes") == false) { throw ex; } // Expected. } finally { writer.close(); } } static class BitFieldRecord { BitSet bs; BitFieldRecord(BitSet bs) { this.bs = bs; } BitFieldRecord() { } static HDF5CompoundMemberInformation[] getMemberInfo() { return HDF5CompoundMemberInformation.create(BitFieldRecord.class, "", mapping("bs") .length(100)); } static HDF5CompoundType getHDF5Type(IHDF5Reader reader) { return reader.compound().getType(BitFieldRecord.class, mapping("bs").length(100)); } @Override public boolean equals(Object obj) { if (obj instanceof BitFieldRecord == false) { return false; } final BitFieldRecord that = (BitFieldRecord) obj; return this.bs.equals(that.bs); } @Override public int hashCode() { return bs.hashCode(); } } @Test public void testBitFieldCompound() { final File file = new File(workingDirectory, "compoundWithBitField.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); HDF5CompoundType compoundType = BitFieldRecord.getHDF5Type(writer); final BitSet bs = new BitSet(); bs.set(39); bs.set(100); final BitFieldRecord recordWritten = new BitFieldRecord(bs); writer.compound().write("/testCompound", compoundType, recordWritten); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); final HDF5CompoundMemberInformation[] memMemberInfo = BitFieldRecord.getMemberInfo(); final HDF5CompoundMemberInformation[] diskMemberInfo = reader.compound().getDataSetInfo("/testCompound"); assertEquals(memMemberInfo.length, diskMemberInfo.length); for (int i = 0; i < memMemberInfo.length; ++i) { assertEquals(memMemberInfo[i], diskMemberInfo[i]); } compoundType = BitFieldRecord.getHDF5Type(reader); final BitFieldRecord recordRead = reader.compound().read("/testCompound", compoundType); assertEquals(recordWritten, recordRead); reader.close(); } @Test public void testCompoundArray() { final File file = new File(workingDirectory, "compoundArray.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); HDF5CompoundType compoundType = Record.getHDF5Type(writer); HDF5EnumerationType enumType = writer.enumeration().getType("someEnumType", new String[] { "1", "Two", "THREE" }, false); Record[] arrayWritten = new Record[] { new Record(1, 2.0f, 100000000L, 3.0, (short) -1, true, "one", new HDF5EnumerationValue(enumType, "THREE"), new int[] { 1, 2, 3 }, new float[] { 8.0f, -17.0f }, new long[] { -10, -11, -12 }, new double[] { 3.14159 }, new short[] { 1000, 2000 }, new byte[] { 11, 12, 13, -14 }, new MDIntArray(new int[][] { { 1, 2 }, { 3, 4 } }), new char[] { 'A', 'b', 'C' }), new Record(2, 3.0f, 100000000L, 4.0, (short) 5, false, "two", new HDF5EnumerationValue(enumType, "1"), new int[] { 4, 5, 6 }, new float[] { 8.0f, -17.0f }, new long[] { -10, -11, -12 }, new double[] { 3.14159 }, new short[] { 1000, 2000 }, new byte[] { 11, 12, 13, 14 }, new MDIntArray(new int[][] { { 5, 6 }, { 7, 8 } }), new char[] { 'A', 'b', 'C' }), }; writer.compound().writeArray("/testCompound", compoundType, arrayWritten, HDF5GenericStorageFeatures.GENERIC_COMPACT); HDF5CompoundType inferredType = writer.compound().getNamedType(Record.class); // Write again, this time with inferred type. writer.compound().writeArray("/testCompound", inferredType, arrayWritten, HDF5GenericStorageFeatures.GENERIC_COMPACT); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); final HDF5CompoundMemberInformation[] memberInfo = reader.compound().getDataSetInfo("/testCompound"); assertEquals(16, memberInfo.length); assertEquals("a", memberInfo[0].getName()); assertTrue(memberInfo[0].getType().isSigned()); assertEquals("d", memberInfo[4].getName()); assertFalse(memberInfo[4].getType().isSigned()); compoundType = Record.getHDF5Type(reader); inferredType = reader.compound().getDataSetType("/testCompound", Record.class); Record[] arrayRead = reader.compound().readArray("/testCompound", inferredType); Record firstElementRead = reader.compound().read("/testCompound", compoundType); assertEquals(arrayRead[0], firstElementRead); for (int i = 0; i < arrayRead.length; ++i) { assertEquals("" + i, arrayWritten[i], arrayRead[i]); } reader.close(); } @Test public void testCompoundArrayBlockWise() { final File file = new File(workingDirectory, "compoundVectorBlockWise.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); HDF5CompoundType compoundType = Record.getHDF5Type(writer); HDF5EnumerationType enumType = writer.enumeration().getType("someEnumType"); writer.compound().createArray("/testCompound", compoundType, 6, 3); Record[] arrayWritten1 = new Record[] { new Record(1, 2.0f, 100000000L, 3.0, (short) 4, true, "one", new HDF5EnumerationValue(enumType, "THREE"), new int[] { 1, 2, 3 }, new float[] { 8.0f, -17.0f }, new long[] { -10, -11, -12 }, new double[] { 3.14159 }, new short[] { 1000, 2000 }, new byte[] { 11, 12, 13, 14 }, new MDIntArray(new int[][] { { 1, 2 }, { 3, 4 } }), new char[] { 'A', 'b', 'C' }), new Record(2, 3.0f, 100000000L, 4.0, (short) 5, false, "two", new HDF5EnumerationValue(enumType, "1"), new int[] { 4, 5, 6 }, new float[] { 8.0f, -17.0f }, new long[] { -10, -11, -12 }, new double[] { 3.14159 }, new short[] { 1000, 2000 }, new byte[] { 11, 12, 13, 14 }, new MDIntArray(new int[][] { { 1, 2 }, { 3, 4 } }), new char[] { 'A', 'b', 'C' }), new Record(3, 3.0f, 100000000L, 5.0, (short) 6, true, "two", new HDF5EnumerationValue(enumType, "Two"), new int[] { -1, -2, -3 }, new float[] { 8.0f, -17.0f }, new long[] { -10, -11, -12 }, new double[] { 3.14159 }, new short[] { 1000, 2000 }, new byte[] { 11, 12, 13, 14 }, new MDIntArray(new int[][] { { 1, 2 }, { 3, 4 } }), new char[] { 'A', 'b', 'C' }), }; Record[] arrayWritten2 = new Record[] { new Record(4, 4.0f, 100000000L, 6.0, (short) 7, false, "two", new HDF5EnumerationValue(enumType, "Two"), new int[] { 100, 200, 300 }, new float[] { 8.0f, -17.0f }, new long[] { -10, -11, -12 }, new double[] { 3.14159 }, new short[] { 1000, 2000 }, new byte[] { 11, 12, 13, 14 }, new MDIntArray(new int[][] { { 6, 7 }, { 8, 9 } }), new char[] { 'A', 'b', 'C' }), new Record(5, 5.0f, 100000000L, 7.0, (short) 8, true, "two", new HDF5EnumerationValue(enumType, "THREE"), new int[] { 400, 500, 600 }, new float[] { 8.0f, -17.0f }, new long[] { -10, -11, -12 }, new double[] { 3.14159 }, new short[] { 1000, 2000 }, new byte[] { 11, 12, 13, 14 }, new MDIntArray(new int[][] { { 6, 7 }, { 8, 9 } }), new char[] { 'A', 'b', 'C' }), new Record(6, 6.0f, 100000000L, 8.0, (short) 9, false, "x", new HDF5EnumerationValue(enumType, "1"), new int[] { -100, -200, -300 }, new float[] { 8.0f, -17.0f }, new long[] { -10, -11, -12 }, new double[] { 3.14159 }, new short[] { 1000, 2000 }, new byte[] { 11, 12, 13, 14 }, new MDIntArray(new int[][] { { 6, 7 }, { 8, 9 } }), new char[] { 'A', 'b', 'C' }), }; writer.compound().writeArrayBlock("/testCompound", compoundType, arrayWritten1, 0); writer.compound().writeArrayBlock("/testCompound", compoundType, arrayWritten2, 1); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); compoundType = Record.getHDF5Type(reader); Record[] arrayRead = reader.compound().readArrayBlock("/testCompound", compoundType, 3, 0); for (int i = 0; i < arrayRead.length; ++i) { assertEquals("" + i, arrayWritten1[i], arrayRead[i]); } arrayRead = reader.compound().readArrayBlock("/testCompound", compoundType, 3, 1); for (int i = 0; i < arrayRead.length; ++i) { assertEquals("" + i, arrayWritten2[i], arrayRead[i]); } arrayRead = reader.compound().readArrayBlockWithOffset("/testCompound", compoundType, 3, 1); for (int i = 1; i < arrayRead.length; ++i) { assertEquals("" + i, arrayWritten1[i], arrayRead[i - 1]); } assertEquals("" + (arrayRead.length - 1), arrayWritten2[0], arrayRead[arrayRead.length - 1]); reader.close(); } @Test public void testCompoundMDArray() { final File file = new File(workingDirectory, "compoundMDArray.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.open(file); writer.compound().writeMDArray( "cpd", new MDArray( new SimpleRecord[] { createSR(1), createSR(2), createSR(3), createSR(4), createSR(5), createSR(6) }, new int[] { 2, 3 })); writer.close(); final IHDF5Reader reader = HDF5Factory.openForReading(file); final MDArray records = reader.compound().readMDArray("cpd", SimpleRecord.class); assertEquals(6, records.size()); assertTrue(ArrayUtils.isEquals(new int[] { 2, 3 }, records.dimensions())); assertEquals(createSR(1), records.get(0, 0)); assertEquals(createSR(2), records.get(0, 1)); assertEquals(createSR(3), records.get(0, 2)); assertEquals(createSR(4), records.get(1, 0)); assertEquals(createSR(5), records.get(1, 1)); assertEquals(createSR(6), records.get(1, 2)); reader.close(); } private static SimpleRecord createSR(int i) { return new SimpleRecord(i, i, (short) i, Integer.toString(i)); } @Test public void testCompoundMDArrayManualMapping() { final File file = new File(workingDirectory, "compoundMDArrayManualMapping.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); HDF5CompoundType compoundType = Record.getHDF5Type(writer); HDF5EnumerationType enumType = writer.enumeration().getType("someEnumType"); final Record[] arrayWritten = new Record[] { new Record(1, 2.0f, 100000000L, 3.0, (short) 4, true, "one", new HDF5EnumerationValue(enumType, "THREE"), new int[] { 1, 2, 3 }, new float[] { 8.0f, -17.0f }, new long[] { -10, -11, -12 }, new double[] { 3.14159 }, new short[] { 1000, 2000 }, new byte[] { 11, 12, 13, 14 }, new MDIntArray(new int[][] { { 6, 7 }, { 8, 9 } }), new char[] { 'A', 'b', 'C' }), new Record(2, 3.0f, 100000000L, 4.0, (short) 5, false, "two", new HDF5EnumerationValue(enumType, "1"), new int[] { 4, 5, 6 }, new float[] { 8.0f, -17.0f }, new long[] { -10, -11, -12 }, new double[] { 3.14159 }, new short[] { 1000, 2000 }, new byte[] { 11, 12, 13, 14 }, new MDIntArray(new int[][] { { 6, 7 }, { 8, 9 } }), new char[] { 'A', 'b', 'C' }), new Record(3, 3.0f, 100000000L, 5.0, (short) 6, true, "two", new HDF5EnumerationValue(enumType, "Two"), new int[] { 7, 8, 9 }, new float[] { 8.0f, -17.0f }, new long[] { -10, -11, -12 }, new double[] { 3.14159 }, new short[] { 1000, 2000 }, new byte[] { 11, 12, 13, 14 }, new MDIntArray(new int[][] { { 6, 7 }, { 8, 9 } }), new char[] { 'A', 'b', 'C' }), new Record(4, 4.0f, 100000000L, 6.0, (short) 7, false, "two", new HDF5EnumerationValue(enumType, "Two"), new int[] { 10, 11, 12 }, new float[] { 8.0f, -17.0f }, new long[] { -10, -11, -12 }, new double[] { 3.14159 }, new short[] { 1000, 2000 }, new byte[] { 11, 12, 13, 14 }, new MDIntArray(new int[][] { { 6, 7 }, { 8, 9 } }), new char[] { 'A', 'b', 'C' }), }; final MDArray mdArrayWritten = new MDArray(arrayWritten, new int[] { 2, 2 }); writer.compound().writeMDArray("/testCompound", compoundType, mdArrayWritten); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); compoundType = Record.getHDF5Type(reader); final MDArray mdArrayRead = reader.compound().readMDArray("/testCompound", compoundType); assertEquals(mdArrayWritten, mdArrayRead); reader.close(); } @Test public void testCompoundMDArrayBlockWise() { final File file = new File(workingDirectory, "compoundMDArrayBlockWise.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); HDF5CompoundType compoundType = Record.getHDF5Type(writer); HDF5EnumerationType enumType = writer.enumeration().getType("someEnumType"); writer.compound().createMDArray("/testCompound", compoundType, new long[] { 2, 2 }, new int[] { 2, 1 }); final Record[] arrayWritten1 = new Record[] { new Record(1, 2.0f, 100000000L, 3.0, (short) 4, true, "one", new HDF5EnumerationValue(enumType, "THREE"), new int[] { 1, 2, 3 }, new float[] { 8.0f, -17.0f }, new long[] { -10, -11, -12 }, new double[] { 3.14159 }, new short[] { 1000, 2000 }, new byte[] { 11, 12, 13, 14 }, new MDIntArray(new int[][] { { 6, 7 }, { 8, 9 } }), new char[] { 'A', 'b', 'C' }), new Record(2, 3.0f, 100000000L, 4.0, (short) 5, false, "two", new HDF5EnumerationValue(enumType, "1"), new int[] { 2, 3, 4 }, new float[] { 8.1f, -17.1f }, new long[] { -10, -13, -12 }, new double[] { 3.1415 }, new short[] { 1000, 2001 }, new byte[] { 11, 12, 13, 17 }, new MDIntArray(new int[][] { { 6, 7 }, { 8, 9 } }), new char[] { 'A', 'b', 'C' }), }; final Record[] arrayWritten2 = new Record[] { new Record(3, 3.0f, 100000000L, 5.0, (short) 6, true, "two", new HDF5EnumerationValue(enumType, "Two"), new int[] { 3, 4, 5 }, new float[] { 8.0f, -17.0f }, new long[] { -10, -11, -12 }, new double[] { 3.14159 }, new short[] { 1000, 2000 }, new byte[] { 11, 12, 13, 14 }, new MDIntArray(new int[][] { { 6, 7 }, { 8, 9 } }), new char[] { 'A', 'b', 'C' }), new Record(4, 4.0f, 100000000L, 6.0, (short) 7, false, "two", new HDF5EnumerationValue(enumType, "Two"), new int[] { 4, 5, 6 }, new float[] { 8.0f, -17.0f }, new long[] { -10, -11, -12 }, new double[] { 3.14159 }, new short[] { 1000, 2000 }, new byte[] { 11, 12, 13, 14 }, new MDIntArray(new int[][] { { 6, 7 }, { 8, 9 } }), new char[] { 'A', 'b', 'C' }), }; final MDArray mdArrayWritten1 = new MDArray(arrayWritten1, new int[] { 2, 1 }); final MDArray mdArrayWritten2 = new MDArray(arrayWritten2, new int[] { 2, 1 }); writer.compound().writeMDArrayBlock("/testCompound", compoundType, mdArrayWritten1, new long[] { 0, 0 }); writer.compound().writeMDArrayBlock("/testCompound", compoundType, mdArrayWritten2, new long[] { 0, 1 }); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); compoundType = Record.getHDF5Type(reader); final MDArray mdArrayRead1 = reader.compound().readMDArrayBlock("/testCompound", compoundType, new int[] { 2, 1 }, new long[] { 0, 0 }); final MDArray mdArrayRead2 = reader.compound().readMDArrayBlock("/testCompound", compoundType, new int[] { 2, 1 }, new long[] { 0, 1 }); assertEquals(mdArrayWritten1, mdArrayRead1); assertEquals(mdArrayWritten2, mdArrayRead2); reader.close(); } static class RecordA { int a; double b; RecordA(int a, float b) { this.a = a; this.b = b; } RecordA() { } static HDF5CompoundType getHDF5Type(IHDF5Reader reader) { return reader.compound().getType(RecordA.class, mapping("a"), mapping("b")); } } static class RecordB { float a; long b; RecordB(float a, int b) { this.a = a; this.b = b; } RecordB() { } static HDF5CompoundType getHDF5Type(IHDF5Reader reader) { return reader.compound().getType(RecordB.class, mapping("a"), mapping("b")); } } static class RecordC { float a; RecordC(float a) { this.a = a; } RecordC() { } } static class RecordD { @CompoundElement(memberName = "a") float b; RecordD(float b) { this.b = b; } RecordD() { } } static class RecordE { int a; RecordE(int a) { this.a = a; } RecordE() { } } static class MatrixElementRecord { int row; int col; MatrixElementRecord() { } MatrixElementRecord(int row, int col) { this.row = row; this.col = col; } boolean equals(@SuppressWarnings("hiding") int row, @SuppressWarnings("hiding") int col) { return this.row == row && this.col == col; } @Override public boolean equals(Object o) { if (o instanceof MatrixElementRecord == false) { return false; } final MatrixElementRecord m = (MatrixElementRecord) o; return equals(m.row, m.col); } @Override public String toString() { return "(" + row + "," + col + ")"; } } @Test public void testIterateOverMDCompoundArrayInNaturalBlocks() { final File datasetFile = new File(workingDirectory, "iterateOverMDCompoundArrayInNaturalBlocks.h5"); datasetFile.delete(); assertFalse(datasetFile.exists()); datasetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(datasetFile); final String dsName = "ds"; final HDF5CompoundType typeW = writer.compound().getInferredType(MatrixElementRecord.class); assertEquals(HDF5Utils.getDataTypeGroup("") + "/Compound_MatrixElementRecord", typeW.tryGetDataTypePath()); assertEquals("COMPOUND(8)", typeW.getDataTypeInformation(HDF5DataTypeInformation.options().all()).toString()); writer.compound().createMDArray(dsName, typeW, new long[] { 4, 4 }, new int[] { 2, 2 }); writer.compound().writeMDArrayBlock( dsName, typeW, new MDArray(new MatrixElementRecord[] { new MatrixElementRecord(1, 1), new MatrixElementRecord(1, 2), new MatrixElementRecord(2, 1), new MatrixElementRecord(2, 2) }, new int[] { 2, 2 }), new long[] { 0, 0 }); writer.compound().writeMDArrayBlock( dsName, typeW, new MDArray(new MatrixElementRecord[] { new MatrixElementRecord(3, 1), new MatrixElementRecord(3, 2), new MatrixElementRecord(4, 1), new MatrixElementRecord(4, 2) }, new int[] { 2, 2 }), new long[] { 1, 0 }); writer.compound().writeMDArrayBlock( dsName, typeW, new MDArray(new MatrixElementRecord[] { new MatrixElementRecord(1, 3), new MatrixElementRecord(1, 4), new MatrixElementRecord(2, 3), new MatrixElementRecord(2, 4) }, new int[] { 2, 2 }), new long[] { 0, 1 }); writer.compound().writeMDArrayBlock( dsName, typeW, new MDArray(new MatrixElementRecord[] { new MatrixElementRecord(3, 3), new MatrixElementRecord(3, 4), new MatrixElementRecord(4, 3), new MatrixElementRecord(4, 4) }, new int[] { 2, 2 }), new long[] { 1, 1 }); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(datasetFile); int i = 0; int j = 0; final HDF5CompoundType typeR = reader.compound().getInferredType(MatrixElementRecord.class); for (HDF5MDDataBlock> block : reader.compound() .getMDArrayBlocks(dsName, typeR)) { final String ij = new MatrixElementRecord(i, j).toString() + ": "; assertTrue(ij + Arrays.toString(block.getIndex()), Arrays.equals(new long[] { i, j }, block.getIndex())); assertTrue(ij + Arrays.toString(block.getData().dimensions()), Arrays.equals(new int[] { 2, 2 }, block.getData().dimensions())); assertTrue(ij + Arrays.toString(block.getData().getAsFlatArray()), Arrays.equals( new MatrixElementRecord[] { new MatrixElementRecord(1 + i * 2, 1 + j * 2), new MatrixElementRecord(1 + i * 2, 2 + j * 2), new MatrixElementRecord(2 + i * 2, 1 + j * 2), new MatrixElementRecord(2 + i * 2, 2 + j * 2) }, block.getData() .getAsFlatArray())); if (++j > 1) { j = 0; ++i; } } assertEquals(2, i); assertEquals(0, j); i = 0; j = 0; for (HDF5MDDataBlock> block : reader.compound() .getMDArrayBlocks(dsName, MatrixElementRecord.class)) { final String ij = new MatrixElementRecord(i, j).toString() + ": "; assertTrue(ij + Arrays.toString(block.getIndex()), Arrays.equals(new long[] { i, j }, block.getIndex())); assertTrue(ij + Arrays.toString(block.getData().dimensions()), Arrays.equals(new int[] { 2, 2 }, block.getData().dimensions())); assertTrue(ij + Arrays.toString(block.getData().getAsFlatArray()), Arrays.equals( new MatrixElementRecord[] { new MatrixElementRecord(1 + i * 2, 1 + j * 2), new MatrixElementRecord(1 + i * 2, 2 + j * 2), new MatrixElementRecord(2 + i * 2, 1 + j * 2), new MatrixElementRecord(2 + i * 2, 2 + j * 2) }, block.getData() .getAsFlatArray())); if (++j > 1) { j = 0; ++i; } } reader.close(); } @Test public void testConfusedCompound() { final File file = new File(workingDirectory, "confusedCompound.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); HDF5CompoundType compoundTypeInt = RecordA.getHDF5Type(writer); final RecordA recordWritten = new RecordA(17, 42.0f); writer.compound().write("/testCompound", compoundTypeInt, recordWritten); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().configureForReading(file).performNumericConversions() .reader(); HDF5CompoundType compoundTypeFloat = RecordB.getHDF5Type(reader); try { reader.compound().read("/testCompound", compoundTypeFloat); fail("Unsuitable data set type not detected."); } catch (HDF5JavaException ex) { assertEquals( "The compound type 'UNKNOWN' does not equal the compound type of data set '/testCompound'.", ex.getMessage()); } reader.close(); } static class SimpleRecord { private float f; private int i; @CompoundElement(typeVariant = HDF5DataTypeVariant.TIME_DURATION_SECONDS) private short d; @CompoundElement(dimensions = 4) private String s; SimpleRecord() { } SimpleRecord(float f, int i, short d, String s) { this.f = f; this.i = i; this.d = d; this.s = s; } public float getF() { return f; } public int getI() { return i; } public short getD() { return d; } public String getS() { return s; } @Override public int hashCode() { final int prime = 31; int result = 1; result = prime * result + d; result = prime * result + Float.floatToIntBits(f); result = prime * result + i; result = prime * result + ((s == null) ? 0 : s.hashCode()); return result; } @Override public boolean equals(Object obj) { if (this == obj) { return true; } if (obj == null) { return false; } if (getClass() != obj.getClass()) { return false; } SimpleRecord other = (SimpleRecord) obj; if (d != other.d) { return false; } if (Float.floatToIntBits(f) != Float.floatToIntBits(other.f)) { return false; } if (i != other.i) { return false; } if (s == null) { if (other.s != null) { return false; } } else if (!s.equals(other.s)) { return false; } return true; } @Override public String toString() { return "SimpleRecord [f=" + f + ", i=" + i + ", d=" + d + ", s=" + s + "]"; } } static class SimpleInheretingRecord extends SimpleRecord { SimpleInheretingRecord() { } @CompoundElement(memberName = "ll", dimensions = { 2, 3 }) private long[][] l; public SimpleInheretingRecord(float f, int i, short d, String s, long[][] l) { super(f, i, d, s); this.l = l; } public long[][] getL() { return l; } @Override public int hashCode() { final int prime = 31; int result = super.hashCode(); result = prime * result + Arrays.hashCode(l); return result; } @Override public boolean equals(Object obj) { if (this == obj) { return true; } if (!super.equals(obj)) { return false; } if (getClass() != obj.getClass()) { return false; } SimpleInheretingRecord other = (SimpleInheretingRecord) obj; if (ArrayUtils.isEquals(l, other.l) == false) { return false; } return true; } @Override public String toString() { return "SimpleInheretingRecord [l=" + ArrayUtils.toString(l) + ", getF()=" + getF() + ", getI()=" + getI() + ", getD()=" + getD() + ", getS()=" + getS() + "]"; } } static class SimpleInheretingRecord2 extends SimpleRecord { SimpleInheretingRecord2() { } private long[][] ll; public SimpleInheretingRecord2(float f, int i, short d, String s, long[][] l) { super(f, i, d, s); this.ll = l; } public long[][] getL() { return ll; } @Override public int hashCode() { final int prime = 31; int result = super.hashCode(); result = prime * result + Arrays.hashCode(ll); return result; } @Override public boolean equals(Object obj) { if (this == obj) { return true; } if (!super.equals(obj)) { return false; } if (getClass() != obj.getClass()) { return false; } SimpleInheretingRecord2 other = (SimpleInheretingRecord2) obj; if (ArrayUtils.isEquals(ll, other.ll) == false) { return false; } return true; } @Override public String toString() { return "SimpleInheretingRecord2 [l=" + ArrayUtils.toString(ll) + ", getF()=" + getF() + ", getI()=" + getI() + ", getD()=" + getD() + ", getS()=" + getS() + "]"; } } static class SimpleInheretingRecord3 extends SimpleRecord { SimpleInheretingRecord3() { } private MDLongArray ll; public SimpleInheretingRecord3(float f, int i, short d, String s, long[][] l) { super(f, i, d, s); this.ll = new MDLongArray(l); } public MDLongArray getL() { return ll; } @Override public int hashCode() { final int prime = 31; int result = super.hashCode(); result = prime * result + ll.hashCode(); return result; } @Override public boolean equals(Object obj) { if (this == obj) { return true; } if (!super.equals(obj)) { return false; } if (getClass() != obj.getClass()) { return false; } SimpleInheretingRecord3 other = (SimpleInheretingRecord3) obj; if (ll.equals(other.ll) == false) { return false; } return true; } @Override public String toString() { return "SimpleInheretingRecord3 [l=" + ll + ", getF()=" + getF() + ", getI()=" + getI() + ", getD()=" + getD() + ", getS()=" + getS() + "]"; } } enum FruitEnum { APPLE, ORANGE, CHERRY } enum ColorEnum { RED, GEEN, BLUE, BLACK } enum StateEnum { PREPARING, READY, ONGOING, DONE } static class JavaEnumCompoundType { FruitEnum fruit; JavaEnumCompoundType() { } JavaEnumCompoundType(FruitEnum fruit) { this.fruit = fruit; } @Override public int hashCode() { final int prime = 31; int result = 1; result = prime * result + ((fruit == null) ? 0 : fruit.hashCode()); return result; } @Override public boolean equals(Object obj) { if (this == obj) { return true; } if (obj == null) { return false; } if (getClass() != obj.getClass()) { return false; } JavaEnumCompoundType other = (JavaEnumCompoundType) obj; if (fruit != other.fruit) { return false; } return true; } } static class JavaMultipleEnumsCompoundType { int i; // Will be ignored, just to be sure a non-enum member doesn't hurt. FruitEnum fruit; ColorEnum color; StateEnum state; JavaMultipleEnumsCompoundType() { } JavaMultipleEnumsCompoundType(FruitEnum fruit, ColorEnum color, StateEnum state) { this.fruit = fruit; this.color = color; this.state = state; } @Override public int hashCode() { final int prime = 31; int result = 1; result = prime * result + ((color == null) ? 0 : color.hashCode()); result = prime * result + ((fruit == null) ? 0 : fruit.hashCode()); result = prime * result + ((state == null) ? 0 : state.hashCode()); return result; } @Override public boolean equals(Object obj) { if (this == obj) { return true; } if (obj == null) { return false; } if (getClass() != obj.getClass()) { return false; } JavaMultipleEnumsCompoundType other = (JavaMultipleEnumsCompoundType) obj; if (color != other.color) { return false; } if (fruit != other.fruit) { return false; } if (state != other.state) { return false; } return true; } } @Test public void testInferredCompoundType() { final File file = new File(workingDirectory, "inferredCompoundType.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); final HDF5CompoundType typeW = writer.compound().getInferredType(SimpleRecord.class); writer.compound().write("sc", typeW, new SimpleRecord(2.2f, 17, (short) 10, "test")); long[][] arrayWritten = new long[][] { { 1, 2, 3 }, { 4, 5, 6 } }; final HDF5CompoundType itype = writer.compound().getInferredType(SimpleInheretingRecord.class); writer.compound().write("sci", itype, new SimpleInheretingRecord(-3.1f, 42, (short) 17, "some", arrayWritten)); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().configureForReading(file).reader(); final HDF5CompoundType typeR = reader.compound().getInferredType(SimpleRecord.class); final SimpleRecord recordRead = reader.compound().read("sc", typeR); final HDF5CompoundType inheritedTypeR = reader.compound().getInferredType(SimpleInheretingRecord.class); final SimpleInheretingRecord recordInheritedRead = reader.compound().read("sci", inheritedTypeR); final HDF5CompoundMemberInformation[] info = reader.compound().getMemberInfo(SimpleRecord.class); assertEquals("d", info[2].getName()); assertEquals(HDF5DataTypeVariant.TIME_DURATION_SECONDS, info[2].getType() .tryGetTypeVariant()); reader.close(); assertEquals(2.2f, recordRead.getF()); assertEquals(17, recordRead.getI()); assertEquals("test", recordRead.getS()); assertEquals(-3.1f, recordInheritedRead.getF()); assertEquals(42, recordInheritedRead.getI()); assertEquals("some", recordInheritedRead.getS()); assertTrue(equals(arrayWritten, recordInheritedRead.getL())); } static class CompleteMappedCompound { @CompoundElement float a; @CompoundElement int b; @CompoundElement(variableLength = true) String c; public CompleteMappedCompound() { } public CompleteMappedCompound(float a, int b, String c) { this.a = a; this.b = b; this.c = c; } } @CompoundType(mapAllFields = false) static class IncompleteMappedCompound { @CompoundElement float a; @CompoundElement int b; // unmapped String c; public IncompleteMappedCompound() { } public IncompleteMappedCompound(float a, int b, String c) { this.a = a; this.b = b; this.c = c; } } @Test public void testInferredIncompletelyMappedCompoundType() { final File file = new File(workingDirectory, "inferredIncompletelyMappedCompoundType.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); writer.compound().write("cpd", new CompleteMappedCompound(-1.111f, 11, "Not mapped")); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().configureForReading(file).reader(); final IncompleteMappedCompound cpd = reader.compound().read("cpd", IncompleteMappedCompound.class); final HDF5CompoundType type = reader.compound().getType("incomplete_mapped_compound", IncompleteMappedCompound.class, false, HDF5CompoundMemberMapping.inferMapping(IncompleteMappedCompound.class)); final IncompleteMappedCompound cpd2 = reader.compound().read("cpd", type); reader.close(); assertEquals(-1.111f, cpd.a); assertEquals(11, cpd.b); assertEquals("Not mapped", cpd.c); assertEquals(-1.111f, cpd2.a); assertEquals(11, cpd2.b); assertNull(cpd2.c); } @Test public void testNameChangeInCompoundMapping() { final File file = new File(workingDirectory, "nameChangeInCompoundMapping.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); final String typeName = "a_float"; HDF5CompoundType compoundTypeInt = writer.compound().getInferredType(typeName, RecordC.class); final RecordC recordWritten = new RecordC(33.33333f); writer.compound().write("/testCompound", compoundTypeInt, recordWritten); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().configureForReading(file).performNumericConversions() .reader(); HDF5CompoundType compoundTypeFloat = reader.compound().getNamedType(typeName, RecordD.class); final RecordD recordRead = reader.compound().read("/testCompound", compoundTypeFloat); assertEquals(recordWritten.a, recordRead.b); reader.close(); } @Test public void testOverwriteCompound() { final File file = new File(workingDirectory, "overwriteCompound.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); IHDF5Writer writer = HDF5FactoryProvider.get().open(file); HDF5CompoundType compoundTypeFloat = writer.compound().getInferredType(RecordC.class); final RecordC recordWritten = new RecordC(33.33333f); writer.compound().write("/testCompound", compoundTypeFloat, recordWritten); writer.close(); writer = HDF5FactoryProvider.get().open(file); final RecordE recordWritten2 = new RecordE(-1); HDF5CompoundType compoundTypeInt = writer.compound().getInferredType(RecordE.class); writer.compound().write("/testCompound", compoundTypeInt, recordWritten2); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().configureForReading(file).performNumericConversions() .reader(); HDF5CompoundType compoundTypeInt2 = reader.compound().getNamedType(RecordE.class); assertEquals(1, compoundTypeInt2.getCompoundMemberInformation().length); assertEquals(HDF5DataClass.INTEGER, compoundTypeInt2.getCompoundMemberInformation()[0] .getType().getDataClass()); assertEquals(-1, reader.compound().read("/testCompound", compoundTypeInt2).a); reader.close(); } @Test public void testOverwriteCompoundKeepType() { final File file = new File(workingDirectory, "overwriteCompoundKeepType.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); IHDF5Writer writer = HDF5FactoryProvider.get().open(file); HDF5CompoundType compoundTypeFloat = writer.compound().getInferredType(RecordC.class); final RecordC recordWritten = new RecordC(33.33333f); writer.compound().write("/testCompound", compoundTypeFloat, recordWritten); writer.close(); writer = HDF5FactoryProvider.get().configure(file).keepDataSetsIfTheyExist().writer(); final RecordE recordWritten2 = new RecordE(-1); HDF5CompoundType compoundTypeInt = writer.compound().getInferredType(RecordE.class); writer.compound().write("/testCompound", compoundTypeInt, recordWritten2); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().configureForReading(file).performNumericConversions() .reader(); HDF5CompoundType compoundTypeInt2 = reader.compound().getDataSetType("/testCompound", RecordE.class); assertEquals(1, compoundTypeInt2.getCompoundMemberInformation().length); assertEquals(HDF5DataClass.FLOAT, compoundTypeInt2.getCompoundMemberInformation()[0] .getType().getDataClass()); assertEquals(-1, reader.compound().read("/testCompound", compoundTypeInt2).a); reader.close(); } static class SimpleRecordWithEnum { HDF5EnumerationValue e; SimpleRecordWithEnum() { } public SimpleRecordWithEnum(HDF5EnumerationValue e) { this.e = e; } } @Test public void testInferredCompoundTypedWithEnum() { final File file = new File(workingDirectory, "inferredCompoundTypeWithEnum.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final String[] alternatives = new String[257]; for (int i = 0; i < alternatives.length; ++i) { alternatives[i] = Integer.toString(i); } final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); final HDF5EnumerationType enumType = writer.enumeration().getType("type", alternatives); final SimpleRecordWithEnum r = new SimpleRecordWithEnum(new HDF5EnumerationValue(enumType, "3")); final HDF5CompoundType typeW = writer.compound().getInferredType(r); writer.compound().write("sce", typeW, r); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().configureForReading(file).reader(); final HDF5CompoundType typeR = reader.compound().getNamedType(SimpleRecordWithEnum.class); final SimpleRecordWithEnum recordRead = reader.compound().read("sce", typeR); assertEquals("3", recordRead.e.getValue()); reader.close(); } static class SimpleRecordWithEnumArray { @CompoundElement(dimensions = 5) HDF5EnumerationValueArray e; SimpleRecordWithEnumArray() { } public SimpleRecordWithEnumArray(HDF5EnumerationValueArray e) { this.e = e; } } @Test public void testInferredCompoundTypeWithEnumArray() { final File file = new File(workingDirectory, "inferredCompoundTypeWithEnumArray.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); final String[] alternatives = new String[512]; for (int i = 0; i < alternatives.length; ++i) { alternatives[i] = Integer.toString(i); } final HDF5EnumerationType enumType = writer.enumeration().getType("type", alternatives); final SimpleRecordWithEnumArray r = new SimpleRecordWithEnumArray(new HDF5EnumerationValueArray(enumType, new String[] { "3", "2", "1", "511", "3" })); final HDF5CompoundType cType = writer.compound().getInferredType(r); writer.compound().write("sce", cType, r); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().configureForReading(file).reader(); final HDF5CompoundType typeR = reader.compound().getNamedType(SimpleRecordWithEnumArray.class); final SimpleRecordWithEnumArray recordRead = reader.compound().read("sce", typeR); reader.close(); assertEquals(5, recordRead.e.getLength()); assertEquals("3", recordRead.e.getValue(0)); assertEquals("2", recordRead.e.getValue(1)); assertEquals("1", recordRead.e.getValue(2)); assertEquals("511", recordRead.e.getValue(3)); assertEquals("3", recordRead.e.getValue(4)); } static class RecordWithMatrix { String s; MDFloatArray fm; public RecordWithMatrix() { } RecordWithMatrix(String s, MDFloatArray fm) { this.s = s; this.fm = fm; } static HDF5CompoundType getHDF5Type(IHDF5Reader reader) { return reader.compound().getType(null, RecordWithMatrix.class, getMapping()); } private static HDF5CompoundMemberMapping[] getMapping() { return new HDF5CompoundMemberMapping[] { mapping("s").length(5), mapping("fm").dimensions(2, 2) }; } } @Test public void testMDArrayCompound() { final File file = new File(workingDirectory, "mdArrayCompound.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); HDF5CompoundType compoundTypeMatrix = RecordWithMatrix.getHDF5Type(writer); final RecordWithMatrix recordWritten = new RecordWithMatrix("tag", new MDFloatArray(new float[][] { { 1, 2 }, { 3, 4 } })); writer.compound().write("/testCompound", compoundTypeMatrix, recordWritten); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); HDF5CompoundType compoundTypeMatrixRead = RecordWithMatrix.getHDF5Type(reader); final RecordWithMatrix recordRead = reader.compound().read("/testCompound", compoundTypeMatrixRead); assertEquals(recordWritten.s, recordRead.s); assertEquals(recordWritten.fm, recordRead.fm); } @Test public void testMDArrayCompoundArray() { final File file = new File(workingDirectory, "mdArrayCompoundArray.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); HDF5CompoundType compoundTypeMatrix = RecordWithMatrix.getHDF5Type(writer); final RecordWithMatrix[] recordArrayWritten = new RecordWithMatrix[] { new RecordWithMatrix("tag1", new MDFloatArray(new float[][] { { 1, 2 }, { 3, 4 } })), new RecordWithMatrix("tag2", new MDFloatArray(new float[][] { { 10, 20 }, { 30, 40 } })), new RecordWithMatrix("tag3", new MDFloatArray(new float[][] { { 100, 200 }, { 300, 400 } })), }; writer.compound().writeArray("/testCompoundArray", compoundTypeMatrix, recordArrayWritten); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); HDF5CompoundType compoundTypeMatrixRead = RecordWithMatrix.getHDF5Type(reader); final RecordWithMatrix[] recordReadArray = reader.compound().readArray("/testCompoundArray", compoundTypeMatrixRead); assertEquals(3, recordReadArray.length); for (int i = 0; i < recordArrayWritten.length; ++i) { assertEquals("" + i, recordArrayWritten[i].s, recordReadArray[i].s); assertEquals("" + i, recordArrayWritten[i].fm, recordReadArray[i].fm); } } @Test public void testSetDataSetSize() { final File file = new File(workingDirectory, "testSetDataSetSize.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); writer.int8().createArray("ds", 0, 10); writer.object().setDataSetSize("ds", 20); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); final HDF5DataSetInformation dsInfo = reader.getDataSetInformation("ds"); assertEquals(20, dsInfo.getSize()); assertTrue(dsInfo.isSigned()); int idx = 0; for (byte b : reader.int8().readArray("ds")) { assertEquals("Position " + (idx++), 0, b); } reader.close(); } @Test public void testNumericConversion() { final File file = new File(workingDirectory, "numericConversions.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); writer.float32().write("pi", 3.14159f); writer.float32().write("INFINITY", Float.POSITIVE_INFINITY); writer.float64().write("DINFINITY", Double.NEGATIVE_INFINITY); writer.float64().write("verySmallFloat", 1e-100); writer.float64().write("veryLargeFloat", 1e+100); writer.float64().setAttr("pi", "eps", 1e-5); writer.int64().write("smallInteger", 17L); writer.int64().write("largeInteger", Long.MAX_VALUE); writer.close(); final IHDF5ReaderConfigurator config = HDF5FactoryProvider.get().configureForReading(file).performNumericConversions(); // If this platform doesn't support numeric conversions, the test would fail. if (config.platformSupportsNumericConversions() == false) { return; } final IHDF5Reader reader = config.reader(); assertEquals(3.14159, reader.float64().read("pi"), 1e-5); assertEquals(3, reader.int32().read("pi")); assertEquals(1e-5f, reader.float32().getAttr("pi", "eps"), 1e-9); assertEquals(17, reader.int8().read("smallInteger")); assertEquals(0.0f, reader.float32().read("verySmallFloat")); assertEquals(Double.POSITIVE_INFINITY, reader.float64().read("INFINITY")); try { reader.int32().read("largeInteger"); fail("Failed to detect overflow"); } catch (HDF5DatatypeInterfaceException ex) { assertEquals(HDF5Constants.H5E_CANTCONVERT, ex.getMinorErrorNumber()); } try { reader.float32().read("veryLargeFloat"); fail("Failed to detect overflow"); } catch (HDF5DatatypeInterfaceException ex) { assertEquals(HDF5Constants.H5E_CANTCONVERT, ex.getMinorErrorNumber()); } try { reader.int64().read("veryLargeFloat"); fail("Failed to detect overflow"); } catch (HDF5DatatypeInterfaceException ex) { assertEquals(HDF5Constants.H5E_CANTCONVERT, ex.getMinorErrorNumber()); } // In HDF5 up to 1.8.10, numeric conversions on sparc don't detect overflows // for INFINITY and DINFINITY values. if (OSUtilities.getCPUArchitecture().startsWith("sparc")) { return; } try { reader.float32().read("DINFINITY"); fail("Failed to detect overflow"); } catch (HDF5DatatypeInterfaceException ex) { assertEquals(HDF5Constants.H5E_CANTCONVERT, ex.getMinorErrorNumber()); } try { reader.int64().read("INFINITY"); fail("Failed to detect overflow"); } catch (HDF5DatatypeInterfaceException ex) { assertEquals(HDF5Constants.H5E_CANTCONVERT, ex.getMinorErrorNumber()); } reader.close(); } @Test public void testNumericConversionWithNumericConversionsSwitchedOff() { final File file = new File(workingDirectory, "numericConversionWithNumericConversionsSwitchedOff.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); writer.float32().write("pi", 3.14159f); writer.float32().write("one", 1.0f); writer.float32().write("INFINITY", Float.POSITIVE_INFINITY); writer.float64().write("DINFINITY", Double.NEGATIVE_INFINITY); writer.float64().write("verySmallFloat", 1e-100); writer.float64().write("veryLargeFloat", 1e+100); writer.float64().setAttr("pi", "eps", 1e-5); writer.int64().write("smallInteger", 17L); writer.int64().write("largeInteger", Long.MAX_VALUE); writer.close(); final IHDF5Reader reader = HDF5Factory.openForReading(file); // <<< Don't try this at home - it is not clean: START assertEquals(3.14159, reader.float64().read("pi"), 1e-5); // SPARC CPUs need numeric conversion to be switched on for this to work. if (OSUtilities.getCPUArchitecture().startsWith("sparc") == false) { assertEquals(1, reader.int32().read("one")); assertEquals(Double.POSITIVE_INFINITY, reader.float64().read("INFINITY")); } assertEquals(1e-5f, reader.float32().getAttr("pi", "eps"), 1e-9); assertEquals(17, reader.int8().read("smallInteger")); assertEquals(0.0f, reader.float32().read("verySmallFloat")); // Don't try this at home - it is not clean: END >>> try { reader.int32().read("largeInteger"); fail("Failed to detect overflow"); } catch (HDF5DatatypeInterfaceException ex) { assertEquals(HDF5Constants.H5E_CANTCONVERT, ex.getMinorErrorNumber()); } try { reader.float32().read("veryLargeFloat"); fail("Failed to detect overflow"); } catch (HDF5DatatypeInterfaceException ex) { assertEquals(HDF5Constants.H5E_CANTCONVERT, ex.getMinorErrorNumber()); } try { reader.int64().read("veryLargeFloat"); fail("Failed to detect overflow"); } catch (HDF5DatatypeInterfaceException ex) { assertEquals(HDF5Constants.H5E_CANTCONVERT, ex.getMinorErrorNumber()); } // In HDF5 up to 1.8.10, numeric conversions on sparc don't detect overflows // for INFINITY and DINFINITY values. if (OSUtilities.getCPUArchitecture().startsWith("sparc")) { return; } try { reader.float32().read("DINFINITY"); fail("Failed to detect overflow"); } catch (HDF5DatatypeInterfaceException ex) { assertEquals(HDF5Constants.H5E_CANTCONVERT, ex.getMinorErrorNumber()); } try { reader.int64().read("INFINITY"); fail("Failed to detect overflow"); } catch (HDF5DatatypeInterfaceException ex) { assertEquals(HDF5Constants.H5E_CANTCONVERT, ex.getMinorErrorNumber()); } reader.close(); } @Test public void testObjectReferenceOverwriteWithKeep() { final File file = new File(workingDirectory, "testObjectReferenceOverwriteWithKeep.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().configure(file).keepDataSetsIfTheyExist().writer(); writer.string().write("a", "TestA"); writer.string().write("aa", "TestAA"); writer.reference().write("b", "aa"); writer.delete("a"); // If keepDataSetsIfTheyExist() was not given above, the dataset would be deleted, the // header of the new dataset would be written at the old position of "a" and the object // reference "b" would be dangling. writer.string().write("aa", "TestX"); assertEquals("/aa", writer.reference().read("/b")); writer.object().move("/aa", "/C"); assertEquals("/C", writer.reference().read("/b")); writer.close(); } @Test public void testObjectReferenceOverwriteWithKeepOverridden() { final File file = new File(workingDirectory, "testObjectReferenceOverwriteWithKeepOverridden.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().configure(file).keepDataSetsIfTheyExist().writer(); writer.string().write("a", "TestA"); writer.string().write("aa", "TestAA"); writer.reference().write("b", "aa"); writer.delete("a"); // As we override keepDataSetsIfTheyExist() by // HDF5GenericStorageFeatures.GENERIC_COMPACT_DELETE, // the dataset will be deleted and the header of the new dataset will be written at the old // position of "a", thus the object // reference "b" will be dangling. writer.string().write("aa", "TestX", HDF5GenericStorageFeatures.GENERIC_COMPACT_DELETE); // Check for dangling reference. assertEquals("", writer.reference().read("/b")); writer.close(); } @Test public void testObjectReference() { final File file = new File(workingDirectory, "testObjectReference.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); writer.string().write("a", "TestA"); writer.reference().write("b", "a"); assertEquals("/a", writer.reference().read("/b")); writer.object().move("/a", "/C"); assertEquals("/C", writer.reference().read("/b")); assertEquals("TestA", writer.readString(writer.reference().read("/b", false))); writer.close(); } @Test public void testObjectReferenceArray() { final File file = new File(workingDirectory, "testObjectReferenceArray.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); writer.string().write("a1", "TestA"); writer.string().write("a2", "TestB"); writer.string().write("a3", "TestC"); writer.reference().writeArray("b", new String[] { "a1", "a2", "a3" }); assertTrue(ArrayUtils.isEquals(new String[] { "/a1", "/a2", "/a3" }, writer.reference().readArray("/b"))); writer.object().move("/a1", "/C"); assertTrue(ArrayUtils.isEquals(new String[] { "/C", "/a2", "/a3" }, writer.reference().readArray("/b"))); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); assertTrue(ArrayUtils.isEquals(new String[] { "/C", "/a2", "/a3" }, reader.reference().readArray("/b"))); final String[] refs = reader.reference().readArray("/b", false); assertEquals("TestA", reader.string().read(refs[0])); assertEquals("/C", reader.reference().resolvePath(refs[0])); assertEquals("TestB", reader.string().read(refs[1])); assertEquals("/a2", reader.reference().resolvePath(refs[1])); assertEquals("TestC", reader.string().read(refs[2])); assertEquals("/a3", reader.reference().resolvePath(refs[2])); reader.close(); } @Test public void testObjectReferenceArrayBlockWise() { final File file = new File(workingDirectory, "testObjectReferenceArrayBlockWise.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); final String[] completeArray = new String[16]; for (int i = 0; i < completeArray.length; ++i) { writer.string().write("a" + (i + 1), "TestA" + i); completeArray[i] = "/a" + (i + 1); } writer.reference().createArray("b", completeArray.length, completeArray.length / 4, HDF5IntStorageFeatures.INT_NO_COMPRESSION); final String[][] chunk = new String[4][4]; System.arraycopy(completeArray, 0, chunk[0], 0, 4); System.arraycopy(completeArray, 4, chunk[1], 0, 4); System.arraycopy(completeArray, 8, chunk[2], 0, 4); System.arraycopy(completeArray, 12, chunk[3], 0, 4); writer.reference().writeArrayBlock("b", chunk[0], 0); writer.reference().writeArrayBlock("b", chunk[2], 2); writer.reference().writeArrayBlock("b", chunk[1], 1); writer.reference().writeArrayBlock("b", chunk[3], 3); assertTrue(ArrayUtils.isEquals(completeArray, writer.reference().readArray("/b"))); writer.object().move("/a1", "/C"); completeArray[0] = "/C"; chunk[0][0] = "/C"; assertTrue(ArrayUtils.isEquals(completeArray, writer.reference().readArray("/b"))); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); int idx = 0; for (HDF5DataBlock block : reader.reference().getArrayNaturalBlocks("b")) { assertTrue("" + idx, ArrayUtils.isEquals(chunk[idx++], block.getData())); } reader.close(); } @Test public void testObjectReferenceMDArray() { final File file = new File(workingDirectory, "testObjectReferenceMDArray.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); writer.string().write("a1", "TestA"); writer.string().write("a2", "TestA"); writer.string().write("a3", "TestA"); writer.string().write("a4", "TestA"); writer.reference().writeMDArray("b", new MDArray(new String[] { "a1", "a2", "a3", "a4" }, new int[] { 2, 2 })); assertEquals(new MDArray(new String[] { "/a1", "/a2", "/a3", "/a4" }, new int[] { 2, 2 }), writer.reference().readMDArray("/b")); writer.object().move("/a1", "/C"); assertEquals(new MDArray(new String[] { "/C", "/a2", "/a3", "/a4" }, new int[] { 2, 2 }), writer.reference().readMDArray("/b")); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); assertEquals(new MDArray(new String[] { "/C", "/a2", "/a3", "/a4" }, new int[] { 2, 2 }), reader.reference().readMDArray("/b")); reader.close(); } @Test public void testObjectReferenceMDArrayBlockWise() { final File file = new File(workingDirectory, "testObjectReferenceMDArrayBlockWise.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); final String[] completeArray = new String[16]; for (int i = 0; i < completeArray.length; ++i) { writer.string().write("a" + (i + 1), "TestA" + i); completeArray[i] = "/a" + (i + 1); } writer.reference().createMDArray("b", new long[] { 4, 4 }, new int[] { 1, 4 }, HDF5IntStorageFeatures.INT_NO_COMPRESSION); final String[][] chunk = new String[4][4]; System.arraycopy(completeArray, 0, chunk[0], 0, 4); System.arraycopy(completeArray, 4, chunk[1], 0, 4); System.arraycopy(completeArray, 8, chunk[2], 0, 4); System.arraycopy(completeArray, 12, chunk[3], 0, 4); writer.reference().writeMDArrayBlock("b", new MDArray(chunk[0], new int[] { 1, 4 }), new long[] { 0, 0 }); writer.reference().writeMDArrayBlock("b", new MDArray(chunk[2], new int[] { 1, 4 }), new long[] { 2, 0 }); writer.reference().writeMDArrayBlock("b", new MDArray(chunk[1], new int[] { 1, 4 }), new long[] { 1, 0 }); writer.reference().writeMDArrayBlock("b", new MDArray(chunk[3], new int[] { 1, 4 }), new long[] { 3, 0 }); assertEquals(new MDArray(completeArray, new int[] { 4, 4 }), writer.reference().readMDArray("/b")); writer.object().move("/a1", "/C"); completeArray[0] = "/C"; chunk[0][0] = "/C"; assertEquals(new MDArray(completeArray, new int[] { 4, 4 }), writer.reference().readMDArray("/b")); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); int idx = 0; for (HDF5MDDataBlock> block : reader.reference().getMDArrayNaturalBlocks( "b")) { assertEquals("" + idx, new MDArray(chunk[idx++], new int[] { 1, 4 }), block.getData()); } reader.close(); } @Test public void testObjectReferenceAttribute() { final File file = new File(workingDirectory, "testObjectReferenceAttribute.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); writer.string().write("a", "TestA"); writer.string().write("b", "TestB"); writer.reference().setAttr("a", "partner", "b"); assertEquals("/b", writer.reference().getAttr("/a", "partner")); writer.object().move("/b", "/C"); assertEquals("/C", writer.reference().getAttr("/a", "partner")); writer.close(); } @Test public void testObjectReferenceArrayAttribute() { final File file = new File(workingDirectory, "testObjectReferenceArrayAttribute.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); writer.string().write("a1", "TestA1"); writer.string().write("a2", "TestA2"); writer.string().write("a3", "TestA3"); writer.string().write("b", "TestB"); writer.reference().setArrayAttr("b", "partner", new String[] { "a1", "a2", "a3" }); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); final String[] referencesRead = reader.reference().getArrayAttr("b", "partner"); assertEquals(3, referencesRead.length); assertEquals("/a1", referencesRead[0]); assertEquals("/a2", referencesRead[1]); assertEquals("/a3", referencesRead[2]); reader.close(); } @Test public void testObjectReferenceMDArrayAttribute() { final File file = new File(workingDirectory, "testObjectReferenceMDArrayAttribute.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(file); writer.string().write("a1", "TestA1"); writer.string().write("a2", "TestA2"); writer.string().write("a3", "TestA3"); writer.string().write("a4", "TestA4"); writer.string().write("b", "TestB"); writer.reference().setMDArrayAttr("b", "partner", new MDArray(new String[] { "a1", "a2", "a3", "a4" }, new int[] { 2, 2 })); writer.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(file); final MDArray referencesRead = reader.reference().getMDArrayAttr("b", "partner"); assertTrue(ArrayUtils.isEquals(new int[] { 2, 2 }, referencesRead.dimensions())); assertEquals("/a1", referencesRead.get(0, 0)); assertEquals("/a2", referencesRead.get(0, 1)); assertEquals("/a3", referencesRead.get(1, 0)); assertEquals("/a4", referencesRead.get(1, 1)); reader.close(); } @Test public void testHDF5FileDetection() throws IOException { final File hdf5File = new File(workingDirectory, "testHDF5FileDetection.h5"); hdf5File.delete(); assertFalse(hdf5File.exists()); hdf5File.deleteOnExit(); final IHDF5Writer writer = HDF5Factory.open(hdf5File); writer.string().write("a", "someString"); writer.close(); assertTrue(HDF5Factory.isHDF5File(hdf5File)); final File noHdf5File = new File(workingDirectory, "testHDF5FileDetection.h5"); noHdf5File.delete(); assertFalse(noHdf5File.exists()); noHdf5File.deleteOnExit(); FileUtils.writeByteArrayToFile(noHdf5File, new byte[] { 1, 2, 3, 4 }); assertFalse(HDF5Factory.isHDF5File(noHdf5File)); } @Test public void testHDFJavaLowLevel() { final File file = new File(workingDirectory, "testHDFJavaLowLevel.h5"); file.delete(); assertFalse(file.exists()); file.deleteOnExit(); int fileId = ch.systemsx.cisd.hdf5.hdf5lib.H5F.H5Fcreate(file.getAbsolutePath(), ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5F_ACC_TRUNC, ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT, ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT); int groupId = ch.systemsx.cisd.hdf5.hdf5lib.H5GLO.H5Gcreate(fileId, "constants", ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT, ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT, ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT); int spcId = ch.systemsx.cisd.hdf5.hdf5lib.H5S .H5Screate(ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_SCALAR); int dsId = ch.systemsx.cisd.hdf5.hdf5lib.H5D.H5Dcreate(groupId, "pi", ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_IEEE_F32LE, spcId, ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT, ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT, ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT); ch.systemsx.cisd.hdf5.hdf5lib.H5D.H5Dwrite(dsId, ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_FLOAT, ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_SCALAR, ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_SCALAR, ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT, new float[] { 3.14159f }); ch.systemsx.cisd.hdf5.hdf5lib.H5D.H5Dclose(dsId); ch.systemsx.cisd.hdf5.hdf5lib.H5S.H5Sclose(spcId); ch.systemsx.cisd.hdf5.hdf5lib.H5GLO.H5Gclose(groupId); ch.systemsx.cisd.hdf5.hdf5lib.H5F.H5Fclose(fileId); fileId = ch.systemsx.cisd.hdf5.hdf5lib.H5F.H5Fopen(file.getAbsolutePath(), ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5F_ACC_RDONLY, ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT); spcId = ch.systemsx.cisd.hdf5.hdf5lib.H5S .H5Screate(ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_SCALAR); dsId = ch.systemsx.cisd.hdf5.hdf5lib.H5D.H5Dopen(fileId, "/constants/pi", ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT); final float[] data = new float[1]; ch.systemsx.cisd.hdf5.hdf5lib.H5D.H5Dread(dsId, ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_NATIVE_FLOAT, ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_ALL, ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_ALL, ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT, data); assertEquals(3.14159f, data[0], 0f); ch.systemsx.cisd.hdf5.hdf5lib.H5D.H5Dclose(dsId); ch.systemsx.cisd.hdf5.hdf5lib.H5S.H5Sclose(spcId); ch.systemsx.cisd.hdf5.hdf5lib.H5F.H5Fclose(fileId); } }libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/HDF5SpeedTest.java000066400000000000000000000071471256564762100274050ustar00rootroot00000000000000/* * Copyright 2008 ETH Zuerich, CISD * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.io.File; import java.io.FileInputStream; import java.io.FileOutputStream; import java.io.ObjectInputStream; import java.io.ObjectOutputStream; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import ch.systemsx.cisd.hdf5.IHDF5WriterConfigurator.SyncMode; /** * @author Bernd Rinn */ public class HDF5SpeedTest { public static void main(String[] args) { final float[] arr = new float[1000000]; for (int i = 0; i < arr.length; ++i) { arr[i] = (float) Math.random(); } long start = System.currentTimeMillis(); final File f1 = new File("speedtest.jo"); try { for (int i = 0; i < 20; ++i) { f1.delete(); final ObjectOutputStream s = new ObjectOutputStream(new FileOutputStream(f1)); s.writeObject(arr); s.close(); } } catch (Exception ex) { ex.printStackTrace(); } final float twj = (System.currentTimeMillis() - start) / 1000.f; System.out.printf("Write Java Serialization: %.2f s\n", twj); final File f2 = new File("speedtest.h5"); f2.delete(); start = System.currentTimeMillis(); try { for (int i = 0; i < 20; ++i) { f2.delete(); final IHDF5Writer writer = HDF5FactoryProvider.get().configure(f2).syncMode(SyncMode.NO_SYNC).writer(); writer.float32().writeArray("/f", arr); writer.close(); } } catch (HDF5LibraryException ex) { System.err.println(ex.getHDF5ErrorStackAsString()); } final float twh = (System.currentTimeMillis() - start) / 1000.f; System.out.printf("Write HDF5: %.2f s (%.2f %%)\n", twh, 100.0 * twh / twj); start = System.currentTimeMillis(); try { for (int i = 0; i < 20; ++i) { final ObjectInputStream s = new ObjectInputStream(new FileInputStream(f1)); s.readObject(); s.close(); } } catch (Exception ex) { ex.printStackTrace(); } final float trj = (System.currentTimeMillis() - start) / 1000.f; System.out.printf("Read Java Serialization: %.2f s\n", trj); start = System.currentTimeMillis(); try { for (int i = 0; i < 20; ++i) { final IHDF5Reader reader = HDF5FactoryProvider.get().configureForReading(f2).reader(); reader.float32().readArray("/f"); reader.close(); } } catch (HDF5LibraryException ex) { System.err.println(ex.getHDF5ErrorStackAsString()); } final float trh = (System.currentTimeMillis() - start) / 1000.f; System.out.printf("Read HDF5: %.2f s (%.2f %%)\n", trh, 100.0 * trh / trj); } } libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/HDF5TimeDurationReaderTest.java000066400000000000000000000034611256564762100320670ustar00rootroot00000000000000/* * Copyright 2013 ETH Zuerich, CISD * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.util.Arrays; import org.testng.annotations.Test; import ch.systemsx.cisd.base.mdarray.MDLongArray; import static org.testng.AssertJUnit.*; /** * Test cases for {@link HDF5TimeDurationReader}. * * @author Bernd Rinn */ public class HDF5TimeDurationReaderTest { @Test public void testConvertUnit() { MDLongArray array = new MDLongArray(new int[] { 5, 5, 5 }); int[] ofs = new int[] { 1, 2, 1 }; int[] dims = new int[] { 4, 3, 4 }; Arrays.fill(array.getAsFlatArray(), 1); HDF5TimeDurationReader.convertUnit(array, HDF5TimeUnit.MINUTES, HDF5TimeUnit.SECONDS, dims, ofs); for (int x = 0; x < 5; ++x) { for (int y = 0; y < 5; ++y) { for (int z = 0; z < 5; ++z) { final boolean converted = (x >= ofs[0] && x < ofs[0] + dims[0] && y >= ofs[1] && y < ofs[1] + dims[1] && z >= ofs[2] && z < ofs[2] + dims[2]); assertEquals(converted ? 60 : 1, array.get(x, y, z)); } } } } } libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/HDF5TimeUnitTest.java000066400000000000000000000041631256564762100300760ustar00rootroot00000000000000/* * Copyright 2009 ETH Zuerich, CISD * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import org.testng.annotations.Test; import static org.testng.AssertJUnit.*; /** * Test cases for {@link HDF5TimeUnit}. * * @author Bernd Rinn */ public class HDF5TimeUnitTest { @Test public void testConversion() { assertEquals(3, HDF5TimeUnit.HOURS.convert(10000L, HDF5TimeUnit.SECONDS)); assertEquals(10000L, HDF5TimeUnit.MILLISECONDS.convert(10L, HDF5TimeUnit.SECONDS)); assertEquals(120L, HDF5TimeUnit.MINUTES.convert(2L, HDF5TimeUnit.HOURS)); assertEquals(2L * 3600 * 1000 * 1000, HDF5TimeUnit.MICROSECONDS.convert(2L, HDF5TimeUnit.HOURS)); // Overflow assertEquals(Long.MIN_VALUE, HDF5TimeUnit.MICROSECONDS.convert(Long.MIN_VALUE / 24, HDF5TimeUnit.DAYS)); } @Test public void testTypeVariant() { assertEquals(HDF5DataTypeVariant.TIME_DURATION_DAYS, HDF5TimeUnit.DAYS.getTypeVariant()); assertEquals(HDF5DataTypeVariant.TIME_DURATION_HOURS, HDF5TimeUnit.HOURS.getTypeVariant()); assertEquals(HDF5DataTypeVariant.TIME_DURATION_SECONDS, HDF5TimeUnit.SECONDS .getTypeVariant()); assertEquals(HDF5DataTypeVariant.TIME_DURATION_MINUTES, HDF5TimeUnit.MINUTES .getTypeVariant()); assertEquals(HDF5DataTypeVariant.TIME_DURATION_MILLISECONDS, HDF5TimeUnit.MILLISECONDS .getTypeVariant()); assertEquals(HDF5DataTypeVariant.TIME_DURATION_MICROSECONDS, HDF5TimeUnit.MICROSECONDS .getTypeVariant()); } } libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/HDF5UtilsTest.java000066400000000000000000000035731256564762100274440ustar00rootroot00000000000000/* * Copyright 2012 ETH Zuerich, CISD * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import org.testng.annotations.Test; import static org.testng.AssertJUnit.*; /** * @author Bernd Rinn */ public class HDF5UtilsTest { /** The attribute to signal that this is a variant of the data type. */ static final String TYPE_VARIANT_ATTRIBUTE_OLD = "__TYPE_VARIANT__"; /** * Returns the type variant attribute for the given attributeName. */ static String createTypeVariantAttributeNameOld(String attributeName) { return TYPE_VARIANT_ATTRIBUTE_OLD + attributeName + "__"; } @Test public void testAttributeTypeVariantAttributeName() { assertEquals("__TYPE_VARIANT__abc__", HDF5Utils.createAttributeTypeVariantAttributeName("abc", "")); assertEquals( "__TYPE_VARIANT____abc____", HDF5Utils.createAttributeTypeVariantAttributeName( HDF5Utils.toHouseKeepingName("abc", ""), "")); assertEquals("TYPE_VARIANT__abcXX", HDF5Utils.createAttributeTypeVariantAttributeName("abc", "XX")); assertEquals( "TYPE_VARIANT__abcXXXX", HDF5Utils.createAttributeTypeVariantAttributeName( HDF5Utils.toHouseKeepingName("abc", "XX"), "XX")); } } libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/HDF5WriteTest.java000066400000000000000000000053061256564762100274320ustar00rootroot00000000000000/* * Copyright 2007 ETH Zuerich, CISD. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import java.io.File; import java.util.BitSet; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; /** * @author Bernd Rinn */ public class HDF5WriteTest { public static void main(String[] args) { final BitSet bs = new BitSet(); bs.set(127); bs.set(64); bs.set(128); // bs.set(191); try { IHDF5Writer writer = HDF5FactoryProvider.get().configure(new File("test.h5")).overwrite().writer(); // writer.write("/Group1/SubGroup1/MyDataSet", new float[] { 1.0f, 2.0f, 3.0f, 4.0f }); // writer.link("/Group1/SubGroup1/MyDataSet", "/Group1/MyDataSet"); // writer.write("/Group1/MyDataSet", new float[] { 4.0f, 3.0f, 2.0f, 1.0f }); // writer.write("/Group1/MyDataSet", new double[] { 4.0, 3.0, 2.0, 1.0 }); writer.writeBitField("/Group1/MyBitSet", bs); writer.float32().writeMatrix("/Group1/MyDataSet", new float[][] { { 4, 3, 2, 1, 0, -1 }, { 0, 1, 2, 3, 4, 5 } }); writer.int64().writeArray("/Group1/MyDataSet2", new long[] { 4, 3, 2, 1 }); writer.int64().writeArray("/Group1/MyDataSet3", new long[] { 1 }); // writer.write("/Group1/MyDataSet", new int[] { 4, 3, 2, 1 }); writer.object().createHardLink("/Group1/MyDataSet", "/Group1/SubGroup1/MyDataSet"); writer.string().write("/Group1/MyString", "Und schon wieder die Geschichte vom Pferd!"); writer.string().setAttr("/Group1/MyDataSet", "foo", "Die Geschichte vom Pferd"); // writer.addAttribute("/Group1/SubGroup1/MyDataSet", "foo", "No story"); writer.float64().setAttr("/", "version", 17.0); writer.bool().setAttr("/Group1", "active", true); writer.int8().writeArray("/empty", new byte[0]); writer.close(); } catch (HDF5LibraryException ex) { System.err.println(ex.getHDF5ErrorStackAsString()); ex.printStackTrace(); } } } libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/MatrixUtilsTest.java000066400000000000000000000043061256564762100302150ustar00rootroot00000000000000/* * Copyright 2013 ETH Zuerich, CISD * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static org.testng.AssertJUnit.assertFalse; import static org.testng.AssertJUnit.assertTrue; import java.util.Arrays; import org.testng.annotations.Test; /** * Tests for {@link MatrixUtils}. * * @author Bernd Rinn */ public class MatrixUtilsTest { @Test public void testIncrementIdx() { int[] blockDims = new int[] { 2, 2, 2 }; int[] offset = new int[] { 1, 2, 3 }; int[] idx = offset.clone(); assertTrue(MatrixUtils.incrementIdx(idx, blockDims, offset)); assertTrue(Arrays.toString(idx), Arrays.equals(new int[] { 1, 2, 4 }, idx)); assertTrue(MatrixUtils.incrementIdx(idx, blockDims, offset)); assertTrue(Arrays.toString(idx), Arrays.equals(new int[] { 1, 3, 3 }, idx)); assertTrue(MatrixUtils.incrementIdx(idx, blockDims, offset)); assertTrue(Arrays.toString(idx), Arrays.equals(new int[] { 1, 3, 4 }, idx)); assertTrue(MatrixUtils.incrementIdx(idx, blockDims, offset)); assertTrue(Arrays.toString(idx), Arrays.equals(new int[] { 2, 2, 3 }, idx)); assertTrue(MatrixUtils.incrementIdx(idx, blockDims, offset)); assertTrue(Arrays.toString(idx), Arrays.equals(new int[] { 2, 2, 4 }, idx)); assertTrue(MatrixUtils.incrementIdx(idx, blockDims, offset)); assertTrue(Arrays.toString(idx), Arrays.equals(new int[] { 2, 3, 3 }, idx)); assertTrue(MatrixUtils.incrementIdx(idx, blockDims, offset)); assertTrue(Arrays.toString(idx), Arrays.equals(new int[] { 2, 3, 4 }, idx)); assertFalse(MatrixUtils.incrementIdx(idx, blockDims, offset)); } } libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/TestLowLevelHDF5.java000066400000000000000000000041421256564762100300660ustar00rootroot00000000000000/* * Copyright 2008 ETH Zuerich, CISD * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.hdf5lib.H5F.*; import static ch.systemsx.cisd.hdf5.hdf5lib.H5D.*; import static ch.systemsx.cisd.hdf5.hdf5lib.H5S.*; import static ch.systemsx.cisd.hdf5.hdf5lib.H5T.*; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.*; import ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants; public class TestLowLevelHDF5 { static class Container { String s; Container() { } } public static void main(String[] args) throws Exception { System.out.println(HDF5Constants.H5S_MAX_RANK); System.exit(0); Container[] cont = new Container[1]; cont[0] = new Container(); cont[0].s = "aaa"; long[] dims = new long[] { cont.length }; int fileId = H5Fcreate("compoundTest.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); int dataSpaceId = H5Screate_simple(1, dims, dims); int dataTypeId = H5Tcreate(H5T_COMPOUND, 5); int stringDataType = H5Tcopy(H5T_C_S1); H5Tset_size(stringDataType, 5); H5Tinsert(dataTypeId, "s", 0, stringDataType); int dataSetId = H5Dcreate(fileId, "ds", dataTypeId, dataSpaceId, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); H5Dwrite(dataSetId, dataTypeId, H5S_ALL, H5S_ALL, H5P_DEFAULT, (cont[0].s + '\0').getBytes()); H5Tclose(dataTypeId); H5Sclose(dataSpaceId); H5Dclose(dataSetId); H5Fclose(fileId); } } libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/UnsignedIntUtilsTest.java000066400000000000000000000047261256564762100312060ustar00rootroot00000000000000/* * Copyright 2013 ETH Zuerich, CISD * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertTrue; import java.math.BigInteger; import org.testng.annotations.Test; import ch.systemsx.cisd.base.convert.NativeData; import ch.systemsx.cisd.base.convert.NativeData.ByteOrder; /** * Test cases for{@link UnsignedIntUtils}. * * @author Bernd Rinn */ public class UnsignedIntUtilsTest { @Test public void testToInt64() { final BigInteger veryLarge = new BigInteger("2").pow(64).subtract(new BigInteger("100")); final long int64 = UnsignedIntUtils.toInt64(veryLarge); assertTrue(int64 < 0); final BigInteger veryLarge2 = new BigInteger(1, NativeData.longToByte(new long[] { int64 }, ByteOrder.BIG_ENDIAN)); assertEquals(veryLarge, veryLarge2); } @Test(expectedExceptions = IllegalArgumentException.class) public void testToInt64_Overflow() { final BigInteger tooLarge = new BigInteger("2").pow(64); UnsignedIntUtils.toInt64(tooLarge); } @Test public void testToUint32() { final long veryLarge = (1L << 32L) - 17; final int veryLargeInt = UnsignedIntUtils.toInt32(veryLarge); assertTrue(veryLargeInt < 0); assertEquals(veryLarge, UnsignedIntUtils.toUint32(veryLargeInt)); } @Test public void testToUint16() { final int veryLarge = 40000; final short veryLargeShort = UnsignedIntUtils.toInt16(veryLarge); assertTrue(veryLargeShort < 0); assertEquals(veryLarge, UnsignedIntUtils.toUint16(veryLargeShort)); } @Test public void testToUint8() { final short veryLarge = 199; final byte veryLargeByte = UnsignedIntUtils.toInt8(veryLarge); assertTrue(veryLargeByte < 0); assertEquals(veryLarge, UnsignedIntUtils.toUint8(veryLargeByte)); } } libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/h5ar/000077500000000000000000000000001256564762100250615ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/h5ar/ArchivingStrategyTest.java000066400000000000000000000112531256564762100322230ustar00rootroot00000000000000/* * Copyright 2012 ETH Zuerich, CISD * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertFalse; import static org.testng.AssertJUnit.assertTrue; import org.testng.annotations.Test; import ch.systemsx.cisd.hdf5.h5ar.ArchivingStrategy.CompressionStrategy; /** * Test cases for {@link ArchivingStrategy}. * * @author Bernd Rinn */ public class ArchivingStrategyTest { @Test public void testCompressDefault() { assertEquals(CompressionStrategy.COMPRESS_NOTHING, ArchivingStrategy.DEFAULT_NO_COMPRESSION.getCompressionStrategy()); assertFalse(ArchivingStrategy.DEFAULT_NO_COMPRESSION.doCompress("/test.txt")); } @Test public void testCompressDefaultWithCompression() { assertEquals(CompressionStrategy.USE_BLACK_WHITE_LISTS, ArchivingStrategy.DEFAULT.getCompressionStrategy()); assertTrue(ArchivingStrategy.DEFAULT.doCompress("/test.txt")); assertFalse(ArchivingStrategy.DEFAULT.doCompress("/test.txt.gz")); assertFalse(ArchivingStrategy.DEFAULT.doCompress("/test.txt.bz2")); assertFalse(ArchivingStrategy.DEFAULT.doCompress("/test.txt.zip")); } @Test public void testCompressAll() { final ArchivingStrategy strategy = new ArchivingStrategy().compressAll(); assertEquals(CompressionStrategy.COMPRESS_ALL, strategy.getCompressionStrategy()); assertTrue(strategy.doCompress("/test.txt")); } @Test public void testCompressBlackList() { final ArchivingStrategy strategyCompressAll = new ArchivingStrategy().compressAll().addToCompressionBlackList(".*\\.txt"); assertEquals(CompressionStrategy.USE_BLACK_WHITE_LISTS, strategyCompressAll.getCompressionStrategy()); final ArchivingStrategy strategy = new ArchivingStrategy().compressAll().addToCompressionBlackList(".*\\.txt"); assertEquals(CompressionStrategy.USE_BLACK_WHITE_LISTS, strategy.getCompressionStrategy()); assertTrue(strategyCompressAll.doCompress("/test.dat")); assertFalse(strategyCompressAll.doCompress("/test.txt")); assertTrue(strategy.doCompress("/test.dat")); assertFalse(strategy.doCompress("/test.txt")); } @Test public void testCompressWhiteList() { final ArchivingStrategy strategyCompressAll = new ArchivingStrategy().compressAll().addToCompressionWhiteList(".*\\.txt"); assertEquals(CompressionStrategy.USE_BLACK_WHITE_LISTS, strategyCompressAll.getCompressionStrategy()); final ArchivingStrategy strategy = new ArchivingStrategy().addToCompressionWhiteList(".*\\.txt"); assertEquals(CompressionStrategy.USE_BLACK_WHITE_LISTS, strategy.getCompressionStrategy()); assertFalse(strategyCompressAll.doCompress("/test.dat")); assertTrue(strategyCompressAll.doCompress("/test.txt")); assertFalse(strategy.doCompress("/test.dat")); assertTrue(strategy.doCompress("/test.txt")); } @Test public void testCompressBlackWhiteList() { final ArchivingStrategy strategyCompressAll = new ArchivingStrategy().compressAll().addToCompressionBlackList(".*a[^/]*\\.txt") .addToCompressionWhiteList(".*\\.txt"); assertEquals(CompressionStrategy.USE_BLACK_WHITE_LISTS, strategyCompressAll.getCompressionStrategy()); final ArchivingStrategy strategy = new ArchivingStrategy().addToCompressionBlackList(".*a[^/]*\\.txt") .addToCompressionWhiteList(".*\\.txt"); assertEquals(CompressionStrategy.USE_BLACK_WHITE_LISTS, strategy.getCompressionStrategy()); assertFalse(strategyCompressAll.doCompress("/test.dat")); assertTrue(strategyCompressAll.doCompress("/test.txt")); assertFalse(strategyCompressAll.doCompress("/atest.txt")); assertFalse(strategy.doCompress("/test.dat")); assertTrue(strategy.doCompress("/test.txt")); assertFalse(strategy.doCompress("/atest.txt")); } } libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/h5ar/DirectoryIndexUpdaterTest.java000066400000000000000000000172571256564762100330610ustar00rootroot00000000000000/* * Copyright 2012 ETH Zuerich, CISD * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import static org.testng.AssertJUnit.assertTrue; import java.io.File; import java.io.IOException; import org.apache.commons.io.FileUtils; import org.hamcrest.Description; import org.hamcrest.TypeSafeMatcher; import org.jmock.Expectations; import org.jmock.Mockery; import org.testng.annotations.BeforeMethod; import org.testng.annotations.BeforeSuite; import org.testng.annotations.Test; import ch.systemsx.cisd.base.exceptions.IErrorStrategy; import ch.systemsx.cisd.base.unix.FileLinkType; /** * Test cases for {@link DirectoryIndexUpdater}. * * @author Bernd Rinn */ public class DirectoryIndexUpdaterTest { private static final File rootDirectory = new File("targets", "unit-test-wd"); private static final File workingDirectory = new File(rootDirectory, "hdf5-directory-index-updater-wd"); private Mockery context; IDirectoryIndexProvider provider; private DirectoryIndexUpdater updater; @BeforeSuite public void init() { workingDirectory.mkdirs(); assertTrue(workingDirectory.isDirectory()); workingDirectory.deleteOnExit(); rootDirectory.deleteOnExit(); } @BeforeMethod public void initTest() throws IOException { FileUtils.cleanDirectory(workingDirectory); this.context = new Mockery(); this.provider = context.mock(IDirectoryIndexProvider.class); context.checking(new Expectations() { { one(provider).getErrorStrategy(); will(returnValue(IErrorStrategy.DEFAULT_ERROR_STRATEGY)); } }); this.updater = new DirectoryIndexUpdater(provider); } @Override protected void finalize() throws Throwable { // Delete the working directory if (workingDirectory.exists() && workingDirectory.canWrite()) { workingDirectory.delete(); } // Delete root directory if (rootDirectory.exists() && rootDirectory.canWrite()) { rootDirectory.delete(); } super.finalize(); } static class LinkEntryEntryMatcher extends TypeSafeMatcher { private final FileLinkType type; private final String name; private final int crc32; private final long lastModified; LinkEntryEntryMatcher(FileLinkType type, String name, int crc32, long lastModified) { this.type = type; this.name = name; this.crc32 = crc32; this.lastModified = lastModified; } static LinkEntryEntryMatcher file(String name, int crc32, long lastModified) { return new LinkEntryEntryMatcher(FileLinkType.REGULAR_FILE, name, crc32, lastModified); } static LinkEntryEntryMatcher dir(String name, long lastModified) { return new LinkEntryEntryMatcher(FileLinkType.DIRECTORY, name, 0, lastModified); } @Override public void describeTo(Description description) { description.appendText(toString()); } @Override public boolean matchesSafely(LinkRecord item) { if (name.equals(item.getLinkName()) == false) { System.err.printf("linkName=%s (expected: %s)\n", item.getLinkName(), name); return false; } if (type != item.getLinkType()) { System.err.printf("linkType=%s (expected: %s) [linkName=%s]\n", item.getLinkType(), type, name); return false; } if (crc32 != item.getCrc32()) { System.err.printf("crc32=%s (expected: %s) [linkName=%s]\n", item.getCrc32(), crc32, name); return false; } if (Math.abs(lastModified - item.getLastModified()) > 1) { System.err.printf("lastModified=%s (expected: %s) [linkName=%s]\n", item.getLastModified(), lastModified, name); return false; } return true; } @Override public String toString() { return "LinkEntryEntryMatcher [type=" + type + ", name=" + name + ", crc32=" + crc32 + ", lastModified=" + lastModified + "]"; } } @Test public void testFileExistsOnFS() throws IOException { final String name = "abc"; final int crc32 = 123; final long lastModified = 543L; final File f = new File(workingDirectory, name); FileUtils.touch(f); f.setLastModified(lastModified * 1000L); context.checking(new Expectations() { { final IDirectoryIndex indexBlaBlub = context.mock(IDirectoryIndex.class, "indexBlaBlub"); one(provider).get("/bla/blub", false); will(returnValue(indexBlaBlub)); one(indexBlaBlub).updateIndex(with(LinkEntryEntryMatcher.file(name, crc32, lastModified))); final IDirectoryIndex indexBla = context.mock(IDirectoryIndex.class, "indexBla"); one(provider).get("/bla", false); will(returnValue(indexBla)); one(indexBla).updateIndex(with(LinkEntryEntryMatcher.dir("blub", System.currentTimeMillis()/1000))); final IDirectoryIndex indexRoot = context.mock(IDirectoryIndex.class, "indexRoot"); one(provider).get("/", false); will(returnValue(indexRoot)); one(indexRoot).updateIndex(with(LinkEntryEntryMatcher.dir("bla", System.currentTimeMillis()/1000))); } }); updater.updateIndicesOnThePath("/bla/blub", f, 123, false); } @Test public void testOnlyFileAndDirExistsOnFS() throws IOException { final String name = "abc"; final int crc32 = 123; final long lastModified = 543L; final File f = new File(new File(workingDirectory, "ttt"), name); f.getParentFile().mkdirs(); FileUtils.touch(f); f.setLastModified(lastModified * 1000L); final long lastModifiedDir = 2222L; f.getParentFile().setLastModified(lastModifiedDir * 1000L); context.checking(new Expectations() { { final IDirectoryIndex indexTtt = context.mock(IDirectoryIndex.class, "indexTtt"); one(provider).get("/ttt", false); will(returnValue(indexTtt)); one(indexTtt).updateIndex(with(LinkEntryEntryMatcher.file(name, crc32, lastModified))); final IDirectoryIndex indexRoot = context.mock(IDirectoryIndex.class, "indexRoot"); one(provider).get("/", false); will(returnValue(indexRoot)); one(indexRoot).updateIndex(with(LinkEntryEntryMatcher.dir("ttt", lastModifiedDir))); } }); updater.updateIndicesOnThePath("/ttt", f, 123, false); } } libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/h5ar/HDF5ArchiverTest.java000066400000000000000000001242001256564762100307350ustar00rootroot00000000000000/* * Copyright 2009 ETH Zuerich, CISD * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertFalse; import static org.testng.AssertJUnit.assertNotNull; import static org.testng.AssertJUnit.assertNull; import static org.testng.AssertJUnit.assertTrue; import java.io.BufferedReader; import java.io.ByteArrayInputStream; import java.io.File; import java.io.IOException; import java.io.InputStreamReader; import java.io.PrintStream; import java.util.Arrays; import java.util.List; import java.util.concurrent.atomic.AtomicInteger; import org.apache.commons.io.FileUtils; import org.apache.commons.lang.ArrayUtils; import org.testng.annotations.AfterTest; import org.testng.annotations.BeforeSuite; import org.testng.annotations.Test; import ch.rinn.restrictions.Friend; import ch.systemsx.cisd.base.unix.FileLinkType; import ch.systemsx.cisd.base.unix.Unix; import ch.systemsx.cisd.base.unix.Unix.Stat; import ch.systemsx.cisd.base.utilities.OSUtilities; import ch.systemsx.cisd.hdf5.HDF5Factory; import ch.systemsx.cisd.hdf5.IHDF5Writer; /** * Tests for {@link HDF5Archiver}. * * @author Bernd Rinn */ @Friend(toClasses = { HDF5Archiver.class, IdCache.class, LinkRecord.class }) public class HDF5ArchiverTest { private static final File rootDirectory = new File("targets", "unit-test-wd"); private static final File workingDirectory = new File(rootDirectory, "hdf5-archivertest-wd"); private static final File srcDirectory = new File("sourceTest/java/ch/systemsx/cisd/hdf5/h5ar"); @BeforeSuite public void init() { workingDirectory.mkdirs(); assertTrue(workingDirectory.isDirectory()); workingDirectory.deleteOnExit(); rootDirectory.deleteOnExit(); } @AfterTest public void cleanup() { deleteAll(workingDirectory); } private void deleteAll(File path) { if (path.isDirectory()) { for (File sub : path.listFiles()) { deleteAll(sub); } } path.delete(); } @Override protected void finalize() throws Throwable { // Delete the working directory if (workingDirectory.exists() && workingDirectory.canWrite()) { workingDirectory.delete(); } // Delete root directory if (rootDirectory.exists() && rootDirectory.canWrite()) { rootDirectory.delete(); } super.finalize(); } @Test public void testGetPermissions() { assertEquals("----------", Utils.permissionsToString(0, false, false)); assertEquals("-rw-rw-rw-", Utils.permissionsToString(0666, false, false)); assertEquals("-r--r--r--", Utils.permissionsToString(0444, false, false)); assertEquals("-rwx------", Utils.permissionsToString(0700, false, false)); assertEquals("-rwsr-xr-x", Utils.permissionsToString(04755, false, false)); assertEquals("-rwSr-xr-x", Utils.permissionsToString(04655, false, false)); assertEquals("-rwxr-sr-x", Utils.permissionsToString(02755, false, false)); assertEquals("-rwxr-Sr-x", Utils.permissionsToString(02745, false, false)); assertEquals("-rwxr-xr-t", Utils.permissionsToString(01755, false, false)); assertEquals("-rwxr-xr-T", Utils.permissionsToString(01754, false, false)); assertEquals("d---------", Utils.permissionsToString(0, true, false)); assertEquals("drwxr-xr-x", Utils.permissionsToString(0755, true, false)); } @Test(groups = { "requires_unix" }) public void testDescribeLink() { final String rootGroupName = OSUtilities.isMacOS() ? "wheel" : "root"; final IdCache idCache = new IdCache(); assertEquals("dir/link_name", new ArchiveEntry("dir", "dir/link_name", new LinkRecord(null, null, null, -1, -1, -1, -1, (short) -1, 0), idCache).describeLink(false, false)); assertEquals(" 100\t00000000\tdir/link_name", new ArchiveEntry("dir", "dir/link_name", new LinkRecord(null, null, FileLinkType.REGULAR_FILE, 100, -1, -1, -1, (short) -1, 0), idCache).describeLink(true, false)); assertEquals("-rwxr-xr-x\troot\t" + rootGroupName + "\t 111\t2000-01-01 00:00:00\t00000000\tdir/link_name", new ArchiveEntry( "dir", "dir/link_name", new LinkRecord(null, null, FileLinkType.REGULAR_FILE, 111L, 946681200491L / 1000L, 0, 0, (short) 0755, 0), idCache).describeLink(true, false)); assertEquals("d---------\troot\t" + rootGroupName + "\t DIR\t2000-01-01 00:00:00\t \tdir/link_name", new ArchiveEntry( "dir", "dir/link_name", new LinkRecord(null, null, FileLinkType.DIRECTORY, 111L, 946681200491L / 1000L, 0, 0, (short) 0, 0), idCache).describeLink(true, false)); assertEquals("755\t0\t0\t 111\t2000-01-01 00:00:00\t" + Utils.crc32ToString(200) + "\tdir/link_name", new ArchiveEntry("dir", "dir/link_name", new LinkRecord(null, null, FileLinkType.REGULAR_FILE, 111L, 946681200491L / 1000L, 0, 0, (short) 0755, 200), idCache).describeLink(true, true)); assertEquals("0\t0\t0\t DIR\t2000-01-01 00:00:00\t \tdir/link_name", new ArchiveEntry("dir", "dir/link_name", new LinkRecord("link_name2", null, FileLinkType.DIRECTORY, 111L, 946681200491L / 1000L, 0, 0, (short) 0, 0), idCache).describeLink(true, true)); assertEquals(" 111\t2000-01-01 00:00:00\t00000000\tdir/link_name", new ArchiveEntry( "dir", "dir/link_name", new LinkRecord("link_name", null, FileLinkType.REGULAR_FILE, 111L, 946681200491L / 1000L, -1, 0, (short) 0755, 0), idCache).describeLink(true, false)); assertEquals(" 111\t00000000\tdir/link_name", new ArchiveEntry("dir", "dir/link_name", new LinkRecord("link_name2", null, FileLinkType.REGULAR_FILE, 111L, -1L, -1, 0, (short) 0755, 0), idCache).describeLink(true, false)); } @Test(groups = { "requires_unix" }) public void testIdCache() { if (Unix.isOperational() == false) { return; } final int uid = Unix.getUid(); final String uname = Unix.tryGetUserNameForUid(uid); final IdCache idCache = new IdCache(); assertEquals("-17", idCache.getUser(-17, true)); assertEquals("root", idCache.getUser(0, false)); assertEquals(uname, idCache.getUser(uid, false)); Integer invalidUid = getInvalidUid(); if (invalidUid != null) { assertEquals(Integer.toString(invalidUid), idCache.getUser(invalidUid, false)); } } private Integer getInvalidUid() { int invalidUid; for (invalidUid = 60000; invalidUid < 65535 && Unix.tryGetUserByUid(invalidUid) != null; ++invalidUid) { } return Unix.tryGetUserByUid(invalidUid) == null ? invalidUid : null; } private void writeToArchive(final IHDF5Archiver a, final String name, final String content) { final byte[] bytes = content.getBytes(); a.archiveFile(NewArchiveEntry.file("/test", name).lastModified(1000000L).uid(100).gid(100), new ByteArrayInputStream(bytes)); } @Test public void testWriteByteArrayToArchive() { final File file = new File(workingDirectory, "writeByteArrayToArchive.h5ar"); file.delete(); file.deleteOnExit(); final IHDF5Archiver a = HDF5ArchiverFactory.open(file); writeToArchive(a, "hello.txt", "Hello World\n"); writeToArchive(a, "hello2.txt", "Yet another Hello World\n"); a.close(); final IHDF5ArchiveReader aro = HDF5ArchiverFactory.openForReading(file); final String content1 = new String(aro.extractFileAsByteArray("/test/hello.txt")); assertEquals("Hello World\n", content1); final String content2 = new String(aro.extractFileAsByteArray("/test/hello2.txt")); assertEquals("Yet another Hello World\n", content2); final List list = aro.list("/", ListParameters.build().nonRecursive().noReadLinkTarget().get()); assertEquals(1, list.size()); assertEquals("755\t100\t100\t DIR\t1970-01-12 14:46:40\t \t/test", list.get(0) .describeLink(true, true)); final List list2 = aro.list("/test", ListParameters.build().testArchive().suppressDirectoryEntries() .get()); assertEquals(2, list2.size()); assertEquals( "755\t100\t100\t 12\t1970-01-12 14:46:40\tb095e5e3\t/test/hello.txt\tOK", list2.get(0).describeLink(true, true)); assertEquals( "755\t100\t100\t 24\t1970-01-12 14:46:40\tee5f3107\t/test/hello2.txt\tOK", list2.get(1).describeLink(true, true)); aro.close(); } @Test public void testWriteFileAsOutputStream() throws Exception { final File file = new File(workingDirectory, "writeFileAsOutputStream.h5ar"); file.delete(); file.deleteOnExit(); final IHDF5Archiver a = HDF5ArchiverFactory.open(file); final PrintStream ps = new PrintStream(a.archiveFileAsOutputStream(NewArchiveEntry.file("test1") .chunkSize(128))); ps.printf("Some %s stuff: %d\n", "more", 17); // Note: we don't close the PrintStream or the underlying OutputStream explicitly. // The flushables take care of things getting written correctly anyway. a.close(); final IHDF5ArchiveReader ar = HDF5ArchiverFactory.openForReading(file); final List entries = ar.list("", ListParameters.build().testArchive().get()); assertEquals(1, entries.size()); assertEquals("test1", entries.get(0).getName()); assertTrue(entries.get(0).isOK()); final BufferedReader r = new BufferedReader(new InputStreamReader(ar.extractFileAsInputStream("test1"))); assertEquals("Some more stuff: 17", r.readLine()); assertNull(r.readLine()); ar.close(); } private File createTestDirectory() throws IOException { return createTestDirectory(null, System.currentTimeMillis()); } private File createTestDirectory(String prefixOrNull, long time) throws IOException { final File prefixDir = (prefixOrNull != null) ? new File(workingDirectory, prefixOrNull) : workingDirectory; prefixDir.delete(); prefixDir.deleteOnExit(); final File dir = new File(prefixDir, "test"); dir.delete(); dir.deleteOnExit(); dir.mkdirs(); final File f1 = new File(dir, "file_test1.txt"); f1.delete(); f1.deleteOnExit(); FileUtils.writeLines(f1, Arrays.asList("Line 1", "Line 2", "Line 3")); f1.setLastModified(time); final File dir2 = new File(dir, "dir_somedir"); dir2.delete(); dir2.mkdir(); dir2.deleteOnExit(); final File f2 = new File(dir2, "file_test2.txt"); f2.delete(); f2.deleteOnExit(); FileUtils.writeLines(f2, Arrays.asList("A", "B", "C")); f2.setLastModified(time); final File dir3 = new File(dir, "dir_someotherdir"); dir3.delete(); dir3.mkdir(); dir3.deleteOnExit(); if (Unix.isOperational()) { final File l1 = new File(dir2, "link_todir3"); l1.delete(); l1.deleteOnExit(); Unix.createSymbolicLink("../" + dir3.getName(), l1.getAbsolutePath()); } dir2.setLastModified(time); dir3.setLastModified(time); dir.setLastModified(time); return dir; } @Test public void testCreateVerifyRoundtripOK() throws IOException { final File dir = createTestDirectory(); final File h5arfile = new File(workingDirectory, "testRoundtrip.h5ar"); h5arfile.delete(); h5arfile.deleteOnExit(); HDF5ArchiverFactory.open(h5arfile).archiveFromFilesystem(dir).close(); final IHDF5ArchiveReader ar = HDF5ArchiverFactory.openForReading(h5arfile); assertTrue(ar.test().isEmpty()); assertTrue(ar.verifyAgainstFilesystem(dir).isEmpty()); ar.close(); } @Test public void testCreateVerifyContentArtificialRootRoundtripOK() throws IOException { final File dir = createTestDirectory(); final File h5arfile = new File(workingDirectory, "testRoundtripContentArtificialRoot.h5ar"); h5arfile.delete(); h5arfile.deleteOnExit(); HDF5ArchiverFactory.open(h5arfile).archiveFromFilesystemBelowDirectory("ttt", dir).close(); final IHDF5ArchiveReader ar = HDF5ArchiverFactory.openForReading(h5arfile); assertTrue(ar.test().isEmpty()); assertTrue(ar.verifyAgainstFilesystem("", dir, "ttt").isEmpty()); ar.close(); } @Test public void testRoundtrip() throws IOException { final long now = System.currentTimeMillis(); final long dirLastChanged = now - 1000L * 3600L * 24 * 5; final File dir = createTestDirectory("original", dirLastChanged); final long dirLastChangedSeconds = dirLastChanged / 1000L; final File h5arfile = new File(workingDirectory, "testRoundtrip.h5ar"); h5arfile.delete(); h5arfile.deleteOnExit(); final AtomicInteger entryCount = new AtomicInteger(0); HDF5ArchiverFactory.open(h5arfile) .archiveFromFilesystemBelowDirectory("/", dir, new IArchiveEntryVisitor() { @Override public void visit(ArchiveEntry entry) { entryCount.incrementAndGet(); final File f = new File(dir, entry.getPath()); assertTrue(entry.getPath(), f.exists()); assertTrue(entry.isOK()); if (entry.isSymLink() == false) { assertEquals(dirLastChangedSeconds, entry.getLastModified()); assertEquals(entry.getPath(), f.isDirectory(), entry.isDirectory()); assertEquals(entry.getPath(), f.isFile(), entry.isRegularFile()); if (entry.isRegularFile()) { assertEquals(entry.getPath(), f.length(), entry.getSize()); } } } }).close(); assertEquals(6, entryCount.intValue()); final IHDF5ArchiveReader ar = HDF5ArchiverFactory.openForReading(h5arfile); entryCount.set(0); ar.list("/", new IArchiveEntryVisitor() { @Override public void visit(ArchiveEntry entry) { entryCount.incrementAndGet(); final File f = new File(dir, entry.getPath()); assertTrue(entry.getPath(), f.exists()); assertTrue(entry.isOK()); if (entry.isSymLink() == false) { assertEquals(dirLastChangedSeconds, entry.getLastModified()); assertEquals(entry.getPath(), f.isDirectory(), entry.isDirectory()); assertEquals(entry.getPath(), f.isFile(), entry.isRegularFile()); if (entry.isRegularFile()) { assertEquals(entry.getPath(), f.length(), entry.getSize()); } } } }); assertEquals(5, entryCount.intValue()); assertTrue(ar.verifyAgainstFilesystem(dir).isEmpty()); final File extracted = new File(dir.getParentFile().getParentFile(), "extracted"); deleteAll(extracted); entryCount.set(0); ar.extractToFilesystem(extracted, "/", new IArchiveEntryVisitor() { @Override public void visit(ArchiveEntry entry) { entryCount.incrementAndGet(); final File f = new File(dir, entry.getPath()); assertTrue(entry.getPath(), f.exists()); assertTrue(entry.isOK()); if (entry.isSymLink() == false) { assertEquals(dirLastChangedSeconds, entry.getLastModified()); assertEquals(entry.getPath(), f.isDirectory(), entry.isDirectory()); assertEquals(entry.getPath(), f.isFile(), entry.isRegularFile()); if (entry.isRegularFile()) { assertEquals(entry.getPath(), f.length(), entry.getSize()); } } } }); assertEquals(5, entryCount.get()); assertTrue(ar.verifyAgainstFilesystem(extracted).isEmpty()); entryCount.set(0); checkDirectoryEntries(dir, extracted, entryCount); assertEquals(5, entryCount.intValue()); final File partiallyExtracted = new File(dir.getParentFile().getParentFile(), "partiallyExtracted"); deleteAll(partiallyExtracted); entryCount.set(0); final String[] pathsInDirSomedir = new String[] { "/dir_somedir", "/dir_somedir/file_test2.txt", "/dir_somedir/link_todir3" }; ar.extractToFilesystemBelowDirectory(partiallyExtracted, "/dir_somedir", new IArchiveEntryVisitor() { @Override public void visit(ArchiveEntry entry) { int idx = entryCount.getAndIncrement(); assertEquals(pathsInDirSomedir[idx], entry.getPath()); } }); assertEquals(3, entryCount.get()); ar.close(); } private void checkDirectoryEntries(final File dir, final File extracted, final AtomicInteger entryCount) { for (File f : extracted.listFiles()) { entryCount.incrementAndGet(); final String relativePath = f.getAbsolutePath().substring(extracted.getAbsolutePath().length() + 1); final File orig = new File(dir, relativePath); assertTrue(relativePath, orig.exists()); assertEquals(relativePath, orig.isDirectory(), f.isDirectory()); assertEquals(relativePath, orig.isFile(), f.isFile()); if (Unix.isOperational()) { final Stat fStat = Unix.getLinkInfo(f.getPath(), true); final Stat origStat = Unix.getLinkInfo(orig.getPath(), true); assertEquals(relativePath, origStat.isSymbolicLink(), fStat.isSymbolicLink()); assertEquals(relativePath, origStat.tryGetSymbolicLink(), fStat.tryGetSymbolicLink()); } if (f.isDirectory()) { checkDirectoryEntries(orig, f, entryCount); } } } @Test public void testRoundtripArtificalRootOK() throws IOException { final File dir = createTestDirectory(); final File h5arfile = new File(workingDirectory, "testRoundtripArtificalRootOK.h5ar"); h5arfile.delete(); h5arfile.deleteOnExit(); HDF5ArchiverFactory.open(h5arfile).archiveFromFilesystem("ttt", dir).close(); final IHDF5ArchiveReader ar = HDF5ArchiverFactory.openForReading(h5arfile); final List list = ar.list("/"); assertEquals(7, list.size()); assertEquals("/ttt", list.get(0).getPath()); assertEquals("/ttt/test", list.get(1).getPath()); assertEquals("/ttt/test/dir_somedir", list.get(2).getPath()); assertEquals("/ttt/test/dir_somedir/file_test2.txt", list.get(3).getPath()); assertEquals("/ttt/test/dir_somedir/link_todir3", list.get(4).getPath()); assertEquals("/ttt/test/dir_someotherdir", list.get(5).getPath()); assertEquals("/ttt/test/file_test1.txt", list.get(6).getPath()); assertEquals("Line 1\nLine 2\nLine 3\n", new String(ar.extractFileAsByteArray("/ttt/test/file_test1.txt"))); assertEquals("A\nB\nC\n", new String(ar.extractFileAsByteArray("/ttt/test/dir_somedir/file_test2.txt"))); assertTrue(ar.test().isEmpty()); List verifyErrors = ar.verifyAgainstFilesystem("/", dir.getParentFile(), "/ttt"); assertTrue(verifyErrors.toString(), verifyErrors.isEmpty()); final List list2 = ar.list("/ttt/test/dir_somedir"); assertEquals(2, list2.size()); assertEquals("file_test2.txt", list2.get(0).getName()); assertEquals("link_todir3", list2.get(1).getName()); final List list3 = ar.list("/ttt/test/dir_somedir", ListParameters.build() .includeTopLevelDirectoryEntry().get()); assertEquals(3, list3.size()); assertEquals("dir_somedir", list3.get(0).getName()); assertEquals("file_test2.txt", list3.get(1).getName()); assertEquals("link_todir3", list3.get(2).getName()); ar.close(); } @Test public void testRoundtripArtificalRootWhichExistsOnFSOK() throws IOException { final long now = System.currentTimeMillis(); final long dirLastChanged = now - 1000L * 3600L * 24 * 3; final File dir = createTestDirectory("ttt", dirLastChanged); // Set some special last modified time and access mode that we can recognize dir.getParentFile().setLastModified(111000L); Unix.setAccessMode(dir.getParent(), (short) 0777); final File h5arfile = new File(workingDirectory, "testRoundtripArtificalRootWhichExistsOnFSOK.h5ar"); h5arfile.delete(); h5arfile.deleteOnExit(); HDF5ArchiverFactory.open(h5arfile).archiveFromFilesystem("ttt", dir).close(); final IHDF5ArchiveReader ar = HDF5ArchiverFactory.openForReading(h5arfile); final List list = ar.list("/"); assertEquals(7, list.size()); assertEquals("/ttt", list.get(0).getPath()); // Does the archive entry have the last modified time and access mode we have set in the // filesystem? assertEquals(111, list.get(0).getLastModified()); assertEquals((short) 0777, list.get(0).getPermissions()); assertEquals("/ttt/test", list.get(1).getPath()); assertEquals("/ttt/test/dir_somedir", list.get(2).getPath()); assertEquals("/ttt/test/dir_somedir/file_test2.txt", list.get(3).getPath()); assertEquals("/ttt/test/dir_somedir/link_todir3", list.get(4).getPath()); assertEquals("/ttt/test/dir_someotherdir", list.get(5).getPath()); assertEquals("/ttt/test/file_test1.txt", list.get(6).getPath()); assertEquals("Line 1\nLine 2\nLine 3\n", new String(ar.extractFileAsByteArray("/ttt/test/file_test1.txt"))); assertEquals("A\nB\nC\n", new String(ar.extractFileAsByteArray("/ttt/test/dir_somedir/file_test2.txt"))); assertTrue(ar.test().isEmpty()); List verifyErrors = ar.verifyAgainstFilesystem("/", dir.getParentFile(), "/ttt"); assertTrue(verifyErrors.toString(), verifyErrors.isEmpty()); ar.close(); } @Test public void testGetInfo() throws IOException { final File dir = createTestDirectory(); final File h5arfile = new File(workingDirectory, "testGetInfo.h5ar"); h5arfile.delete(); h5arfile.deleteOnExit(); HDF5ArchiverFactory.open(h5arfile).archiveFromFilesystem(dir).close(); final IHDF5ArchiveReader ar = HDF5ArchiverFactory.openForReading(h5arfile); assertTrue(ar.exists("file_test1.txt")); assertTrue(ar.isRegularFile("file_test1.txt")); assertFalse(ar.isDirectory("file_test1.txt")); assertFalse(ar.isSymLink("file_test1.txt")); assertTrue(ar.exists("dir_somedir")); assertFalse(ar.isRegularFile("dir_somedir")); assertFalse(ar.isSymLink("dir_somedir")); assertTrue(ar.isDirectory("dir_somedir")); assertTrue(ar.exists("dir_somedir/link_todir3")); assertFalse(ar.isRegularFile("dir_somedir/link_todir3")); assertFalse(ar.isDirectory("dir_somedir/link_todir3")); assertTrue(ar.isSymLink("dir_somedir/link_todir3")); assertEquals("../dir_someotherdir", ar.tryGetEntry("dir_somedir/link_todir3", true) .getLinkTarget()); ar.close(); } private static final String ARCHIVE_LISTING = "775\t1001\t1001\t DIR\t2015-02-21 14:01:31\t \t/tmp\n" + "775\t1001\t1001\t DIR\t2015-02-21 14:01:40\t \t/tmp/c\n" + "664\t1001\t1001\t 7\t2015-02-21 14:01:40\t046d0418\t/tmp/c/d\n" + "664\t1001\t1001\t 7\t2015-02-21 14:01:21\t791af05d\t/tmp/a\n" + "664\t1001\t1001\t 7\t2015-02-21 14:01:27\t5237a39e\t/tmp/b"; @Test public void testReadExistingArchive() { final File h5arfile = new File(srcDirectory, "test.h5ar"); System.out.println(h5arfile); assertTrue(h5arfile.exists()); final IHDF5ArchiveReader ar = HDF5ArchiverFactory.openForReading(h5arfile); assertEquals(ARCHIVE_LISTING, toStringNumeric(ar)); final List testResult = ar.test(); assertTrue(ArrayUtils.toString(testResult), testResult.isEmpty()); ar.close(); } @Test public void testReadLegacy_14_12_0_Archive() { final File h5arfile = new File(srcDirectory, "test_14_12_0.h5ar"); System.out.println(h5arfile); assertTrue(h5arfile.exists()); final IHDF5ArchiveReader ar = HDF5ArchiverFactory.openForReading(h5arfile); assertEquals(ARCHIVE_LISTING, toStringNumeric(ar)); final List testResult = ar.test(); assertTrue(ArrayUtils.toString(testResult), testResult.isEmpty()); ar.close(); } private String toStringNumeric(final IHDF5ArchiveReader ar) { final StringBuilder b = new StringBuilder(); for (ArchiveEntry e : ar.list()) { b.append(e.describeLink(true, true)); b.append('\n'); } b.setLength(b.length() - 1); return b.toString(); } private void checkSorted(List entries) { boolean dirs = true; for (int i = 1; i < entries.size(); ++i) { if (dirs && entries.get(i).isDirectory() == false) { dirs = false; } else { assertTrue(entries.get(i - 1).getName().compareTo(entries.get(i).getName()) < 0); } } } @Test public void testManyFiles() { workingDirectory.mkdirs(); final File h5arfile = new File(workingDirectory, "testManyFiles.h5ar"); h5arfile.delete(); h5arfile.deleteOnExit(); final IHDF5Archiver a = HDF5ArchiverFactory.open(h5arfile); for (int i = 999; i >= 0; --i) { a.archiveFile(Integer.toString(i), new byte[0]); } a.archiveSymlink("symlink", "500"); a.archiveDirectory(NewArchiveEntry.directory("/dir")); a.archiveFile("dir/hello", "hello world".getBytes()); final List entries = a.list("/"); assertEquals(1003, entries.size()); final ArchiveEntry symLinkEntry = a.tryGetEntry("symlink", true); assertNotNull(symLinkEntry); assertTrue(symLinkEntry.isSymLink()); assertTrue(symLinkEntry.hasLinkTarget()); assertEquals("500", symLinkEntry.getLinkTarget()); final ArchiveEntry dirEntry = a.tryGetEntry("dir", true); assertNotNull(dirEntry); assertTrue(dirEntry.isDirectory()); assertFalse(dirEntry.isRegularFile()); assertFalse(dirEntry.isSymLink()); final List entriesDir = a.list("/dir"); assertEquals(1, entriesDir.size()); assertEquals("hello", entriesDir.get(0).getName()); a.close(); final IHDF5ArchiveReader ra = HDF5ArchiverFactory.openForReading(h5arfile); final List entriesRead = ra.list("/", ListParameters.build().nonRecursive().get()); assertEquals(1002, entriesRead.size()); checkSorted(entriesRead); for (int i = 1; i < entriesRead.size() - 1; ++i) { assertTrue(entriesRead.get(i).isRegularFile()); } assertTrue(entriesRead.get(0).isDirectory()); assertTrue(entriesRead.get(entriesRead.size() - 1).isSymLink()); for (int i = 1; i < 1001; ++i) { assertTrue(ra.isRegularFile(Integer.toString(i - 1))); assertFalse(ra.isDirectory(Integer.toString(i - 1))); assertFalse(ra.isSymLink(Integer.toString(i - 1))); } assertTrue(ra.isSymLink("symlink")); assertFalse(ra.isDirectory("symlink")); assertFalse(ra.isRegularFile("symlink")); assertEquals("500", ra.tryGetEntry("symlink", true).getLinkTarget()); assertTrue(ra.isDirectory("dir")); assertFalse(ra.isSymLink("dir")); assertFalse(ra.isRegularFile("dir")); ra.close(); } @Test public void testFollowSymbolicLinks() { workingDirectory.mkdirs(); final File h5arfile = new File(workingDirectory, "testFollowSymbolicLinks.h5ar"); h5arfile.delete(); h5arfile.deleteOnExit(); final IHDF5Archiver a = HDF5ArchiverFactory.open(h5arfile); a.archiveDirectory(NewArchiveEntry.directory("aDir")); a.archiveFile(NewArchiveEntry.file("aDir/aFile"), "Some file content".getBytes()); a.archiveSymlink(NewArchiveEntry.symlink("aLinkToAFile", "aDir/aFile")); a.archiveSymlink(NewArchiveEntry.symlink("aLinkToADir", "aDir")); a.close(); final IHDF5ArchiveReader ra = HDF5ArchiverFactory.openForReading(h5arfile); final List entries = ra.list("/", ListParameters.build() ./* resolveSymbolicLinks(). */followSymbolicLinks().get()); assertEquals(5, entries.size()); assertEquals("/aDir", entries.get(0).getPath()); assertTrue(entries.get(0).isDirectory()); assertEquals("/aDir/aFile", entries.get(1).getPath()); assertTrue(entries.get(1).isRegularFile()); assertEquals("/aLinkToADir", entries.get(2).getPath()); assertTrue(entries.get(2).isSymLink()); assertEquals("/aLinkToADir/aFile", entries.get(3).getPath()); assertTrue(entries.get(3).isRegularFile()); assertEquals("/aLinkToAFile", entries.get(4).getPath()); assertTrue(entries.get(4).isSymLink()); ra.close(); } @Test public void testFollowAndResolveSymbolicLinks() { workingDirectory.mkdirs(); final File h5arfile = new File(workingDirectory, "testFollowAndResolveSymbolicLinks.h5ar"); h5arfile.delete(); h5arfile.deleteOnExit(); final IHDF5Archiver a = HDF5ArchiverFactory.open(h5arfile); a.archiveDirectory(NewArchiveEntry.directory("aDir")); a.archiveFile(NewArchiveEntry.file("aDir/aFile"), "Some file content".getBytes()); a.archiveSymlink(NewArchiveEntry.symlink("aLinkToAFile", "aDir/aFile")); a.archiveSymlink(NewArchiveEntry.symlink("aLinkToADir", "aDir")); a.close(); final IHDF5ArchiveReader ra = HDF5ArchiverFactory.openForReading(h5arfile); final List entries = ra.list("/", ListParameters.build().resolveSymbolicLinks().followSymbolicLinks() .get()); assertEquals(5, entries.size()); assertEquals("/aDir", entries.get(0).getPath()); assertTrue(entries.get(0).isDirectory()); assertEquals("/aDir/aFile", entries.get(1).getPath()); assertTrue(entries.get(1).isRegularFile()); assertEquals("/aLinkToADir", entries.get(2).getPath()); assertEquals("/aDir", entries.get(2).getRealPath()); assertTrue(entries.get(2).isDirectory()); assertEquals("/aLinkToADir/aFile", entries.get(3).getPath()); assertTrue(entries.get(3).isRegularFile()); assertEquals("/aLinkToAFile", entries.get(4).getPath()); assertEquals("/aDir/aFile", entries.get(4).getRealPath()); assertTrue(entries.get(4).isRegularFile()); ra.close(); } @Test public void testResolveLinks() { workingDirectory.mkdirs(); final File h5arfile = new File(workingDirectory, "testResolveLinks.h5ar"); h5arfile.delete(); h5arfile.deleteOnExit(); final IHDF5Archiver a = HDF5ArchiverFactory.open(h5arfile); a.archiveFile(NewArchiveEntry.file("aFile"), "Some file content".getBytes()); a.archiveDirectory(NewArchiveEntry.directory("aDir")); a.archiveSymlink(NewArchiveEntry.symlink("aLinkToAFile", "aFile")); a.archiveSymlink(NewArchiveEntry.symlink("aLinkToADir", "aDir")); a.archiveSymlink(NewArchiveEntry.symlink("aNonsenseLink", "../outOfFS")); a.archiveSymlink(NewArchiveEntry.symlink("aLinkToANonexistingFile", "nonexistingFile")); a.archiveSymlink(NewArchiveEntry.symlink("aDir/aLinkToALinkToAFile", "../aLinkToAFile")); a.archiveSymlink(NewArchiveEntry.symlink("aDir/aLinkToALinkToADir", "/aLinkToADir")); // A loop a.archiveDirectory(NewArchiveEntry.directory("z")); a.archiveSymlink(NewArchiveEntry.symlink("z/y", "..")); a.close(); final IHDF5ArchiveReader ra = HDF5ArchiverFactory.openForReading(h5arfile); // A file is resolved to itself final ArchiveEntry aFileLink = ra.tryGetEntry("aFile", false); assertEquals(aFileLink, ra.tryResolveLink(aFileLink)); // A directory is resolved to itself final ArchiveEntry aDirLink = ra.tryGetEntry("aDir", false); assertEquals(aDirLink, ra.tryResolveLink(aDirLink)); // A symlink to a file is correctly resolved... final ArchiveEntry aSymLinkToAFile = ra.tryGetEntry("aLinkToAFile", true); final ArchiveEntry aResolvedLinkToAFile = ra.tryResolveLink(aSymLinkToAFile); assertNotNull(aResolvedLinkToAFile); assertEquals(aFileLink.getPath(), aResolvedLinkToAFile.getPath()); // .. even when the link target was not read final ArchiveEntry aSymLinkToAFileWithoutTarget = ra.tryGetEntry("aLinkToAFile", false); final ArchiveEntry aResolvedLinkToAFileWithoutTarget = ra.tryResolveLink(aSymLinkToAFileWithoutTarget); assertNotNull(aResolvedLinkToAFileWithoutTarget); assertEquals(aFileLink.getPath(), aResolvedLinkToAFileWithoutTarget.getPath()); // A symlink to a dir is correctly resolved as well final ArchiveEntry aSymLinkToADir = ra.tryGetEntry("aLinkToADir", true); final ArchiveEntry aResolvedLinkToADir = ra.tryResolveLink(aSymLinkToADir); assertNotNull(aResolvedLinkToADir); assertEquals(aDirLink.getPath(), aResolvedLinkToADir.getPath()); // A nonsense link ('/../outOfFS') is resolved to null assertNull(ra.tryResolveLink(ra.tryGetEntry("aNonsenseLink", true))); // A link to a non-existing file is resolved to null assertNull(ra.tryResolveLink(ra.tryGetEntry("aLinkToANonexistingFile", true))); // A link to a link to a file final ArchiveEntry aSymLinkToALinkToAFile = ra.tryGetEntry("/aDir/aLinkToALinkToAFile", false); final ArchiveEntry aResolvedSymLinkToALinkToAFile = ra.tryResolveLink(aSymLinkToALinkToAFile); assertNotNull(aResolvedSymLinkToALinkToAFile); assertEquals(aFileLink.getPath(), aResolvedSymLinkToALinkToAFile.getPath()); final ArchiveEntry aSymLinkToALinkToAFileWithPathInfoKept = ra.tryGetResolvedEntry("/aDir/aLinkToALinkToAFile", true); assertEquals("/aDir", aSymLinkToALinkToAFileWithPathInfoKept.getParentPath()); assertEquals("aLinkToALinkToAFile", aSymLinkToALinkToAFileWithPathInfoKept.getName()); assertTrue(aSymLinkToALinkToAFileWithPathInfoKept.isRegularFile()); assertEquals(ra.tryGetEntry("aFile", false).getSize(), aSymLinkToALinkToAFileWithPathInfoKept.getSize()); // A link to a link to a dir final ArchiveEntry aSymLinkToALinkToADir = ra.tryGetEntry("/aDir/aLinkToALinkToADir", false); final ArchiveEntry aResolvedSymLinkToALinkToADir = ra.tryResolveLink(aSymLinkToALinkToADir); assertNotNull(aResolvedSymLinkToALinkToADir); assertEquals(aDirLink.getPath(), aResolvedSymLinkToALinkToADir.getPath()); final List entries = ra.list("/", ListParameters.build().resolveSymbolicLinks().get()); assertEquals(8, entries.size()); assertEquals("/aDir", entries.get(0).getPath()); assertTrue(entries.get(0).isDirectory()); assertEquals("/aDir/aLinkToALinkToADir", entries.get(1).getPath()); assertEquals("/aDir", entries.get(1).getRealPath()); assertTrue(entries.get(1).isDirectory()); assertEquals("/aDir/aLinkToALinkToAFile", entries.get(2).getPath()); assertEquals("/aFile", entries.get(2).getRealPath()); assertTrue(entries.get(2).isRegularFile()); assertEquals("/z", entries.get(3).getPath()); assertTrue(entries.get(3).isDirectory()); assertEquals("/z/y", entries.get(4).getPath()); assertEquals("/", entries.get(4).getRealPath()); assertTrue(entries.get(4).isDirectory()); assertEquals("/aFile", entries.get(5).getPath()); assertTrue(entries.get(5).isRegularFile()); assertEquals("/aLinkToADir", entries.get(6).getPath()); assertTrue(entries.get(6).isDirectory()); assertEquals("/aLinkToAFile", entries.get(7).getPath()); assertTrue(entries.get(7).isRegularFile()); assertEquals(entries.get(5).getCrc32(), entries.get(7).getCrc32()); assertEquals("/", ra.tryGetResolvedEntry("z/y", false).getPath()); ra.close(); } @Test public void testResolveLinksWithLoops() { workingDirectory.mkdirs(); final File h5arfile = new File(workingDirectory, "testResolveLinksWithLoops.h5ar"); h5arfile.delete(); h5arfile.deleteOnExit(); final IHDF5Archiver a = HDF5ArchiverFactory.open(h5arfile); a.archiveSymlink(NewArchiveEntry.symlink("a", "b")); a.archiveSymlink(NewArchiveEntry.symlink("b", "a")); a.archiveSymlink(NewArchiveEntry.symlink("c", "d")); a.archiveSymlink(NewArchiveEntry.symlink("d", "e")); a.archiveSymlink(NewArchiveEntry.symlink("e", "c")); a.close(); final IHDF5ArchiveReader ra = HDF5ArchiverFactory.openForReading(h5arfile); assertNull(ra.tryGetResolvedEntry("a", false)); assertNull(ra.tryGetResolvedEntry("d", false)); assertTrue(ra.list("/", ListParameters.build().resolveSymbolicLinks().followSymbolicLinks().get()) .isEmpty()); ra.close(); } @Test(expectedExceptions = ListArchiveTooManySymbolicLinksException.class) public void testResolveLinksWithLoopsInPath() { workingDirectory.mkdirs(); final File h5arfile = new File(workingDirectory, "testResolveLinksWithLoopsInPath.h5ar"); h5arfile.delete(); h5arfile.deleteOnExit(); final IHDF5Archiver a = HDF5ArchiverFactory.open(h5arfile); // A loop in the paths a.archiveDirectory(NewArchiveEntry.directory("1")); a.archiveDirectory(NewArchiveEntry.directory("2")); a.archiveSymlink(NewArchiveEntry.symlink("1/3", "/2")); a.archiveSymlink(NewArchiveEntry.symlink("2/4", "/1")); a.close(); final IHDF5ArchiveReader ra = HDF5ArchiverFactory.openForReading(h5arfile); try { // Will throw ListArchiveTooManySymbolicLinksException ra.list("/", ListParameters.build().resolveSymbolicLinks().followSymbolicLinks().get()); } finally { ra.close(); } } @Test public void testIntegrityCheck() throws IOException { final File dir = createTestDirectory(); final File h5arfile = new File(workingDirectory, "testIntegrityCheck.h5ar"); h5arfile.delete(); h5arfile.deleteOnExit(); HDF5ArchiverFactory.open(h5arfile).archiveFromFilesystem("ttt", dir).close(); IHDF5Writer w = HDF5Factory.open(h5arfile); w.string().write("/ttt/test/file_test1.txt", "changed behind the back."); w.int8().writeArray("/ttt/test/dir_somedir/file_test2.txt", "A\nB\nD\n".getBytes()); w.close(); final IHDF5ArchiveReader ar = HDF5ArchiverFactory.openForReading(h5arfile); final List failed = ar.test(); ar.close(); assertEquals(2, failed.size()); assertEquals("/ttt/test/dir_somedir/file_test2.txt", failed.get(0).getPath()); assertFalse(failed.get(0).isOK()); assertTrue(failed.get(0).sizeOK()); assertFalse(failed.get(0).checksumOK()); assertEquals("/ttt/test/file_test1.txt", failed.get(1).getPath()); assertFalse(failed.get(1).isOK()); assertFalse(failed.get(1).sizeOK()); assertFalse(failed.get(1).checksumOK()); } } libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/h5ar/UtilsTest.java000066400000000000000000000034241256564762100276670ustar00rootroot00000000000000/* * Copyright 2012 ETH Zuerich, CISD * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.h5ar; import static org.testng.AssertJUnit.assertEquals; import org.testng.annotations.Test; /** * Test cases for {@link Utils}. * * @author Bernd Rinn */ public class UtilsTest { @Test public void testNormalizePath() { assertEquals("/", Utils.normalizePath("/")); assertEquals("/a", Utils.normalizePath("a")); assertEquals("/a", Utils.normalizePath("a/")); assertEquals("/a", Utils.normalizePath("/a/")); assertEquals("/a/b/c", Utils.normalizePath("a/b/c")); assertEquals("/a/c", Utils.normalizePath("a/b/../c/./")); } @Test public void testGetParentPath() { assertEquals("", Utils.getParentPath("/")); assertEquals("/", Utils.getParentPath("/dir")); assertEquals("/some", Utils.getParentPath("/some/dir")); } @Test public void testConcatLink() { assertEquals("/", Utils.concatLink(Utils.getParentPath("/"), Utils.getName("/"))); assertEquals("/a", Utils.concatLink(Utils.getParentPath("/a"), Utils.getName("/a"))); assertEquals("/a/b", Utils.concatLink(Utils.getParentPath("/a/b"), Utils.getName("/a/b"))); } } libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/h5ar/test.h5ar000066400000000000000000000373501256564762100266310ustar00rootroot00000000000000‰HDF  ÿÿÿÿÿÿÿÿè>ÿÿÿÿÿÿÿÿ`ˆ¨ 8¸TREEÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿàHEAPXÈDATA_TYPESÀ€@hPTREEÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿàHEAPXˆPSNOD Hh0(FALSETRUEÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ èP H@(String_VariableLength¸° h @__HOUSEKEEPING_SUFFIX__ P+ __STRING_LENGTH____HOUSEKEEPING_SUFFIX____ ØHTREEÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿàHEAPXX Pÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ  DATA_TYPESÀ€ 05@˜HTREEÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿàHEAPX€Pÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ ð0FILEH Opaque_FILE  àÁèT€ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ x@Test D Test B Test A ´èTéé´m´èTééý¡èTéé´]ðy§èTéé´ž£7R«èTééý çÂèT€00bà îÂèT€`*@a dÂèT ( CRC32 \¼H@pà 8  INDEXNAMESÀ€`PHREGULAR_FILEDIRECTORYSYMLINKOTHERˆH  Enum_linkType¸#linkNameLength linkTypeREGULAR_FILEDIRECTORYSYMLINKOTHERsize@lastModified @uid gid permissionschecksum  Enum_Boolean(  Compound_Link`ÿÿÿÿÿÿÿÿ`!#ÂèT ( CRC32 CÖì•PdˆINDEXÀ€ÐTREEÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ#õ#cabÂèT ( CRC32 Ã/ p°+8  INDEXNAMESÀ€H)ÿÿÿÿÿÿÿÿ`è+#ÂèT ( CRC32 5‚a[Pc INDEXÀ€ *TREEÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿi#tmpÂèT ( CRC32 RÉ)ªp€68  INDEXNAMESÀ€4ÿÿÿÿÿÿÿÿ`¸6#ÂèT ( CRC32 ±ÄrPtmpðINDEXÀ€p5TREEÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ##libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/h5ar/test_14_12_0.h5ar000066400000000000000000000373501256564762100276560ustar00rootroot00000000000000‰HDF  ÿÿÿÿÿÿÿÿè>ÿÿÿÿÿÿÿÿ`ˆ¨ 8¸TREEÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿàHEAPXÈDATA_TYPESÀ€@X`TREEÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿàHEAPXˆPSNOD Hh ø@ (String_VariableLength(0(FALSETRUEH@ Enum_Boolean¸° h @__HOUSEKEEPING_SUFFIX__ P+ __STRING_LENGTH____HOUSEKEEPING_SUFFIX____ ØHTREEÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿàHEAPXX Pÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ  DATA_TYPESÀ€ 05@˜HTREEÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿàHEAPX€Pÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ ð0FILEH Opaque_FILE  àéïèT€ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ x@Test D Test B Test A ´èTéé´m´èTééý¡èTéé´]ðy§èTéé´ž£7R«èTééý çéïèT€00bà îéïèT€`*@a déïèT ( CRC32 \¼H@pà 8  INDEXNAMESÀ€`PHREGULAR_FILEDIRECTORYSYMLINKOTHERˆH  Enum_linkType¸#linkNameLength linkTypeREGULAR_FILEDIRECTORYSYMLINKOTHERsize@lastModified @uid gid permissionschecksum ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ  Compound_Link`ÿÿÿÿÿÿÿÿ`!#éïèT ( CRC32 ÒŒn†PdˆINDEXÀ€ÐTREEÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ#õ#cabéïèT ( CRC32 Ã/ p°+8  INDEXNAMESÀ€H)ÿÿÿÿÿÿÿÿ`è+#éïèT ( CRC32  nb)Pc INDEXÀ€ *TREEÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿi#tmpéïèT ( CRC32 RÉ)ªp€68  INDEXNAMESÀ€4ÿÿÿÿÿÿÿÿ`¸6#éïèT ( CRC32 pÃEÁPtmpðINDEXÀ€p5TREEÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ##libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/io/000077500000000000000000000000001256564762100246315ustar00rootroot00000000000000HDF5DataSetRandomAccessFileTest.java000066400000000000000000001240121256564762100332740ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/io/* * Copyright 2011 ETH Zuerich, CISD * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.io; import static ch.systemsx.cisd.hdf5.io.HDF5IOAdapterFactory.asInputStream; import static ch.systemsx.cisd.hdf5.io.HDF5IOAdapterFactory.asOutputStream; import static ch.systemsx.cisd.hdf5.io.HDF5IOAdapterFactory.asRandomAccessFile; import static ch.systemsx.cisd.hdf5.io.HDF5IOAdapterFactory.asRandomAccessFileReadOnly; import static ch.systemsx.cisd.hdf5.io.HDF5IOAdapterFactory.asRandomAccessFileReadWrite; import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertFalse; import static org.testng.AssertJUnit.assertNotNull; import static org.testng.AssertJUnit.assertNull; import static org.testng.AssertJUnit.assertTrue; import java.io.ByteArrayInputStream; import java.io.File; import java.io.IOException; import java.io.InputStream; import java.io.OutputStream; import java.io.UnsupportedEncodingException; import org.apache.commons.io.IOUtils; import org.apache.commons.lang.ArrayUtils; import org.testng.annotations.BeforeSuite; import org.testng.annotations.Test; import ch.systemsx.cisd.base.convert.NativeData; import ch.systemsx.cisd.base.convert.NativeData.ByteOrder; import ch.systemsx.cisd.base.io.AdapterIInputStreamToInputStream; import ch.systemsx.cisd.hdf5.HDF5DataSetInformation; import ch.systemsx.cisd.hdf5.HDF5FactoryProvider; import ch.systemsx.cisd.hdf5.HDF5GenericStorageFeatures; import ch.systemsx.cisd.hdf5.HDF5StorageLayout; import ch.systemsx.cisd.hdf5.IHDF5Reader; import ch.systemsx.cisd.hdf5.IHDF5Writer; /** * Test cases for {@link HDF5DataSetRandomAccessFile}. * * @author Bernd Rinn */ public class HDF5DataSetRandomAccessFileTest { private static final File rootDirectory = new File("targets", "unit-test-wd"); private static final File workingDirectory = new File(rootDirectory, "hdf5-dataset-random-access-file-wd"); @BeforeSuite public void init() { workingDirectory.mkdirs(); assertTrue(workingDirectory.isDirectory()); workingDirectory.deleteOnExit(); rootDirectory.deleteOnExit(); } @Override protected void finalize() throws Throwable { // Delete the working directory if (workingDirectory.exists() && workingDirectory.canWrite()) { workingDirectory.delete(); } // Delete root directory if (rootDirectory.exists() && rootDirectory.canWrite()) { rootDirectory.delete(); } super.finalize(); } @Test public void testWriterOpenAfterRAFileClosed() { final File dataSetFile = new File(workingDirectory, "testReaderOpenAfterRAFileClosed.h5"); final String dataSetName = "ds"; dataSetFile.delete(); assertFalse(dataSetFile.exists()); dataSetFile.deleteOnExit(); final IHDF5Writer writer = HDF5FactoryProvider.get().open(dataSetFile); final HDF5DataSetRandomAccessFile raFile = asRandomAccessFile(writer, dataSetName); raFile.close(); // Checks that reader is still open writer.exists("/"); writer.close(); } @Test public void testReadContiguousByteByByte() { final File dataSetFile = new File(workingDirectory, "testReadContiguousByteByByte.h5"); final String dataSetName = "ds"; dataSetFile.delete(); assertFalse(dataSetFile.exists()); dataSetFile.deleteOnExit(); final byte[] referenceArray = new byte[1000]; for (int i = 0; i < referenceArray.length; ++i) { referenceArray[i] = (byte) i; } final IHDF5Writer writer = HDF5FactoryProvider.get().configure(dataSetFile).dontUseExtendableDataTypes() .writer(); writer.int8().writeArray(dataSetName, referenceArray); assertEquals(HDF5StorageLayout.CONTIGUOUS, writer.getDataSetInformation(dataSetName) .getStorageLayout()); writer.close(); final byte[] arrayRead = new byte[referenceArray.length]; final HDF5DataSetRandomAccessFile raFile = asRandomAccessFileReadOnly(dataSetFile, dataSetName); int b; int idx = 0; while ((b = raFile.read()) >= 0) { arrayRead[idx++] = (byte) b; assertEquals(referenceArray.length - idx, raFile.available()); } assertEquals(referenceArray.length, idx); assertTrue(ArrayUtils.isEquals(referenceArray, arrayRead)); raFile.close(); } @Test public void testReadChunkedByteByByte() { final File dataSetFile = new File(workingDirectory, "testReadChunkedByteByByte.h5"); final String dataSetName = "ds"; dataSetFile.delete(); assertFalse(dataSetFile.exists()); dataSetFile.deleteOnExit(); final byte[] referenceArray = new byte[1000]; final int chunkSize = referenceArray.length / 10; for (int i = 0; i < referenceArray.length; ++i) { referenceArray[i] = (byte) i; } final IHDF5Writer writer = HDF5FactoryProvider.get().configure(dataSetFile).keepDataSetsIfTheyExist().writer(); writer.int8().createArray(dataSetName, referenceArray.length, chunkSize); writer.int8().writeArray(dataSetName, referenceArray); assertEquals(HDF5StorageLayout.CHUNKED, writer.getDataSetInformation(dataSetName) .getStorageLayout()); writer.close(); final byte[] arrayRead = new byte[referenceArray.length]; final HDF5DataSetRandomAccessFile raFile = asRandomAccessFileReadOnly(dataSetFile, dataSetName); int b; int idx = 0; while ((b = raFile.read()) >= 0) { arrayRead[idx++] = (byte) b; assertEquals(referenceArray.length - idx, raFile.available()); } assertEquals(referenceArray.length, idx); assertTrue(ArrayUtils.isEquals(referenceArray, arrayRead)); raFile.close(); } @Test public void testReadContiguousBlockwise() { final File dataSetFile = new File(workingDirectory, "testReadContiguousBlockwise.h5"); final String dataSetName = "ds"; dataSetFile.delete(); assertFalse(dataSetFile.exists()); dataSetFile.deleteOnExit(); final byte[] referenceArray = new byte[1000]; for (int i = 0; i < referenceArray.length; ++i) { referenceArray[i] = (byte) i; } final IHDF5Writer writer = HDF5FactoryProvider.get().configure(dataSetFile).dontUseExtendableDataTypes() .writer(); writer.int8().writeArray(dataSetName, referenceArray); assertEquals(HDF5StorageLayout.CONTIGUOUS, writer.getDataSetInformation(dataSetName) .getStorageLayout()); writer.close(); final byte[] arrayRead = new byte[referenceArray.length]; final HDF5DataSetRandomAccessFile raFile = asRandomAccessFileReadOnly(dataSetFile, dataSetName); int idx = 0; int bsize = referenceArray.length / 10; int bytesRead; while ((bytesRead = raFile.read(arrayRead, idx, bsize)) >= 0) { idx += bytesRead; assertEquals(referenceArray.length - idx, raFile.available()); } assertEquals(referenceArray.length, idx); assertTrue(ArrayUtils.isEquals(referenceArray, arrayRead)); raFile.close(); } @Test public void testReadChunkedBlockwiseMatch() { final File dataSetFile = new File(workingDirectory, "testReadChunkedBlockwiseMatch.h5"); final String dataSetName = "ds"; dataSetFile.delete(); assertFalse(dataSetFile.exists()); dataSetFile.deleteOnExit(); final byte[] referenceArray = new byte[1000]; final int chunkSize = referenceArray.length / 10; for (int i = 0; i < referenceArray.length; ++i) { referenceArray[i] = (byte) i; } final IHDF5Writer writer = HDF5FactoryProvider.get().configure(dataSetFile).keepDataSetsIfTheyExist().writer(); writer.int8().createArray(dataSetName, referenceArray.length, chunkSize); writer.int8().writeArray(dataSetName, referenceArray); assertEquals(HDF5StorageLayout.CHUNKED, writer.getDataSetInformation(dataSetName) .getStorageLayout()); writer.close(); final byte[] arrayRead = new byte[referenceArray.length]; final HDF5DataSetRandomAccessFile raFile = asRandomAccessFileReadOnly(dataSetFile, dataSetName); int idx = 0; int bsize = chunkSize; int bytesRead; while ((bytesRead = raFile.read(arrayRead, idx, bsize)) >= 0) { idx += bytesRead; assertEquals(referenceArray.length - idx, raFile.available()); } assertEquals(referenceArray.length, idx); assertTrue(ArrayUtils.isEquals(referenceArray, arrayRead)); raFile.close(); } @Test public void testReadChunkedBlockwiseMismatch() { final File dataSetFile = new File(workingDirectory, "testReadChunkedBlockwiseMismatch.h5"); final String dataSetName = "ds"; dataSetFile.delete(); assertFalse(dataSetFile.exists()); dataSetFile.deleteOnExit(); final byte[] referenceArray = new byte[1000]; final int chunkSize = referenceArray.length / 10; for (int i = 0; i < referenceArray.length; ++i) { referenceArray[i] = (byte) i; } final IHDF5Writer writer = HDF5FactoryProvider.get().configure(dataSetFile).keepDataSetsIfTheyExist().writer(); writer.int8().createArray(dataSetName, referenceArray.length, chunkSize); writer.int8().writeArray(dataSetName, referenceArray); assertEquals(HDF5StorageLayout.CHUNKED, writer.getDataSetInformation(dataSetName) .getStorageLayout()); writer.close(); final byte[] arrayRead = new byte[referenceArray.length]; final HDF5DataSetRandomAccessFile raFile = asRandomAccessFileReadOnly(dataSetFile, dataSetName); int idx = 0; int bsize = chunkSize + 1; int bytesRead; while ((bytesRead = raFile.read(arrayRead, idx, bsize)) >= 0) { idx += bytesRead; assertEquals(referenceArray.length - idx, raFile.available()); } assertEquals(referenceArray.length, idx); for (int i = 0; i < idx; ++i) { if (referenceArray[i] != arrayRead[i]) { System.err.println("Mismatch " + i + ": " + referenceArray[i] + ":" + arrayRead[i]); break; } } assertTrue(ArrayUtils.isEquals(referenceArray, arrayRead)); raFile.close(); } @Test public void testSkip() { final File dataSetFile = new File(workingDirectory, "testSkip.h5"); final String dataSetName = "ds"; dataSetFile.delete(); assertFalse(dataSetFile.exists()); dataSetFile.deleteOnExit(); final byte[] referenceArray = new byte[1000]; final int chunkSize = referenceArray.length / 10; for (int i = 0; i < referenceArray.length; ++i) { referenceArray[i] = (byte) i; } final IHDF5Writer writer = HDF5FactoryProvider.get().configure(dataSetFile).keepDataSetsIfTheyExist().writer(); writer.int8().createArray(dataSetName, referenceArray.length, chunkSize); writer.int8().writeArray(dataSetName, referenceArray); assertEquals(HDF5StorageLayout.CHUNKED, writer.getDataSetInformation(dataSetName) .getStorageLayout()); writer.close(); final byte[] arrayRead = new byte[referenceArray.length]; final HDF5DataSetRandomAccessFile raFile = asRandomAccessFileReadOnly(dataSetFile, dataSetName); int idx = 0; int bsize = chunkSize + 1; int bytesRead = raFile.read(arrayRead, idx, bsize); assertEquals(bsize, bytesRead); final int skipSize = 73; assertEquals(referenceArray.length - bsize, raFile.available()); assertEquals(skipSize, raFile.skip(skipSize)); assertEquals(referenceArray.length - bsize - skipSize, raFile.available()); assertEquals(skipSize, raFile.skip(skipSize)); assertEquals(referenceArray.length - bsize - 2 * skipSize, raFile.available()); assertEquals(referenceArray[bsize + 2 * skipSize], (byte) raFile.read()); raFile.close(); } @Test public void testMarkSupport() { final File dataSetFile = new File(workingDirectory, "testMarkSupport.h5"); final String dataSetName = "ds"; dataSetFile.delete(); assertFalse(dataSetFile.exists()); dataSetFile.deleteOnExit(); final byte[] referenceArray = new byte[1000]; final int chunkSize = referenceArray.length / 10; for (int i = 0; i < referenceArray.length; ++i) { referenceArray[i] = (byte) i; } final IHDF5Writer writer = HDF5FactoryProvider.get().configure(dataSetFile).keepDataSetsIfTheyExist().writer(); writer.int8().createArray(dataSetName, referenceArray.length, chunkSize); writer.int8().writeArray(dataSetName, referenceArray); assertEquals(HDF5StorageLayout.CHUNKED, writer.getDataSetInformation(dataSetName) .getStorageLayout()); writer.close(); final byte[] arrayRead = new byte[referenceArray.length]; final HDF5DataSetRandomAccessFile raFile = asRandomAccessFileReadOnly(dataSetFile, dataSetName); int idx = 0; int bsize = chunkSize + 1; int bytesRead = raFile.read(arrayRead, idx, bsize); assertEquals(bsize, bytesRead); assertTrue(raFile.markSupported()); long markedFilePointer = raFile.getFilePointer(); raFile.mark(0); assertEquals(markedFilePointer, raFile.getFilePointer()); byte markedByte = (byte) raFile.read(); assertEquals(markedFilePointer + 1, raFile.getFilePointer()); final int skipSize = 73; assertEquals(skipSize, raFile.skip(skipSize)); assertEquals(markedFilePointer + 1 + skipSize, raFile.getFilePointer()); raFile.reset(); assertEquals(markedFilePointer, raFile.getFilePointer()); assertEquals(markedByte, (byte) raFile.read()); assertEquals(skipSize, raFile.skip(skipSize)); assertEquals(skipSize, raFile.skip(skipSize)); assertEquals(markedFilePointer + 1 + 2 * skipSize, raFile.getFilePointer()); raFile.reset(); assertEquals(markedFilePointer, raFile.getFilePointer()); assertEquals(markedByte, (byte) raFile.read()); assertEquals(skipSize, raFile.skip(skipSize)); assertEquals(skipSize, raFile.skip(skipSize)); assertEquals(skipSize, raFile.skip(skipSize)); markedFilePointer = raFile.getFilePointer(); raFile.mark(0); assertEquals(markedFilePointer, raFile.getFilePointer()); markedByte = (byte) raFile.read(); assertEquals(markedFilePointer + 1, raFile.getFilePointer()); assertEquals(skipSize, raFile.skip(skipSize)); assertEquals(markedFilePointer + 1 + skipSize, raFile.getFilePointer()); raFile.reset(); assertEquals(markedFilePointer, raFile.getFilePointer()); assertEquals(markedByte, (byte) raFile.read()); raFile.close(); } @Test public void testWriteTwiceSmallBuffer() throws IOException { final File dataSetFile = new File(workingDirectory, "testWriteTwiceSmallBuffer.h5"); final String dataSetName = "ds"; dataSetFile.delete(); assertFalse(dataSetFile.exists()); dataSetFile.deleteOnExit(); final byte[] referenceArray = new byte[10]; for (int i = 0; i < referenceArray.length; ++i) { referenceArray[i] = (byte) i; } final IHDF5Writer writer = HDF5FactoryProvider.get().configure(dataSetFile).keepDataSetsIfTheyExist().writer(); final HDF5DataSetRandomAccessFile raFile = asRandomAccessFile(writer, dataSetName, HDF5GenericStorageFeatures.GENERIC_CHUNKED, 11, null); raFile.write(referenceArray); raFile.write(referenceArray); raFile.flush(); final HDF5DataSetInformation dsInfo = writer.getDataSetInformation(dataSetName); assertEquals(HDF5StorageLayout.CHUNKED, dsInfo.getStorageLayout()); assertEquals(referenceArray.length * 2, dsInfo.getSize()); assertNull(dsInfo.getTypeInformation().tryGetOpaqueTag()); final byte[] arrayRead = writer.int8().readArray(dataSetName); assertEquals(referenceArray.length * 2, arrayRead.length); for (int i = 0; i < referenceArray.length; ++i) { assertEquals(i, referenceArray[i], arrayRead[i]); } for (int i = 0; i < referenceArray.length; ++i) { assertEquals(i, referenceArray[i], arrayRead[referenceArray.length + i]); } raFile.close(); } @Test public void testWriteTwiceLargeBuffer() throws IOException { final File dataSetFile = new File(workingDirectory, "testWriteTwiceLargeBuffer.h5"); final String dataSetName = "ds"; dataSetFile.delete(); assertFalse(dataSetFile.exists()); dataSetFile.deleteOnExit(); final byte[] referenceArray = new byte[10]; for (int i = 0; i < referenceArray.length; ++i) { referenceArray[i] = (byte) i; } final IHDF5Writer writer = HDF5FactoryProvider.get().configure(dataSetFile).keepDataSetsIfTheyExist().writer(); final HDF5DataSetRandomAccessFile raFile = asRandomAccessFile(writer, dataSetName, HDF5GenericStorageFeatures.GENERIC_CHUNKED, 100, null); raFile.write(referenceArray); raFile.write(referenceArray); raFile.flush(); final HDF5DataSetInformation dsInfo = writer.getDataSetInformation(dataSetName); assertEquals(HDF5StorageLayout.CHUNKED, dsInfo.getStorageLayout()); assertEquals(referenceArray.length * 2, dsInfo.getSize()); assertNull(dsInfo.getTypeInformation().tryGetOpaqueTag()); final byte[] arrayRead = writer.int8().readArray(dataSetName); assertEquals(referenceArray.length * 2, arrayRead.length); for (int i = 0; i < referenceArray.length; ++i) { assertEquals(i, referenceArray[i], arrayRead[i]); } for (int i = 0; i < referenceArray.length; ++i) { assertEquals(i, referenceArray[i], arrayRead[referenceArray.length + i]); } raFile.close(); } @Test public void testCopyIOUtils() throws IOException { final File dataSetFile = new File(workingDirectory, "testCopyIOUtils.h5"); final String dataSetName = "ds"; dataSetFile.delete(); assertFalse(dataSetFile.exists()); dataSetFile.deleteOnExit(); final byte[] referenceArray = new byte[10000]; for (int i = 0; i < referenceArray.length; ++i) { referenceArray[i] = (byte) i; } final IHDF5Writer writer = HDF5FactoryProvider.get().configure(dataSetFile).keepDataSetsIfTheyExist().writer(); final OutputStream ostream = asOutputStream(writer, dataSetName, HDF5GenericStorageFeatures.GENERIC_CHUNKED, 12000, null); IOUtils.copyLarge(new ByteArrayInputStream(referenceArray), ostream); ostream.flush(); final HDF5DataSetInformation dsInfo = writer.getDataSetInformation(dataSetName); assertEquals(HDF5StorageLayout.CHUNKED, dsInfo.getStorageLayout()); assertEquals(referenceArray.length, dsInfo.getSize()); writer.close(); final InputStream istream = asInputStream(dataSetFile, dataSetName); final byte[] arrayRead = IOUtils.toByteArray(istream); assertTrue(ArrayUtils.isEquals(referenceArray, arrayRead)); istream.close(); } @Test public void testSeek() throws IOException { final File dataSetFile = new File(workingDirectory, "testSeek.h5"); final String dataSetName = "ds"; dataSetFile.delete(); assertFalse(dataSetFile.exists()); dataSetFile.deleteOnExit(); final byte[] referenceArray = new byte[10000]; final int chunkSize = referenceArray.length / 10; for (int i = 0; i < referenceArray.length; ++i) { referenceArray[i] = (byte) i; } final IHDF5Writer writer = HDF5FactoryProvider.get().configure(dataSetFile).keepDataSetsIfTheyExist().writer(); writer.int8().createArray(dataSetName, referenceArray.length, chunkSize); writer.int8().writeArray(dataSetName, referenceArray); assertEquals(HDF5StorageLayout.CHUNKED, writer.getDataSetInformation(dataSetName) .getStorageLayout()); writer.close(); final HDF5DataSetRandomAccessFile raFile = asRandomAccessFileReadOnly(dataSetFile, dataSetName); byte[] arrayRead = IOUtils.toByteArray(new AdapterIInputStreamToInputStream(raFile)); assertTrue(ArrayUtils.isEquals(referenceArray, arrayRead)); raFile.seek(0); arrayRead = IOUtils.toByteArray(new AdapterIInputStreamToInputStream(raFile)); assertTrue(ArrayUtils.isEquals(referenceArray, arrayRead)); raFile.seek(1113); assertEquals(referenceArray[1113], (byte) raFile.read()); raFile.close(); } @Test public void testLength() throws IOException { final File dataSetFile = new File(workingDirectory, "testLength.h5"); final String dataSetName = "ds"; dataSetFile.delete(); assertFalse(dataSetFile.exists()); dataSetFile.deleteOnExit(); final byte[] referenceArray = new byte[10000]; final int chunkSize = referenceArray.length / 10; for (int i = 0; i < referenceArray.length; ++i) { referenceArray[i] = (byte) i; } final IHDF5Writer writer = HDF5FactoryProvider.get().configure(dataSetFile).keepDataSetsIfTheyExist().writer(); writer.int8().createArray(dataSetName, referenceArray.length, chunkSize); writer.int8().writeArray(dataSetName, referenceArray); assertEquals(HDF5StorageLayout.CHUNKED, writer.getDataSetInformation(dataSetName) .getStorageLayout()); writer.close(); final HDF5DataSetRandomAccessFile raFile = asRandomAccessFileReadOnly(dataSetFile, dataSetName); assertEquals(referenceArray.length, raFile.length()); raFile.close(); } @Test public void testReadChunkedShortBigEndian() { final File dataSetFile = new File(workingDirectory, "testReadChunkedShortBigEndian.h5"); final String dataSetName = "ds"; dataSetFile.delete(); assertFalse(dataSetFile.exists()); dataSetFile.deleteOnExit(); final short[] referenceArrayShort = new short[50000]; for (int i = 0; i < referenceArrayShort.length; ++i) { referenceArrayShort[i] = (short) i; } final byte[] referenceArrayByte = NativeData.shortToByte(referenceArrayShort, ByteOrder.BIG_ENDIAN); final int chunkSize = referenceArrayByte.length / 10; final IHDF5Writer writer = HDF5FactoryProvider.get().configure(dataSetFile).keepDataSetsIfTheyExist().writer(); writer.int8().createArray(dataSetName, referenceArrayByte.length, chunkSize); writer.int8().writeArray(dataSetName, referenceArrayByte); assertEquals(HDF5StorageLayout.CHUNKED, writer.getDataSetInformation(dataSetName) .getStorageLayout()); writer.close(); final short[] arrayRead = new short[referenceArrayShort.length]; final HDF5DataSetRandomAccessFile raFile = asRandomAccessFileReadOnly(dataSetFile, dataSetName); int idx = 0; while (raFile.available() >= 2) { arrayRead[idx++] = raFile.readShort(); assertEquals(referenceArrayByte.length - idx * 2, raFile.available()); } assertEquals(referenceArrayByte.length, idx * 2); assertTrue(ArrayUtils.isEquals(referenceArrayShort, arrayRead)); raFile.close(); } @Test public void testReadChunkedShortLittleEndian() { final File dataSetFile = new File(workingDirectory, "testReadChunkedShortLittleEndian.h5"); final String dataSetName = "ds"; dataSetFile.delete(); assertFalse(dataSetFile.exists()); dataSetFile.deleteOnExit(); final short[] referenceArrayShort = new short[50000]; for (int i = 0; i < referenceArrayShort.length; ++i) { referenceArrayShort[i] = (short) i; } final byte[] referenceArrayByte = NativeData.shortToByte(referenceArrayShort, ByteOrder.LITTLE_ENDIAN); final int chunkSize = referenceArrayByte.length / 10; final IHDF5Writer writer = HDF5FactoryProvider.get().configure(dataSetFile).keepDataSetsIfTheyExist().writer(); writer.int8().createArray(dataSetName, referenceArrayByte.length, chunkSize); writer.int8().writeArray(dataSetName, referenceArrayByte); assertEquals(HDF5StorageLayout.CHUNKED, writer.getDataSetInformation(dataSetName) .getStorageLayout()); writer.close(); final short[] arrayRead = new short[referenceArrayShort.length]; final HDF5DataSetRandomAccessFile raFile = asRandomAccessFileReadOnly(dataSetFile, dataSetName); raFile.setByteOrder(java.nio.ByteOrder.LITTLE_ENDIAN); int idx = 0; while (raFile.available() >= 2) { arrayRead[idx++] = raFile.readShort(); assertEquals(referenceArrayByte.length - idx * 2, raFile.available()); } assertEquals(referenceArrayByte.length, idx * 2); assertTrue(ArrayUtils.isEquals(referenceArrayShort, arrayRead)); raFile.close(); } @Test public void testReadChunkedDoubleBigEndian() { final File dataSetFile = new File(workingDirectory, "testReadChunkedDoubleBigEndian.h5"); final String dataSetName = "ds"; dataSetFile.delete(); assertFalse(dataSetFile.exists()); dataSetFile.deleteOnExit(); final double[] referenceArrayDouble = new double[12500]; for (int i = 0; i < referenceArrayDouble.length; ++i) { referenceArrayDouble[i] = i; } final byte[] referenceArrayByte = NativeData.doubleToByte(referenceArrayDouble, ByteOrder.BIG_ENDIAN); final int chunkSize = referenceArrayByte.length / 10; final IHDF5Writer writer = HDF5FactoryProvider.get().configure(dataSetFile).keepDataSetsIfTheyExist().writer(); writer.int8().createArray(dataSetName, referenceArrayByte.length, chunkSize); writer.int8().writeArray(dataSetName, referenceArrayByte); assertEquals(HDF5StorageLayout.CHUNKED, writer.getDataSetInformation(dataSetName) .getStorageLayout()); writer.close(); final double[] arrayRead = new double[referenceArrayDouble.length]; final HDF5DataSetRandomAccessFile raFile = asRandomAccessFileReadOnly(dataSetFile, dataSetName); int idx = 0; while (raFile.available() >= 2) { arrayRead[idx++] = raFile.readDouble(); assertEquals(referenceArrayByte.length - idx * 8, raFile.available()); } assertEquals(referenceArrayByte.length, idx * 8); assertTrue(ArrayUtils.isEquals(referenceArrayDouble, arrayRead)); raFile.close(); } @Test public void testReadChunkedDoubleLittleEndian() { final File dataSetFile = new File(workingDirectory, "testReadChunkedDoubleLittleEndian.h5"); final String dataSetName = "ds"; dataSetFile.delete(); assertFalse(dataSetFile.exists()); dataSetFile.deleteOnExit(); final double[] referenceArrayDouble = new double[12500]; for (int i = 0; i < referenceArrayDouble.length; ++i) { referenceArrayDouble[i] = i; } final byte[] referenceArrayByte = NativeData.doubleToByte(referenceArrayDouble, ByteOrder.LITTLE_ENDIAN); final int chunkSize = referenceArrayByte.length / 10; final IHDF5Writer writer = HDF5FactoryProvider.get().configure(dataSetFile).keepDataSetsIfTheyExist().writer(); writer.int8().createArray(dataSetName, referenceArrayByte.length, chunkSize); writer.int8().writeArray(dataSetName, referenceArrayByte); assertEquals(HDF5StorageLayout.CHUNKED, writer.getDataSetInformation(dataSetName) .getStorageLayout()); writer.close(); final double[] arrayRead = new double[referenceArrayDouble.length]; final HDF5DataSetRandomAccessFile raFile = asRandomAccessFileReadOnly(dataSetFile, dataSetName); raFile.setByteOrder(java.nio.ByteOrder.LITTLE_ENDIAN); int idx = 0; while (raFile.available() >= 2) { arrayRead[idx++] = raFile.readDouble(); assertEquals(referenceArrayByte.length - idx * 8, raFile.available()); } assertEquals(referenceArrayByte.length, idx * 8); assertTrue(ArrayUtils.isEquals(referenceArrayDouble, arrayRead)); raFile.close(); } @Test public void testReadChunkedStringReadline() throws UnsupportedEncodingException { final File dataSetFile = new File(workingDirectory, "testReadChunkedStringReadline.h5"); final String dataSetName = "ds"; dataSetFile.delete(); assertFalse(dataSetFile.exists()); dataSetFile.deleteOnExit(); final String reference = "One\nTwo\nThree\r\nFour"; final byte[] bytesReference = reference.getBytes("ASCII"); final int chunkSize = 4; final IHDF5Writer writer = HDF5FactoryProvider.get().configure(dataSetFile).keepDataSetsIfTheyExist().writer(); writer.int8().createArray(dataSetName, bytesReference.length, chunkSize); writer.int8().writeArray(dataSetName, bytesReference); assertEquals(HDF5StorageLayout.CHUNKED, writer.getDataSetInformation(dataSetName) .getStorageLayout()); writer.close(); final HDF5DataSetRandomAccessFile raFile = asRandomAccessFileReadOnly(dataSetFile, dataSetName); assertEquals("One", raFile.readLine()); assertEquals("Two", raFile.readLine()); assertEquals("Three", raFile.readLine()); assertEquals("Four", raFile.readLine()); assertEquals(0, raFile.available()); raFile.close(); } @Test public void testWriteByteByByte() throws IOException { final File dataSetFile = new File(workingDirectory, "testWriteByteByByte.h5"); final String dataSetName = "ds"; dataSetFile.delete(); assertFalse(dataSetFile.exists()); dataSetFile.deleteOnExit(); final int chunkSize = 10; final IHDF5Writer writer = HDF5FactoryProvider.get().configure(dataSetFile).keepDataSetsIfTheyExist().writer(); writer.int8().createArray(dataSetName, 0, chunkSize); writer.close(); final HDF5DataSetRandomAccessFile raFile = asRandomAccessFileReadWrite(dataSetFile, dataSetName); raFile.mark(0); for (int i = 0; i < 256; ++i) { raFile.write(i); } raFile.reset(); final byte[] arrayRead = IOUtils.toByteArray(new AdapterIInputStreamToInputStream(raFile)); assertEquals(256, arrayRead.length); for (int i = 0; i < 256; ++i) { assertEquals(Integer.toString(i), (byte) i, arrayRead[i]); } raFile.close(); } @Test public void testWriteByteBlock() throws IOException { final File dataSetFile = new File(workingDirectory, "testWriteByteBlock.h5"); final String dataSetName = "ds"; dataSetFile.delete(); assertFalse(dataSetFile.exists()); dataSetFile.deleteOnExit(); final int chunkSize = 10; final IHDF5Writer writer = HDF5FactoryProvider.get().configure(dataSetFile).keepDataSetsIfTheyExist().writer(); writer.int8().createArray(dataSetName, 0, chunkSize); writer.close(); final HDF5DataSetRandomAccessFile raFile = asRandomAccessFileReadWrite(dataSetFile, dataSetName); raFile.mark(0); final byte[] arr = new byte[256]; for (int i = 0; i < 256; ++i) { arr[i] = (byte) i; } raFile.write(arr); raFile.reset(); final byte[] arrayRead = IOUtils.toByteArray(new AdapterIInputStreamToInputStream(raFile)); assertEquals(256, arrayRead.length); for (int i = 0; i < 256; ++i) { assertEquals(Integer.toString(i), (byte) i, arrayRead[i]); } raFile.close(); } @Test public void testWriteDouble() throws IOException { final File dataSetFile = new File(workingDirectory, "testWriteDouble.h5"); final String dataSetName = "ds"; dataSetFile.delete(); assertFalse(dataSetFile.exists()); dataSetFile.deleteOnExit(); final int chunkSize = 10; final IHDF5Writer writer = HDF5FactoryProvider.get().configure(dataSetFile).keepDataSetsIfTheyExist().writer(); writer.int8().createArray(dataSetName, 0, chunkSize); writer.close(); final HDF5DataSetRandomAccessFile raFile = asRandomAccessFileReadWrite(dataSetFile, dataSetName); raFile.mark(0); for (int i = 0; i < 256; ++i) { raFile.writeDouble(i); } raFile.reset(); for (int i = 0; i < 256; ++i) { assertEquals(Integer.toString(i), (double) i, raFile.readDouble()); } assertEquals(0, raFile.available()); raFile.close(); } @Test public void testWriteBytesOfString() throws IOException { final File dataSetFile = new File(workingDirectory, "testWriteBytesOfString.h5"); final String dataSetName = "ds"; dataSetFile.delete(); assertFalse(dataSetFile.exists()); dataSetFile.deleteOnExit(); final int chunkSize = 10; final IHDF5Writer writer = HDF5FactoryProvider.get().configure(dataSetFile).keepDataSetsIfTheyExist().writer(); writer.int8().createArray(dataSetName, 0, chunkSize); writer.close(); final HDF5DataSetRandomAccessFile raFile = asRandomAccessFileReadWrite(dataSetFile, dataSetName); raFile.mark(0); raFile.writeBytes("TestString\n"); raFile.reset(); assertEquals("TestString", raFile.readLine()); raFile.close(); } @Test public void testWriteStringUTF8() throws IOException { final File dataSetFile = new File(workingDirectory, "testWriteStringUTF8.h5"); final String dataSetName = "ds"; dataSetFile.delete(); assertFalse(dataSetFile.exists()); dataSetFile.deleteOnExit(); final int chunkSize = 10; final IHDF5Writer writer = HDF5FactoryProvider.get().configure(dataSetFile).keepDataSetsIfTheyExist().writer(); writer.int8().createArray(dataSetName, 0, chunkSize); writer.close(); final HDF5DataSetRandomAccessFile raFile = asRandomAccessFileReadWrite(dataSetFile, dataSetName); raFile.mark(0); raFile.writeUTF("TestString\u1873"); raFile.reset(); assertEquals("TestString\u1873", raFile.readUTF()); raFile.close(); } @Test public void testPendingExtension() throws IOException { final File dataSetFile = new File(workingDirectory, "testPendingExtension.h5"); final String dataSetName = "ds"; dataSetFile.delete(); assertFalse(dataSetFile.exists()); dataSetFile.deleteOnExit(); final int chunkSize = 10; final IHDF5Writer writer = HDF5FactoryProvider.get().configure(dataSetFile).keepDataSetsIfTheyExist().writer(); writer.int8().createArray(dataSetName, 0, chunkSize); writer.close(); final HDF5DataSetRandomAccessFile raFile = asRandomAccessFileReadWrite(dataSetFile, dataSetName); raFile.seek(20); raFile.write(42); assertEquals(21, raFile.length()); raFile.seek(0); final byte[] arrayRead = IOUtils.toByteArray(new AdapterIInputStreamToInputStream(raFile)); assertEquals(42, arrayRead[20]); for (int i = 0; i < 20; ++i) { assertEquals("Position " + i, 0, arrayRead[0]); } raFile.close(); } @Test public void testEmptyDatasetDefaultParameters() throws IOException { final File dataSetFile = new File(workingDirectory, "testEmptyDatasetDefaultParameters.h5"); final String dataSetName = "ds"; dataSetFile.delete(); assertFalse(dataSetFile.exists()); dataSetFile.deleteOnExit(); final HDF5DataSetRandomAccessFile raFile = asRandomAccessFileReadWrite(dataSetFile, dataSetName); raFile.seek(20); raFile.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(dataSetFile); assertTrue(reader.exists(dataSetName)); final HDF5DataSetInformation info = reader.getDataSetInformation(dataSetName); assertEquals(0, info.getSize()); assertEquals(HDF5StorageLayout.CHUNKED, info.getStorageLayout()); assertEquals("FILE", info.getTypeInformation().tryGetOpaqueTag()); final int[] chunkSizesOrNull = info.tryGetChunkSizes(); assertNotNull(chunkSizesOrNull); assertEquals(1, chunkSizesOrNull.length); assertEquals(1024 * 1024, chunkSizesOrNull[0]); reader.close(); } @Test public void testEmptyDatasetOpaqueSmallChunkSize() throws IOException { final File dataSetFile = new File(workingDirectory, "testEmptyDatasetOpaqueSmallChunkSize.h5"); final String dataSetName = "ds"; dataSetFile.delete(); assertFalse(dataSetFile.exists()); dataSetFile.deleteOnExit(); final int chunkSize = 10 * 1024; final HDF5DataSetRandomAccessFile raFile = asRandomAccessFile(dataSetFile, dataSetName, HDF5GenericStorageFeatures.GENERIC_CHUNKED, chunkSize, "FILE"); raFile.seek(20); raFile.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(dataSetFile); assertTrue(reader.exists(dataSetName)); final HDF5DataSetInformation info = reader.getDataSetInformation(dataSetName); assertEquals(0, info.getSize()); assertEquals(HDF5StorageLayout.CHUNKED, info.getStorageLayout()); assertEquals("FILE", info.getTypeInformation().tryGetOpaqueTag()); final int[] chunkSizesOrNull = info.tryGetChunkSizes(); assertNotNull(chunkSizesOrNull); assertEquals(1, chunkSizesOrNull.length); assertEquals(chunkSize, chunkSizesOrNull[0]); reader.close(); } @Test public void testEmptyDatasetContiguous() throws IOException { final File dataSetFile = new File(workingDirectory, "testEmptyDatasetContiguous.h5"); final String dataSetName = "ds"; dataSetFile.delete(); assertFalse(dataSetFile.exists()); dataSetFile.deleteOnExit(); final HDF5DataSetRandomAccessFile raFile = asRandomAccessFile(dataSetFile, dataSetName, HDF5GenericStorageFeatures.GENERIC_CONTIGUOUS, 1024, null); raFile.seek(20); raFile.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(dataSetFile); assertTrue(reader.exists(dataSetName)); final HDF5DataSetInformation info = reader.getDataSetInformation(dataSetName); assertEquals(1024, info.getSize()); assertEquals(HDF5StorageLayout.CONTIGUOUS, info.getStorageLayout()); assertNull(info.getTypeInformation().tryGetOpaqueTag()); final int[] chunkSizesOrNull = info.tryGetChunkSizes(); assertNull(chunkSizesOrNull); reader.close(); } @Test public void testEmptyDatasetCompact() throws IOException { final File dataSetFile = new File(workingDirectory, "testEmptyDatasetCompact.h5"); final String dataSetName = "ds"; dataSetFile.delete(); assertFalse(dataSetFile.exists()); dataSetFile.deleteOnExit(); final HDF5DataSetRandomAccessFile raFile = asRandomAccessFile(dataSetFile, dataSetName, HDF5GenericStorageFeatures.GENERIC_COMPACT, 1024, null); raFile.seek(20); raFile.close(); final IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(dataSetFile); assertTrue(reader.exists(dataSetName)); final HDF5DataSetInformation info = reader.getDataSetInformation(dataSetName); assertEquals(1024, info.getSize()); assertEquals(HDF5StorageLayout.COMPACT, info.getStorageLayout()); assertNull(info.getTypeInformation().tryGetOpaqueTag()); final int[] chunkSizesOrNull = info.tryGetChunkSizes(); assertNull(chunkSizesOrNull); reader.close(); } } libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/tools/000077500000000000000000000000001256564762100253625ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/tools/HDF5CodeGenerator.java000066400000000000000000000347351256564762100313710ustar00rootroot00000000000000/* * Copyright 2008 ETH Zuerich, CISD * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5.tools; import java.io.File; import java.io.IOException; import java.io.PrintStream; import org.apache.commons.io.FileUtils; import org.apache.commons.lang.StringUtils; /** * A code generator for the identical parts of the HDF5 Java classes class for different numerical * types. * * @author Bernd Rinn */ public class HDF5CodeGenerator { static class TemplateParameters { final String name; final String capitalizedName; final String capitalizedClassName; final String upperCaseClassName; final String wrapperName; final String storageType; final String featureBasedStorageType; final String storageTypeImport; final String memoryType; final String elementSize; final boolean isUnsigned; final boolean isInteger; TemplateParameters(String name, String capitalizedName, String capitalizedClassName, String wrapperName, String storageType, String featureBasedStorageType, String storageTypeImport, String memoryType, String elementSize, boolean isUnsigned, boolean isInteger) { this.name = name; this.capitalizedName = capitalizedName; this.capitalizedClassName = capitalizedClassName; this.upperCaseClassName = capitalizedClassName.toUpperCase(); this.wrapperName = wrapperName; this.storageType = storageType; this.featureBasedStorageType = featureBasedStorageType; this.storageTypeImport = storageTypeImport; this.memoryType = memoryType; this.elementSize = elementSize; this.isUnsigned = isUnsigned; this.isInteger = isInteger; } } static TemplateParameters tp(String name, String capitalizedName, String capitalizedClassName, String wrapperName, String storageType, String featureBasedStorageType, String storageTypeImport, String memoryType, String elementSize, boolean isUnsigned, boolean isInteger) { return new TemplateParameters(name, capitalizedName, capitalizedClassName, wrapperName, storageType, featureBasedStorageType, storageTypeImport, memoryType, elementSize, isUnsigned, isInteger); } static final TemplateParameters PLACEHOLDERS = tp("__name__", "__Name__", "__Classname__", "__Wrappername__", "__Storagetype__", "__FeatureBasedStoragetype__", "__StoragetypeImport__", "__Memorytype__", "__elementsize__", false, false); static final TemplateParameters[] NUMERICAL_TYPES = new TemplateParameters[] { tp("byte", "Byte", "Int", "Byte", "H5T_STD_I8LE", "features.isSigned() ? H5T_STD_I8LE : H5T_STD_U8LE", "import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_I8LE;\n" + "import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_U8LE;", "H5T_NATIVE_INT8", "1", false, true), tp("byte", "Byte", "Int", "Byte", "H5T_STD_U8LE", "H5T_STD_U8LE", "import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_U8LE;", "H5T_NATIVE_UINT8", "1", true, true), tp("short", "Short", "Int", "Short", "H5T_STD_I16LE", "features.isSigned() ? H5T_STD_I16LE : H5T_STD_U16LE", "import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_I16LE;\n" + "import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_U16LE;", "H5T_NATIVE_INT16", "2", false, true), tp("short", "Short", "Int", "Short", "H5T_STD_U16LE", "H5T_STD_U16LE", "import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_U16LE;", "H5T_NATIVE_UINT16", "2", true, true), tp("int", "Int", "Int", "Integer", "H5T_STD_I32LE", "features.isSigned() ? H5T_STD_I32LE : H5T_STD_U32LE", "import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_I32LE;\n" + "import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_U32LE;", "H5T_NATIVE_INT32", "4", false, true), tp("int", "Int", "Int", "Integer", "H5T_STD_U32LE", "H5T_STD_U32LE", "import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_U32LE;", "H5T_NATIVE_UINT32", "4", true, true), tp("long", "Long", "Int", "Long", "H5T_STD_I64LE", "features.isSigned() ? H5T_STD_I64LE : H5T_STD_U64LE", "import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_I64LE;\n" + "import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_U64LE;", "H5T_NATIVE_INT64", "8", false, true), tp("long", "Long", "Int", "Long", "H5T_STD_U64LE", "H5T_STD_U64LE", "import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_STD_U64LE;", "H5T_NATIVE_UINT64", "8", true, true), tp("float", "Float", "Float", "Float", "H5T_IEEE_F32LE", "H5T_IEEE_F32LE", "import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_IEEE_F32LE;", "H5T_NATIVE_FLOAT", "4", false, false), tp("double", "Double", "Float", "Double", "H5T_IEEE_F64LE", "H5T_IEEE_F64LE", "import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_IEEE_F64LE;", "H5T_NATIVE_DOUBLE", "8", false, false) }; /** * Generate the code for all numerical types from codeTemplate and write it to * stdout. */ static void generateCode(final String codeTemplate) { for (TemplateParameters t : NUMERICAL_TYPES) { generateCode(codeTemplate, t, System.out); } } /** * Generate the code for all numerical types from codeTemplate and write it to * out. */ static void generateCode(final String codeTemplate, final TemplateParameters params, final PrintStream out) { String s = codeTemplate; if (params.isInteger) { s = StringUtils.replace(s, "__SuperInterface__", "IHDF5Unsigned__Name__Writer"); s = StringUtils.replace(s, "__OverrideIfInt__", "@Override\n "); s = StringUtils .replace( s, "__SupressWarning__ ", " // Note: It is a trick for keeping backward compatibility to let this interface extend \n" + " // IHDF5Unsigned__Name__Writer instead of IHDF5__Name__Reader as it logically should.\n" + " // Once we remove IHDF5Unsigned__Name__Writer, uncomment the following line and remove\n" + " // all @Override annotations and we are fine again.\n" + "//public interface IHDF5__Name__Writer extends IHDF5__Name__Reader\n" + "@SuppressWarnings(\"deprecation\")\n"); s = StringUtils .replace( s, "__NoteUnsigned__", " *

\n" + " * Note: If you need to convert from and to unsigned values, use the methods of \n" + " * {@link UnsignedIntUtils}.\n"); } else { s = StringUtils.replace(s, "__SuperInterface__", "IHDF5__Name__Reader"); s = StringUtils.replace(s, "__OverrideIfInt__", ""); s = StringUtils.replace(s, "__SupressWarning__ ", ""); s = StringUtils.replace(s, "__NoteUnsigned__", ""); } s = StringUtils.replace(s, PLACEHOLDERS.name, params.name); s = StringUtils.replace(s, PLACEHOLDERS.capitalizedName, params.capitalizedName); s = StringUtils.replace(s, PLACEHOLDERS.capitalizedClassName, params.capitalizedClassName); s = StringUtils.replace(s, PLACEHOLDERS.upperCaseClassName, params.upperCaseClassName); s = StringUtils.replace(s, PLACEHOLDERS.wrapperName, params.wrapperName); s = StringUtils.replace(s, PLACEHOLDERS.storageType, params.storageType); s = StringUtils.replace(s, PLACEHOLDERS.featureBasedStorageType, params.featureBasedStorageType); s = StringUtils.replace(s, PLACEHOLDERS.storageTypeImport, params.storageTypeImport); s = StringUtils.replace(s, PLACEHOLDERS.memoryType, params.memoryType); s = StringUtils.replace(s, PLACEHOLDERS.elementSize, params.elementSize); out.println(s); } public static void main(String[] args) throws IOException { for (TemplateParameters t : NUMERICAL_TYPES) { if (t.isUnsigned == false) { final String interfaceTemplateReader = FileUtils .readFileToString(new File( "sourceTest/java/ch/systemsx/cisd/hdf5/tools/IHDF5PrimitiveReader.java.templ")); final PrintStream outInterfaceReader = new PrintStream(new File("source/java/ch/systemsx/cisd/hdf5/IHDF5" + t.capitalizedName + "Reader.java")); generateCode(interfaceTemplateReader, t, outInterfaceReader); outInterfaceReader.close(); } final String classTemplateReader = FileUtils .readFileToString(new File( t.isUnsigned ? "sourceTest/java/ch/systemsx/cisd/hdf5/tools/HDF5UnsignedPrimitiveReader.java.templ" : "sourceTest/java/ch/systemsx/cisd/hdf5/tools/HDF5PrimitiveReader.java.templ")); final PrintStream outclassReader = new PrintStream(new File("source/java/ch/systemsx/cisd/hdf5/HDF5" + (t.isUnsigned ? "Unsigned" : "") + t.capitalizedName + "Reader.java")); generateCode(classTemplateReader, t, outclassReader); outclassReader.close(); final String interfaceTemplateWriter = FileUtils .readFileToString(new File( t.isUnsigned ? "sourceTest/java/ch/systemsx/cisd/hdf5/tools/IHDF5UnsignedPrimitiveWriter.java.templ" : "sourceTest/java/ch/systemsx/cisd/hdf5/tools/IHDF5PrimitiveWriter.java.templ")); final PrintStream outInterfaceWriter = new PrintStream(new File("source/java/ch/systemsx/cisd/hdf5/IHDF5" + (t.isUnsigned ? "Unsigned" : "") + t.capitalizedName + "Writer.java")); generateCode(interfaceTemplateWriter, t, outInterfaceWriter); outInterfaceWriter.close(); final String classTemplateWriter = FileUtils .readFileToString(new File( t.isUnsigned ? "sourceTest/java/ch/systemsx/cisd/hdf5/tools/HDF5UnsignedPrimitiveWriter.java.templ" : "sourceTest/java/ch/systemsx/cisd/hdf5/tools/HDF5PrimitiveWriter.java.templ")); final PrintStream outclassWriter = new PrintStream(new File("source/java/ch/systemsx/cisd/hdf5/HDF5" + (t.isUnsigned ? "Unsigned" : "") + t.capitalizedName + "Writer.java")); generateCode(classTemplateWriter, t, outclassWriter); outclassWriter.close(); } } } libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/tools/HDF5PrimitiveReader.java.templ000066400000000000000000001030461256564762100330530ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.MatrixUtils.cardinalityBoundIndices; import static ch.systemsx.cisd.hdf5.MatrixUtils.checkBoundIndices; import static ch.systemsx.cisd.hdf5.MatrixUtils.createFullBlockDimensionsAndOffset; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_ARRAY; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.__Memorytype__; import java.util.Arrays; import java.util.Iterator; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import ncsa.hdf.hdf5lib.exceptions.HDF5SpaceRankMismatch; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MD__Name__Array; import ch.systemsx.cisd.hdf5.HDF5BaseReader.DataSpaceParameters; import ch.systemsx.cisd.hdf5.HDF5DataTypeInformation.DataTypeInfoOptions; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; import ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants; /** * The implementation of {@link IHDF5__Name__Reader}. * * @author Bernd Rinn */ class HDF5__Name__Reader implements IHDF5__Name__Reader { private final HDF5BaseReader baseReader; HDF5__Name__Reader(HDF5BaseReader baseReader) { assert baseReader != null; this.baseReader = baseReader; } // For Unit tests only. HDF5BaseReader getBaseReader() { return baseReader; } // ///////////////////// // Attributes // ///////////////////// @Override public __name__ getAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp<__Wrappername__> getAttributeRunnable = new ICallableWithCleanUp<__Wrappername__>() { @Override public __Wrappername__ call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final __name__[] data = baseReader.h5.readAttributeAs__Name__Array(attributeId, __Memorytype__, 1); return data[0]; } }; return baseReader.runner.call(getAttributeRunnable); } @Override public __name__[] getArrayAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp<__name__[]> getAttributeRunnable = new ICallableWithCleanUp<__name__[]>() { @Override public __name__[] call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); return get__Name__ArrayAttribute(objectId, attributeName, registry); } }; return baseReader.runner.call(getAttributeRunnable); } @Override public MD__Name__Array getMDArrayAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public MD__Name__Array call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); return get__Name__MDArrayAttribute(objectId, attributeName, registry); } }; return baseReader.runner.call(getAttributeRunnable); } @Override public __name__[][] getMatrixAttr(final String objectPath, final String attributeName) throws HDF5JavaException { final MD__Name__Array array = getMDArrayAttr(objectPath, attributeName); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } // ///////////////////// // Data Sets // ///////////////////// @Override public __name__ read(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp<__Wrappername__> readCallable = new ICallableWithCleanUp<__Wrappername__>() { @Override public __Wrappername__ call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final __name__[] data = new __name__[1]; baseReader.h5.readDataSet(dataSetId, __Memorytype__, data); return data[0]; } }; return baseReader.runner.call(readCallable); } @Override public __name__[] readArray(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp<__name__[]> readCallable = new ICallableWithCleanUp<__name__[]>() { @Override public __name__[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); return read__Name__Array(dataSetId, registry); } }; return baseReader.runner.call(readCallable); } private __name__[] read__Name__Array(int dataSetId, ICleanUpRegistry registry) { try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); final __name__[] data = new __name__[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, __Memorytype__, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return data; } catch (HDF5LibraryException ex) { if (ex.getMajorErrorNumber() == HDF5Constants.H5E_DATATYPE && ex.getMinorErrorNumber() == HDF5Constants.H5E_CANTINIT) { // Check whether it is an array data type. final int dataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); if (baseReader.h5.getClassType(dataTypeId) == HDF5Constants.H5T_ARRAY) { return read__Name__ArrayFromArrayType(dataSetId, dataTypeId, registry); } } throw ex; } } private __name__[] read__Name__ArrayFromArrayType(int dataSetId, final int dataTypeId, ICleanUpRegistry registry) { final int spaceId = baseReader.h5.createScalarDataSpace(); final int[] dimensions = baseReader.h5.getArrayDimensions(dataTypeId); final __name__[] data = new __name__[HDF5Utils.getOneDimensionalArraySize(dimensions)]; final int memoryDataTypeId = baseReader.h5.createArrayType(__Memorytype__, data.length, registry); baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceId, spaceId, data); return data; } @Override public int[] readToMDArrayWithOffset(final String objectPath, final MD__Name__Array array, final int[] memoryOffset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getBlockSpaceParameters(dataSetId, memoryOffset, array .dimensions(), registry); final int nativeDataTypeId = baseReader.getNativeDataTypeId(dataSetId, __Memorytype__, registry); baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, array. getAsFlatArray()); return MDArray.toInt(spaceParams.dimensions); } }; return baseReader.runner.call(readCallable); } @Override public int[] readToMDArrayBlockWithOffset(final String objectPath, final MD__Name__Array array, final int[] blockDimensions, final long[] offset, final int[] memoryOffset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getBlockSpaceParameters(dataSetId, memoryOffset, array .dimensions(), offset, blockDimensions, registry); final int nativeDataTypeId = baseReader.getNativeDataTypeId(dataSetId, __Memorytype__, registry); baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, array .getAsFlatArray()); return MDArray.toInt(spaceParams.dimensions); } }; return baseReader.runner.call(readCallable); } @Override public __name__[] readArrayBlock(final String objectPath, final int blockSize, final long blockNumber) { return readArrayBlockWithOffset(objectPath, blockSize, blockNumber * blockSize); } @Override public __name__[] readArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp<__name__[]> readCallable = new ICallableWithCleanUp<__name__[]>() { @Override public __name__[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockSize, registry); final __name__[] data = new __name__[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, __Memorytype__, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return data; } }; return baseReader.runner.call(readCallable); } @Override public __name__[][] readMatrix(final String objectPath) throws HDF5JavaException { final MD__Name__Array array = readMDArray(objectPath); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public __name__[][] readMatrixBlock(final String objectPath, final int blockSizeX, final int blockSizeY, final long blockNumberX, final long blockNumberY) throws HDF5JavaException { final MD__Name__Array array = readMDArrayBlock(objectPath, new int[] { blockSizeX, blockSizeY }, new long[] { blockNumberX, blockNumberY }); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public __name__[][] readMatrixBlockWithOffset(final String objectPath, final int blockSizeX, final int blockSizeY, final long offsetX, final long offsetY) throws HDF5JavaException { final MD__Name__Array array = readMDArrayBlockWithOffset(objectPath, new int[] { blockSizeX, blockSizeY }, new long[] { offsetX, offsetY }); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public MD__Name__Array readMDArraySlice(String objectPath, IndexMap boundIndices) { baseReader.checkOpen(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; final int cardBoundIndices = cardinalityBoundIndices(boundIndices); checkBoundIndices(objectPath, fullDimensions, cardBoundIndices); final int[] effectiveBlockDimensions = new int[fullBlockDimensions.length - cardBoundIndices]; Arrays.fill(effectiveBlockDimensions, -1); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, null, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MD__Name__Array result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); if (fullBlockDimensions.length == cardBoundIndices) // no free indices { return new MD__Name__Array(result.getAsFlatArray(), new int[] { 1 }); } else { return new MD__Name__Array(result.getAsFlatArray(), effectiveBlockDimensions); } } @Override public MD__Name__Array readMDArraySlice(String objectPath, long[] boundIndices) { baseReader.checkOpen(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; final int cardBoundIndices = cardinalityBoundIndices(boundIndices); checkBoundIndices(objectPath, fullDimensions, boundIndices); final int[] effectiveBlockDimensions = new int[fullBlockDimensions.length - cardBoundIndices]; Arrays.fill(effectiveBlockDimensions, -1); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, null, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MD__Name__Array result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); if (fullBlockDimensions.length == cardBoundIndices) // no free indices { return new MD__Name__Array(result.getAsFlatArray(), new int[] { 1 }); } else { return new MD__Name__Array(result.getAsFlatArray(), effectiveBlockDimensions); } } @Override public MD__Name__Array readMDArray(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public MD__Name__Array call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); return read__Name__MDArray(dataSetId, registry); } }; return baseReader.runner.call(readCallable); } MD__Name__Array read__Name__MDArray(int dataSetId, ICleanUpRegistry registry) { try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); final __name__[] data = new __name__[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, __Memorytype__, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return new MD__Name__Array(data, spaceParams.dimensions); } catch (HDF5LibraryException ex) { if (ex.getMajorErrorNumber() == HDF5Constants.H5E_DATATYPE && ex.getMinorErrorNumber() == HDF5Constants.H5E_CANTINIT) { // Check whether it is an array data type. final int dataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); if (baseReader.h5.getClassType(dataTypeId) == HDF5Constants.H5T_ARRAY) { return read__Name__MDArrayFromArrayType(dataSetId, dataTypeId, registry); } } throw ex; } } private MD__Name__Array read__Name__MDArrayFromArrayType(int dataSetId, final int dataTypeId, ICleanUpRegistry registry) { final int[] arrayDimensions = baseReader.h5.getArrayDimensions(dataTypeId); final int memoryDataTypeId = baseReader.h5.createArrayType(__Memorytype__, arrayDimensions, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); if (spaceParams.blockSize == 0) { final int spaceId = baseReader.h5.createScalarDataSpace(); final __name__[] data = new __name__[MDArray.getLength(arrayDimensions)]; baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceId, spaceId, data); return new MD__Name__Array(data, arrayDimensions); } else { final __name__[] data = new __name__[MDArray.getLength(arrayDimensions) * spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return new MD__Name__Array(data, MatrixUtils.concat(MDArray.toInt(spaceParams.dimensions), arrayDimensions)); } } @Override public MD__Name__Array readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, IndexMap boundIndices) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readSlicedMDArrayBlockWithOffset(objectPath, blockDimensions, offset, boundIndices); } @Override public MD__Name__Array readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, long[] boundIndices) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readSlicedMDArrayBlockWithOffset(objectPath, blockDimensions, offset, boundIndices); } @Override public MD__Name__Array readMDArrayBlock(final String objectPath, final int[] blockDimensions, final long[] blockNumber) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readMDArrayBlockWithOffset(objectPath, blockDimensions, offset); } @Override public MD__Name__Array readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, IndexMap boundIndices) { baseReader.checkOpen(); final int[] effectiveBlockDimensions = blockDimensions.clone(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; checkBoundIndices(objectPath, fullDimensions, blockDimensions, cardinalityBoundIndices(boundIndices)); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, offset, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MD__Name__Array result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); return new MD__Name__Array(result.getAsFlatArray(), effectiveBlockDimensions); } @Override public MD__Name__Array readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, long[] boundIndices) { baseReader.checkOpen(); final int[] effectiveBlockDimensions = blockDimensions.clone(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; checkBoundIndices(objectPath, fullDimensions, blockDimensions, cardinalityBoundIndices(boundIndices)); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, offset, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MD__Name__Array result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); return new MD__Name__Array(result.getAsFlatArray(), effectiveBlockDimensions); } @Override public MD__Name__Array readMDArrayBlockWithOffset(final String objectPath, final int[] blockDimensions, final long[] offset) { assert objectPath != null; assert blockDimensions != null; assert offset != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public MD__Name__Array call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockDimensions, registry); final __name__[] dataBlock = new __name__[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, __Memorytype__, spaceParams.memorySpaceId, spaceParams.dataSpaceId, dataBlock); return new MD__Name__Array(dataBlock, spaceParams.dimensions); } catch (HDF5SpaceRankMismatch ex) { final HDF5DataSetInformation info = baseReader.getDataSetInformation(objectPath, DataTypeInfoOptions.MINIMAL, false); if (ex.getSpaceRankExpected() - ex.getSpaceRankFound() == info .getTypeInformation().getRank()) { return readMDArrayBlockOfArrays(dataSetId, blockDimensions, offset, info, ex.getSpaceRankFound(), registry); } else { throw ex; } } } }; return baseReader.runner.call(readCallable); } private MD__Name__Array readMDArrayBlockOfArrays(final int dataSetId, final int[] blockDimensions, final long[] offset, final HDF5DataSetInformation info, final int spaceRank, final ICleanUpRegistry registry) { final int[] arrayDimensions = info.getTypeInformation().getDimensions(); int[] effectiveBlockDimensions = blockDimensions; // We do not support block-wise reading of array types, check // that we do not have to and bail out otherwise. for (int i = 0; i < arrayDimensions.length; ++i) { final int j = spaceRank + i; if (effectiveBlockDimensions[j] < 0) { if (effectiveBlockDimensions == blockDimensions) { effectiveBlockDimensions = blockDimensions.clone(); } effectiveBlockDimensions[j] = arrayDimensions[i]; } if (effectiveBlockDimensions[j] != arrayDimensions[i]) { throw new HDF5JavaException( "Block-wise reading of array type data sets is not supported."); } } final int[] spaceBlockDimensions = Arrays.copyOfRange(effectiveBlockDimensions, 0, spaceRank); final long[] spaceOfs = Arrays.copyOfRange(offset, 0, spaceRank); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, spaceOfs, spaceBlockDimensions, registry); final __name__[] dataBlock = new __name__[spaceParams.blockSize * info.getTypeInformation().getNumberOfElements()]; final int memoryDataTypeId = baseReader.h5.createArrayType(__Memorytype__, info.getTypeInformation() .getDimensions(), registry); baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, dataBlock); return new MD__Name__Array(dataBlock, effectiveBlockDimensions); } @Override public Iterable> getArrayNaturalBlocks(final String dataSetPath) throws HDF5JavaException { baseReader.checkOpen(); final HDF5NaturalBlock1DParameters params = new HDF5NaturalBlock1DParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlock1DParameters.HDF5NaturalBlock1DIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5DataBlock<__name__[]> next() { final long offset = index.computeOffsetAndSizeGetOffset(); final __name__[] block = readArrayBlockWithOffset(dataSetPath, index .getBlockSize(), offset); return new HDF5DataBlock<__name__[]>(block, index.getAndIncIndex(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } @Override public Iterable> getMDArrayNaturalBlocks(final String dataSetPath) { baseReader.checkOpen(); final HDF5NaturalBlockMDParameters params = new HDF5NaturalBlockMDParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlockMDParameters.HDF5NaturalBlockMDIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5MDDataBlock next() { final long[] offset = index.computeOffsetAndSizeGetOffsetClone(); final MD__Name__Array data = readMDArrayBlockWithOffset(dataSetPath, index .getBlockSize(), offset); return new HDF5MDDataBlock(data, index .getIndexClone(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } __name__[] get__Name__ArrayAttribute(final int objectId, final String attributeName, ICleanUpRegistry registry) { final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, registry); final int memoryTypeId; final int len; if (baseReader.h5.getClassType(attributeTypeId) == H5T_ARRAY) { final int[] arrayDimensions = baseReader.h5.getArrayDimensions(attributeTypeId); if (arrayDimensions.length != 1) { throw new HDF5JavaException( "Array needs to be of rank 1, but is of rank " + arrayDimensions.length); } len = arrayDimensions[0]; memoryTypeId = baseReader.h5.createArrayType(__Memorytype__, len, registry); } else { final long[] arrayDimensions = baseReader.h5.getDataDimensionsForAttribute(attributeId, registry); memoryTypeId = __Memorytype__; len = HDF5Utils.getOneDimensionalArraySize(arrayDimensions); } final __name__[] data = baseReader.h5.readAttributeAs__Name__Array(attributeId, memoryTypeId, len); return data; } MD__Name__Array get__Name__MDArrayAttribute(final int objectId, final String attributeName, ICleanUpRegistry registry) { try { final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, registry); final int memoryTypeId; final int[] arrayDimensions; if (baseReader.h5.getClassType(attributeTypeId) == H5T_ARRAY) { arrayDimensions = baseReader.h5.getArrayDimensions(attributeTypeId); memoryTypeId = baseReader.h5.createArrayType(__Memorytype__, arrayDimensions, registry); } else { arrayDimensions = MDArray.toInt(baseReader.h5.getDataDimensionsForAttribute( attributeId, registry)); memoryTypeId = __Memorytype__; } final int len = MDArray.getLength(arrayDimensions); final __name__[] data = baseReader.h5.readAttributeAs__Name__Array(attributeId, memoryTypeId, len); return new MD__Name__Array(data, arrayDimensions); } catch (IllegalArgumentException ex) { throw new HDF5JavaException(ex.getMessage()); } } }libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/tools/HDF5PrimitiveWriter.java.templ000066400000000000000000000670261256564762100331340ustar00rootroot00000000000000/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.HDF5__Classname__StorageFeatures.__CLASSNAME___NO_COMPRESSION; import static ch.systemsx.cisd.hdf5.hdf5lib.H5D.H5Dwrite; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_ALL; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.__Memorytype__; __StoragetypeImport__ import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MD__Name__Array; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; /** * The implementation of {@link IHDF5__Name__Writer}. * * @author Bernd Rinn */ class HDF5__Name__Writer extends HDF5__Name__Reader implements IHDF5__Name__Writer { private final HDF5BaseWriter baseWriter; HDF5__Name__Writer(HDF5BaseWriter baseWriter) { super(baseWriter); assert baseWriter != null; this.baseWriter = baseWriter; } // ///////////////////// // Attributes // ///////////////////// @Override public void setAttr(final String objectPath, final String name, final __name__ value) { assert objectPath != null; assert name != null; baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { 1 }, registry); baseWriter.setAttribute(objectPath, name, __Storagetype__, __Memorytype__, dataSpaceId, new __name__[] { value }, registry); } else { baseWriter.setAttribute(objectPath, name, __Storagetype__, __Memorytype__, -1, new __name__[] { value }, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void setArrayAttr(final String objectPath, final String name, final __name__[] value) { assert objectPath != null; assert name != null; assert value != null; baseWriter.checkOpen(); final ICallableWithCleanUp setAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { value.length }, registry); baseWriter.setAttribute(objectPath, name, __Storagetype__, __Memorytype__, dataSpaceId, value, registry); } else { final int memoryTypeId = baseWriter.h5.createArrayType(__Memorytype__, value.length, registry); final int storageTypeId = baseWriter.h5.createArrayType(__Storagetype__, value.length, registry); baseWriter.setAttribute(objectPath, name, storageTypeId, memoryTypeId, -1, value, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(setAttributeRunnable); } @Override public void setMDArrayAttr(final String objectPath, final String name, final MD__Name__Array value) { assert objectPath != null; assert name != null; assert value != null; baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(value.longDimensions(), registry); baseWriter.setAttribute(objectPath, name, __Storagetype__, __Memorytype__, dataSpaceId, value.getAsFlatArray(), registry); } else { final int memoryTypeId = baseWriter.h5.createArrayType(__Memorytype__, value.dimensions(), registry); final int storageTypeId = baseWriter.h5.createArrayType(__Storagetype__, value.dimensions(), registry); baseWriter.setAttribute(objectPath, name, storageTypeId, memoryTypeId, -1, value.getAsFlatArray(), registry); } return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void setMatrixAttr(final String objectPath, final String name, final __name__[][] value) { setMDArrayAttr(objectPath, name, new MD__Name__Array(value)); } // ///////////////////// // Data Sets // ///////////////////// @Override public void write(final String objectPath, final __name__ value) { assert objectPath != null; baseWriter.checkOpen(); baseWriter.writeScalar(objectPath, __Storagetype__, __Memorytype__, value); } @Override public void writeArray(final String objectPath, final __name__[] data) { writeArray(objectPath, data, __CLASSNAME___NO_COMPRESSION); } @Override public void writeArray(final String objectPath, final __name__[] data, final HDF5__Classname__StorageFeatures features) { assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, __FeatureBasedStoragetype__, new long[] { data.length }, __elementsize__, features, registry); H5Dwrite(dataSetId, __Memorytype__, H5S_ALL, H5S_ALL, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createArray(final String objectPath, final int size) { createArray(objectPath, size, __CLASSNAME___NO_COMPRESSION); } @Override public void createArray(final String objectPath, final long size, final int blockSize) { createArray(objectPath, size, blockSize, __CLASSNAME___NO_COMPRESSION); } @Override public void createArray(final String objectPath, final int size, final HDF5__Classname__StorageFeatures features) { assert objectPath != null; assert size >= 0; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (features.requiresChunking()) { baseWriter.createDataSet(objectPath, __FeatureBasedStoragetype__, features, new long[] { 0 }, new long[] { size }, __elementsize__, registry); } else { baseWriter.createDataSet(objectPath, __FeatureBasedStoragetype__, features, new long[] { size }, null, __elementsize__, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void createArray(final String objectPath, final long size, final int blockSize, final HDF5__Classname__StorageFeatures features) { assert objectPath != null; assert size >= 0; assert blockSize >= 0 && (blockSize <= size || size == 0); baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { baseWriter.createDataSet(objectPath, __FeatureBasedStoragetype__, features, new long[] { size }, new long[] { blockSize }, __elementsize__, registry); return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void writeArrayBlock(final String objectPath, final __name__[] data, final long blockNumber) { writeArrayBlockWithOffset(objectPath, data, data.length, data.length * blockNumber); } @Override public void writeArrayBlockWithOffset(final String objectPath, final __name__[] data, final int dataSize, final long offset) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] blockDimensions = new long[] { dataSize }; final long[] slabStartOrNull = new long[] { offset }; final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, new long[] { offset + dataSize }, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, slabStartOrNull, blockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(blockDimensions, registry); H5Dwrite(dataSetId, __Memorytype__, memorySpaceId, dataSpaceId, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } /** * Writes out a __name__ matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ @Override public void writeMatrix(final String objectPath, final __name__[][] data) { writeMatrix(objectPath, data, __CLASSNAME___NO_COMPRESSION); } @Override public void writeMatrix(final String objectPath, final __name__[][] data, final HDF5__Classname__StorageFeatures features) { assert objectPath != null; assert data != null; assert HDF5Utils.areMatrixDimensionsConsistent(data); writeMDArray(objectPath, new MD__Name__Array(data), features); } @Override public void createMatrix(final String objectPath, final int sizeX, final int sizeY) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; createMDArray(objectPath, new int[] { sizeX, sizeY }); } @Override public void createMatrix(final String objectPath, final int sizeX, final int sizeY, final HDF5__Classname__StorageFeatures features) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; createMDArray(objectPath, new int[] { sizeX, sizeY }, features); } @Override public void createMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; assert blockSizeX >= 0 && (blockSizeX <= sizeX || sizeX == 0); assert blockSizeY >= 0 && (blockSizeY <= sizeY || sizeY == 0); createMDArray(objectPath, new long[] { sizeX, sizeY }, new int[] { blockSizeX, blockSizeY }); } @Override public void createMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY, final HDF5__Classname__StorageFeatures features) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; assert blockSizeX >= 0 && (blockSizeX <= sizeX || sizeX == 0); assert blockSizeY >= 0 && (blockSizeY <= sizeY || sizeY == 0); createMDArray(objectPath, new long[] { sizeX, sizeY }, new int[] { blockSizeX, blockSizeY }, features); } @Override public void writeMatrixBlock(final String objectPath, final __name__[][] data, final long blockNumberX, final long blockNumberY) { assert objectPath != null; assert data != null; writeMDArrayBlock(objectPath, new MD__Name__Array(data), new long[] { blockNumberX, blockNumberY }); } @Override public void writeMatrixBlockWithOffset(final String objectPath, final __name__[][] data, final long offsetX, final long offsetY) { assert objectPath != null; assert data != null; writeMDArrayBlockWithOffset(objectPath, new MD__Name__Array(data, new int[] { data.length, data[0].length }), new long[] { offsetX, offsetY }); } @Override public void writeMatrixBlockWithOffset(final String objectPath, final __name__[][] data, final int dataSizeX, final int dataSizeY, final long offsetX, final long offsetY) { assert objectPath != null; assert data != null; writeMDArrayBlockWithOffset(objectPath, new MD__Name__Array(data, new int[] { dataSizeX, dataSizeY }), new long[] { offsetX, offsetY }); } @Override public void writeMDArray(final String objectPath, final MD__Name__Array data) { writeMDArray(objectPath, data, __CLASSNAME___NO_COMPRESSION); } @Override public void writeMDArraySlice(String objectPath, MD__Name__Array data, IndexMap boundIndices) { baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), null, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MD__Name__Array(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArraySlice(String objectPath, MD__Name__Array data, long[] boundIndices) { baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), null, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MD__Name__Array(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArray(final String objectPath, final MD__Name__Array data, final HDF5__Classname__StorageFeatures features) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, __FeatureBasedStoragetype__, data.longDimensions(), __elementsize__, features, registry); H5Dwrite(dataSetId, __Memorytype__, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createMDArray(final String objectPath, final int[] dimensions) { createMDArray(objectPath, dimensions, __CLASSNAME___NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions) { createMDArray(objectPath, dimensions, blockDimensions, __CLASSNAME___NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final int[] dimensions, final HDF5__Classname__StorageFeatures features) { assert objectPath != null; assert dimensions != null; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (features.requiresChunking()) { final long[] nullDimensions = new long[dimensions.length]; baseWriter.createDataSet(objectPath, __FeatureBasedStoragetype__, features, nullDimensions, MDArray.toLong(dimensions), __elementsize__, registry); } else { baseWriter.createDataSet(objectPath, __FeatureBasedStoragetype__, features, MDArray.toLong(dimensions), null, __elementsize__, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void createMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions, final HDF5__Classname__StorageFeatures features) { assert objectPath != null; assert dimensions != null; assert blockDimensions != null; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { baseWriter.createDataSet(objectPath, __FeatureBasedStoragetype__, features, dimensions, MDArray.toLong(blockDimensions), __elementsize__, registry); return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void writeMDArrayBlock(final String objectPath, final MD__Name__Array data, final long[] blockNumber) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeMDArrayBlockWithOffset(objectPath, data, offset); } @Override public void writeSlicedMDArrayBlock(final String objectPath, final MD__Name__Array data, final long[] blockNumber, IndexMap boundIndices) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeSlicedMDArrayBlockWithOffset(objectPath, data, offset, boundIndices); } @Override public void writeSlicedMDArrayBlock(String objectPath, MD__Name__Array data, long[] blockNumber, long[] boundIndices) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeSlicedMDArrayBlockWithOffset(objectPath, data, offset, boundIndices); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final MD__Name__Array data, final long[] offset) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] dimensions = data.longDimensions(); assert dimensions.length == offset.length; final long[] dataSetDimensions = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + dimensions[i]; } final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, dimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(dimensions, registry); H5Dwrite(dataSetId, __Memorytype__, memorySpaceId, dataSpaceId, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeSlicedMDArrayBlockWithOffset(String objectPath, MD__Name__Array data, long[] offset, IndexMap boundIndices) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), offset, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MD__Name__Array(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeSlicedMDArrayBlockWithOffset(String objectPath, MD__Name__Array data, long[] offset, long[] boundIndices) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), offset, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MD__Name__Array(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final MD__Name__Array data, final int[] blockDimensions, final long[] offset, final int[] memoryOffset) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] memoryDimensions = data.longDimensions(); assert memoryDimensions.length == offset.length; final long[] longBlockDimensions = MDArray.toLong(blockDimensions); assert longBlockDimensions.length == offset.length; final long[] dataSetDimensions = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + blockDimensions[i]; } final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, longBlockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(memoryDimensions, registry); baseWriter.h5.setHyperslabBlock(memorySpaceId, MDArray.toLong(memoryOffset), longBlockDimensions); H5Dwrite(dataSetId, __Memorytype__, memorySpaceId, dataSpaceId, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } }HDF5UnsignedPrimitiveReader.java.templ000066400000000000000000001031021256564762100344620ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/tools/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.MatrixUtils.cardinalityBoundIndices; import static ch.systemsx.cisd.hdf5.MatrixUtils.checkBoundIndices; import static ch.systemsx.cisd.hdf5.MatrixUtils.createFullBlockDimensionsAndOffset; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5T_ARRAY; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.__Memorytype__; import java.util.Arrays; import java.util.Iterator; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import ncsa.hdf.hdf5lib.exceptions.HDF5SpaceRankMismatch; import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MD__Name__Array; import ch.systemsx.cisd.hdf5.HDF5BaseReader.DataSpaceParameters; import ch.systemsx.cisd.hdf5.HDF5DataTypeInformation.DataTypeInfoOptions; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; import ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants; /** * The implementation of {@link IHDF5__Name__Reader}. * * @author Bernd Rinn */ class HDF5Unsigned__Name__Reader implements IHDF5__Name__Reader { private final HDF5BaseReader baseReader; HDF5Unsigned__Name__Reader(HDF5BaseReader baseReader) { assert baseReader != null; this.baseReader = baseReader; } // For Unit tests only. HDF5BaseReader getBaseReader() { return baseReader; } // ///////////////////// // Attributes // ///////////////////// @Override public __name__ getAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp<__Wrappername__> getAttributeRunnable = new ICallableWithCleanUp<__Wrappername__>() { @Override public __Wrappername__ call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final __name__[] data = baseReader.h5.readAttributeAs__Name__Array(attributeId, __Memorytype__, 1); return data[0]; } }; return baseReader.runner.call(getAttributeRunnable); } @Override public __name__[] getArrayAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp<__name__[]> getAttributeRunnable = new ICallableWithCleanUp<__name__[]>() { @Override public __name__[] call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); return get__Name__ArrayAttribute(objectId, attributeName, registry); } }; return baseReader.runner.call(getAttributeRunnable); } @Override public MD__Name__Array getMDArrayAttr(final String objectPath, final String attributeName) { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp getAttributeRunnable = new ICallableWithCleanUp() { @Override public MD__Name__Array call(ICleanUpRegistry registry) { final int objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); return get__Name__MDArrayAttribute(objectId, attributeName, registry); } }; return baseReader.runner.call(getAttributeRunnable); } @Override public __name__[][] getMatrixAttr(final String objectPath, final String attributeName) throws HDF5JavaException { final MD__Name__Array array = getMDArrayAttr(objectPath, attributeName); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } // ///////////////////// // Data Sets // ///////////////////// @Override public __name__ read(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp<__Wrappername__> readCallable = new ICallableWithCleanUp<__Wrappername__>() { @Override public __Wrappername__ call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final __name__[] data = new __name__[1]; baseReader.h5.readDataSet(dataSetId, __Memorytype__, data); return data[0]; } }; return baseReader.runner.call(readCallable); } @Override public __name__[] readArray(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp<__name__[]> readCallable = new ICallableWithCleanUp<__name__[]>() { @Override public __name__[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); return read__Name__Array(dataSetId, registry); } }; return baseReader.runner.call(readCallable); } private __name__[] read__Name__Array(int dataSetId, ICleanUpRegistry registry) { try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); final __name__[] data = new __name__[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, __Memorytype__, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return data; } catch (HDF5LibraryException ex) { if (ex.getMajorErrorNumber() == HDF5Constants.H5E_DATATYPE && ex.getMinorErrorNumber() == HDF5Constants.H5E_CANTINIT) { // Check whether it is an array data type. final int dataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); if (baseReader.h5.getClassType(dataTypeId) == HDF5Constants.H5T_ARRAY) { return read__Name__ArrayFromArrayType(dataSetId, dataTypeId, registry); } } throw ex; } } private __name__[] read__Name__ArrayFromArrayType(int dataSetId, final int dataTypeId, ICleanUpRegistry registry) { final int spaceId = baseReader.h5.createScalarDataSpace(); final int[] dimensions = baseReader.h5.getArrayDimensions(dataTypeId); final __name__[] data = new __name__[HDF5Utils.getOneDimensionalArraySize(dimensions)]; final int memoryDataTypeId = baseReader.h5.createArrayType(__Memorytype__, data.length, registry); baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceId, spaceId, data); return data; } @Override public int[] readToMDArrayWithOffset(final String objectPath, final MD__Name__Array array, final int[] memoryOffset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getBlockSpaceParameters(dataSetId, memoryOffset, array .dimensions(), registry); final int nativeDataTypeId = baseReader.getNativeDataTypeId(dataSetId, __Memorytype__, registry); baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, array. getAsFlatArray()); return MDArray.toInt(spaceParams.dimensions); } }; return baseReader.runner.call(readCallable); } @Override public int[] readToMDArrayBlockWithOffset(final String objectPath, final MD__Name__Array array, final int[] blockDimensions, final long[] offset, final int[] memoryOffset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public int[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getBlockSpaceParameters(dataSetId, memoryOffset, array .dimensions(), offset, blockDimensions, registry); final int nativeDataTypeId = baseReader.getNativeDataTypeId(dataSetId, __Memorytype__, registry); baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, array .getAsFlatArray()); return MDArray.toInt(spaceParams.dimensions); } }; return baseReader.runner.call(readCallable); } @Override public __name__[] readArrayBlock(final String objectPath, final int blockSize, final long blockNumber) { return readArrayBlockWithOffset(objectPath, blockSize, blockNumber * blockSize); } @Override public __name__[] readArrayBlockWithOffset(final String objectPath, final int blockSize, final long offset) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp<__name__[]> readCallable = new ICallableWithCleanUp<__name__[]>() { @Override public __name__[] call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockSize, registry); final __name__[] data = new __name__[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, __Memorytype__, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return data; } }; return baseReader.runner.call(readCallable); } @Override public __name__[][] readMatrix(final String objectPath) throws HDF5JavaException { final MD__Name__Array array = readMDArray(objectPath); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public __name__[][] readMatrixBlock(final String objectPath, final int blockSizeX, final int blockSizeY, final long blockNumberX, final long blockNumberY) throws HDF5JavaException { final MD__Name__Array array = readMDArrayBlock(objectPath, new int[] { blockSizeX, blockSizeY }, new long[] { blockNumberX, blockNumberY }); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public __name__[][] readMatrixBlockWithOffset(final String objectPath, final int blockSizeX, final int blockSizeY, final long offsetX, final long offsetY) throws HDF5JavaException { final MD__Name__Array array = readMDArrayBlockWithOffset(objectPath, new int[] { blockSizeX, blockSizeY }, new long[] { offsetX, offsetY }); if (array.rank() != 2) { throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank " + array.rank()); } return array.toMatrix(); } @Override public MD__Name__Array readMDArraySlice(String objectPath, IndexMap boundIndices) { baseReader.checkOpen(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; final int cardBoundIndices = cardinalityBoundIndices(boundIndices); checkBoundIndices(objectPath, fullDimensions, cardBoundIndices); final int[] effectiveBlockDimensions = new int[fullBlockDimensions.length - cardBoundIndices]; Arrays.fill(effectiveBlockDimensions, -1); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, null, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MD__Name__Array result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); if (fullBlockDimensions.length == cardBoundIndices) // no free indices { return new MD__Name__Array(result.getAsFlatArray(), new int[] { 1 }); } else { return new MD__Name__Array(result.getAsFlatArray(), effectiveBlockDimensions); } } @Override public MD__Name__Array readMDArraySlice(String objectPath, long[] boundIndices) { baseReader.checkOpen(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; final int cardBoundIndices = cardinalityBoundIndices(boundIndices); checkBoundIndices(objectPath, fullDimensions, boundIndices); final int[] effectiveBlockDimensions = new int[fullBlockDimensions.length - cardBoundIndices]; Arrays.fill(effectiveBlockDimensions, -1); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, null, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MD__Name__Array result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); if (fullBlockDimensions.length == cardBoundIndices) // no free indices { return new MD__Name__Array(result.getAsFlatArray(), new int[] { 1 }); } else { return new MD__Name__Array(result.getAsFlatArray(), effectiveBlockDimensions); } } @Override public MD__Name__Array readMDArray(final String objectPath) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public MD__Name__Array call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); return read__Name__MDArray(dataSetId, registry); } }; return baseReader.runner.call(readCallable); } MD__Name__Array read__Name__MDArray(int dataSetId, ICleanUpRegistry registry) { try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); final __name__[] data = new __name__[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, __Memorytype__, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return new MD__Name__Array(data, spaceParams.dimensions); } catch (HDF5LibraryException ex) { if (ex.getMajorErrorNumber() == HDF5Constants.H5E_DATATYPE && ex.getMinorErrorNumber() == HDF5Constants.H5E_CANTINIT) { // Check whether it is an array data type. final int dataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry); if (baseReader.h5.getClassType(dataTypeId) == HDF5Constants.H5T_ARRAY) { return read__Name__MDArrayFromArrayType(dataSetId, dataTypeId, registry); } } throw ex; } } private MD__Name__Array read__Name__MDArrayFromArrayType(int dataSetId, final int dataTypeId, ICleanUpRegistry registry) { final int[] arrayDimensions = baseReader.h5.getArrayDimensions(dataTypeId); final int memoryDataTypeId = baseReader.h5.createArrayType(__Memorytype__, arrayDimensions, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); if (spaceParams.blockSize == 0) { final int spaceId = baseReader.h5.createScalarDataSpace(); final __name__[] data = new __name__[MDArray.getLength(arrayDimensions)]; baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceId, spaceId, data); return new MD__Name__Array(data, arrayDimensions); } else { final __name__[] data = new __name__[MDArray.getLength(arrayDimensions) * spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return new MD__Name__Array(data, MatrixUtils.concat(MDArray.toInt(spaceParams.dimensions), arrayDimensions)); } } @Override public MD__Name__Array readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, IndexMap boundIndices) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readSlicedMDArrayBlockWithOffset(objectPath, blockDimensions, offset, boundIndices); } @Override public MD__Name__Array readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, long[] boundIndices) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readSlicedMDArrayBlockWithOffset(objectPath, blockDimensions, offset, boundIndices); } @Override public MD__Name__Array readMDArrayBlock(final String objectPath, final int[] blockDimensions, final long[] blockNumber) { final long[] offset = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * blockDimensions[i]; } return readMDArrayBlockWithOffset(objectPath, blockDimensions, offset); } @Override public MD__Name__Array readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, IndexMap boundIndices) { baseReader.checkOpen(); final int[] effectiveBlockDimensions = blockDimensions.clone(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; checkBoundIndices(objectPath, fullDimensions, blockDimensions, cardinalityBoundIndices(boundIndices)); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, offset, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MD__Name__Array result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); return new MD__Name__Array(result.getAsFlatArray(), effectiveBlockDimensions); } @Override public MD__Name__Array readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, long[] boundIndices) { baseReader.checkOpen(); final int[] effectiveBlockDimensions = blockDimensions.clone(); final long[] fullDimensions = baseReader.getDimensions(objectPath); final int[] fullBlockDimensions = new int[fullDimensions.length]; final long[] fullOffset = new long[fullDimensions.length]; checkBoundIndices(objectPath, fullDimensions, blockDimensions, cardinalityBoundIndices(boundIndices)); createFullBlockDimensionsAndOffset(effectiveBlockDimensions, offset, boundIndices, fullDimensions, fullBlockDimensions, fullOffset); final MD__Name__Array result = readMDArrayBlockWithOffset(objectPath, fullBlockDimensions, fullOffset); return new MD__Name__Array(result.getAsFlatArray(), effectiveBlockDimensions); } @Override public MD__Name__Array readMDArrayBlockWithOffset(final String objectPath, final int[] blockDimensions, final long[] offset) { assert objectPath != null; assert blockDimensions != null; assert offset != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public MD__Name__Array call(ICleanUpRegistry registry) { final int dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); try { final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, offset, blockDimensions, registry); final __name__[] dataBlock = new __name__[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, __Memorytype__, spaceParams.memorySpaceId, spaceParams.dataSpaceId, dataBlock); return new MD__Name__Array(dataBlock, spaceParams.dimensions); } catch (HDF5SpaceRankMismatch ex) { final HDF5DataSetInformation info = baseReader.getDataSetInformation(objectPath, DataTypeInfoOptions.MINIMAL, false); if (ex.getSpaceRankExpected() - ex.getSpaceRankFound() == info .getTypeInformation().getRank()) { return readMDArrayBlockOfArrays(dataSetId, blockDimensions, offset, info, ex.getSpaceRankFound(), registry); } else { throw ex; } } } }; return baseReader.runner.call(readCallable); } private MD__Name__Array readMDArrayBlockOfArrays(final int dataSetId, final int[] blockDimensions, final long[] offset, final HDF5DataSetInformation info, final int spaceRank, final ICleanUpRegistry registry) { final int[] arrayDimensions = info.getTypeInformation().getDimensions(); int[] effectiveBlockDimensions = blockDimensions; // We do not support block-wise reading of array types, check // that we do not have to and bail out otherwise. for (int i = 0; i < arrayDimensions.length; ++i) { final int j = spaceRank + i; if (effectiveBlockDimensions[j] < 0) { if (effectiveBlockDimensions == blockDimensions) { effectiveBlockDimensions = blockDimensions.clone(); } effectiveBlockDimensions[j] = arrayDimensions[i]; } if (effectiveBlockDimensions[j] != arrayDimensions[i]) { throw new HDF5JavaException( "Block-wise reading of array type data sets is not supported."); } } final int[] spaceBlockDimensions = Arrays.copyOfRange(effectiveBlockDimensions, 0, spaceRank); final long[] spaceOfs = Arrays.copyOfRange(offset, 0, spaceRank); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, spaceOfs, spaceBlockDimensions, registry); final __name__[] dataBlock = new __name__[spaceParams.blockSize * info.getTypeInformation().getNumberOfElements()]; final int memoryDataTypeId = baseReader.h5.createArrayType(__Memorytype__, info.getTypeInformation() .getDimensions(), registry); baseReader.h5.readDataSet(dataSetId, memoryDataTypeId, spaceParams.memorySpaceId, spaceParams.dataSpaceId, dataBlock); return new MD__Name__Array(dataBlock, effectiveBlockDimensions); } @Override public Iterable> getArrayNaturalBlocks(final String dataSetPath) throws HDF5JavaException { baseReader.checkOpen(); final HDF5NaturalBlock1DParameters params = new HDF5NaturalBlock1DParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlock1DParameters.HDF5NaturalBlock1DIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5DataBlock<__name__[]> next() { final long offset = index.computeOffsetAndSizeGetOffset(); final __name__[] block = readArrayBlockWithOffset(dataSetPath, index .getBlockSize(), offset); return new HDF5DataBlock<__name__[]>(block, index.getAndIncIndex(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } @Override public Iterable> getMDArrayNaturalBlocks(final String dataSetPath) { baseReader.checkOpen(); final HDF5NaturalBlockMDParameters params = new HDF5NaturalBlockMDParameters(baseReader.getDataSetInformation(dataSetPath)); return new Iterable>() { @Override public Iterator> iterator() { return new Iterator>() { final HDF5NaturalBlockMDParameters.HDF5NaturalBlockMDIndex index = params.getNaturalBlockIndex(); @Override public boolean hasNext() { return index.hasNext(); } @Override public HDF5MDDataBlock next() { final long[] offset = index.computeOffsetAndSizeGetOffsetClone(); final MD__Name__Array data = readMDArrayBlockWithOffset(dataSetPath, index .getBlockSize(), offset); return new HDF5MDDataBlock(data, index .getIndexClone(), offset); } @Override public void remove() { throw new UnsupportedOperationException(); } }; } }; } __name__[] get__Name__ArrayAttribute(final int objectId, final String attributeName, ICleanUpRegistry registry) { final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, registry); final int memoryTypeId; final int len; if (baseReader.h5.getClassType(attributeTypeId) == H5T_ARRAY) { final int[] arrayDimensions = baseReader.h5.getArrayDimensions(attributeTypeId); if (arrayDimensions.length != 1) { throw new HDF5JavaException( "Array needs to be of rank 1, but is of rank " + arrayDimensions.length); } len = arrayDimensions[0]; memoryTypeId = baseReader.h5.createArrayType(__Memorytype__, len, registry); } else { final long[] arrayDimensions = baseReader.h5.getDataDimensionsForAttribute(attributeId, registry); memoryTypeId = __Memorytype__; len = HDF5Utils.getOneDimensionalArraySize(arrayDimensions); } final __name__[] data = baseReader.h5.readAttributeAs__Name__Array(attributeId, memoryTypeId, len); return data; } MD__Name__Array get__Name__MDArrayAttribute(final int objectId, final String attributeName, ICleanUpRegistry registry) { try { final int attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final int attributeTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, registry); final int memoryTypeId; final int[] arrayDimensions; if (baseReader.h5.getClassType(attributeTypeId) == H5T_ARRAY) { arrayDimensions = baseReader.h5.getArrayDimensions(attributeTypeId); memoryTypeId = baseReader.h5.createArrayType(__Memorytype__, arrayDimensions, registry); } else { arrayDimensions = MDArray.toInt(baseReader.h5.getDataDimensionsForAttribute( attributeId, registry)); memoryTypeId = __Memorytype__; } final int len = MDArray.getLength(arrayDimensions); final __name__[] data = baseReader.h5.readAttributeAs__Name__Array(attributeId, memoryTypeId, len); return new MD__Name__Array(data, arrayDimensions); } catch (IllegalArgumentException ex) { throw new HDF5JavaException(ex.getMessage()); } } }HDF5UnsignedPrimitiveWriter.java.templ000066400000000000000000000670561256564762100345550ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/tools/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import static ch.systemsx.cisd.hdf5.HDF5__Classname__StorageFeatures.__CLASSNAME___NO_COMPRESSION; import static ch.systemsx.cisd.hdf5.hdf5lib.H5D.H5Dwrite; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5P_DEFAULT; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.H5S_ALL; import static ch.systemsx.cisd.hdf5.hdf5lib.HDF5Constants.__Memorytype__; __StoragetypeImport__ import ch.systemsx.cisd.base.mdarray.MDArray; import ch.systemsx.cisd.base.mdarray.MD__Name__Array; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; /** * The implementation of {@link IHDF5__Name__Writer}. * * @author Bernd Rinn */ class HDF5Unsigned__Name__Writer extends HDF5Unsigned__Name__Reader implements IHDF5__Name__Writer { private final HDF5BaseWriter baseWriter; HDF5Unsigned__Name__Writer(HDF5BaseWriter baseWriter) { super(baseWriter); assert baseWriter != null; this.baseWriter = baseWriter; } // ///////////////////// // Attributes // ///////////////////// @Override public void setAttr(final String objectPath, final String name, final __name__ value) { assert objectPath != null; assert name != null; baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Object call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { 1 }, registry); baseWriter.setAttribute(objectPath, name, __Storagetype__, __Memorytype__, dataSpaceId, new __name__[] { value }, registry); } else { baseWriter.setAttribute(objectPath, name, __Storagetype__, __Memorytype__, -1, new __name__[] { value }, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void setArrayAttr(final String objectPath, final String name, final __name__[] value) { assert objectPath != null; assert name != null; assert value != null; baseWriter.checkOpen(); final ICallableWithCleanUp setAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(new long[] { value.length }, registry); baseWriter.setAttribute(objectPath, name, __Storagetype__, __Memorytype__, dataSpaceId, value, registry); } else { final int memoryTypeId = baseWriter.h5.createArrayType(__Memorytype__, value.length, registry); final int storageTypeId = baseWriter.h5.createArrayType(__Storagetype__, value.length, registry); baseWriter.setAttribute(objectPath, name, storageTypeId, memoryTypeId, -1, value, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(setAttributeRunnable); } @Override public void setMDArrayAttr(final String objectPath, final String name, final MD__Name__Array value) { assert objectPath != null; assert name != null; assert value != null; baseWriter.checkOpen(); final ICallableWithCleanUp addAttributeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (baseWriter.useSimpleDataSpaceForAttributes) { final int dataSpaceId = baseWriter.h5.createSimpleDataSpace(value.longDimensions(), registry); baseWriter.setAttribute(objectPath, name, __Storagetype__, __Memorytype__, dataSpaceId, value.getAsFlatArray(), registry); } else { final int memoryTypeId = baseWriter.h5.createArrayType(__Memorytype__, value.dimensions(), registry); final int storageTypeId = baseWriter.h5.createArrayType(__Storagetype__, value.dimensions(), registry); baseWriter.setAttribute(objectPath, name, storageTypeId, memoryTypeId, -1, value.getAsFlatArray(), registry); } return null; // Nothing to return. } }; baseWriter.runner.call(addAttributeRunnable); } @Override public void setMatrixAttr(final String objectPath, final String name, final __name__[][] value) { setMDArrayAttr(objectPath, name, new MD__Name__Array(value)); } // ///////////////////// // Data Sets // ///////////////////// @Override public void write(final String objectPath, final __name__ value) { assert objectPath != null; baseWriter.checkOpen(); baseWriter.writeScalar(objectPath, __Storagetype__, __Memorytype__, value); } @Override public void writeArray(final String objectPath, final __name__[] data) { writeArray(objectPath, data, __CLASSNAME___NO_COMPRESSION); } @Override public void writeArray(final String objectPath, final __name__[] data, final HDF5__Classname__StorageFeatures features) { assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, __FeatureBasedStoragetype__, new long[] { data.length }, __elementsize__, features, registry); H5Dwrite(dataSetId, __Memorytype__, H5S_ALL, H5S_ALL, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createArray(final String objectPath, final int size) { createArray(objectPath, size, __CLASSNAME___NO_COMPRESSION); } @Override public void createArray(final String objectPath, final long size, final int blockSize) { createArray(objectPath, size, blockSize, __CLASSNAME___NO_COMPRESSION); } @Override public void createArray(final String objectPath, final int size, final HDF5__Classname__StorageFeatures features) { assert objectPath != null; assert size >= 0; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (features.requiresChunking()) { baseWriter.createDataSet(objectPath, __FeatureBasedStoragetype__, features, new long[] { 0 }, new long[] { size }, __elementsize__, registry); } else { baseWriter.createDataSet(objectPath, __FeatureBasedStoragetype__, features, new long[] { size }, null, __elementsize__, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void createArray(final String objectPath, final long size, final int blockSize, final HDF5__Classname__StorageFeatures features) { assert objectPath != null; assert size >= 0; assert blockSize >= 0 && (blockSize <= size || size == 0); baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { baseWriter.createDataSet(objectPath, __FeatureBasedStoragetype__, features, new long[] { size }, new long[] { blockSize }, __elementsize__, registry); return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void writeArrayBlock(final String objectPath, final __name__[] data, final long blockNumber) { writeArrayBlockWithOffset(objectPath, data, data.length, data.length * blockNumber); } @Override public void writeArrayBlockWithOffset(final String objectPath, final __name__[] data, final int dataSize, final long offset) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] blockDimensions = new long[] { dataSize }; final long[] slabStartOrNull = new long[] { offset }; final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, new long[] { offset + dataSize }, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, slabStartOrNull, blockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(blockDimensions, registry); H5Dwrite(dataSetId, __Memorytype__, memorySpaceId, dataSpaceId, H5P_DEFAULT, data); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } /** * Writes out a __name__ matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ @Override public void writeMatrix(final String objectPath, final __name__[][] data) { writeMatrix(objectPath, data, __CLASSNAME___NO_COMPRESSION); } @Override public void writeMatrix(final String objectPath, final __name__[][] data, final HDF5__Classname__StorageFeatures features) { assert objectPath != null; assert data != null; assert HDF5Utils.areMatrixDimensionsConsistent(data); writeMDArray(objectPath, new MD__Name__Array(data), features); } @Override public void createMatrix(final String objectPath, final int sizeX, final int sizeY) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; createMDArray(objectPath, new int[] { sizeX, sizeY }); } @Override public void createMatrix(final String objectPath, final int sizeX, final int sizeY, final HDF5__Classname__StorageFeatures features) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; createMDArray(objectPath, new int[] { sizeX, sizeY }, features); } @Override public void createMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; assert blockSizeX >= 0 && (blockSizeX <= sizeX || sizeX == 0); assert blockSizeY >= 0 && (blockSizeY <= sizeY || sizeY == 0); createMDArray(objectPath, new long[] { sizeX, sizeY }, new int[] { blockSizeX, blockSizeY }); } @Override public void createMatrix(final String objectPath, final long sizeX, final long sizeY, final int blockSizeX, final int blockSizeY, final HDF5__Classname__StorageFeatures features) { assert objectPath != null; assert sizeX >= 0; assert sizeY >= 0; assert blockSizeX >= 0 && (blockSizeX <= sizeX || sizeX == 0); assert blockSizeY >= 0 && (blockSizeY <= sizeY || sizeY == 0); createMDArray(objectPath, new long[] { sizeX, sizeY }, new int[] { blockSizeX, blockSizeY }, features); } @Override public void writeMatrixBlock(final String objectPath, final __name__[][] data, final long blockNumberX, final long blockNumberY) { assert objectPath != null; assert data != null; writeMDArrayBlock(objectPath, new MD__Name__Array(data), new long[] { blockNumberX, blockNumberY }); } @Override public void writeMatrixBlockWithOffset(final String objectPath, final __name__[][] data, final long offsetX, final long offsetY) { assert objectPath != null; assert data != null; writeMDArrayBlockWithOffset(objectPath, new MD__Name__Array(data, new int[] { data.length, data[0].length }), new long[] { offsetX, offsetY }); } @Override public void writeMatrixBlockWithOffset(final String objectPath, final __name__[][] data, final int dataSizeX, final int dataSizeY, final long offsetX, final long offsetY) { assert objectPath != null; assert data != null; writeMDArrayBlockWithOffset(objectPath, new MD__Name__Array(data, new int[] { dataSizeX, dataSizeY }), new long[] { offsetX, offsetY }); } @Override public void writeMDArray(final String objectPath, final MD__Name__Array data) { writeMDArray(objectPath, data, __CLASSNAME___NO_COMPRESSION); } @Override public void writeMDArraySlice(String objectPath, MD__Name__Array data, IndexMap boundIndices) { baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), null, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MD__Name__Array(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArraySlice(String objectPath, MD__Name__Array data, long[] boundIndices) { baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), null, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MD__Name__Array(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArray(final String objectPath, final MD__Name__Array data, final HDF5__Classname__StorageFeatures features) { assert objectPath != null; assert data != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final int dataSetId = baseWriter.getOrCreateDataSetId(objectPath, __FeatureBasedStoragetype__, data.longDimensions(), __elementsize__, features, registry); H5Dwrite(dataSetId, __Memorytype__, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void createMDArray(final String objectPath, final int[] dimensions) { createMDArray(objectPath, dimensions, __CLASSNAME___NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions) { createMDArray(objectPath, dimensions, blockDimensions, __CLASSNAME___NO_COMPRESSION); } @Override public void createMDArray(final String objectPath, final int[] dimensions, final HDF5__Classname__StorageFeatures features) { assert objectPath != null; assert dimensions != null; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { if (features.requiresChunking()) { final long[] nullDimensions = new long[dimensions.length]; baseWriter.createDataSet(objectPath, __FeatureBasedStoragetype__, features, nullDimensions, MDArray.toLong(dimensions), __elementsize__, registry); } else { baseWriter.createDataSet(objectPath, __FeatureBasedStoragetype__, features, MDArray.toLong(dimensions), null, __elementsize__, registry); } return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void createMDArray(final String objectPath, final long[] dimensions, final int[] blockDimensions, final HDF5__Classname__StorageFeatures features) { assert objectPath != null; assert dimensions != null; assert blockDimensions != null; baseWriter.checkOpen(); final ICallableWithCleanUp createRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { baseWriter.createDataSet(objectPath, __FeatureBasedStoragetype__, features, dimensions, MDArray.toLong(blockDimensions), __elementsize__, registry); return null; // Nothing to return. } }; baseWriter.runner.call(createRunnable); } @Override public void writeMDArrayBlock(final String objectPath, final MD__Name__Array data, final long[] blockNumber) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeMDArrayBlockWithOffset(objectPath, data, offset); } @Override public void writeSlicedMDArrayBlock(final String objectPath, final MD__Name__Array data, final long[] blockNumber, IndexMap boundIndices) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeSlicedMDArrayBlockWithOffset(objectPath, data, offset, boundIndices); } @Override public void writeSlicedMDArrayBlock(String objectPath, MD__Name__Array data, long[] blockNumber, long[] boundIndices) { assert blockNumber != null; final long[] dimensions = data.longDimensions(); final long[] offset = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { offset[i] = blockNumber[i] * dimensions[i]; } writeSlicedMDArrayBlockWithOffset(objectPath, data, offset, boundIndices); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final MD__Name__Array data, final long[] offset) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] dimensions = data.longDimensions(); assert dimensions.length == offset.length; final long[] dataSetDimensions = new long[dimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + dimensions[i]; } final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, dimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(dimensions, registry); H5Dwrite(dataSetId, __Memorytype__, memorySpaceId, dataSpaceId, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } @Override public void writeSlicedMDArrayBlockWithOffset(String objectPath, MD__Name__Array data, long[] offset, IndexMap boundIndices) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), offset, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MD__Name__Array(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeSlicedMDArrayBlockWithOffset(String objectPath, MD__Name__Array data, long[] offset, long[] boundIndices) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final int fullRank = baseWriter.getRank(objectPath); final int[] fullBlockDimensions = new int[fullRank]; final long[] fullOffset = new long[fullRank]; MatrixUtils.createFullBlockDimensionsAndOffset(data.dimensions(), offset, boundIndices, fullRank, fullBlockDimensions, fullOffset); writeMDArrayBlockWithOffset(objectPath, new MD__Name__Array(data.getAsFlatArray(), fullBlockDimensions), fullOffset); } @Override public void writeMDArrayBlockWithOffset(final String objectPath, final MD__Name__Array data, final int[] blockDimensions, final long[] offset, final int[] memoryOffset) { assert objectPath != null; assert data != null; assert offset != null; baseWriter.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Void call(ICleanUpRegistry registry) { final long[] memoryDimensions = data.longDimensions(); assert memoryDimensions.length == offset.length; final long[] longBlockDimensions = MDArray.toLong(blockDimensions); assert longBlockDimensions.length == offset.length; final long[] dataSetDimensions = new long[blockDimensions.length]; for (int i = 0; i < offset.length; ++i) { dataSetDimensions[i] = offset[i] + blockDimensions[i]; } final int dataSetId = baseWriter.h5.openAndExtendDataSet(baseWriter.fileId, objectPath, baseWriter.fileFormat, dataSetDimensions, -1, registry); final int dataSpaceId = baseWriter.h5.getDataSpaceForDataSet(dataSetId, registry); baseWriter.h5.setHyperslabBlock(dataSpaceId, offset, longBlockDimensions); final int memorySpaceId = baseWriter.h5.createSimpleDataSpace(memoryDimensions, registry); baseWriter.h5.setHyperslabBlock(memorySpaceId, MDArray.toLong(memoryOffset), longBlockDimensions); H5Dwrite(dataSetId, __Memorytype__, memorySpaceId, dataSpaceId, H5P_DEFAULT, data.getAsFlatArray()); return null; // Nothing to return. } }; baseWriter.runner.call(writeRunnable); } }IHDF5PrimitiveReader.java.templ000066400000000000000000000427631256564762100331150ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/tools/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.base.mdarray.MD__Name__Array; /** * An interface that provides methods for reading __name__ values from HDF5 files. *

* Note: This interface supports block access and sliced access (which is a special cases of * block access) to arrays. The performance of this block access can vary greatly depending on how * the data are layed out in the HDF5 file. For best performance, the block (or slice) dimension should * be chosen to be equal to the chunk dimensions of the array, as in this case the block written / read * are stored as consecutive value in the HDF5 file and one write / read access will suffice. *

* Note: If the values read are unsigned, use the methods in {@link UnsignedIntUtils} to convert * to a larger Java integer type that can hold all values as unsigned. * * @author Bernd Rinn */ public interface IHDF5__Name__Reader { // ///////////////////// // Attributes // ///////////////////// /** * Reads a __name__ attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. */ public __name__ getAttr(String objectPath, String attributeName); /** * Reads a __name__[] attribute named attributeName from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute value read from the data set. */ public __name__[] getArrayAttr(String objectPath, String attributeName); /** * Reads a multi-dimensional array __name__ attribute named attributeName * from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute array value read from the data set. */ public MD__Name__Array getMDArrayAttr(String objectPath, String attributeName); /** * Reads a __name__ matrix attribute named attributeName * from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param attributeName The name of the attribute to read. * @return The attribute matrix value read from the data set. */ public __name__[][] getMatrixAttr(String objectPath, String attributeName) throws HDF5JavaException; // ///////////////////// // Data Sets // ///////////////////// /** * Reads a __name__ value from the data set objectPath. This method * doesn't check the data space but simply reads the first value. * * @param objectPath The name (including path information) of the data set object in the file. * @return The value read from the data set. */ public __name__ read(String objectPath); /** * Reads a __name__ array (of rank 1) from the data set objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. */ public __name__[] readArray(String objectPath); /** * Reads a multi-dimensional __name__ array data set objectPath * into a given array in memory. * * @param objectPath The name (including path information) of the data set object in the file. * @param array The array to read the data into. * @param memoryOffset The offset in the array to write the data to. * @return The effective dimensions of the block in array that was filled. */ public int[] readToMDArrayWithOffset(String objectPath, MD__Name__Array array, int[] memoryOffset); /** * Reads a block of the multi-dimensional __name__ array data set * objectPath into a given array in memory. * * @param objectPath The name (including path information) of the data set object in the file. * @param array The array to read the data into. * @param blockDimensions The size of the block to read along each axis. * @param offset The offset of the block in the data set. * @param memoryOffset The offset of the block in the array to write the data to. * @return The effective dimensions of the block in array that was filled. */ public int[] readToMDArrayBlockWithOffset(String objectPath, MD__Name__Array array, int[] blockDimensions, long[] offset, int[] memoryOffset); /** * Reads a block from a __name__ array (of rank 1) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the __name__[] returned * if the data set is long enough). * @param blockNumber The number of the block to read (starting with 0, offset: multiply with * blockSize). * @return The data read from the data set. The length will be min(size - blockSize*blockNumber, * blockSize). */ public __name__[] readArrayBlock(String objectPath, int blockSize, long blockNumber); /** * Reads a block from __name__ array (of rank 1) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSize The block size (this will be the length of the __name__[] * returned). * @param offset The offset of the block in the data set to start reading from (starting with 0). * @return The data block read from the data set. */ public __name__[] readArrayBlockWithOffset(String objectPath, int blockSize, long offset); /** * Reads a __name__ matrix (array of arrays) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. * * @throws HDF5JavaException If the data set objectPath is not of rank 2. */ public __name__[][] readMatrix(String objectPath) throws HDF5JavaException; /** * Reads a __name__ matrix (array of arrays) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSizeX The size of the block in the x dimension. * @param blockSizeY The size of the block in the y dimension. * @param blockNumberX The block number in the x dimension (offset: multiply with * blockSizeX). * @param blockNumberY The block number in the y dimension (offset: multiply with * blockSizeY). * @return The data block read from the data set. * * @throws HDF5JavaException If the data set objectPath is not of rank 2. */ public __name__[][] readMatrixBlock(String objectPath, int blockSizeX, int blockSizeY, long blockNumberX, long blockNumberY) throws HDF5JavaException; /** * Reads a __name__ matrix (array of arrays) from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockSizeX The size of the block in the x dimension. * @param blockSizeY The size of the block in the y dimension. * @param offsetX The offset in x dimension in the data set to start reading from. * @param offsetY The offset in y dimension in the data set to start reading from. * @return The data block read from the data set. * * @throws HDF5JavaException If the data set objectPath is not of rank 2. */ public __name__[][] readMatrixBlockWithOffset(String objectPath, int blockSizeX, int blockSizeY, long offsetX, long offsetY) throws HDF5JavaException; /** * Reads a multi-dimensional __name__ array from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @return The data read from the data set. */ public MD__Name__Array readMDArray(String objectPath); /** * Reads a slice of a multi-dimensional __name__ array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MD__Name__Array readMDArraySlice(String objectPath, IndexMap boundIndices); /** * Reads a slice of a multi-dimensional __name__ array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MD__Name__Array readMDArraySlice(String objectPath, long[] boundIndices); /** * Reads a block from a multi-dimensional __name__ array from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @return The data block read from the data set. */ public MD__Name__Array readMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber); /** * Reads a sliced block from a multi-dimensional __name__ array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MD__Name__Array readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, IndexMap boundIndices); /** * Reads a sliced block from a multi-dimensional __name__ array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param blockNumber The block number in each dimension (offset: multiply with the * blockDimensions in the according dimension). * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MD__Name__Array readSlicedMDArrayBlock(String objectPath, int[] blockDimensions, long[] blockNumber, long[] boundIndices); /** * Reads a block from a multi-dimensional __name__ array from the data set * objectPath. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @return The data block read from the data set. */ public MD__Name__Array readMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset); /** * Reads a sliced block of a multi-dimensional __name__ array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MD__Name__Array readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, IndexMap boundIndices); /** * Reads a sliced block of a multi-dimensional __name__ array from the data set * objectPath. The slice is defined by "bound indices", each of which is fixed to a * given value. The returned data block only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param blockDimensions The extent of the block in each dimension. * @param offset The offset in the data set to start reading from in each dimension. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. * @return The data block read from the data set. */ public MD__Name__Array readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions, long[] offset, long[] boundIndices); /** * Provides all natural blocks of this one-dimensional data set to iterate over. * * @see HDF5DataBlock * @throws HDF5JavaException If the data set is not of rank 1. */ public Iterable> getArrayNaturalBlocks( String dataSetPath) throws HDF5JavaException; /** * Provides all natural blocks of this multi-dimensional data set to iterate over. * * @see HDF5MDDataBlock */ public Iterable> getMDArrayNaturalBlocks( String dataSetPath); }IHDF5PrimitiveWriter.java.templ000066400000000000000000000716201256564762100331610ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/tools/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ch.systemsx.cisd.base.mdarray.MD__Name__Array; /** * An interface that provides methods for writing __name__ values to HDF5 files. *

* Note: This interface supports block access and sliced access (which is a special cases of * block access) to arrays. The performance of this block access can vary greatly depending on how * the data are layed out in the HDF5 file. For best performance, the block (or slice) dimension should * be chosen to be equal to the chunk dimensions of the array, as in this case the block written / read * are stored as consecutive value in the HDF5 file and one write / read access will suffice. __NoteUnsigned__ * * @author Bernd Rinn */ __SupressWarning__ public interface IHDF5__Name__Writer extends __SuperInterface__ { // ///////////////////// // Attributes // ///////////////////// /** * Set a __name__ attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ __OverrideIfInt__public void setAttr(String objectPath, String name, __name__ value); /** * Set a __name__[] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ __OverrideIfInt__public void setArrayAttr(String objectPath, String name, __name__[] value); /** * Set a multi-dimensional code>__name__ attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ __OverrideIfInt__public void setMDArrayAttr(String objectPath, String name, MD__Name__Array value); /** * Set a __name__[][] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ __OverrideIfInt__public void setMatrixAttr(String objectPath, String name, __name__[][] value); // ///////////////////// // Data Sets // ///////////////////// /** * Writes out a __name__ value. * * @param objectPath The name (including path information) of the data set object in the file. * @param value The value to write. */ __OverrideIfInt__public void write(String objectPath, __name__ value); /** * Writes out a __name__ array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ __OverrideIfInt__public void writeArray(String objectPath, __name__[] data); /** * Writes out a __name__ array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param features The storage features of the data set. */ __OverrideIfInt__public void writeArray(String objectPath, __name__[] data, HDF5__Classname__StorageFeatures features); /** * Creates a __name__ array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size When the writer is configured to use extendable data types (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be size. When the writer is * configured to enforce a non-extendable data set, the initial size equals the * total size and will be size. */ __OverrideIfInt__public void createArray(String objectPath, int size); /** * Creates a __name__ array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the __name__ array to create. When using extendable data sets * ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data * set smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). */ __OverrideIfInt__public void createArray(String objectPath, long size, int blockSize); /** * Creates a __name__ array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the __name__ array to create. When requesting a * chunked data set (e.g. {@link HDF5__Classname__StorageFeatures#__CLASSNAME___CHUNKED}), * the initial size of the array will be 0 and the chunk size will be arraySize. * When allowing a chunked data set (e.g. * {@link HDF5__Classname__StorageFeatures#__CLASSNAME___NO_COMPRESSION} when the writer is * not configured to avoid extendable data types, see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be arraySize. When enforcing a * on-extendable data set (e.g. * {@link HDF5__Classname__StorageFeatures#__CLASSNAME___CONTIGUOUS}), the initial size equals * the total size and will be arraySize. * @param features The storage features of the data set. */ __OverrideIfInt__public void createArray(String objectPath, int size, HDF5__Classname__StorageFeatures features); /** * Creates a __name__ array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the __name__ array to create. When using extendable data sets * ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data * set smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) and * features is HDF5__Classname__StorageFeature.__CLASSNAME___NO_COMPRESSION. * @param features The storage features of the data set. */ __OverrideIfInt__public void createArray(String objectPath, long size, int blockSize, HDF5__Classname__StorageFeatures features); /** * Writes out a block of a __name__ array (of rank 1). The data set needs to have * been created by {@link #createArray(String, long, int, HDF5__Classname__StorageFeatures)} * beforehand. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumber The number of the block to write. */ __OverrideIfInt__public void writeArrayBlock(String objectPath, __name__[] data, long blockNumber); /** * Writes out a block of a __name__ array (of rank 1). The data set needs to have * been created by {@link #createArray(String, long, int, HDF5__Classname__StorageFeatures)} * beforehand. *

* Use this method instead of {@link #writeArrayBlock(String, __name__[], long)} if the * total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param dataSize The (real) size of data (needs to be <= data.length * ) * @param offset The offset in the data set to start writing to. */ __OverrideIfInt__public void writeArrayBlockWithOffset(String objectPath, __name__[] data, int dataSize, long offset); /** * Writes out a __name__ matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ __OverrideIfInt__public void writeMatrix(String objectPath, __name__[][] data); /** * Writes out a __name__ matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. */ __OverrideIfInt__public void writeMatrix(String objectPath, __name__[][] data, HDF5__Classname__StorageFeatures features); /** * Creates a __name__ matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of one block in the x dimension. See * {@link #createMDArray(String, int[])} on the different * meanings of this parameter. * @param sizeY The size of one block in the y dimension. See * {@link #createMDArray(String, int[])} on the different * meanings of this parameter. */ __OverrideIfInt__public void createMatrix(String objectPath, int sizeX, int sizeY); /** * Creates a __name__ matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of one block in the x dimension. See * {@link #createMDArray(String, int[], HDF5__Classname__StorageFeatures)} on the different * meanings of this parameter. * @param sizeY The size of one block in the y dimension. See * {@link #createMDArray(String, int[], HDF5__Classname__StorageFeatures)} on the different * meanings of this parameter. * @param features The storage features of the data set. */ __OverrideIfInt__public void createMatrix(String objectPath, int sizeX, int sizeY, HDF5__Classname__StorageFeatures features); /** * Creates a __name__ matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the __name__ matrix to create. * @param sizeY The size of the y dimension of the __name__ matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. */ __OverrideIfInt__public void createMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY); /** * Creates a __name__ matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the __name__ matrix to create. * @param sizeY The size of the y dimension of the __name__ matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. * @param features The storage features of the data set. */ __OverrideIfInt__public void createMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY, HDF5__Classname__StorageFeatures features); /** * Writes out a block of a __name__ matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5__Classname__StorageFeatures)} beforehand. *

* Use this method instead of * {@link #createMatrix(String, long, long, int, int, HDF5__Classname__StorageFeatures)} if the total * size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumberX The block number in the x dimension (offset: multiply with * data.length). * @param blockNumberY The block number in the y dimension (offset: multiply with * data[0.length). */ __OverrideIfInt__public void writeMatrixBlock(String objectPath, __name__[][] data, long blockNumberX, long blockNumberY); /** * Writes out a block of a __name__ matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5__Classname__StorageFeatures)} beforehand. *

* Use this method instead of {@link #writeMatrixBlock(String, __name__[][], long, long)} if * the total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. */ __OverrideIfInt__public void writeMatrixBlockWithOffset(String objectPath, __name__[][] data, long offsetX, long offsetY); /** * Writes out a block of a __name__ matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5__Classname__StorageFeatures)} beforehand. *

* Use this method instead of {@link #writeMatrixBlock(String, __name__[][], long, long)} if * the total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param dataSizeX The (real) size of data along the x axis (needs to be * <= data.length ) * @param dataSizeY The (real) size of data along the y axis (needs to be * <= data[0].length ) * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. */ __OverrideIfInt__public void writeMatrixBlockWithOffset(String objectPath, __name__[][] data, int dataSizeX, int dataSizeY, long offsetX, long offsetY); /** * Writes out a multi-dimensional __name__ array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ __OverrideIfInt__public void writeMDArray(String objectPath, MD__Name__Array data); /** * Writes out a multi-dimensional __name__ array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. */ __OverrideIfInt__public void writeMDArray(String objectPath, MD__Name__Array data, HDF5__Classname__StorageFeatures features); /** * Writes out a slice of a multi-dimensional __name__ array. The slice is defined by * "bound indices", each of which is fixed to a given value. The data object only * contains the free (i.e. non-fixed) indices. *

* Note:The object identified by objectPath needs to exist when this method is * called. This method will not create the array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. */ public void writeMDArraySlice(String objectPath, MD__Name__Array data, IndexMap boundIndices); /** * Writes out a slice of a multi-dimensional __name__ array. The slice is defined by * "bound indices", each of which is fixed to a given value. The data object only * contains the free (i.e. non-fixed) indices. *

* Note:The object identified by objectPath needs to exist when this method is * called. This method will not create the array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. */ public void writeMDArraySlice(String objectPath, MD__Name__Array data, long[] boundIndices); /** * Creates a multi-dimensional __name__ array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions When the writer is configured to use extendable data types (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial dimensions * and the dimensions of a chunk of the array will be dimensions. When the * writer is configured to enforce a non-extendable data set, the initial dimensions * equal the dimensions and will be dimensions. */ __OverrideIfInt__public void createMDArray(String objectPath, int[] dimensions); /** * Creates a multi-dimensional __name__ array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. */ __OverrideIfInt__public void createMDArray(String objectPath, long[] dimensions, int[] blockDimensions); /** * Creates a multi-dimensional __name__ array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the __name__ array to create. When requesting * a chunked data set (e.g. {@link HDF5__Classname__StorageFeatures#__CLASSNAME___CHUNKED}), * the initial size of the array will be 0 and the chunk size will be dimensions. * When allowing a chunked data set (e.g. * {@link HDF5__Classname__StorageFeatures#__CLASSNAME___NO_COMPRESSION} when the writer is * not configured to avoid extendable data types, see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be dimensions. When enforcing a * on-extendable data set (e.g. * {@link HDF5__Classname__StorageFeatures#__CLASSNAME___CONTIGUOUS}), the initial size equals * the total size and will be dimensions. * @param features The storage features of the data set. */ __OverrideIfInt__public void createMDArray(String objectPath, int[] dimensions, HDF5__Classname__StorageFeatures features); /** * Creates a multi-dimensional __name__ array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. * @param features The storage features of the data set. */ __OverrideIfInt__public void createMDArray(String objectPath, long[] dimensions, int[] blockDimensions, HDF5__Classname__StorageFeatures features); /** * Writes out a block of a multi-dimensional __name__ array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). */ __OverrideIfInt__public void writeMDArrayBlock(String objectPath, MD__Name__Array data, long[] blockNumber); /** * Writes out a sliced block of a multi-dimensional __name__ array. The slice is * defined by "bound indices", each of which is fixed to a given value. The data * object only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. */ public void writeSlicedMDArrayBlock(String objectPath, MD__Name__Array data, long[] blockNumber, IndexMap boundIndices); /** * Writes out a sliced block of a multi-dimensional __name__ array. The slice is * defined by "bound indices", each of which is fixed to a given value. The data * object only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). * @param boundIndices The mapping of indices to index values which should be bound. For example * a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound * indices and binds them to the values 5 and 7, respectively. */ public void writeSlicedMDArrayBlock(String objectPath, MD__Name__Array data, long[] blockNumber, long[] boundIndices); /** * Writes out a block of a multi-dimensional __name__ array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. */ __OverrideIfInt__public void writeMDArrayBlockWithOffset(String objectPath, MD__Name__Array data, long[] offset); /** * Writes out a sliced block of a multi-dimensional __name__ array. The slice is * defined by "bound indices", each of which is fixed to a given value. The data * object only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. */ public void writeSlicedMDArrayBlockWithOffset(String objectPath, MD__Name__Array data, long[] offset, IndexMap boundIndices); /** * Writes out a sliced block of a multi-dimensional __name__ array. The slice is * defined by "bound indices", each of which is fixed to a given value. The data * object only contains the free (i.e. non-fixed) indices. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. * @param boundIndices The array containing the values of the bound indices at the respective * index positions, and -1 at the free index positions. For example an array of * new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and * binds them to the values 5 and 7, respectively. */ public void writeSlicedMDArrayBlockWithOffset(String objectPath, MD__Name__Array data, long[] offset, long[] boundIndices); /** * Writes out a block of a multi-dimensional __name__ array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param blockDimensions The dimensions of the block to write to the data set. * @param offset The offset of the block in the data set to start writing to in each dimension. * @param memoryOffset The offset of the block in the data array. */ __OverrideIfInt__public void writeMDArrayBlockWithOffset(String objectPath, MD__Name__Array data, int[] blockDimensions, long[] offset, int[] memoryOffset); }IHDF5UnsignedPrimitiveWriter.java.templ000066400000000000000000000541761256564762100346650ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/sourceTest/java/ch/systemsx/cisd/hdf5/tools/* * Copyright 2007 - 2014 ETH Zuerich, CISD and SIS. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ch.systemsx.cisd.hdf5; import ch.systemsx.cisd.base.mdarray.MD__Name__Array; /** * An interface that provides methods for writing unsigned __name__ values to HDF5 files. *

* Note: This interface supports block access and sliced access (which is a special cases of * block access) to arrays. The performance of this block access can vary greatly depending on how * the data are layed out in the HDF5 file. For best performance, the block (or slice) dimension should * be chosen to be equal to the chunk dimensions of the array, as in this case the block written / read * are stored as consecutive value in the HDF5 file and one write / read access will suffice. *

* Note: Use the methods in {@link UnsignedIntUtils} to convert from and to unsigned values. * * @deprecated Use {@link IHDF5__Name__Writer} instead, it has all methods of this interface. * * @author Bernd Rinn */ @Deprecated public interface IHDF5Unsigned__Name__Writer extends IHDF5__Name__Reader { // ///////////////////// // Attributes // ///////////////////// /** * Set a __name__ attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setAttr(String objectPath, String name, __name__ value); /** * Set a __name__[] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setArrayAttr(String objectPath, String name, __name__[] value); /** * Set a multi-dimensional code>__name__ attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setMDArrayAttr(String objectPath, String name, MD__Name__Array value); /** * Set a __name__[][] attribute on the referenced object. *

* The referenced object must exist, that is it need to have been written before by one of the * write() methods. * * @param objectPath The name of the object to add the attribute to. * @param name The name of the attribute. * @param value The value of the attribute. */ public void setMatrixAttr(String objectPath, String name, __name__[][] value); // ///////////////////// // Data Sets // ///////////////////// /** * Writes out a __name__ value. * * @param objectPath The name (including path information) of the data set object in the file. * @param value The value to write. */ public void write(String objectPath, __name__ value); /** * Writes out a __name__ array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. */ public void writeArray(String objectPath, __name__[] data); /** * Writes out a __name__ array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param features The storage features of the data set. */ public void writeArray(String objectPath, __name__[] data, HDF5__Classname__StorageFeatures features); /** * Creates a __name__ array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size When the writer is configured to use extendable data types (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be size. When the writer is * configured to enforce a non-extendable data set, the initial size equals the * total size and will be size. */ public void createArray(String objectPath, int size); /** * Creates a __name__ array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the __name__ array to create. When using extendable data sets * ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data * set smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}). */ public void createArray(String objectPath, long size, int blockSize); /** * Creates a __name__ array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the __name__ array to create. When requesting a * chunked data set (e.g. {@link HDF5__Classname__StorageFeatures#__CLASSNAME___CHUNKED}), * the initial size of the array will be 0 and the chunk size will be arraySize. * When allowing a chunked data set (e.g. * {@link HDF5__Classname__StorageFeatures#__CLASSNAME___NO_COMPRESSION} when the writer is * not configured to avoid extendable data types, see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be arraySize. When enforcing a * on-extendable data set (e.g. * {@link HDF5__Classname__StorageFeatures#__CLASSNAME___CONTIGUOUS}), the initial size equals * the total size and will be arraySize. * @param features The storage features of the data set. */ public void createArray(String objectPath, int size, HDF5__Classname__StorageFeatures features); /** * Creates a __name__ array (of rank 1). * * @param objectPath The name (including path information) of the data set object in the file. * @param size The size of the __name__ array to create. When using extendable data sets * ((see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()})), then no data * set smaller than this size can be created, however data sets may be larger. * @param blockSize The size of one block (for block-wise IO). Ignored if no extendable data * sets are used (see {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}) and * features is HDF5__Classname__StorageFeature.__CLASSNAME___NO_COMPRESSION. * @param features The storage features of the data set. */ public void createArray(String objectPath, long size, int blockSize, HDF5__Classname__StorageFeatures features); /** * Writes out a block of a __name__ array (of rank 1). The data set needs to have * been created by {@link #createArray(String, long, int, HDF5__Classname__StorageFeatures)} * beforehand. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumber The number of the block to write. */ public void writeArrayBlock(String objectPath, __name__[] data, long blockNumber); /** * Writes out a block of a __name__ array (of rank 1). The data set needs to have * been created by {@link #createArray(String, long, int, HDF5__Classname__StorageFeatures)} * beforehand. *

* Use this method instead of {@link #writeArrayBlock(String, __name__[], long)} if the * total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param dataSize The (real) size of data (needs to be <= data.length * ) * @param offset The offset in the data set to start writing to. */ public void writeArrayBlockWithOffset(String objectPath, __name__[] data, int dataSize, long offset); /** * Writes out a __name__ matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ public void writeMatrix(String objectPath, __name__[][] data); /** * Writes out a __name__ matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. */ public void writeMatrix(String objectPath, __name__[][] data, HDF5__Classname__StorageFeatures features); /** * Creates a __name__ matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of one block in the x dimension. See * {@link #createMDArray(String, int[])} on the different * meanings of this parameter. * @param sizeY The size of one block in the y dimension. See * {@link #createMDArray(String, int[])} on the different * meanings of this parameter. */ public void createMatrix(String objectPath, int sizeX, int sizeY); /** * Creates a __name__ matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of one block in the x dimension. See * {@link #createMDArray(String, int[], HDF5__Classname__StorageFeatures)} on the different * meanings of this parameter. * @param sizeY The size of one block in the y dimension. See * {@link #createMDArray(String, int[], HDF5__Classname__StorageFeatures)} on the different * meanings of this parameter. * @param features The storage features of the data set. */ public void createMatrix(String objectPath, int sizeX, int sizeY, HDF5__Classname__StorageFeatures features); /** * Creates a __name__ matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the __name__ matrix to create. * @param sizeY The size of the y dimension of the __name__ matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. */ public void createMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY); /** * Creates a __name__ matrix (array of rank 2). * * @param objectPath The name (including path information) of the data set object in the file. * @param sizeX The size of the x dimension of the __name__ matrix to create. * @param sizeY The size of the y dimension of the __name__ matrix to create. * @param blockSizeX The size of one block in the x dimension. * @param blockSizeY The size of one block in the y dimension. * @param features The storage features of the data set. */ public void createMatrix(String objectPath, long sizeX, long sizeY, int blockSizeX, int blockSizeY, HDF5__Classname__StorageFeatures features); /** * Writes out a block of a __name__ matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5__Classname__StorageFeatures)} beforehand. *

* Use this method instead of * {@link #createMatrix(String, long, long, int, int, HDF5__Classname__StorageFeatures)} if the total * size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. The length defines the block size. Must not be * null or of length 0. * @param blockNumberX The block number in the x dimension (offset: multiply with * data.length). * @param blockNumberY The block number in the y dimension (offset: multiply with * data[0.length). */ public void writeMatrixBlock(String objectPath, __name__[][] data, long blockNumberX, long blockNumberY); /** * Writes out a block of a __name__ matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5__Classname__StorageFeatures)} beforehand. *

* Use this method instead of {@link #writeMatrixBlock(String, __name__[][], long, long)} if * the total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. */ public void writeMatrixBlockWithOffset(String objectPath, __name__[][] data, long offsetX, long offsetY); /** * Writes out a block of a __name__ matrix (array of rank 2). The data set needs to * have been created by * {@link #createMatrix(String, long, long, int, int, HDF5__Classname__StorageFeatures)} beforehand. *

* Use this method instead of {@link #writeMatrixBlock(String, __name__[][], long, long)} if * the total size of the data set is not a multiple of the block size. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. * @param dataSizeX The (real) size of data along the x axis (needs to be * <= data.length ) * @param dataSizeY The (real) size of data along the y axis (needs to be * <= data[0].length ) * @param offsetX The x offset in the data set to start writing to. * @param offsetY The y offset in the data set to start writing to. */ public void writeMatrixBlockWithOffset(String objectPath, __name__[][] data, int dataSizeX, int dataSizeY, long offsetX, long offsetY); /** * Writes out a multi-dimensional __name__ array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. */ public void writeMDArray(String objectPath, MD__Name__Array data); /** * Writes out a multi-dimensional __name__ array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param features The storage features of the data set. */ public void writeMDArray(String objectPath, MD__Name__Array data, HDF5__Classname__StorageFeatures features); /** * Creates a multi-dimensional __name__ array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions When the writer is configured to use extendable data types (see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial dimensions * and the dimensions of a chunk of the array will be dimensions. When the * writer is configured to enforce a non-extendable data set, the initial dimensions * equal the dimensions and will be dimensions. */ public void createMDArray(String objectPath, int[] dimensions); /** * Creates a multi-dimensional __name__ array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. */ public void createMDArray(String objectPath, long[] dimensions, int[] blockDimensions); /** * Creates a multi-dimensional __name__ array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the __name__ array to create. When requesting * a chunked data set (e.g. {@link HDF5__Classname__StorageFeatures#__CLASSNAME___CHUNKED}), * the initial size of the array will be 0 and the chunk size will be dimensions. * When allowing a chunked data set (e.g. * {@link HDF5__Classname__StorageFeatures#__CLASSNAME___NO_COMPRESSION} when the writer is * not configured to avoid extendable data types, see * {@link IHDF5WriterConfigurator#dontUseExtendableDataTypes()}), the initial size * and the chunk size of the array will be dimensions. When enforcing a * on-extendable data set (e.g. * {@link HDF5__Classname__StorageFeatures#__CLASSNAME___CONTIGUOUS}), the initial size equals * the total size and will be dimensions. * @param features The storage features of the data set. */ public void createMDArray(String objectPath, int[] dimensions, HDF5__Classname__StorageFeatures features); /** * Creates a multi-dimensional __name__ array. * * @param objectPath The name (including path information) of the data set object in the file. * @param dimensions The dimensions of the array. * @param blockDimensions The dimensions of one block (chunk) of the array. * @param features The storage features of the data set. */ public void createMDArray(String objectPath, long[] dimensions, int[] blockDimensions, HDF5__Classname__StorageFeatures features); /** * Writes out a block of a multi-dimensional __name__ array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param blockNumber The block number in each dimension (offset: multiply with the extend in * the according dimension). */ public void writeMDArrayBlock(String objectPath, MD__Name__Array data, long[] blockNumber); /** * Writes out a block of a multi-dimensional __name__ array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. All columns need to have the * same length. * @param offset The offset in the data set to start writing to in each dimension. */ public void writeMDArrayBlockWithOffset(String objectPath, MD__Name__Array data, long[] offset); /** * Writes out a block of a multi-dimensional __name__ array. * * @param objectPath The name (including path information) of the data set object in the file. * @param data The data to write. Must not be null. * @param blockDimensions The dimensions of the block to write to the data set. * @param offset The offset of the block in the data set to start writing to in each dimension. * @param memoryOffset The offset of the block in the data array. */ public void writeMDArrayBlockWithOffset(String objectPath, MD__Name__Array data, int[] blockDimensions, long[] offset, int[] memoryOffset); }libsis-jhdf5-java-14.12.1/sourceTest/java/test/000077500000000000000000000000001256564762100211405ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/000077500000000000000000000000001256564762100224555ustar00rootroot00000000000000libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/TestAll.java000066400000000000000000000046721256564762100247010ustar00rootroot00000000000000package test.hdf5lib; import java.io.File; import java.io.FileOutputStream; import java.io.IOException; import java.io.InputStream; import java.io.OutputStream; import org.apache.commons.io.IOUtils; import org.junit.BeforeClass; import org.junit.runner.RunWith; import org.junit.runners.Suite; import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel; import ch.systemsx.cisd.base.utilities.ResourceUtilities; @RunWith(Suite.class) @Suite.SuiteClasses( { TestH5.class, TestH5Eregister.class, TestH5Edefault.class, TestH5E.class, TestH5Fparams.class, TestH5Fbasic.class, TestH5F.class, TestH5Gbasic.class, TestH5G.class, TestH5Giterate.class, TestH5Sbasic.class, TestH5S.class, TestH5Tparams.class, TestH5Tbasic.class, TestH5T.class, TestH5Dparams.class, TestH5D.class, TestH5Dplist.class, TestH5Lparams.class, TestH5Lbasic.class, TestH5Lcreate.class, TestH5R.class, TestH5P.class, TestH5PData.class, TestH5Pfapl.class, TestH5A.class, TestH5Oparams.class, TestH5Obasic.class, TestH5Ocopy.class, TestH5Ocreate.class, TestH5Z.class }) public class TestAll { @BeforeClass public static void setUp() { InputStream resourceStream = null; try { final File dir = new File("sourceTest/java/test/hdf5lib"); if (dir.isDirectory() == false) { dir.mkdirs(); } final File file = new File(dir, "h5ex_g_iterate.hdf"); if (file.exists() == false) { resourceStream = ResourceUtilities.class.getResourceAsStream("/h5ex_g_iterate.hdf"); if (resourceStream == null) { throw new IllegalArgumentException("Resource 'h5ex_g_iterate.hdf' not found."); } final OutputStream fileStream = new FileOutputStream(file); try { IOUtils.copy(resourceStream, fileStream); fileStream.close(); } finally { IOUtils.closeQuietly(fileStream); } } } catch (final IOException ex) { throw CheckedExceptionTunnel.wrapIfNecessary(ex); } finally { IOUtils.closeQuietly(resourceStream); } } } libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/TestH5.java000066400000000000000000000152611256564762100244410ustar00rootroot00000000000000/** * */ package test.hdf5lib; import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertFalse; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import java.io.ByteArrayOutputStream; import java.io.File; import java.io.FileInputStream; import java.io.FileOutputStream; import java.io.IOException; import java.io.ObjectInputStream; import java.io.ObjectOutputStream; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.HDF5Constants; import org.junit.Test; /** * @author xcao * */ @SuppressWarnings("all") public class TestH5 { /** * Test method for {@link ncsa.hdf.hdf5lib.H5#J2C(int)}. */ @Test public void testJ2C() { int H5F_ACC_RDONLY = 0x0000; int H5F_ACC_RDWR = 0x0001; int H5F_ACC_TRUNC = 0x0002; int H5F_ACC_EXCL = 0x0004; int H5F_ACC_DEBUG = 0x0008; int H5F_ACC_CREAT = 0x0010; int H5F_OBJ_FILE = 0x0001; int H5F_OBJ_DATASET = 0x0002; int H5F_OBJ_GROUP = 0x0004; int H5F_OBJ_DATATYPE = 0x0008; int H5F_OBJ_ATTR = 0x0010; int H5F_OBJ_ALL = H5F_OBJ_FILE | H5F_OBJ_DATASET | H5F_OBJ_GROUP | H5F_OBJ_DATATYPE | H5F_OBJ_ATTR; int H5F_OBJ_LOCAL = 0x0020; int definedValues[] = { H5F_ACC_RDONLY, H5F_ACC_RDWR, H5F_ACC_TRUNC, H5F_ACC_EXCL, H5F_ACC_DEBUG, H5F_ACC_CREAT, H5F_OBJ_FILE, H5F_OBJ_DATASET, H5F_OBJ_GROUP, H5F_OBJ_DATATYPE, H5F_OBJ_ATTR, H5F_OBJ_ALL, H5F_OBJ_LOCAL }; int j2cValues[] = { HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5F_ACC_EXCL, HDF5Constants.H5F_ACC_DEBUG, HDF5Constants.H5F_ACC_CREAT, HDF5Constants.H5F_OBJ_FILE, HDF5Constants.H5F_OBJ_DATASET, HDF5Constants.H5F_OBJ_GROUP, HDF5Constants.H5F_OBJ_DATATYPE, HDF5Constants.H5F_OBJ_ATTR, HDF5Constants.H5F_OBJ_ALL, HDF5Constants.H5F_OBJ_LOCAL }; for (int i = 0; i < definedValues.length; i++) { assertEquals(definedValues[i], j2cValues[i]); } assertFalse(H5F_ACC_RDONLY == HDF5Constants.H5F_ACC_RDWR); assertFalse(H5F_OBJ_FILE == HDF5Constants.H5F_OBJ_GROUP); } /** * Test method for {@link ncsa.hdf.hdf5lib.H5#H5error_off()}. */ @Test public void testH5error_off() { try { H5.H5error_off(); } catch (Throwable err) { fail("H5.H5error_off failed: " + err); } } /** * Test method for {@link ncsa.hdf.hdf5lib.H5#H5open()}. */ @Test public void testH5open() { try { H5.H5open(); } catch (Throwable err) { fail("H5.H5open failed: " + err); } } /** * Test method for {@link ncsa.hdf.hdf5lib.H5#H5garbage_collect()}. */ @Test public void testH5garbage_collect() { try { H5.H5garbage_collect(); } catch (Throwable err) { fail("H5.H5garbage_collect failed: " + err); } } /** * Test method for * {@link ncsa.hdf.hdf5lib.H5#H5set_free_list_limits(int, int, int, int, int, int)} * . */ @Test public void testH5set_free_list_limits() { int reg_global_lim = 1; int reg_list_lim = 1; int arr_global_lim = 1; int arr_list_lim = 1; int blk_global_lim = 1; int blk_list_lim = 1; try { H5.H5set_free_list_limits(reg_global_lim, reg_list_lim, arr_global_lim, arr_list_lim, blk_global_lim, blk_list_lim); } catch (Throwable err) { fail("H5.H5set_free_list_limits failed: " + err); } } /** * Test method for {@link ncsa.hdf.hdf5lib.H5#H5get_libversion(int[])}. */ @Test public void testH5get_libversion() { int libversion[] = { 0, 0, 0 }; try { H5.H5get_libversion(libversion); } catch (Throwable err) { fail("H5.H5get_libversion: " + err); } for (int i = 0; i < 3; i++) assertEquals(libversion[i], H5.LIB_VERSION[i]); for (int i = 0; i < 3; i++) assertFalse(libversion[i] == 0); } /** * Test method for * {@link ncsa.hdf.hdf5lib.H5#H5check_version(int, int, int)}. */ @Test public void testH5check_version() { int majnum = 1, minnum = 8, relnum = 10; try { H5.H5check_version(majnum, minnum, relnum); } catch (Throwable err) { fail("H5.H5check_version failed: " + err); } try { H5.H5check_version(-1, 0, 0); } catch (Throwable err) { fail("H5.H5check_version failed: " + err); } } @Test public void testIsSerializable() { H5 test = new H5(); ByteArrayOutputStream out = new ByteArrayOutputStream(); ObjectOutputStream oos; try { oos = new ObjectOutputStream(out); oos.writeObject(test); oos.close(); } catch (IOException err) { err.printStackTrace(); fail("ObjectOutputStream failed: " + err); } assertTrue(out.toByteArray().length > 0); } @SuppressWarnings("static-access") @Test public void serializeToDisk() { try { H5 test = new H5(); FileOutputStream fos = new FileOutputStream("temph5.ser"); ObjectOutputStream oos = new ObjectOutputStream(fos); oos.writeObject(test); oos.close(); } catch (Exception ex) { fail("Exception thrown during test: " + ex.toString()); } try { FileInputStream fis = new FileInputStream("temph5.ser"); ObjectInputStream ois = new ObjectInputStream(fis); H5 test = (ncsa.hdf.hdf5lib.H5) ois.readObject(); ois.close(); assertTrue("H5.LIB_VERSION[0]", test.LIB_VERSION[0]==H5.LIB_VERSION[0]); assertTrue("H5.LIB_VERSION[1]", test.LIB_VERSION[1]==H5.LIB_VERSION[1]); assertTrue("H5.LIB_VERSION[2]", test.LIB_VERSION[2]==H5.LIB_VERSION[2]); // Clean up the file new File("temph5.ser").delete(); } catch (Exception ex) { fail("Exception thrown during test: " + ex.toString()); } } } libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/TestH5A.java000066400000000000000000000766141256564762100245530ustar00rootroot00000000000000package test.hdf5lib; import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertFalse; import static org.junit.Assert.assertNotNull; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import java.io.File; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.HDF5Constants; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import ncsa.hdf.hdf5lib.structs.H5A_info_t; import org.junit.After; import org.junit.Before; import org.junit.Test; @SuppressWarnings("all") public class TestH5A { private static final String H5_FILE = "test.h5"; private static final int DIM_X = 4; private static final int DIM_Y = 6; int H5fid = -1; int H5dsid = -1; int H5did = -1; long[] H5dims = { DIM_X, DIM_Y }; int type_id = -1; int space_id = -1; int lapl_id = -1; private final void _deleteFile(String filename) { File file = new File(filename); if (file.exists()) { try {file.delete();} catch (SecurityException e) {} } } private final int _createDataset(int fid, int dsid, String name, int dapl) { int did = -1; try { did = H5.H5Dcreate(fid, name, HDF5Constants.H5T_STD_I32BE, dsid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, dapl); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Dcreate: " + err); } assertTrue("TestH5D._createDataset: ", did > 0); return did; } @Before public void createH5file() throws NullPointerException, HDF5Exception { assertTrue("H5 open ids is 0", H5.getOpenIDCount() == 0); try { H5fid = H5.H5Fcreate(H5_FILE, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); assertTrue("TestH5D.createH5file: H5.H5Fcreate: ", H5fid > 0); H5dsid = H5.H5Screate_simple(2, H5dims, null); assertTrue("TestH5D.createH5file: H5.H5Screate_simple: ", H5dsid > 0); H5did = _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT); assertTrue("TestH5D.createH5file: _createDataset: ", H5did > 0); space_id = H5.H5Screate(HDF5Constants.H5S_NULL); assertTrue(space_id > 0); lapl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_ACCESS); assertTrue(lapl_id > 0); type_id = H5.H5Tenum_create(HDF5Constants.H5T_STD_I32LE); assertTrue(type_id > 0); int status = H5.H5Tenum_insert(type_id, "test", 1); assertTrue(status >= 0); } catch (Throwable err) { err.printStackTrace(); fail("TestH5D.createH5file: " + err); } H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); } @After public void deleteH5file() throws HDF5LibraryException { if (H5dsid > 0) try {H5.H5Sclose(H5dsid);} catch (Exception ex) {} if (H5did > 0) try {H5.H5Dclose(H5did);} catch (Exception ex) {} if (H5fid > 0) try {H5.H5Fclose(H5fid);} catch (Exception ex) {} _deleteFile(H5_FILE); if (type_id > 0) try {H5.H5Tclose(type_id);} catch (Exception ex) {} if (space_id > 0) try {H5.H5Sclose(space_id);} catch (Exception ex) {} if (lapl_id > 0) try {H5.H5Pclose(lapl_id);} catch (Exception ex) {} } @Test public void testH5Acreate2() { int attr_id = -1; try { attr_id = H5.H5Acreate(H5did, "dset", type_id, space_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); assertTrue("testH5Acreate2", attr_id >= 0); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Acreate2: " + err); } finally { if (attr_id > 0) try {H5.H5Aclose(attr_id);} catch (Exception ex) {} } } @Test(expected = HDF5LibraryException.class) public void testH5Acreate2_invalidobject() throws Throwable { H5.H5Acreate(H5dsid, "dset", type_id, space_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); } @Test(expected = NullPointerException.class) public void testH5Acreate2_nullname() throws Throwable { H5.H5Acreate(H5did, null, type_id, space_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); } @Test public void testH5Aopen() { String attr_name = "dset"; int attribute_id = -1; int attr_id = -1; try { attr_id = H5.H5Acreate(H5did, attr_name, type_id, space_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); // Opening the existing attribute, attr_name(Created by H5ACreate2) // attached to an object identifier. attribute_id = H5.H5Aopen(H5did, attr_name, HDF5Constants.H5P_DEFAULT); assertTrue("testH5Aopen: H5Aopen", attribute_id >= 0); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Aopen: " + err); } finally { if (attr_id > 0) try {H5.H5Aclose(attr_id);} catch (Exception ex) {} if (attribute_id > 0) try {H5.H5Aclose(attribute_id);} catch (Exception ex) {} } } @Test(expected = HDF5LibraryException.class) public void testH5Aopen_invalidname() throws Throwable { H5.H5Aopen(H5did, "attr_name", HDF5Constants.H5P_DEFAULT); } @Test public void testH5Aopen_by_idx() { int loc_id = H5did; String obj_name = "."; int idx_type = HDF5Constants.H5_INDEX_CRT_ORDER; int order = HDF5Constants.H5_ITER_INC; long n = 0; int attr_id = -1; int attribute_id = -1; int aapl_id = HDF5Constants.H5P_DEFAULT; try { attr_id = H5.H5Acreate(H5did, "file", type_id, space_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); // Opening the existing attribute, obj_name(Created by H5ACreate2) // by index, attached to an object identifier. attribute_id = H5.H5Aopen_by_idx(H5did, ".", HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, 0, HDF5Constants.H5P_DEFAULT, lapl_id); assertTrue("testH5Aopen_by_idx: H5Aopen_by_idx", attribute_id >= 0); // Negative test- Error should be thrown when H5Aopen_by_idx is // called // with n=5 and we do not have 5 attributes created. try { n = 5; H5.H5Aopen_by_idx(loc_id, obj_name, idx_type, order, n, aapl_id, lapl_id); fail("Negative Test Failed:- Error not Thrown when n is invalid."); } catch (AssertionError err) { fail("H5.H5Aopen_by_idx: " + err); } catch (HDF5LibraryException err) {} // Negative test- Error should be thrown when H5Aopen_by_idx is // called // with an invalid object name(which hasn't been created). try { n = 0; obj_name = "file"; H5.H5Aopen_by_idx(loc_id, obj_name, idx_type, order, n, aapl_id, lapl_id); fail("Negative Test Failed:- Error not Thrown when attribute name is invalid."); } catch (AssertionError err) { fail("H5.H5Aopen_by_idx: " + err); } catch (HDF5LibraryException err) {} } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Aopen_by_idx: " + err); } finally { if (attr_id > 0) try {H5.H5Aclose(attr_id);} catch (Exception ex) {} if (attribute_id > 0) try {H5.H5Aclose(attribute_id);} catch (Exception ex) {} } } @Test public void testH5Acreate_by_name() { String obj_name = "."; String attr_name = "DATASET"; int attribute_id = -1; boolean bool_val = false; try { attribute_id = H5.H5Acreate_by_name(H5fid, obj_name, attr_name, type_id, space_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id); assertTrue("testH5Acreate_by_name: H5Acreate_by_name", attribute_id >= 0); // Check if the name of attribute attached to the object specified // by loc_id and obj_name exists.It should be true. bool_val = H5.H5Aexists_by_name(H5fid, obj_name, attr_name, lapl_id); assertTrue("testH5Acreate_by_name: H5Aexists_by_name", bool_val == true); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Acreate_by_name " + err); } finally { if (attribute_id > 0) try {H5.H5Aclose(attribute_id);} catch (Exception ex) {} } } @Test public void testH5Arename() throws Throwable, HDF5LibraryException, NullPointerException { int loc_id = H5fid; String old_attr_name = "old"; String new_attr_name = "new"; int attr_id = -1; int ret_val = -1; boolean bool_val = false; try { attr_id = H5.H5Acreate(loc_id, old_attr_name, type_id, space_id, HDF5Constants.H5P_DEFAULT, lapl_id); ret_val = H5.H5Arename(loc_id, old_attr_name, new_attr_name); // Check the return value.It should be non negative. assertTrue("testH5Arename: H5Arename", ret_val >= 0); // Check if the new name of attribute attached to the object // specified by loc_id and obj_name exists.It should be true. bool_val = H5.H5Aexists(loc_id, new_attr_name); assertTrue("testH5Arename: H5Aexists", bool_val == true); // Check if the old name of attribute attached to the object // specified by loc_id and obj_name exists. It should equal false. bool_val = H5.H5Aexists(loc_id, old_attr_name); assertEquals(bool_val, false); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Arename " + err); } finally { if (attr_id > 0) try {H5.H5Aclose(attr_id);} catch (Exception ex) {} } } @Test public void testH5Arename_by_name() { int loc_id = H5fid; String obj_name = "."; String old_attr_name = "old"; String new_attr_name = "new"; int attr_id = -1; int ret_val = -1; boolean bool_val = false; try { attr_id = H5.H5Acreate_by_name(loc_id, obj_name, old_attr_name, type_id, space_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id); ret_val = H5.H5Arename_by_name(loc_id, obj_name, old_attr_name, new_attr_name, lapl_id); // Check the return value.It should be non negative. assertTrue("testH5Arename_by_name: H5Arename_by_name", ret_val >= 0); // Check if the new name of attribute attached to the object // specified by loc_id and obj_name exists.It should be true. bool_val = H5.H5Aexists_by_name(loc_id, obj_name, new_attr_name, lapl_id); assertTrue("testH5Arename_by_name: H5Aexists_by_name", bool_val == true); // Check if the old name of attribute attached to the object // specified by loc_id and obj_name exists. It should equal false. bool_val = H5.H5Aexists_by_name(loc_id, obj_name, old_attr_name, lapl_id); assertEquals(bool_val, false); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Arename_by_name " + err); } finally { if (attr_id > 0) try {H5.H5Aclose(attr_id);} catch (Exception ex) {} } } @Test public void testH5Aget_name_by_idx() { int loc_id = H5fid; String obj_name = "."; String attr_name = "DATASET1", attr2_name = "DATASET2"; String ret_name = null; int idx_type = HDF5Constants.H5_INDEX_NAME; int order = HDF5Constants.H5_ITER_INC; int n = 0; int attr1_id = -1; int attr2_id = -1; try { attr1_id = H5.H5Acreate_by_name(loc_id, obj_name, attr_name, type_id, space_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id); attr2_id = H5.H5Acreate_by_name(loc_id, obj_name, attr2_name, type_id, space_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id); // getting the 1st attribute name(n=0). ret_name = H5.H5Aget_name_by_idx(loc_id, obj_name, idx_type, order, n, lapl_id); assertFalse("H5Aget_name_by_idx ", ret_name == null); assertEquals(ret_name, attr_name); // getting the second attribute name(n=1) ret_name = H5.H5Aget_name_by_idx(loc_id, obj_name, idx_type, order, 1, lapl_id); assertFalse("H5Aget_name_by_idx ", ret_name == null); assertEquals(ret_name, attr2_name); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Aget_name_by_idx " + err); } finally { if (attr1_id > 0) try {H5.H5Aclose(attr1_id);} catch (Exception ex) {} if (attr2_id > 0) try {H5.H5Aclose(attr2_id);} catch (Exception ex) {} } } @Test public void testH5Aget_storage_size() { int attr_id = -1; long attr_size = -1; try { attr_id = H5.H5Acreate(H5did, "dset", type_id, space_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); attr_size = H5.H5Aget_storage_size(attr_id); assertTrue("The size of attribute is :", attr_size == 0); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Aget_storage_size: " + err); } finally { if (attr_id > 0) try {H5.H5Aclose(attr_id);} catch (Exception ex) {} } } @Test public void testH5Aget_info() { H5A_info_t attr_info = null; int attribute_id = -1; int attr_id = -1; try { attr_id = H5.H5Acreate(H5did, "dset", type_id, space_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); attribute_id = H5.H5Aopen(H5did, "dset", HDF5Constants.H5P_DEFAULT); // Calling H5Aget_info with attribute_id returned from H5Aopen. attr_info = H5.H5Aget_info(attribute_id); assertFalse("H5Aget_info ", attr_info == null); assertTrue("Corder_Valid should be false", attr_info.corder_valid == false); assertTrue("Character set used for attribute name", attr_info.cset == HDF5Constants.H5T_CSET_ASCII); assertTrue("Corder ", attr_info.corder == 0); assertEquals(attr_info.data_size, H5.H5Aget_storage_size(attr_id)); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Aget_info: " + err); } finally { if (attr_id > 0) try {H5.H5Aclose(attr_id);} catch (Exception ex) {} if (attribute_id > 0) try {H5.H5Aclose(attribute_id);} catch (Exception ex) {} } } @Test public void testH5Aget_info1() { H5A_info_t attr_info = null; int attribute_id = -1; int attr_id = -1; int order = HDF5Constants.H5_ITER_INC; try { attr_id = H5.H5Acreate(H5did, ".", type_id, space_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); attribute_id = H5.H5Aopen_by_idx(H5did, ".", HDF5Constants.H5_INDEX_CRT_ORDER, order, 0, HDF5Constants.H5P_DEFAULT, lapl_id); // Calling H5Aget_info with attribute_id returned from // H5Aopen_by_idx. attr_info = H5.H5Aget_info(attribute_id); assertFalse("H5Aget_info ", attr_info == null); assertTrue("Corder_Valid should be true", attr_info.corder_valid == true); assertTrue("Character set", attr_info.cset == HDF5Constants.H5T_CSET_ASCII); assertTrue("Corder ", attr_info.corder == 0); assertEquals(attr_info.data_size, H5.H5Aget_storage_size(attr_id)); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Aget_info1: " + err); } finally { if (attr_id > 0) try {H5.H5Aclose(attr_id);} catch (Exception ex) {} if (attribute_id > 0) try {H5.H5Aclose(attribute_id);} catch (Exception ex) {} } } @Test public void testH5Aget_info_by_idx() { int attr_id = -1; int attr2_id = -1;; H5A_info_t attr_info = null; try { attr_id = H5.H5Acreate(H5did, "dset1", type_id, space_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); attr2_id = H5.H5Acreate(H5did, "dataset2", type_id, space_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); //Verify info for 1st attribute, in increasing creation order attr_info = H5.H5Aget_info_by_idx(H5did, ".", HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, 0, lapl_id); assertNotNull(attr_info); assertTrue("Corder ", attr_info.corder == 0);//should equal 0 as this is the order of 1st attribute created. assertEquals(attr_info.data_size, H5.H5Aget_storage_size(attr_id)); //Verify info for 2nd attribute, in increasing creation order attr_info = H5.H5Aget_info_by_idx(H5did, ".", HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, 1, lapl_id); assertNotNull(attr_info); assertTrue("Corder", attr_info.corder == 1); assertEquals(attr_info.data_size, H5.H5Aget_storage_size(attr2_id)); //verify info for 2nd attribute, in decreasing creation order attr_info = H5.H5Aget_info_by_idx(H5did, ".", HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_DEC, 0, lapl_id); assertNotNull(attr_info); assertTrue("Corder", attr_info.corder == 1); //should equal 1 as this is the order of 2nd attribute created. //verify info for 1st attribute, in decreasing creation order attr_info = H5.H5Aget_info_by_idx(H5did, ".", HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_DEC, 1, lapl_id); assertNotNull(attr_info); assertTrue("Corder", attr_info.corder == 0); //should equal 0 as this is the order of 1st attribute created. //verify info for 1st attribute, in increasing name order attr_info = H5.H5Aget_info_by_idx(H5did, ".", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, 1, lapl_id); assertNotNull(attr_info); assertTrue("Corder", attr_info.corder == 0); //should equal 0 as this is the order of 1st attribute created. //verify info for 2nd attribute, in decreasing name order attr_info = H5.H5Aget_info_by_idx(H5did, ".", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_DEC, 1, lapl_id); assertNotNull(attr_info); assertTrue("Corder", attr_info.corder == 1); //should equal 1 as this is the order of 2nd attribute created. } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Aget_info_by_idx:" + err); } finally { if (attr_id > 0) try {H5.H5Aclose(attr_id);} catch (Exception ex) {} if (attr2_id > 0) try {H5.H5Aclose(attr2_id);} catch (Exception ex) {} } } @Test public void testH5Aget_info_by_name() { int attr_id = -1; H5A_info_t attr_info = null; String obj_name = "."; String attr_name = "DATASET"; try { attr_id = H5.H5Acreate_by_name(H5fid, obj_name, attr_name, type_id, space_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id); attr_info = H5.H5Aget_info_by_name(H5fid, obj_name, attr_name, lapl_id); assertNotNull(attr_info); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Aget_info_by_name:" + err); } finally { if (attr_id > 0) try {H5.H5Aclose(attr_id);} catch (Exception ex) {} } } @Test public void testH5Adelete_by_name() { int attr_id = -1; int ret_val = -1; boolean bool_val = false; boolean exists = false; try { attr_id = H5.H5Acreate_by_name(H5fid, ".", "DATASET", type_id, space_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id); ret_val = H5.H5Adelete_by_name(H5fid, ".", "DATASET", lapl_id); assertTrue("H5Adelete_by_name", ret_val >= 0); // Check if the Attribute still exists. bool_val = H5.H5Aexists_by_name(H5fid, ".", "DATASET", lapl_id); assertFalse("testH5Adelete_by_name: H5Aexists_by_name", bool_val); exists = H5.H5Aexists(H5fid, "DATASET"); assertFalse("testH5Adelete_by_name: H5Aexists ",exists); // Negative test. Error thrown when we try to delete an attribute // that has already been deleted. try{ ret_val = H5.H5Adelete_by_name(H5fid, ".", "DATASET", lapl_id); fail("Negative Test Failed: Error Not thrown."); } catch (AssertionError err) { fail("H5.H5Adelete_by_name: " + err); } catch (HDF5LibraryException err) {} } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Adelete_by_name " + err); } finally { if (attr_id > 0) try {H5.H5Aclose(attr_id);} catch (Exception ex) {} } } @Test public void testH5Aexists() { boolean exists = false; int attr_id = -1; int attribute_id = -1; try { exists = H5.H5Aexists(H5fid, "None"); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Aexists: " + err); } assertFalse("H5Aexists ", exists); try { attr_id = H5.H5Acreate(H5fid, "dset", type_id, space_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); exists = H5.H5Aexists(H5fid, "dset"); assertTrue("H5Aexists ", exists); attribute_id = H5.H5Acreate_by_name(H5fid, ".", "attribute", type_id, space_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id); exists = H5.H5Aexists(H5fid, "attribute"); assertTrue("H5Aexists ", exists); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Aexists: " + err); } finally { if (attr_id > 0) try {H5.H5Aclose(attr_id);} catch (Exception ex) {} if (attribute_id > 0) try {H5.H5Aclose(attribute_id);} catch (Exception ex) {} } } @Test public void testH5Adelete_by_idx_order() { boolean exists = false; int attr1_id = -1; int attr2_id = -1; int attr3_id = -1; int attr4_id = -1; try { attr1_id = H5.H5Acreate_by_name(H5fid, ".", "attribute1", type_id, space_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id); attr2_id = H5.H5Acreate_by_name(H5fid, ".", "attribute2", type_id, space_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id); attr3_id = H5.H5Acreate_by_name(H5fid, ".", "attribute3", type_id, space_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id); attr4_id = H5.H5Acreate_by_name(H5fid, ".", "attribute4", type_id, space_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id); H5.H5Adelete_by_idx(H5fid, ".", HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, 3, lapl_id); exists = H5.H5Aexists(H5fid, "attribute4"); assertFalse("H5Adelete_by_idx: H5Aexists", exists); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Adelete_by_idx: " + err); } finally { if (attr1_id > 0) try {H5.H5Aclose(attr1_id);} catch (Exception ex) {} if (attr2_id > 0) try {H5.H5Aclose(attr2_id);} catch (Exception ex) {} if (attr3_id > 0) try {H5.H5Aclose(attr3_id);} catch (Exception ex) {} if (attr4_id > 0) try {H5.H5Aclose(attr4_id);} catch (Exception ex) {} } } @Test public void testH5Adelete_by_idx_name1() { boolean exists = false; int attr1_id = -1; int attr2_id = -1; int attr3_id = -1; try { attr1_id = H5.H5Acreate_by_name(H5fid, ".", "attribute1", type_id, space_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id); attr2_id = H5.H5Acreate_by_name(H5fid, ".", "attribute2", type_id, space_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id); attr3_id = H5.H5Acreate_by_name(H5fid, ".", "attribute3", type_id, space_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id); H5.H5Adelete_by_idx(H5fid, ".", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, 2, lapl_id); exists = H5.H5Aexists(H5fid, "attribute3"); assertFalse("H5Adelete_by_idx: H5Aexists", exists); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Adelete_by_idx: " + err); } finally { if (attr1_id > 0) try {H5.H5Aclose(attr1_id);} catch (Exception ex) {} if (attr2_id > 0) try {H5.H5Aclose(attr2_id);} catch (Exception ex) {} if (attr3_id > 0) try {H5.H5Aclose(attr3_id);} catch (Exception ex) {} } } @Test public void testH5Adelete_by_idx_name2() { boolean exists = false; int attr1_id = -1; int attr2_id = -1; int attr3_id = -1; int attr4_id = -1; try { attr1_id = H5.H5Acreate_by_name(H5fid, ".", "attribute1", type_id, space_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id); attr2_id = H5.H5Acreate_by_name(H5fid, ".", "attribute2", type_id, space_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id); attr3_id = H5.H5Acreate_by_name(H5fid, ".", "attribute3", type_id, space_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id); attr4_id = H5.H5Acreate_by_name(H5fid, ".", "attribute4", type_id, space_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id); H5.H5Adelete_by_idx(H5fid, ".", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_DEC, 3, lapl_id); exists = H5.H5Aexists(H5fid, "attribute1"); assertFalse("H5Adelete_by_idx: H5Aexists", exists); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Adelete_by_idx: " + err); } finally { if (attr1_id > 0) try {H5.H5Aclose(attr1_id);} catch (Exception ex) {} if (attr2_id > 0) try {H5.H5Aclose(attr2_id);} catch (Exception ex) {} if (attr3_id > 0) try {H5.H5Aclose(attr3_id);} catch (Exception ex) {} if (attr4_id > 0) try {H5.H5Aclose(attr4_id);} catch (Exception ex) {} } } @Test(expected = NullPointerException.class) public void testH5Adelete_by_idx_null() throws Throwable { H5.H5Adelete_by_idx(H5fid, null, HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, 0, lapl_id); } @Test(expected = HDF5LibraryException.class) public void testH5Adelete_by_idx_invalidobject() throws Throwable { H5.H5Adelete_by_idx(H5fid, "invalid", HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, 0, lapl_id); } @Test public void testH5Aopen_by_name() { String obj_name = "."; String attr_name = "DATASET"; int attribute_id = -1; int aid = -1; try { attribute_id = H5.H5Acreate_by_name(H5fid, obj_name, attr_name, type_id, space_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id); //open Attribute by name if(attribute_id >= 0) { try { aid = H5.H5Aopen_by_name(H5fid, obj_name, attr_name, HDF5Constants.H5P_DEFAULT, lapl_id); assertTrue("testH5Aopen_by_name: ", aid>=0); } catch(Throwable err) { err.printStackTrace(); fail("H5.H5Aopen_by_name " + err); } } } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Aopen_by_name " + err); } finally { if (aid > 0) try {H5.H5Aclose(aid);} catch (Exception ex) {} if (attribute_id > 0) try {H5.H5Aclose(attribute_id);} catch (Exception ex) {} } } } libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/TestH5D.java000066400000000000000000000743541256564762100245550ustar00rootroot00000000000000package test.hdf5lib; import static org.junit.Assert.assertFalse; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import java.io.File; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.HDF5Constants; import ncsa.hdf.hdf5lib.HDFNativeData; import ncsa.hdf.hdf5lib.callbacks.H5D_iterate_cb; import ncsa.hdf.hdf5lib.callbacks.H5D_iterate_t; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import org.junit.After; import org.junit.Before; import org.junit.Test; @SuppressWarnings("all") public class TestH5D { private static final String H5_FILE = "test.h5"; private static final int DIM_X = 4; private static final int DIM_Y = 6; private static final int RANK = 2; int H5fid = -1; int H5dsid = -1; int H5dtid = -1; int H5did = -1; int H5did0 = -1; int H5dcpl_id = -1; long[] H5dims = { DIM_X, DIM_Y }; // Values for the status of space allocation enum H5D_space_status { H5D_SPACE_STATUS_ERROR(-1), H5D_SPACE_STATUS_NOT_ALLOCATED(0), H5D_SPACE_STATUS_PART_ALLOCATED( 1), H5D_SPACE_STATUS_ALLOCATED(2); private int code; H5D_space_status(int space_status) { this.code = space_status; } public int getCode() { return this.code; } } private final void _deleteFile(String filename) { File file = new File(filename); if (file.exists()) { try {file.delete();} catch (SecurityException e) {} } } private final void _createPDataset(int fid, int dsid, String name, int dcpl_val) { try { H5dcpl_id = H5.H5Pcreate(dcpl_val); } catch (Exception err) { err.printStackTrace(); fail("H5.H5Pcreate: " + err); } assertTrue("testH5D._createPDataset: H5.H5Pcreate: ", H5dcpl_id > 0); // Set the allocation time to "early". This way we can be sure // that reading from the dataset immediately after creation will // return the fill value. try { H5.H5Pset_alloc_time(H5dcpl_id, HDF5Constants.H5D_ALLOC_TIME_EARLY); } catch (Exception e) { e.printStackTrace(); } try { H5did0 = H5.H5Dcreate(fid, name, HDF5Constants.H5T_STD_I32BE, dsid, HDF5Constants.H5P_DEFAULT, H5dcpl_id, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Dcreate: " + err); } assertTrue("TestH5D._createPDataset: ", H5did0 > 0); } private final void _createDataset(int fid, int dsid, String name, int dapl) { try { H5did = H5.H5Dcreate(fid, name, HDF5Constants.H5T_STD_I32BE, dsid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, dapl); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Dcreate: " + err); } assertTrue("TestH5D._createDataset: ", H5did > 0); } private final void _createVLDataset(int fid, int dsid, String name, int dapl) { try { H5dtid = H5.H5Tcopy(HDF5Constants.H5T_C_S1); H5.H5Tset_size(H5dtid, HDF5Constants.H5T_VARIABLE); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Tcopy: " + err); } assertTrue("TestH5D._createVLDataset: ", H5dtid > 0); try { H5did = H5.H5Dcreate(fid, name, H5dtid, dsid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, dapl); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Dcreate: " + err); } assertTrue("TestH5D._createVLDataset: ", H5did > 0); } private final void _closeH5file() throws HDF5LibraryException { if (H5dcpl_id >= 0) try {H5.H5Pclose(H5dcpl_id);} catch (Exception ex) {} if (H5did0 >= 0) try {H5.H5Dclose(H5did0);} catch (Exception ex) {} if (H5did >= 0) try {H5.H5Dclose(H5did);} catch (Exception ex) {} if (H5dtid > 0) try {H5.H5Tclose(H5dtid);} catch (Exception ex) {} if (H5dsid > 0) try {H5.H5Sclose(H5dsid);} catch (Exception ex) {} if (H5fid > 0) try {H5.H5Fclose(H5fid);} catch (Exception ex) {} } private final void _openH5file(String name, int dapl) { try { H5fid = H5.H5Fopen(H5_FILE, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); H5did = H5.H5Dopen(H5fid, name, dapl); H5dsid = H5.H5Dget_space(H5did); } catch (Throwable err) { err.printStackTrace(); fail("TestH5D._openH5file: " + err); } assertTrue("TestH5D._openH5file: H5.H5Fopen: ",H5fid > 0); assertTrue("TestH5D._openH5file: H5.H5Screate_simple: ",H5dsid > 0); } @Before public void createH5file() throws NullPointerException, HDF5Exception { assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0); try { H5fid = H5.H5Fcreate(H5_FILE, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); H5dsid = H5.H5Screate_simple(RANK, H5dims, null); } catch (Throwable err) { err.printStackTrace(); fail("TestH5D.createH5file: " + err); } assertTrue("TestH5D.createH5file: H5.H5Fcreate: ",H5fid > 0); assertTrue("TestH5D.createH5file: H5.H5Screate_simple: ",H5dsid > 0); H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); } @After public void deleteH5file() throws HDF5LibraryException { if (H5dcpl_id >= 0) try {H5.H5Pclose(H5dcpl_id);} catch (Exception ex) {} if (H5did0 >= 0) try {H5.H5Dclose(H5did0);} catch (Exception ex) {} if (H5did >= 0) try {H5.H5Dclose(H5did);} catch (Exception ex) {} if (H5dtid > 0) try {H5.H5Tclose(H5dtid);} catch (Exception ex) {} if (H5dsid > 0) try {H5.H5Sclose(H5dsid);} catch (Exception ex) {} if (H5fid > 0) try {H5.H5Fclose(H5fid);} catch (Exception ex) {} _deleteFile(H5_FILE); } @Test public void testH5Dcreate() { int dataset_id = -1; try { dataset_id = H5.H5Dcreate(H5fid, "dset", HDF5Constants.H5T_STD_I32BE, H5dsid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); } catch (Exception err) { err.printStackTrace(); fail("testH5Dcreate: " + err); } assertTrue(dataset_id > 0); // End access to the dataset and release resources used by it. try { if (dataset_id >= 0) H5.H5Dclose(dataset_id); } catch (Exception err) { err.printStackTrace(); } } @Test public void testH5Dcreate_anon() { int dataset_id = -1; try { dataset_id = H5.H5Dcreate_anon(H5fid, HDF5Constants.H5T_STD_I32BE, H5dsid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); } catch (Exception err) { err.printStackTrace(); fail("testH5Dcreate_anon: " + err); } assertTrue(dataset_id > 0); // End access to the dataset and release resources used by it. try { if (dataset_id >= 0) H5.H5Dclose(dataset_id); } catch (Exception err) { err.printStackTrace(); } } @Test public void testH5Dopen() { int dataset_id = -1; _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT); try { H5.H5Dclose(H5did); H5did = -1; dataset_id = H5.H5Dopen(H5fid, "dset", HDF5Constants.H5P_DEFAULT); } catch (Exception err) { err.printStackTrace(); fail("testH5Dopen: " + err); } assertTrue("testH5Dopen: ", dataset_id > 0); // End access to the dataset and release resources used by it. try { if (dataset_id >= 0) H5.H5Dclose(dataset_id); } catch (Exception err) { err.printStackTrace(); } } @Test public void testH5Dget_storage_size_empty() { long storage_size = 0; _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT); try { storage_size = H5.H5Dget_storage_size(H5did); } catch (Exception err) { err.printStackTrace(); fail("testH5Dget_storage_size: " + err); } assertTrue("testH5Dget_storage_size: ", storage_size == 0); } @Test public void testH5Dget_storage_size() { long storage_size = 0; int[][] dset_data = new int[DIM_X][DIM_Y]; int FILLVAL = 99; _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT); // Initialize the dataset. for (int indx = 0; indx < DIM_X; indx++) for (int jndx = 0; jndx < DIM_Y; jndx++) dset_data[indx][jndx] = FILLVAL; try { if (H5did >= 0) H5.H5Dwrite(H5did, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data[0]); } catch (Exception e) { e.printStackTrace(); } try { storage_size = H5.H5Dget_storage_size(H5did); } catch (Exception err) { err.printStackTrace(); fail("testH5Dget_storage_size: " + err); } assertTrue("testH5Dget_storage_size: "+storage_size, storage_size == DIM_X*DIM_Y*4); } @Test public void testH5Dget_access_plist() { int dapl_id = -1; int pequal = -1; int test_dapl_id = -1; try { test_dapl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_ACCESS); } catch (Exception err) { err.printStackTrace(); fail("testH5Dget_access_plist: H5.H5Pcreate: " + err); } assertTrue("testH5Dget_access_plist: test_dapl_id: ", test_dapl_id > 0); _createDataset(H5fid, H5dsid, "dset", test_dapl_id); try { dapl_id = H5.H5Dget_access_plist(H5did); assertTrue("testH5Dget_access_plist: dapl_id: ", dapl_id > 0); pequal = H5.H5Pequal(dapl_id, test_dapl_id); } catch (Exception err) { err.printStackTrace(); fail("testH5Dget_access_plist: H5.H5Dget_access_plist: " + err); } // End access to the dataset and release resources used by it. try { if (dapl_id >= 0) H5.H5Pclose(dapl_id); } catch (Exception err) { err.printStackTrace(); } try { if (test_dapl_id >= 0) H5.H5Pclose(test_dapl_id); } catch (Exception err) { err.printStackTrace(); } assertTrue("testH5Dget_access_plist: ", pequal > 0); } @Test public void testH5Dget_space_status() { int[][] write_dset_data = new int[DIM_X][DIM_Y]; int[] space_status = new int[1]; int[] space_status0 = new int[1]; // Initialize the dataset. for (int indx = 0; indx < DIM_X; indx++) for (int jndx = 0; jndx < DIM_Y; jndx++) write_dset_data[indx][jndx] = indx * jndx - jndx; _createPDataset(H5fid, H5dsid, "dset0", HDF5Constants.H5P_DATASET_CREATE); _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT); // Retrieve and print space status and storage size for dset0. try { H5.H5Dget_space_status(H5did0, space_status0); } catch (Exception e) { e.printStackTrace(); } assertTrue("testH5Dget_space_status0 - H5.H5Dget_space_status: ", space_status0[0] == H5D_space_status.H5D_SPACE_STATUS_ALLOCATED.getCode()); // Retrieve and print space status and storage size for dset. try { H5.H5Dget_space_status(H5did, space_status); } catch (Exception e) { e.printStackTrace(); } assertFalse("testH5Dget_space_status - H5.H5Dget_space_status: ", space_status[0] == H5D_space_status.H5D_SPACE_STATUS_ALLOCATED.getCode()); // Write the data to the dataset. try { H5.H5Dwrite(H5did, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, write_dset_data); } catch (Exception e) { e.printStackTrace(); } // Retrieve and print space status and storage size for dset. try { H5.H5Dget_space_status(H5did, space_status); } catch (Exception e) { e.printStackTrace(); } assertTrue("testH5Dget_space_status - H5.H5Dget_space_status: ", space_status[0] == H5D_space_status.H5D_SPACE_STATUS_ALLOCATED.getCode()); } @Test(expected = HDF5LibraryException.class) public void testH5Dget_space_closed() throws Throwable { int dataset_id = -1; try { dataset_id = H5.H5Dcreate(H5fid, "dset", HDF5Constants.H5T_STD_I32BE, H5dsid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Dcreate: " + err); } assertTrue("TestH5D.testH5Dget_space_closed: ", dataset_id > 0); H5.H5Dclose(dataset_id); H5.H5Dget_space(dataset_id); } @Test public void testH5Dget_space() { int dataspace_id = -1; _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT); try { dataspace_id = H5.H5Dget_space(H5did); } catch (Exception err) { err.printStackTrace(); fail("H5.H5Dget_space: " + err); } assertTrue("TestH5D.testH5Dget_space: ", dataspace_id > 0); // End access to the dataspace and release resources used by it. try { if (dataspace_id >= 0) H5.H5Sclose(dataspace_id); } catch (Exception err) { err.printStackTrace(); } } @Test(expected = HDF5LibraryException.class) public void testH5Dget_type_closed() throws Throwable { int dataset_id = -1; try { dataset_id = H5.H5Dcreate(H5fid, "dset", HDF5Constants.H5T_STD_I32BE, H5dsid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Dcreate: " + err); } assertTrue("TestH5D.testH5Dget_type_closed: ", dataset_id > 0); H5.H5Dclose(dataset_id); H5.H5Dget_type(dataset_id); } @Test public void testH5Dget_type() { int datatype_id = -1; _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT); try { datatype_id = H5.H5Dget_type(H5did); } catch (Exception err) { err.printStackTrace(); fail("H5.H5Dget_type: " + err); } assertTrue("TestH5D.testH5Dget_type: ", datatype_id > 0); // End access to the datatype and release resources used by it. try { if (datatype_id >= 0) H5.H5Tclose(datatype_id); } catch (Exception err) { err.printStackTrace(); } } @Test public void testH5Dget_offset() { int[][] write_dset_data = new int[DIM_X][DIM_Y]; long dset_address = 0; _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT); try { // Test dataset address. Should be undefined. dset_address = H5.H5Dget_offset(H5did); } catch (HDF5LibraryException hdfex) { ; } catch (Exception err) { err.printStackTrace(); fail("H5.H5Dget_offset: " + err); } // Write the data to the dataset. try { H5.H5Dwrite(H5did, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, write_dset_data); } catch (Exception e) { e.printStackTrace(); } try { // Test dataset address. dset_address = H5.H5Dget_offset(H5did); } catch (Exception err) { err.printStackTrace(); fail("H5.H5Dget_offset: " + err); } assertTrue("TestH5D.testH5Dget_offset: ", dset_address > 0); } @Test public void testH5Dfill_null() { int[] buf_data = new int[DIM_X*DIM_Y]; // Initialize memory buffer for (int indx = 0; indx < DIM_X; indx++) for (int jndx = 0; jndx < DIM_Y; jndx++) { buf_data[(indx * DIM_Y) + jndx] = indx * jndx - jndx; } byte[] buf_array = HDFNativeData.intToByte(0, DIM_X*DIM_Y, buf_data); // Fill selection in memory try { H5.H5Dfill(null, HDF5Constants.H5T_NATIVE_UINT, buf_array, HDF5Constants.H5T_NATIVE_UINT, H5dsid); } catch (Exception err) { err.printStackTrace(); fail("H5.H5Dfill: " + err); } buf_data = HDFNativeData.byteToInt(buf_array); // Verify memory buffer the hard way for (int indx = 0; indx < DIM_X; indx++) for (int jndx = 0; jndx < DIM_Y; jndx++) assertTrue("H5.H5Dfill: [" + indx+","+jndx + "] ", buf_data[(indx * DIM_Y) + jndx] == 0); } @Test public void testH5Dfill() { int[] buf_data = new int[DIM_X*DIM_Y]; byte[] fill_value = HDFNativeData.intToByte(254); // Initialize memory buffer for (int indx = 0; indx < DIM_X; indx++) for (int jndx = 0; jndx < DIM_Y; jndx++) { buf_data[(indx * DIM_Y) + jndx] = indx * jndx - jndx; } byte[] buf_array = HDFNativeData.intToByte(0, DIM_X*DIM_Y, buf_data); // Fill selection in memory try { H5.H5Dfill(fill_value, HDF5Constants.H5T_NATIVE_UINT, buf_array, HDF5Constants.H5T_NATIVE_UINT, H5dsid); } catch (Exception err) { err.printStackTrace(); fail("H5.H5Dfill: " + err); } buf_data = HDFNativeData.byteToInt(buf_array); // Verify memory buffer the hard way for (int indx = 0; indx < DIM_X; indx++) for (int jndx = 0; jndx < DIM_Y; jndx++) assertTrue("H5.H5Dfill: [" + indx+","+jndx + "] ", buf_data[(indx * DIM_Y) + jndx] == 254); } @Test public void testH5Diterate() { final int SPACE_RANK = 2; final int SPACE_FILL = 254; class H5D_iter_data implements H5D_iterate_t { public int fill_value; /* The fill value to check */ public long fill_curr_coord; /* Current coordinate to examine */ public long[] fill_coords; /* Pointer to selection's coordinates */ } H5D_iterate_t iter_data = new H5D_iter_data(); class H5D_iter_callback implements H5D_iterate_cb { public int callback(byte[] elem_buf, int elem_id, int ndim, long[] point, H5D_iterate_t op_data) { //Check value in current buffer location int element = HDFNativeData.byteToInt(elem_buf, 0); if(element != ((H5D_iter_data)op_data).fill_value) return -1; //Check number of dimensions if(ndim != SPACE_RANK) return(-1); //Check Coordinates long[] fill_coords = new long[2]; fill_coords[0] = ((H5D_iter_data)op_data).fill_coords[(int) (2 * ((H5D_iter_data)op_data).fill_curr_coord)]; fill_coords[1] = ((H5D_iter_data)op_data).fill_coords[(int) (2 * ((H5D_iter_data)op_data).fill_curr_coord) + 1]; ((H5D_iter_data)op_data).fill_curr_coord++; if(fill_coords[0] != point[0]) return(-1); if(fill_coords[1] != point[1]) return(-1); return(0); } } int[] buf_data = new int[DIM_X*DIM_Y]; byte[] fill_value = HDFNativeData.intToByte(SPACE_FILL); // Initialize memory buffer for (int indx = 0; indx < DIM_X; indx++) for (int jndx = 0; jndx < DIM_Y; jndx++) { buf_data[(indx * DIM_Y) + jndx] = indx * jndx - jndx; } byte[] buf_array = HDFNativeData.intToByte(0, DIM_X*DIM_Y, buf_data); // Fill selection in memory try { H5.H5Dfill(fill_value, HDF5Constants.H5T_NATIVE_UINT, buf_array, HDF5Constants.H5T_NATIVE_UINT, H5dsid); } catch (Exception err) { err.printStackTrace(); fail("H5.H5Diterate: " + err); } // Initialize the iterator structure ((H5D_iter_data)iter_data).fill_value = SPACE_FILL; ((H5D_iter_data)iter_data).fill_curr_coord = 0; // Set the coordinates of the selection ((H5D_iter_data)iter_data).fill_coords = new long[DIM_X*DIM_Y*SPACE_RANK]; /* Coordinates of selection */ for (int indx = 0; indx < DIM_X; indx++) for (int jndx = 0; jndx < DIM_Y; jndx++) { ((H5D_iter_data)iter_data).fill_coords[2*(indx * DIM_Y + jndx)] = indx; ((H5D_iter_data)iter_data).fill_coords[2*(indx * DIM_Y + jndx) + 1] = jndx; } /* end for */ // Iterate through selection, verifying correct data H5D_iterate_cb iter_cb = new H5D_iter_callback(); int op_status = -1; try { op_status = H5.H5Diterate(buf_array, HDF5Constants.H5T_NATIVE_UINT, H5dsid, iter_cb, iter_data); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Diterate: " + err); } assertTrue("H5Diterate ", op_status == 0); } @Test public void testH5Diterate_write() { final int SPACE_RANK = 2; final int SPACE_FILL = 254; class H5D_iter_data implements H5D_iterate_t { public int fill_value; /* The fill value to check */ public long fill_curr_coord; /* Current coordinate to examine */ public long[] fill_coords; /* Pointer to selection's coordinates */ } H5D_iterate_t iter_data = new H5D_iter_data(); class H5D_iter_callback implements H5D_iterate_cb { public int callback(byte[] elem_buf, int elem_id, int ndim, long[] point, H5D_iterate_t op_data) { //Check value in current buffer location int element = HDFNativeData.byteToInt(elem_buf, 0); if(element != ((H5D_iter_data)op_data).fill_value) return -1; //Check number of dimensions if(ndim != SPACE_RANK) return(-1); //Check Coordinates long[] fill_coords = new long[2]; fill_coords[0] = ((H5D_iter_data)op_data).fill_coords[(int) (2 * ((H5D_iter_data)op_data).fill_curr_coord)]; fill_coords[1] = ((H5D_iter_data)op_data).fill_coords[(int) (2 * ((H5D_iter_data)op_data).fill_curr_coord) + 1]; ((H5D_iter_data)op_data).fill_curr_coord++; if(fill_coords[0] != point[0]) return(-1); if(fill_coords[1] != point[1]) return(-1); element -= 128; byte[] new_elembuf = HDFNativeData.intToByte(element); elem_buf[0] = new_elembuf[0]; elem_buf[1] = new_elembuf[1]; elem_buf[2] = new_elembuf[2]; elem_buf[3] = new_elembuf[3]; return(0); } } int[] buf_data = new int[DIM_X*DIM_Y]; byte[] fill_value = HDFNativeData.intToByte(SPACE_FILL); // Initialize memory buffer for (int indx = 0; indx < DIM_X; indx++) for (int jndx = 0; jndx < DIM_Y; jndx++) { buf_data[(indx * DIM_Y) + jndx] = indx * jndx - jndx; } byte[] buf_array = HDFNativeData.intToByte(0, DIM_X*DIM_Y, buf_data); // Fill selection in memory try { H5.H5Dfill(fill_value, HDF5Constants.H5T_NATIVE_UINT, buf_array, HDF5Constants.H5T_NATIVE_UINT, H5dsid); } catch (Exception err) { err.printStackTrace(); fail("H5.H5Diterate: " + err); } // Initialize the iterator structure ((H5D_iter_data)iter_data).fill_value = SPACE_FILL; ((H5D_iter_data)iter_data).fill_curr_coord = 0; // Set the coordinates of the selection ((H5D_iter_data)iter_data).fill_coords = new long[DIM_X*DIM_Y*SPACE_RANK]; /* Coordinates of selection */ for (int indx = 0; indx < DIM_X; indx++) for (int jndx = 0; jndx < DIM_Y; jndx++) { ((H5D_iter_data)iter_data).fill_coords[2*(indx * DIM_Y + jndx)] = indx; ((H5D_iter_data)iter_data).fill_coords[2*(indx * DIM_Y + jndx) + 1] = jndx; } /* end for */ // Iterate through selection, verifying correct data H5D_iterate_cb iter_cb = new H5D_iter_callback(); int op_status = -1; try { op_status = H5.H5Diterate(buf_array, HDF5Constants.H5T_NATIVE_UINT, H5dsid, iter_cb, iter_data); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Diterate: " + err); } assertTrue("H5Diterate ", op_status == 0); buf_data = HDFNativeData.byteToInt(buf_array); // Verify memory buffer the hard way for (int indx = 0; indx < DIM_X; indx++) for (int jndx = 0; jndx < DIM_Y; jndx++) assertTrue("H5.H5Diterate: [" + indx+","+jndx + "] "+buf_data[(indx * DIM_Y) + jndx], buf_data[(indx * DIM_Y) + jndx] == 126); } @Test public void testH5Dvlen_get_buf_size() { String[] str_data = { "Parting", "is such", "sweet", "sorrow.", "Testing", "one", "two", "three.", "Dog,", "man's", "best", "friend.", "Diamonds", "are", "a", "girls!", "S A", "T U R", "D A Y", "night", "That's", "all", "folks", "!!!" }; int[] size = new int[2]; long str_data_bytes = 0; for (int idx = 0; idx < str_data.length; idx++) str_data_bytes += str_data[idx].length() + 1; //Account for terminating null _createVLDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT); try { if ((H5did >= 0) && (H5dtid >= 0)) H5.H5DwriteString(H5did, H5dtid, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, str_data); _closeH5file(); _openH5file("dset", HDF5Constants.H5P_DEFAULT); H5dtid = H5.H5Dget_type(H5did); } catch (Exception e) { e.printStackTrace(); } try { H5.H5Dvlen_get_buf_size(H5did, H5dtid, H5dsid, size); } catch (Exception e) { e.printStackTrace(); } assertTrue("H5Dvlen_get_buf_size "+ size[0] + " == " + str_data_bytes, size[0] == str_data_bytes); } @Test public void testH5Dvlen_get_buf_size_long() { String[] str_data = { "Parting", "is such", "sweet", "sorrow.", "Testing", "one", "two", "three.", "Dog,", "man's", "best", "friend.", "Diamonds", "are", "a", "girls!", "S A", "T U R", "D A Y", "night", "That's", "all", "folks", "!!!" }; long vl_size = -1; /* Number of bytes used */ long str_data_bytes = 0; for (int idx = 0; idx < str_data.length; idx++) str_data_bytes += str_data[idx].length() + 1; //Account for terminating null _createVLDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT); try { if ((H5did >= 0) && (H5dtid >= 0)) H5.H5DwriteString(H5did, H5dtid, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, str_data); } catch (Exception e) { e.printStackTrace(); } try { vl_size = H5.H5Dvlen_get_buf_size_long(H5did, H5dtid, H5dsid); } catch (Exception e) { e.printStackTrace(); } assertTrue("H5Dvlen_get_buf_size_long " + vl_size + " == " + str_data_bytes, vl_size == str_data_bytes); } @Test(expected = IllegalArgumentException.class) public void testH5Dvlen_read_invalid_buffer() throws Throwable { String[] str_data = { "Parting", "is such", "sweet", "sorrow.", "Testing", "one", "two", "three.", "Dog,", "man's", "best", "friend.", "Diamonds", "are", "a", "girls!", "S A", "T U R", "D A Y", "night", "That's", "all", "folks", "!!!" }; byte[] read_data = new byte[512]; _createVLDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT); try { H5.H5DwriteString(H5did, H5dtid, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, str_data); } catch (Exception e) { e.printStackTrace(); } H5.H5Dread(H5did, H5dtid, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, read_data); } } libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/TestH5Dparams.java000066400000000000000000000067201256564762100257510ustar00rootroot00000000000000package test.hdf5lib; import static org.junit.Assert.assertTrue; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import org.junit.Before; import org.junit.Test; public class TestH5Dparams { @Before public void checkOpenIDs() { assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0); } @Test(expected = NullPointerException.class) public void testH5Dcreate_null() throws Throwable { H5.H5Dcreate(-1, null, 0, 0, 0, 0, 0); } @Test(expected = HDF5LibraryException.class) public void testH5Dcreate_invalid() throws Throwable { H5.H5Dcreate(-1, "Bogus", -1, -1, -1, -1, -1); } @Test(expected = HDF5LibraryException.class) public void testH5Dcreate_anon_invalid() throws Throwable { H5.H5Dcreate_anon(-1, -1, -1, -1, -1); } @Test(expected = HDF5LibraryException.class) public void testH5Dget_access_plist_invalid() throws Throwable { H5.H5Dget_access_plist(-1); } @Test(expected = HDF5LibraryException.class) public void testH5Dget_create_plist_invalid() throws Throwable { H5.H5Dget_create_plist(-1); } @Test(expected = HDF5LibraryException.class) public void testH5Dget_offset_invalid() throws Throwable { H5.H5Dget_offset(-1); } @Test(expected = HDF5LibraryException.class) public void testH5Dget_space_invalid() throws Throwable { H5.H5Dget_space(-1); } @Test(expected = HDF5LibraryException.class) public void testH5Dget_type_invalid() throws Throwable { H5.H5Dget_type(-1); } @Test(expected = HDF5LibraryException.class) public void testH5Dget_space_status_invalid() throws Throwable { int[] status = new int[2]; H5.H5Dget_space_status(-1, status); } @Test(expected = NullPointerException.class) public void testH5Dget_space_status_null() throws Throwable { H5.H5Dget_space_status(-1, null); } @Test(expected = HDF5LibraryException.class) public void testH5Dset_extent_status_invalid() throws Throwable { long[] size = new long[2]; H5.H5Dset_extent(-1, size); } @Test(expected = NullPointerException.class) public void testH5Dset_extent_status_null() throws Throwable { H5.H5Dset_extent(-1, null); } @Test(expected = NullPointerException.class) public void testH5Dopen_null() throws Throwable { H5.H5Dopen(-1, null, 0); } @Test(expected = HDF5LibraryException.class) public void testH5Dopen_invalid() throws Throwable { H5.H5Dopen(-1, "Bogus", 0); } @Test(expected = HDF5LibraryException.class) public void testH5Dvlen_get_buf_size_invalid() throws Throwable { int[] size = new int[2]; H5.H5Dvlen_get_buf_size(-1, -1, -1, size); } @Test(expected = NullPointerException.class) public void testH5Dvlen_get_buf_size_null() throws Throwable { H5.H5Dvlen_get_buf_size(-1, -1, -1, null); } @Test(expected = HDF5LibraryException.class) public void testH5Dvlen_reclaim_invalid() throws Throwable { byte[] buf = new byte[2]; H5.H5Dvlen_reclaim(-1, -1, -1, buf); } @Test(expected = NullPointerException.class) public void testH5Dvlen_reclaim_null() throws Throwable { H5.H5Dvlen_reclaim(-1, -1, -1, null); } @Test(expected = IllegalArgumentException.class) public void testH5Dget_storage_size_invalid() throws Throwable { H5.H5Dget_storage_size(-1); } } libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/TestH5Dplist.java000066400000000000000000000146361256564762100256260ustar00rootroot00000000000000package test.hdf5lib; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import java.io.File; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.HDF5Constants; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import org.junit.After; import org.junit.Before; import org.junit.Test; public class TestH5Dplist { private static final String H5_FILE = "test.h5"; private static final int DIM_X = 4; private static final int DIM_Y = 7; private static final int EDIM_X = 6; private static final int EDIM_Y = 10; private static final int CHUNK_X = 4; private static final int CHUNK_Y = 4; private static final int NDIMS = 2; private static final int FILLVAL = 99; private static final int RANK = 2; int H5fid = -1; int H5dsid = -1; int H5did = -1; int H5dcpl_id = -1; long[] H5dims = { DIM_X, DIM_Y }; long[] H5extdims = { EDIM_X, EDIM_Y }; long[] H5chunk_dims = { CHUNK_X, CHUNK_Y }; long[] H5maxdims = { HDF5Constants.H5S_UNLIMITED, HDF5Constants.H5S_UNLIMITED }; private final void _deleteFile(String filename) { File file = new File(filename); if (file.exists()) { try {file.delete();} catch (SecurityException e) {} } } private final void _createPDataset(int fid, int dsid, String name, int dcpl_val) { try { H5dcpl_id = H5.H5Pcreate(dcpl_val); } catch (Exception err) { err.printStackTrace(); fail("H5.H5Pcreate: " + err); } assertTrue("TestH5Dplist._createPDataset: ", H5dcpl_id > 0); // Set the chunk size. try { H5.H5Pset_chunk(H5dcpl_id, NDIMS, H5chunk_dims); } catch (Exception e) { e.printStackTrace(); } // Set the fill value for the dataset try { int[] fill_value = { FILLVAL }; H5.H5Pset_fill_value(H5dcpl_id, HDF5Constants.H5T_NATIVE_INT, fill_value); } catch (Exception e) { e.printStackTrace(); } // Set the allocation time to "early". This way we can be sure // that reading from the dataset immediately after creation will // return the fill value. try { H5.H5Pset_alloc_time(H5dcpl_id, HDF5Constants.H5D_ALLOC_TIME_EARLY); } catch (Exception e) { e.printStackTrace(); } _createDataset(H5fid, H5dsid, "dset", H5dcpl_id, HDF5Constants.H5P_DEFAULT); } private final void _createDataset(int fid, int dsid, String name, int dcpl, int dapl) { try { H5did = H5.H5Dcreate(fid, name, HDF5Constants.H5T_STD_I32BE, dsid, HDF5Constants.H5P_DEFAULT, dcpl, dapl); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Dcreate: " + err); } assertTrue("TestH5Dplist._createDataset: ",H5did > 0); } @Before public void createH5file() throws NullPointerException, HDF5Exception { assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0); try { H5fid = H5.H5Fcreate(H5_FILE, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); H5dsid = H5.H5Screate_simple(RANK, H5dims, H5maxdims); } catch (Throwable err) { err.printStackTrace(); fail("TestH5Dplist.createH5file: " + err); } assertTrue("TestH5Dplist.createH5file: H5.H5Fcreate: ",H5fid > 0); assertTrue("TestH5Dplist.createH5file: H5.H5Screate_simple: ",H5dsid > 0); H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); } @After public void deleteH5file() throws HDF5LibraryException { if (H5dcpl_id >= 0) try {H5.H5Pclose(H5dcpl_id);} catch (Exception ex) {} if (H5did > 0) try {H5.H5Dclose(H5did);} catch (Exception ex) {} if (H5dsid > 0) try {H5.H5Sclose(H5dsid);} catch (Exception ex) {} if (H5fid > 0) try {H5.H5Fclose(H5fid);} catch (Exception ex) {} _deleteFile(H5_FILE); } @Test public void testH5Dset_extent() { int[][] write_dset_data = new int[DIM_X][DIM_Y]; int[][] read_dset_data = new int[DIM_X][DIM_Y]; int[][] extend_dset_data = new int[EDIM_X][EDIM_Y]; // Initialize the dataset. for (int indx = 0; indx < DIM_X; indx++) for (int jndx = 0; jndx < DIM_Y; jndx++) write_dset_data[indx][jndx] = indx * jndx - jndx; _createPDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DATASET_CREATE); // Read values from the dataset, which has not been written to yet. try { H5.H5Dread(H5did, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, read_dset_data); } catch (Exception e) { e.printStackTrace(); } assertTrue("testH5Dset_extent - H5.H5Dread: ", read_dset_data[0][0] == 99); // Write the data to the dataset. try { H5.H5Dwrite(H5did, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, write_dset_data); } catch (Exception e) { e.printStackTrace(); } // Read the data back. try { H5.H5Dread(H5did, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, read_dset_data); } catch (Exception e) { e.printStackTrace(); } assertTrue("testH5Dset_extent - H5.H5Dread: ", read_dset_data[3][6] == 12); // Extend the dataset. try { H5.H5Dset_extent(H5did, H5extdims); } catch (Exception e) { e.printStackTrace(); } // Read from the extended dataset. try { H5.H5Dread(H5did, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, extend_dset_data); } catch (Exception e) { e.printStackTrace(); } assertTrue("testH5Dset_extent - H5.H5Dread: ", extend_dset_data[3][6] == 12); assertTrue("testH5Dset_extent - H5.H5Dread: ", extend_dset_data[4][8] == 99); } } libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/TestH5E.java000066400000000000000000000253171256564762100245510ustar00rootroot00000000000000package test.hdf5lib; import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertFalse; import static org.junit.Assert.assertNotNull; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.HDF5Constants; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import org.junit.After; import org.junit.Before; import org.junit.Ignore; import org.junit.Test; public class TestH5E { int hdf_java_classid = -1; int current_stackid = -1; @Before public void H5Eget_stack_class() { assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0); hdf_java_classid = -1; try { hdf_java_classid = H5.H5Eregister_class("HDF-Java-Error", "hdf-java", "2.5"); current_stackid = H5.H5Eget_current_stack(); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eget_stack_class: " + err); } } @After public void H5Erestore_stack_class() { try { H5.H5Eunregister_class(hdf_java_classid); hdf_java_classid = -1; H5.H5Eclose_stack(current_stackid); current_stackid = -1; } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Erestore_stack_class: " + err); } } @Test public void testH5Eget_class_name() { try { String class_name = H5.H5Eget_class_name(hdf_java_classid); assertNotNull("H5.H5Eget_class_name: " + class_name, class_name); assertEquals("H5.H5Eget_class_name: ", "HDF-Java-Error", class_name); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eget_class_name: " + err); } } @Test public void testH5Eprint2() { try { assertFalse(current_stackid < 0); H5.H5Eprint2(current_stackid, null); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eprint2: " + err); } } @Ignore("Tested with create_msg_major[minor]") public void testH5Eclose_msg() { fail("Not yet implemented"); } @Test(expected = NullPointerException.class) public void testH5Ecreate_msg_name_null() throws Throwable { H5.H5Ecreate_msg(hdf_java_classid, HDF5Constants.H5E_MAJOR, null); } @Test public void testH5Ecreate_msg_major() { try { int err_id = H5.H5Ecreate_msg(hdf_java_classid, HDF5Constants.H5E_MAJOR, "Error in Test"); assertFalse("H5.H5Ecreate_msg_major: " + err_id, err_id < 0); H5.H5Eclose_msg(err_id); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Ecreate_msg_major: " + err); } } @Test public void testH5Ecreate_msg_minor() { try { int err_id = H5.H5Ecreate_msg(hdf_java_classid, HDF5Constants.H5E_MINOR, "Error in Test Function"); assertFalse("H5.H5Ecreate_msg_minor: " + err_id, err_id < 0); H5.H5Eclose_msg(err_id); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Ecreate_msg_minor: " + err); } } @Test public void testH5Eget_msg() { int[] error_msg_type = { HDF5Constants.H5E_MINOR }; int err_id = -1; String msg = null; try { err_id = H5.H5Ecreate_msg(hdf_java_classid, HDF5Constants.H5E_MAJOR, "Error in Test"); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eget_msg: " + err); } assertFalse("H5.H5Eget_msg: H5Ecreate_msg - " + err_id, err_id < 0); try { msg = H5.H5Eget_msg(err_id, error_msg_type); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eget_msg: " + err); } assertNotNull("H5.H5Eget_msg: " + msg, msg); assertEquals("H5.H5Eget_msg: ", "Error in Test", msg); assertEquals("H5.H5Eget_msg: ", HDF5Constants.H5E_MAJOR, error_msg_type[0]); try { H5.H5Eclose_msg(err_id); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eget_msg: " + err); } } @Test public void testH5Eget_msg_major() { try { H5.H5Fopen("test", 0, 1); } catch (HDF5LibraryException hdferr) { int[] error_msg_type = { HDF5Constants.H5E_MAJOR }; String msg = null; try { msg = H5.H5Eget_msg(hdferr.getMajorErrorNumber(), error_msg_type); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eget_msg: " + err); } assertNotNull("H5.H5Eget_msg: " + msg, msg); assertEquals("H5.H5Eget_msg: ", "Invalid arguments to routine", msg); assertEquals("H5.H5Eget_msg: ", HDF5Constants.H5E_MAJOR, error_msg_type[0]); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eget_msg: " + err); } } @Test public void testH5Eget_msg_minor() { try { H5.H5Fopen("test", 0, 1); } catch (HDF5LibraryException hdferr) { int[] error_msg_type = { HDF5Constants.H5E_MINOR }; String msg = null; try { msg = H5.H5Eget_msg(hdferr.getMinorErrorNumber(), error_msg_type); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eget_msg: " + err); } assertNotNull("H5.H5Eget_msg: " + msg, msg); assertEquals("H5.H5Eget_msg: ", "Inappropriate type", msg); assertEquals("H5.H5Eget_msg: ", HDF5Constants.H5E_MINOR, error_msg_type[0]); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eget_msg: " + err); } } @Test public void testH5Ecreate_stack() { int stk_id = -1; try { stk_id = H5.H5Ecreate_stack(); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Ecreate_stack: " + err); } assertFalse("H5.H5Ecreate_stack: " + stk_id, stk_id < 0); try { H5.H5Eclose_stack(stk_id); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Ecreate_stack: " + err); } } @Test public void testH5Epop() { try { H5.H5Eset_current_stack(current_stackid); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Epop: " + err); } try { H5.H5Fopen("test", 0, 1); } catch (Throwable err) { } // save current stack contents try { current_stackid = H5.H5Eget_current_stack(); } catch (HDF5LibraryException err) { err.printStackTrace(); fail("H5.H5Epop: " + err); } long num_msg = -1; try { num_msg = H5.H5Eget_num(HDF5Constants.H5E_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Epop: " + err); } assertTrue("H5.H5Epop #:" + num_msg, num_msg == 0); try { num_msg = H5.H5Eget_num(current_stackid); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Epop: " + err); } assertTrue("H5.H5Epop #:" + num_msg, num_msg == 2); try { H5.H5Epop(current_stackid, 1); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Epop: " + err); } try { num_msg = H5.H5Eget_num(current_stackid); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Epop: " + err); } assertTrue("H5.H5Epop", num_msg == 1); } @Test public void testH5EprintInt() { assertFalse(current_stackid < 0); try { H5.H5Eprint2(current_stackid, null); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5EprintInt: " + err); } } @Test public void testH5EclearInt() { try { H5.H5Eclear(current_stackid); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5EclearInt: " + err); } } @Test public void testH5Eclear2() { try { H5.H5Eclear2(current_stackid); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eclear2: " + err); } } @Test public void testH5Eauto_is_v2() { boolean is_v2 = false; try { is_v2 = H5.H5Eauto_is_v2(current_stackid); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eauto_is_v2: " + err); } assertTrue("H5.H5Eauto_is_v2: ", is_v2); } @Test public void testH5Eget_num() { long num_msg = -1; try { num_msg = H5.H5Eget_num(current_stackid); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eget_num: " + err); } assertTrue("H5.H5Eget_num", num_msg == 0); } @Test public void testH5Eget_num_with_msg() { try { H5.H5Eset_current_stack(current_stackid); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Epop: " + err); } try { H5.H5Fopen("test", 0, 1); } catch (Throwable err) { } // save current stack contents try { current_stackid = H5.H5Eget_current_stack(); } catch (HDF5LibraryException err) { err.printStackTrace(); fail("H5.H5Epop: " + err); } long num_msg = -1; try { num_msg = H5.H5Eget_num(current_stackid); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Epop: " + err); } assertTrue("H5.H5Eget_num_with_msg #:" + num_msg, num_msg > 0); } @Ignore("API1.6") public void testH5Eprint() { fail("Not yet implemented"); } @Ignore("API1.6") public void testH5Eclear() { fail("Not yet implemented"); } } libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/TestH5Edefault.java000066400000000000000000000400401256564762100261040ustar00rootroot00000000000000package test.hdf5lib; import static org.junit.Assert.assertFalse; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.HDF5Constants; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import org.junit.Before; import org.junit.Test; public class TestH5Edefault { @Before public void H5Eset_default_stack() { assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0); try { // Clear any active stack messages H5.H5Eclear2(HDF5Constants.H5E_DEFAULT); } catch (HDF5LibraryException err) { err.printStackTrace(); fail("H5Eset_default_stack: " + err); } } @Test(expected = IllegalArgumentException.class) public void testH5Eprint2_invalid_classid() throws Throwable { H5.H5Eprint2(-1, null); } @Test public void testH5Eprint() { try { H5.H5Fopen("test", 0, 1); } catch (Throwable err) { } try { H5.H5Eprint2(HDF5Constants.H5E_DEFAULT, null); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eprint: " + err); } } @Test public void testH5Eget_current_stack() { long num_msg = -1; long num_msg_default = -1; int stack_id = -1; int stack_id_default = HDF5Constants.H5E_DEFAULT; try { H5.H5Fopen("test", 0, 1); } catch (Throwable err) { //default stack id will be different after exception stack_id_default = HDF5Constants.H5E_DEFAULT; //err.printStackTrace(); //This will clear the error stack } // Verify we have the correct number of messages try { num_msg_default = H5.H5Eget_num(stack_id_default); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eget_current_stack: " + err); } assertTrue("H5.H5Eget_current_stack: get_num #:" + num_msg_default, num_msg_default == 2); //Save a copy of the current stack and clears the current stack try { stack_id = H5.H5Eget_current_stack(); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eget_current_stack: " + err); } assertFalse("H5.H5Eget_current_stack: get_current_stack - " + stack_id, stack_id < 0); assertFalse("H5.H5Eget_current_stack: get_current_stack - " + stack_id, stack_id == stack_id_default); // Verify we have the correct number of messages try { num_msg_default = H5.H5Eget_num(stack_id_default); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eget_current_stack: " + err); } assertTrue("H5.H5Eget_current_stack: get_num #:" + num_msg_default, num_msg_default == 0); //Verify the copy has the correct number of messages try { num_msg = H5.H5Eget_num(stack_id); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eget_current_stack: " + err); } assertTrue("H5.H5Eget_current_stack: get_num #:" + num_msg, num_msg == 2); try { H5.H5Eclose_stack(stack_id); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eget_current_stack: " + err); } } @Test public void testH5Eget_current_stack_pop() { long num_msg = -1; long num_msg_default = -1; int stack_id = -1; try { H5.H5Fopen("test", 0, 1); } catch (Throwable err) { //err.printStackTrace(); //This will clear the error stack } // Verify we have the correct number of messages try { num_msg_default = H5.H5Eget_num(HDF5Constants.H5E_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eget_current_stack: " + err); } assertTrue("H5.H5Eget_current_stack: get_num #:" + num_msg_default, num_msg_default == 2); //Save a copy of the current stack and clears the current stack try { stack_id = H5.H5Eget_current_stack(); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eget_current_stack: " + err); } assertFalse("H5.H5Eget_current_stack: get_current_stack - " + stack_id, stack_id < 0); assertFalse("H5.H5Eget_current_stack: get_current_stack - " + stack_id, stack_id == HDF5Constants.H5E_DEFAULT); // Verify we have the correct number of messages try { num_msg_default = H5.H5Eget_num(HDF5Constants.H5E_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eget_current_stack: " + err); } assertTrue("H5.H5Eget_current_stack: get_num #:" + num_msg_default, num_msg_default == 0); //Verify the copy has the correct number of messages try { num_msg = H5.H5Eget_num(stack_id); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eget_current_stack: " + err); } assertTrue("H5.H5Eget_current_stack: get_num #:" + num_msg, num_msg == 2); //Generate errors on default stack try { H5.H5Fopen("test", 0, 1); } catch (Throwable err) { //err.printStackTrace(); //This will clear the error stack } // Verify we have the correct number of messages try { num_msg_default = H5.H5Eget_num(HDF5Constants.H5E_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eget_current_stack: " + err); } assertTrue("H5.H5Eget_current_stack: get_num #:" + num_msg_default, num_msg_default == 2); //Remove one message from the current stack try { H5.H5Epop(HDF5Constants.H5E_DEFAULT, 1); num_msg_default = H5.H5Eget_num(HDF5Constants.H5E_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eget_current_stack: " + err); } assertTrue("H5.H5Eget_current_stack: pop #:" + num_msg_default, num_msg_default == 1); //Verify the copy still has the correct number of messages try { num_msg = H5.H5Eget_num(stack_id); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eget_current_stack: " + err); } assertTrue("H5.H5Eget_current_stack: get_num #:" + num_msg, num_msg == 2); } @Test(expected = IllegalArgumentException.class) public void testH5Eclose_stack_invalid_stackid() throws Throwable { H5.H5Eclose_stack(-1); } @Test(expected = IllegalArgumentException.class) public void testH5Eget_class_name_invalid_classid() throws Throwable { H5.H5Eget_class_name(-1); } @Test(expected = IllegalArgumentException.class) public void testH5Eget_class_name_invalid_classname() throws Throwable { H5.H5Eget_class_name(HDF5Constants.H5E_DEFAULT); } @Test(expected = IllegalArgumentException.class) public void testH5Eclose_msg_invalid_errid() throws Throwable { H5.H5Eclose_msg(-1); } @Test(expected = IllegalArgumentException.class) public void testH5Ecreate_msg_invalid_errid() throws Throwable { H5.H5Ecreate_msg(-1, HDF5Constants.H5E_MAJOR, "null"); } @Test(expected = IllegalArgumentException.class) public void testH5Eget_msg_invalid_msgid() throws Throwable { H5.H5Eget_msg(-1, null); } @Test public void testH5Ecreate_stack() { try { int stack_id = H5.H5Ecreate_stack(); assertTrue("H5.H5Ecreate_stack", stack_id > 0); H5.H5Eclose_stack(stack_id); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Ecreate_stack: " + err); } } @Test(expected = IllegalArgumentException.class) public void testH5Eset_current_stack_invalid_stkid() throws Throwable { H5.H5Eset_current_stack(-1); } @Test public void testH5Eset_current_stack() { long num_msg = -1; int stack_id = -1; try { H5.H5Fopen("test", 0, 1); } catch (Throwable err) { //err.printStackTrace(); //This will clear the error stack } // Verify we have the correct number of messages try { num_msg = H5.H5Eget_num(HDF5Constants.H5E_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eset_current_stack: " + err); } assertTrue("H5.H5Eset_current_stack: get_num #:" + num_msg, num_msg == 2); //Save a copy of the current stack try { stack_id = H5.H5Eget_current_stack(); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eset_current_stack: " + err); } assertFalse("H5.H5Eset_current_stack: get_current_stack - " + stack_id, stack_id < 0); assertFalse("H5.H5Eset_current_stack: get_current_stack - " + stack_id, stack_id == HDF5Constants.H5E_DEFAULT); //Verify the copy has the correct number of messages try { num_msg = H5.H5Eget_num(stack_id); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eset_current_stack: " + err); } assertTrue("H5.H5Eset_current_stack: get_num #:" + num_msg, num_msg == 2); //Generate errors on default stack try { H5.H5Fopen("test", 0, 1); } catch (Throwable err) { //err.printStackTrace(); //This will clear the error stack } // Verify we have the correct number of messages try { num_msg = H5.H5Eget_num(HDF5Constants.H5E_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eget_current_stack: " + err); } assertTrue("H5.H5Eset_current_stack: get_num #:" + num_msg, num_msg == 2); //Remove one message from the current stack try { H5.H5Epop(HDF5Constants.H5E_DEFAULT, 1); num_msg = H5.H5Eget_num(HDF5Constants.H5E_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eset_current_stack: " + err); } assertTrue("H5.H5Eset_current_stack: pop #:" + num_msg, num_msg == 1); //Verify the copy still has the correct number of messages try { num_msg = H5.H5Eget_num(stack_id); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eset_current_stack: " + err); } assertTrue("H5.H5Eset_current_stack: get_num #:" + num_msg, num_msg == 2); try { H5.H5Eset_current_stack(stack_id); num_msg = H5.H5Eget_num(HDF5Constants.H5E_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eset_current_stack: " + err); } assertTrue("H5.H5Eset_current_stack: get_num - " + num_msg, num_msg == 2); } @Test(expected = IllegalArgumentException.class) public void testH5Epop_invalid_stkid() throws Throwable { H5.H5Epop(-1, 0); } @Test public void testH5Epop() throws Throwable { long num_msg = -1; try { H5.H5Fopen("test", 0, 1); } catch (Throwable err) { } try { num_msg = H5.H5Eget_num(HDF5Constants.H5E_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Epop: " + err); } assertTrue("H5.H5Epop before #:" + num_msg, num_msg == 2); try { H5.H5Epop(HDF5Constants.H5E_DEFAULT, 1); num_msg = H5.H5Eget_num(HDF5Constants.H5E_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Epop: " + err); } assertTrue("H5.H5Epop after #:" + num_msg, num_msg == 1); } @Test(expected = IllegalArgumentException.class) public void testH5EprintInt_invalid_classid() throws Throwable { H5.H5Eprint2(-1, null); } @Test public void testH5EprintInt() { try { H5.H5Fopen("test", 0, 1); } catch (Throwable err) { } try { H5.H5Eprint2(HDF5Constants.H5E_DEFAULT, null); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5EprintInt: " + err); } } @Test public void testH5EclearInt() { try { H5.H5Eclear(HDF5Constants.H5E_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5EclearInt: " + err); } } @Test(expected = IllegalArgumentException.class) public void testH5Eclear2_invalid_stkid() throws Throwable { H5.H5Eclear2(-1); } @Test public void testH5Eclear() { try { H5.H5Eclear2(HDF5Constants.H5E_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eclear2: " + err); } } @Test public void testH5Eclear2_with_msg() { long num_msg = -1; try { H5.H5Fopen("test", 0, 1); } catch (Throwable err) { } try { num_msg = H5.H5Eget_num(HDF5Constants.H5E_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eclear2_with_msg: " + err); } assertTrue("H5.H5Eclear2_with_msg before #:" + num_msg, num_msg == 2); try { H5.H5Eclear2(HDF5Constants.H5E_DEFAULT); num_msg = H5.H5Eget_num(HDF5Constants.H5E_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eclear2_with_msg: " + err); } assertTrue("H5.H5Eclear2_with_msg after #:" + num_msg, num_msg == 0); } @Test(expected = IllegalArgumentException.class) public void testH5Eauto_is_v2_invalid_stkid() throws Throwable { H5.H5Eauto_is_v2(-1); } @Test public void testH5Eauto_is_v2() { boolean is_v2 = false; try { is_v2 = H5.H5Eauto_is_v2(HDF5Constants.H5E_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eauto_is_v2: " + err); } assertTrue("H5.H5Eauto_is_v2: ", is_v2); } @Test(expected = IllegalArgumentException.class) public void testH5Eget_num_invalid_stkid() throws Throwable { H5.H5Eget_num(-1); } @Test public void testH5Eget_num() { long num_msg = -1; try { num_msg = H5.H5Eget_num(HDF5Constants.H5E_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eget_num: " + err); } assertTrue("H5.H5Eget_num #:" + num_msg, num_msg == 0); } @Test public void testH5Eget_num_with_msg() { long num_msg = -1; try { H5.H5Fopen("test", 0, 1); } catch (Throwable err) { } try { num_msg = H5.H5Eget_num(HDF5Constants.H5E_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Eget_num_with_msg: " + err); } assertTrue("H5.H5Eget_num_with_msg #:" + num_msg, num_msg > 0); } } libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/TestH5Eregister.java000066400000000000000000000030221256564762100263030ustar00rootroot00000000000000package test.hdf5lib; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import ncsa.hdf.hdf5lib.H5; import org.junit.Before; import org.junit.Test; public class TestH5Eregister { @Before public void checkOpenIDs() { assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0); } @Test(expected = NullPointerException.class) public void testH5Eregister_class_cls_name_null() throws Throwable { H5.H5Eregister_class(null, "libname", "version"); } @Test(expected = NullPointerException.class) public void testH5Eregister_class_lib_name_null() throws Throwable { H5.H5Eregister_class("clsname", null, "version"); } @Test(expected = NullPointerException.class) public void testH5Eregister_class_version_null() throws Throwable { H5.H5Eregister_class("clsname", "libname", null); } @Test(expected = IllegalArgumentException.class) public void testH5Eunregister_class_invalid_classid() throws Throwable { H5.H5Eunregister_class(-1); } @Test public void testH5Eregister_class() { int hdf_java_classid = -1; try { hdf_java_classid = H5.H5Eregister_class("HDF-Java-Error", "hdf-java", "2.5"); } catch (Throwable err) { fail("H5.H5Eregister_class: " + err); } try { H5.H5Eunregister_class(hdf_java_classid); } catch (Throwable err) { fail("H5.H5Eunregister_class: " + err); } } } libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/TestH5F.java000066400000000000000000000152001256564762100245400ustar00rootroot00000000000000package test.hdf5lib; import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import java.io.File; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.HDF5Constants; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import org.junit.After; import org.junit.Before; import org.junit.Test; public class TestH5F { private static final String H5_FILE = "test.h5"; private static final int COUNT_OBJ_FILE = 1; private static final int COUNT_OBJ_DATASET = 0; private static final int COUNT_OBJ_GROUP = 0; private static final int COUNT_OBJ_DATATYPE = 0; private static final int COUNT_OBJ_ATTR = 0; private static final int COUNT_OBJ_ALL = (COUNT_OBJ_FILE + COUNT_OBJ_DATASET + COUNT_OBJ_GROUP + COUNT_OBJ_DATATYPE + COUNT_OBJ_ATTR); private static final int[] OBJ_COUNTS = { COUNT_OBJ_FILE, COUNT_OBJ_DATASET, COUNT_OBJ_GROUP, COUNT_OBJ_DATATYPE, COUNT_OBJ_ATTR, COUNT_OBJ_ALL }; private static final int[] OBJ_TYPES = { HDF5Constants.H5F_OBJ_FILE, HDF5Constants.H5F_OBJ_DATASET, HDF5Constants.H5F_OBJ_GROUP, HDF5Constants.H5F_OBJ_DATATYPE, HDF5Constants.H5F_OBJ_ATTR, HDF5Constants.H5F_OBJ_ALL }; int H5fid = -1; private final void _deleteFile(String filename) { File file = new File(filename); if (file.exists()) { try {file.delete();} catch (SecurityException e) {} } } @Before public void createH5file() throws HDF5LibraryException, NullPointerException { assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0); H5fid = H5.H5Fcreate(H5_FILE, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); } @After public void deleteH5file() throws HDF5LibraryException { if (H5fid > 0) { try {H5.H5Fclose(H5fid);} catch (Exception ex) {} } _deleteFile(H5_FILE); } @Test public void testH5Fget_create_plist() { int plist = -1; try { plist = H5.H5Fget_create_plist(H5fid); } catch (Throwable err) { fail("H5.H5Fget_create_plist: " + err); } assertTrue(plist > 0); try {H5.H5Pclose(plist);} catch (HDF5LibraryException e) {e.printStackTrace();} } @Test(expected = HDF5LibraryException.class) public void testH5Fget_create_plist_closed() throws Throwable { int fid = -1; try { fid = H5.H5Fopen(H5_FILE, HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { fail("H5.H5Fopen: " + err); } try { H5.H5Fclose(fid); } catch (Exception ex) { } // it should fail because the file was closed. H5.H5Fget_create_plist(fid); } @Test public void testH5Fget_access_plist() { int plist = -1; try { plist = H5.H5Fget_access_plist(H5fid); } catch (Throwable err) { fail("H5.H5Fget_access_plist: " + err); } assertTrue(plist > 0); try {H5.H5Pclose(plist);} catch (HDF5LibraryException e) {e.printStackTrace();} } @Test(expected = HDF5LibraryException.class) public void testH5Fget_access_plist_closed() throws Throwable { int fid = -1; try { fid = H5.H5Fopen(H5_FILE, HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { fail("H5.H5Fopen: " + err); } try { H5.H5Fclose(fid); } catch (Exception ex) { } // it should fail because the file was closed. H5.H5Fget_access_plist(fid); } @Test public void testH5Fget_intent_rdwr() { int intent = 0; int fid = -1; try { fid = H5.H5Fopen(H5_FILE, HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { fail("H5.H5Fopen: " + err); } try { intent = H5.H5Fget_intent(fid); } catch (Throwable err) { fail("H5.H5Fget_intent: " + err); } assertEquals(intent, HDF5Constants.H5F_ACC_RDWR); try { H5.H5Fclose(fid); } catch (Exception ex) { } } @Test public void testH5Fget_intent_rdonly() { int intent = 0; int fid = -1; try { fid = H5.H5Fopen(H5_FILE, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { fail("H5.H5Fopen: " + err); } try { intent = H5.H5Fget_intent(fid); System.err.println(intent); } catch (Throwable err) { fail("H5.H5Fget_intent: " + err); } try { H5.H5Fclose(fid); } catch (Exception ex) { } // BROKEN in HDF5 1.8.13 and HDF-Java 2.10.1 //assertEquals(intent, HDF5Constants.H5F_ACC_RDONLY); } @Test public void testH5Fget_obj_count() { long count = -1; for (int i = 0; i < OBJ_TYPES.length; i++) { try { count = H5.H5Fget_obj_count_long(H5fid, OBJ_TYPES[i]); } catch (Throwable err) { fail("H5.H5Fget_obj_count: " + err); } assertEquals(count, OBJ_COUNTS[i]); } } @Test public void testH5Fget_obj_ids() { long count = 0; int max_objs = 100; int[] obj_id_list = new int[max_objs]; int[] open_obj_counts = new int[OBJ_TYPES.length]; for (int i = 0; i < OBJ_TYPES.length; i++) open_obj_counts[i] = 0; open_obj_counts[0] = 1; for (int i = 0; i < OBJ_TYPES.length - 1; i++) open_obj_counts[OBJ_TYPES.length - 1] += open_obj_counts[i]; for (int i = 0; i < OBJ_TYPES.length; i++) { try { count = H5.H5Fget_obj_ids_long(H5fid, OBJ_TYPES[i], max_objs, obj_id_list); } catch (Throwable err) { fail("H5.H5Fget_obj_ids: " + err); } assertEquals(count, open_obj_counts[i]); } } } libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/TestH5Fbasic.java000066400000000000000000000160311256564762100255450ustar00rootroot00000000000000package test.hdf5lib; import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertNotNull; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import java.io.File; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.HDF5Constants; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import org.junit.After; import org.junit.Before; import org.junit.Test; @SuppressWarnings("all") public class TestH5Fbasic { private static final String H5_FILE = "test.h5"; private static final String TXT_FILE = "test.txt"; int H5fid = -1; private final void _deleteFile(String filename) { File file = new File(filename); if (file.exists()) { try {file.delete();} catch (SecurityException e) {} } } @Before public void createH5file() throws HDF5LibraryException, NullPointerException { assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0); H5fid = H5.H5Fcreate(H5_FILE, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); } @After public void deleteH5file() throws HDF5LibraryException { if (H5fid > 0) { try {H5.H5Fclose(H5fid);} catch (Exception ex) {} } _deleteFile(H5_FILE); } @Test public void testH5Fcreate() { assertTrue(H5fid > 0); } @Test public void testH5Fis_hdf5() { boolean isH5 = false; try { isH5 = H5.H5Fis_hdf5(H5_FILE); } catch (Throwable err) { fail("H5.H5Fis_hdf5 failed on " + H5_FILE + ": " + err); } assertTrue(isH5 == true); } @Test(expected = HDF5LibraryException.class) public void testH5Fcreate_EXCL() throws Throwable { H5.H5Fcreate(H5_FILE, HDF5Constants.H5F_ACC_EXCL, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); } @Test(expected = HDF5LibraryException.class) public void testH5Fopen_read_only() throws Throwable { int fid = -1; try { fid = H5.H5Fopen(H5_FILE, HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { fail("H5.H5Fopen: " + err); } try { H5.H5Fclose(fid); } catch (Exception ex) { } // set the file to read-only File file = new File(H5_FILE); if (file.setReadOnly()) { // this should fail. fid = H5.H5Fopen(H5_FILE, HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT); try { H5.H5Fclose(fid); } catch (Exception ex) { } } else { fail("File.setWritable(true) failed."); } } @Test(expected = HDF5LibraryException.class) public void testH5Freopen_closed() throws Throwable { int fid = -1; int fid2 = -1; try { fid = H5.H5Fopen(H5_FILE, HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { fail("H5.H5Fopen: " + err); } try { H5.H5Fclose(fid); } catch (Exception ex) { } // should fail because the file was closed. fid2 = H5.H5Freopen(fid); } @Test public void testH5Freopen() { int fid = -1; int fid2 = -1; try { fid = H5.H5Fopen(H5_FILE, HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { fail("H5.H5Fopen: " + err); } try { fid2 = H5.H5Freopen(fid); } catch (Throwable err) { fail("H5.H5Freopen: " + err); } assertTrue(fid2 > 0); try { H5.H5Fclose(fid2); } catch (Exception ex) { } try { H5.H5Fclose(fid); } catch (Exception ex) { } } @Test public void testH5Fclose() { int fid = -1; try { fid = H5.H5Fopen(H5_FILE, HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { fail("H5.H5Fopen: " + err); } try { H5.H5Fclose(fid); } catch (Throwable err) { fail("H5.H5Fclose: " + err); } } @Test(expected = HDF5LibraryException.class) public void testH5Fclose_twice() throws Throwable { int fid = -1; try { fid = H5.H5Fopen(H5_FILE, HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { fail("H5.H5Fopen: " + err); } try { H5.H5Fclose(fid); } catch (Throwable err) { fail("H5.H5Fclose: " + err); } // it should fail since the file was closed. H5.H5Fclose(fid); } @Test public void testH5Fget_freespace() { long freeSpace = 0; try { freeSpace = H5.H5Fget_freespace(H5fid); } catch (Throwable err) { fail("H5.H5Fget_freespace: " + err); } assertEquals(freeSpace, 0); } @Test public void testH5Fget_filesize() { long fileSize = 0; try { fileSize = H5.H5Fget_filesize(H5fid); } catch (Throwable err) { fail("H5.H5Fget_freespace: " + err); } assertTrue(fileSize > 0); } @Test public void testH5Fget_mdc_hit_rate() { double rate; try { rate = H5.H5Fget_mdc_hit_rate(H5fid); } catch (Throwable err) { fail("H5.H5Fget_mdc_hit_rate: " + err); } } @Test public void testH5Fget_mdc_size() { int nentries = -1; long cache_sizes[] = new long[3]; try { nentries = H5.H5Fget_mdc_size(H5fid, cache_sizes); } catch (Throwable err) { fail("H5.H5Fget_mdc_size: " + err); } assertTrue("H5.H5Fget_mdc_size #:" + nentries, nentries == 4); } @Test public void testH5Freset_mdc_hit_rate_stats() { try { H5.H5Freset_mdc_hit_rate_stats(H5fid); } catch (Throwable err) { fail("H5.H5Freset_mdc_hit_rate_stats: " + err); } } @Test public void testH5Fget_name() { String fname = null; try { fname = H5.H5Fget_name(H5fid); } catch (Throwable err) { fail("H5.H5Fget_name: " + err); } assertNotNull(fname); assertEquals(fname, H5_FILE); } } libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/TestH5Fparams.java000066400000000000000000000076331256564762100257570ustar00rootroot00000000000000package test.hdf5lib; import static org.junit.Assert.assertFalse; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import java.io.File; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.HDF5Constants; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import org.junit.Before; import org.junit.Test; @SuppressWarnings("all") public class TestH5Fparams { @Before public void checkOpenIDs() { assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0); } @Test(expected = NullPointerException.class) public void testH5Fcreate_null() throws Throwable { H5.H5Fcreate(null, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); } @Test(expected = NullPointerException.class) public void testH5Fopen_null() throws Throwable { H5.H5Fopen(null, HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT); } @Test(expected = NullPointerException.class) public void testH5Fis_hdf5_null() throws Throwable { H5.H5Fis_hdf5(null); } @Test(expected = NullPointerException.class) public void testH5Fmount_null() throws Throwable { H5.H5Fmount(-1, null, -1, HDF5Constants.H5P_DEFAULT); } @Test(expected = NullPointerException.class) public void testH5Funmount_null() throws Throwable { H5.H5Funmount(-1, null); } @Test public void testH5Fis_hdf5_text() { File txtFile = null; boolean isH5 = false; try { txtFile = new File("test.txt"); if (!txtFile.exists()) txtFile.createNewFile(); isH5 = H5.H5Fis_hdf5("test.txt"); } catch (Throwable err) { fail("H5.H5Fis_hdf5 failed on test.txt: " + err); } assertFalse(isH5); try { txtFile.delete(); } catch (SecurityException e) { ;// e.printStackTrace(); } } @Test public void testH5Fcreate() { int fid = -1; File file = null; try { fid = H5.H5Fcreate("test.h5", HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); if (fid > 0) { H5.H5Fclose(fid); } file = new File("test.h5"); } catch (Throwable err) { fail("H5.H5Fopen: " + err); } if (file.exists()) { try { file.delete(); } catch (SecurityException e) { ;// e.printStackTrace(); } } } @Test public void testH5Fflush_global() { int fid = -1; try { fid = H5.H5Fcreate("test.h5", HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { fail("H5.H5Fopen: " + err); } try { H5.H5Fflush(fid, HDF5Constants.H5F_SCOPE_GLOBAL); } catch (Throwable err) { fail("H5.H5Fflush: " + err); } try { H5.H5Fclose(fid); } catch (Exception ex) { } } @Test public void testH5Fflush_local() { int fid = -1; try { fid = H5.H5Fcreate("test.h5", HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { fail("H5.H5Fopen: " + err); } try { H5.H5Fflush(fid, HDF5Constants.H5F_SCOPE_LOCAL); } catch (Throwable err) { fail("H5.H5Fflush: " + err); } try { H5.H5Fclose(fid); } catch (Exception ex) { } } } libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/TestH5G.java000066400000000000000000000361771256564762100245610ustar00rootroot00000000000000package test.hdf5lib; import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertNotNull; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import java.io.File; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.HDF5Constants; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import ncsa.hdf.hdf5lib.structs.H5G_info_t; import org.junit.After; import org.junit.Before; import org.junit.Test; @SuppressWarnings("all") public class TestH5G { private static final String H5_FILE = "test.h5"; private static final String H5_FILE2 = "test2.h5"; private static final String[] GROUPS = { "/G1", "/G1/G11", "/G1/G12", "/G1/G11/G111", "/G1/G11/G112", "/G1/G11/G113", "/G1/G11/G114" }; private static final String[] GROUPS2 = { "/G1", "/G1/G14", "/G1/G12", "/G1/G13", "/G1/G11"}; int H5fid = -1; int H5fid2 = -1; private final int _createGroup(int fid, String name) { int gid = -1; try { gid = H5.H5Gcreate(fid, name, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gcreate: " + err); } return gid; } private final int _createGroup2(int fid, String name) { int gid = -1; int gcpl = -1; try{ gcpl = H5.H5Pcreate(HDF5Constants.H5P_GROUP_CREATE); //create gcpl if (gcpl >= 0) { H5.H5Pset_link_creation_order(gcpl, HDF5Constants.H5P_CRT_ORDER_TRACKED + HDF5Constants.H5P_CRT_ORDER_INDEXED);//Set link creation order } } catch (final Exception ex) { fail("H5.H5Pcreate() failed. " + ex); } try { gid = H5.H5Gcreate(fid, name, HDF5Constants.H5P_DEFAULT, gcpl, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gcreate: " + err); } try {H5.H5Pclose(gcpl);} catch (final Exception ex) {} return gid; } private final int _openGroup(int fid, String name) { int gid = -1; try { gid = H5.H5Gopen(fid, name, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { gid = -1; err.printStackTrace(); fail("H5.H5Gopen: " + err); } return gid; } private final void _deleteFile(String filename) { File file = new File(filename); if (file.exists()) { try {file.delete();} catch (SecurityException e) {} } } @Before public void createH5file() throws HDF5LibraryException, NullPointerException { assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0); H5fid = H5.H5Fcreate(H5_FILE, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); H5fid2 = H5.H5Fcreate(H5_FILE2, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); int gid = -1; for (int i = 0; i < GROUPS.length; i++) { gid = _createGroup(H5fid, GROUPS[i]); assertTrue(gid > 0); try {H5.H5Gclose(gid);} catch (Exception ex) {} } for (int i = 0; i < GROUPS2.length; i++) { gid = _createGroup2(H5fid2, GROUPS2[i]); assertTrue(gid > 0); try {H5.H5Gclose(gid);} catch (Exception ex) {} } H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); H5.H5Fflush(H5fid2, HDF5Constants.H5F_SCOPE_LOCAL); } @After public void deleteH5file() throws HDF5LibraryException { if (H5fid > 0) { try {H5.H5Fclose(H5fid);} catch (Exception ex) {} } if (H5fid2 > 0) { try {H5.H5Fclose(H5fid2);} catch (Exception ex) {} } _deleteFile(H5_FILE); _deleteFile(H5_FILE2); } @Test public void testH5Gopen() { for (int i = 0; i < GROUPS.length; i++) { int gid = _openGroup(H5fid, GROUPS[i]); assertTrue(gid > 0); try { H5.H5Gclose(gid); } catch (Exception ex) { } } } @Test public void testH5Gget_create_plist() { int gid = -1; int pid = -1; for (int i = 0; i < GROUPS.length; i++) { gid = _openGroup(H5fid, GROUPS[i]); assertTrue(gid > 0); try { pid = H5.H5Gget_create_plist(gid); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gget_create_plist: " + err); } assertTrue(pid > 0); try { H5.H5Gclose(gid); } catch (Exception ex) { } } } @Test public void testH5Gget_info() { H5G_info_t info = null; for (int i = 0; i < GROUPS.length; i++) { try { info = H5.H5Gget_info(H5fid); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gget_info: " + err); } assertNotNull(info); } } @Test public void testH5Gget_info_by_name() { H5G_info_t info = null; for (int i = 0; i < GROUPS.length; i++) { try { info = H5.H5Gget_info_by_name(H5fid, GROUPS[i], HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gget_info_by_name: " + err); } assertNotNull(info); } } @Test public void testH5Gget_info_by_idx() { H5G_info_t info = null; for (int i = 0; i < 2; i++) { try { info = H5.H5Gget_info_by_idx(H5fid, "/G1", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, i, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gget_info_by_idx: " + err); } assertNotNull(info); } } @Test public void testH5Gget_obj_info_all() { H5G_info_t info = null; int gid = _openGroup(H5fid, GROUPS[0]); try { info = H5.H5Gget_info(gid); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gget_info: " + err); } try { H5.H5Gclose(gid); } catch (Exception ex) { } assertNotNull(info); assertTrue("number of links is empty", info.nlinks > 0); String objNames[] = new String[(int) info.nlinks]; int objTypes[] = new int[(int) info.nlinks]; int lnkTypes[] = new int[(int) info.nlinks]; long objRefs[] = new long[(int) info.nlinks]; int names_found = 0; try { names_found = H5.H5Gget_obj_info_all(H5fid, GROUPS[0], objNames, objTypes, lnkTypes, objRefs, HDF5Constants.H5_INDEX_NAME); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gget_obj_info_all: " + err); } assertTrue("number found[" + names_found + "] different than expected[" + objNames.length + "]", names_found == objNames.length); for (int i = 0; i < objNames.length; i++) { assertNotNull("name #" + i + " does not exist", objNames[i]); assertTrue(objNames[i].length() > 0); } } @Test public void testH5Gget_obj_info_all_gid() { H5G_info_t info = null; int gid = _openGroup(H5fid, GROUPS[0]); try { info = H5.H5Gget_info(gid); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gget_info: " + err); } assertNotNull(info); assertTrue("number of links is empty", info.nlinks > 0); String objNames[] = new String[(int) info.nlinks]; long objRefs[] = new long[(int) info.nlinks]; int lnkTypes[] = new int[(int) info.nlinks]; int objTypes[] = new int[(int) info.nlinks]; int names_found = 0; try { names_found = H5.H5Gget_obj_info_all(gid, null, objNames, objTypes, lnkTypes, objRefs, HDF5Constants.H5_INDEX_NAME); } catch (Throwable err) { try { H5.H5Gclose(gid); } catch (Exception ex) { } err.printStackTrace(); fail("H5.H5Gget_obj_info_all: " + err); } try { H5.H5Gclose(gid); } catch (Exception ex) { } assertTrue("number found[" + names_found + "] different than expected[" + objNames.length + "]", names_found == objNames.length); for (int i = 0; i < objNames.length; i++) { assertNotNull("name #" + i + " does not exist", objNames[i]); assertTrue(objNames[i].length() > 0); } } @Test public void testH5Gget_obj_info_all_gid2() { H5G_info_t info = null; int gid = _openGroup(H5fid, GROUPS[1]); try { info = H5.H5Gget_info(gid); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gget_info: " + err); } assertNotNull(info); assertTrue("number of links is empty", info.nlinks > 0); String objNames[] = new String[(int) info.nlinks]; long objRefs[] = new long[(int) info.nlinks]; int lnkTypes[] = new int[(int) info.nlinks]; int objTypes[] = new int[(int) info.nlinks]; int names_found = 0; try { names_found = H5.H5Gget_obj_info_all(gid, null, objNames, objTypes, lnkTypes, objRefs, HDF5Constants.H5_INDEX_NAME); } catch (Throwable err) { try { H5.H5Gclose(gid); } catch (Exception ex) { } err.printStackTrace(); fail("H5.H5Gget_obj_info_all: " + err); } try { H5.H5Gclose(gid); } catch (Exception ex) { } assertTrue("number found[" + names_found + "] different than expected[" + objNames.length + "]", names_found == objNames.length); for (int i = 0; i < objNames.length; i++) { assertNotNull("name #" + i + " does not exist", objNames[i]); assertTrue(objNames[i].length() > 0); } } @Test public void testH5Gget_obj_info_max() { int gid = _openGroup(H5fid, GROUPS[0]); int groups_max_size = GROUPS.length + 1; String objNames[] = new String[groups_max_size]; int objTypes[] = new int[groups_max_size]; int lnkTypes[] = new int[groups_max_size]; long objRefs[] = new long[groups_max_size]; int names_found = 0; try { names_found = H5.H5Gget_obj_info_max(gid, objNames, objTypes, lnkTypes, objRefs, groups_max_size); } catch (Throwable err) { try { H5.H5Gclose(gid); } catch (Exception ex) { } err.printStackTrace(); fail("H5.H5Gget_obj_info_max: " + err); } try { H5.H5Gclose(gid); } catch (Exception ex) { } // expected number does not include root group assertTrue("number found[" + names_found + "] different than expected[" + (GROUPS.length - 1) + "]", names_found == (GROUPS.length - 1)); for (int i = 0; i < GROUPS.length-1; i++) { assertNotNull("name #"+i+" does not exist",objNames[i]); assertTrue(objNames[i].length()>0); } } @Test public void testH5Gget_obj_info_max_limit() { int gid = _openGroup(H5fid, GROUPS[0]); int groups_max_size = GROUPS.length - 3; String objNames[] = new String[groups_max_size]; int objTypes[] = new int[groups_max_size]; int lnkTypes[] = new int[groups_max_size]; long objRefs[] = new long[groups_max_size]; int names_found = 0; try { names_found = H5.H5Gget_obj_info_max(gid, objNames, objTypes, lnkTypes, objRefs, groups_max_size); } catch (Throwable err) { try { H5.H5Gclose(gid); } catch (Exception ex) { } err.printStackTrace(); fail("H5.H5Gget_obj_info_max: " + err); } try { H5.H5Gclose(gid); } catch (Exception ex) { } assertTrue("number found[" + names_found + "] different than expected[" + groups_max_size + "]", names_found == groups_max_size); for (int i = 0; i < objNames.length; i++) { assertNotNull("name #" + i + " does not exist", objNames[i]); assertTrue(objNames[i].length() > 0); } } @Test public void testH5Gget_obj_info_all_byIndexType() { H5G_info_t info = null; int gid = _openGroup(H5fid2, GROUPS2[0]); try { info = H5.H5Gget_info(gid); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gget_info: " + err); } try { H5.H5Gclose(gid); } catch (Exception ex) { } assertNotNull(info); assertTrue("number of links is empty", info.nlinks > 0); String objNames[] = new String[(int) info.nlinks]; int objTypes[] = new int[(int) info.nlinks]; int lnkTypes[] = new int[(int) info.nlinks]; long objRefs[] = new long[(int) info.nlinks]; try { H5.H5Gget_obj_info_all(H5fid2, GROUPS2[0], objNames, objTypes, lnkTypes, objRefs, HDF5Constants.H5_INDEX_CRT_ORDER); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gget_obj_info_all: " + err); } assertEquals("G12",objNames[1]); assertEquals("G13", objNames[2] ); assertEquals("G11", objNames[3] ); try { H5.H5Gget_obj_info_all(H5fid2, GROUPS2[0], objNames, objTypes, lnkTypes, objRefs, HDF5Constants.H5_INDEX_NAME); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gget_obj_info_all: " + err); } assertEquals("G12",objNames[1]); assertEquals("G13", objNames[2] ); assertEquals("G14", objNames[3] ); } } libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/TestH5Gbasic.java000066400000000000000000000252221256564762100255500ustar00rootroot00000000000000package test.hdf5lib; import static org.junit.Assert.assertNotNull; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import java.io.File; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.HDF5Constants; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import ncsa.hdf.hdf5lib.structs.H5G_info_t; import org.junit.After; import org.junit.Before; import org.junit.Test; public class TestH5Gbasic { private static final String H5_FILE = "test.h5"; int H5fid = -1; private final int _createGroup(int fid, String name) { int gid = -1; try { gid = H5.H5Gcreate(fid, name, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gcreate: " + err); } return gid; } private final void _deleteFile(String filename) { File file = new File(filename); if (file.exists()) { try {file.delete();} catch (SecurityException e) {} } } @Before public void createH5file() throws HDF5LibraryException, NullPointerException { assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0); H5fid = H5.H5Fcreate(H5_FILE, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); } @After public void deleteH5file() throws HDF5LibraryException { if (H5fid > 0) { try {H5.H5Fclose(H5fid);} catch (Exception ex) {} } _deleteFile(H5_FILE); } @Test(expected = NullPointerException.class) public void testH5Gcreate_null() throws Throwable { int gid = -1; // it should fail because the group name is null gid = H5.H5Gcreate(H5fid, null, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); try {H5.H5Gclose(gid);} catch (Exception ex) {} } @Test(expected = HDF5LibraryException.class) public void testH5Gcreate_invalid() throws Throwable { H5.H5Gcreate(-1, "Invalid ID", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); } @Test public void testH5Gcreate() { int gid = -1; try { gid = H5.H5Gcreate(H5fid, "/testH5Gcreate", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gcreate: " + err); } assertTrue(gid > 0); try {H5.H5Gclose(gid);} catch (Exception ex) {} } @Test public void testH5Gclose() { int gid = _createGroup(H5fid, "/testH5Gcreate"); assertTrue(gid > 0); try { H5.H5Gclose(gid); } catch (Throwable err) { fail("H5Gclose: " + err); } } @Test(expected = HDF5LibraryException.class) public void testH5Gcreate_exists() throws Throwable { int gid = _createGroup(H5fid, "/testH5Gcreate"); assertTrue(gid > 0); try {H5.H5Gclose(gid);} catch (Exception ex) {} // it should failed now because the group already exists in file gid = H5.H5Gcreate(H5fid, "/testH5Gcreate", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); } @Test public void testH5Gcreate_anon() { int gid = -1; try { gid = H5.H5Gcreate_anon(H5fid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gcreate_anon: " + err); } assertTrue(gid > 0); try {H5.H5Gclose(gid);} catch (Exception ex) {} } @Test(expected = NullPointerException.class) public void testH5Gopen_null() throws Throwable { int gid = -1; gid = H5.H5Gopen(H5fid, null, HDF5Constants.H5P_DEFAULT); try {H5.H5Gclose(gid);} catch (Exception ex) {} } @Test(expected = HDF5LibraryException.class) public void testH5Gopen_invalid() throws Throwable { H5.H5Gopen(-1, "Invalid ID", HDF5Constants.H5P_DEFAULT); } @Test(expected = HDF5LibraryException.class) public void testH5Gopen_not_exists() throws Throwable { int gid = -1; gid = H5.H5Gopen(H5fid, "Never_created", HDF5Constants.H5P_DEFAULT); try {H5.H5Gclose(gid);} catch (Exception ex) {} } @Test public void testH5Gopen() { int gid = _createGroup(H5fid, "/testH5Gcreate"); assertTrue(gid > 0); try {H5.H5Gclose(gid);} catch (Exception ex) {} try { gid = H5.H5Gopen(H5fid, "/testH5Gcreate", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gopen: " + err); } assertTrue(gid > 0); try {H5.H5Gclose(gid);} catch (Exception ex) {} } @Test(expected = HDF5LibraryException.class) public void testH5Gget_create_plist_invalid() throws Throwable { H5.H5Gget_create_plist(-1); } @Test public void testH5Gget_create_plist() { int pid = -1; int gid = _createGroup(H5fid, "/testH5Gcreate"); assertTrue(gid > 0); try { pid = H5.H5Gget_create_plist(gid); } catch (Throwable err) { try {H5.H5Gclose(gid);} catch (Exception ex) {} err.printStackTrace(); fail("H5.H5Gget_create_plist: " + err); } assertTrue(pid > 0); try {H5.H5Pclose(pid);} catch (Exception ex) {} try {H5.H5Gclose(gid);} catch (Exception ex) {} } @Test(expected = HDF5LibraryException.class) public void testH5Gget_info_invalid() throws Throwable { H5.H5Gget_info(-1); } @Test public void testH5Gget_info() { H5G_info_t info = null; int gid = _createGroup(H5fid, "/testH5Gcreate"); assertTrue(gid > 0); try { info = H5.H5Gget_info(gid); } catch (Throwable err) { try {H5.H5Gclose(gid);} catch (Exception ex) {} err.printStackTrace(); fail("H5.H5Gget_info: " + err); } assertNotNull(info); try {H5.H5Gclose(gid);} catch (Exception ex) {} } @Test(expected = NullPointerException.class) public void testH5Gget_info_by_name_null() throws Throwable { H5.H5Gget_info_by_name(-1, null, HDF5Constants.H5P_DEFAULT); } @Test(expected = HDF5LibraryException.class) public void testH5Gget_info_by_name_invalid() throws Throwable { H5.H5Gget_info_by_name(-1, "/testH5Gcreate", HDF5Constants.H5P_DEFAULT); } @Test(expected = HDF5LibraryException.class) public void testH5Gget_info_by_name_not_exists() throws Throwable { H5.H5Gget_info_by_name(H5fid, "/testH5Gcreate", HDF5Constants.H5P_DEFAULT); } @Test public void testH5Gget_info_by_name() { H5G_info_t info = null; int gid = _createGroup(H5fid, "/testH5Gcreate"); assertTrue(gid > 0); try { info = H5.H5Gget_info_by_name(gid, "/testH5Gcreate", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { try {H5.H5Gclose(gid);} catch (Exception ex) {} err.printStackTrace(); fail("H5.H5Gget_info_by_name: " + err); } assertNotNull(info); try {H5.H5Gclose(gid);} catch (Exception ex) {} } @Test public void testH5Gget_info_by_name_fileid() { H5G_info_t info = null; int gid = _createGroup(H5fid, "/testH5Gcreate"); assertTrue(gid > 0); try {H5.H5Gclose(gid);} catch (Exception ex) {} try { info = H5.H5Gget_info_by_name(H5fid, "/testH5Gcreate", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { try {H5.H5Gclose(gid);} catch (Exception ex) {} err.printStackTrace(); fail("H5.H5Gget_info_by_name: " + err); } assertNotNull(info); try {H5.H5Gclose(gid);} catch (Exception ex) {} } @Test(expected = NullPointerException.class) public void testH5Gget_info_by_idx_null() throws Throwable { H5.H5Gget_info_by_idx(-1, null, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5_ITER_INC, 1, HDF5Constants.H5P_DEFAULT); } @Test(expected = HDF5LibraryException.class) public void testH5Gget_info_by_idx_invalid() throws Throwable { H5.H5Gget_info_by_idx(-1, "/testH5Gcreate", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5_ITER_INC, 1, HDF5Constants.H5P_DEFAULT); } @Test(expected = HDF5LibraryException.class) public void testH5Gget_info_by_idx_not_exists() throws Throwable { H5.H5Gget_info_by_idx(H5fid, "/testH5Gcreate", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, 1, HDF5Constants.H5P_DEFAULT); } @Test public void testH5Gget_info_by_idx() { H5G_info_t info = null; int gid = _createGroup(H5fid, "/testH5Gcreate"); assertTrue(gid > 0); try { info = H5.H5Gget_info_by_idx(gid, "/", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, 0, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gget_info_by_idx: " + err); } assertNotNull(info); try {H5.H5Gclose(gid);} catch (Exception ex) {} } @Test public void testH5Gget_info_by_idx_fileid() { H5G_info_t info = null; int gid = _createGroup(H5fid, "/testH5Gcreate"); assertTrue(gid > 0); try {H5.H5Gclose(gid);} catch (Exception ex) {} try { info = H5.H5Gget_info_by_idx(H5fid, "/", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, 0, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gget_info_by_idx: " + err); } assertNotNull(info); } } libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/TestH5Giterate.java000066400000000000000000000077341256564762100261340ustar00rootroot00000000000000package test.hdf5lib; import static org.junit.Assert.assertNotNull; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.HDF5Constants; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import ncsa.hdf.hdf5lib.structs.H5G_info_t; import org.junit.After; import org.junit.Before; import org.junit.Test; @SuppressWarnings("all") public class TestH5Giterate { private static final String H5_FILE = "sourceTest/java/test/hdf5lib/h5ex_g_iterate.hdf"; int H5fid = -1; private final int _openGroup(int fid, String name) { int gid = -1; try { gid = H5.H5Gopen(fid, name, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { gid = -1; err.printStackTrace(); fail("H5.H5Gcreate: " + err); } return gid; } @Before public void openH5file() throws HDF5LibraryException, NullPointerException { assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0); try { H5fid = H5.H5Fopen(H5_FILE, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Fopen: openH5file: " + err); } } @After public void deleteH5file() throws HDF5LibraryException { if (H5fid > 0) { try {H5.H5Fclose(H5fid);} catch (Exception ex) {} } } @Test public void testH5Gget_obj_info_all() { H5G_info_t info = null; int gid = _openGroup(H5fid, "/"); try { info = H5.H5Gget_info(gid); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gget_info: " + err); } try { H5.H5Gclose(gid); } catch (Exception ex) { } assertNotNull(info); assertTrue("number of links is empty", info.nlinks > 0); String objNames[] = new String[(int) info.nlinks]; int objTypes[] = new int[(int) info.nlinks]; int lnkTypes[] = new int[(int) info.nlinks]; long objRefs[] = new long[(int) info.nlinks]; int names_found = 0; try { names_found = H5.H5Gget_obj_info_all(H5fid, "/", objNames, objTypes, lnkTypes, objRefs, HDF5Constants.H5_INDEX_NAME); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gget_obj_info_all: " + err); } assertTrue("number found[" + names_found + "] different than expected[" + objNames.length + "]", names_found == objNames.length); for (int i = 0; i < objNames.length; i++) { assertNotNull("name #" + i + " does not exist", objNames[i]); assertTrue(objNames[i].length() > 0); if (objTypes[i]==HDF5Constants.H5O_TYPE_GROUP) { assertTrue("Group is index: "+i + " ",i==2); assertTrue("Group is : "+objNames[i] + " ",objNames[i].compareToIgnoreCase("G1")==0); } else if (objTypes[i]==HDF5Constants.H5O_TYPE_DATASET) { assertTrue("Dataset is index: "+i + " ",(i==0)||(i==3)); if(i==0) assertTrue("Dataset is : "+objNames[i] + " ",objNames[i].compareToIgnoreCase("DS1")==0); else assertTrue("Dataset is : "+objNames[i] + " ",objNames[i].compareToIgnoreCase("L1")==0); } else if (objTypes[i]==HDF5Constants.H5O_TYPE_NAMED_DATATYPE) { assertTrue("Datatype is index: "+i + " ",i==1); assertTrue("Datatype is : "+objNames[i] + " ",objNames[i].compareToIgnoreCase("DT1")==0); } else { fail(" Unknown at index: " + i + " " + objNames[i]); } } } } libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/TestH5Lbasic.java000066400000000000000000000352371256564762100255640ustar00rootroot00000000000000package test.hdf5lib; import static org.junit.Assert.assertFalse; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import java.util.ArrayList; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.HDF5Constants; import ncsa.hdf.hdf5lib.callbacks.H5L_iterate_cb; import ncsa.hdf.hdf5lib.callbacks.H5L_iterate_t; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import ncsa.hdf.hdf5lib.structs.H5L_info_t; import org.junit.After; import org.junit.Before; import org.junit.Test; @SuppressWarnings("all") public class TestH5Lbasic { private static final String H5_FILE = "sourceTest/java/test/hdf5lib/h5ex_g_iterate.hdf"; int H5fid = -1; @Before public void openH5file() throws HDF5LibraryException, NullPointerException { assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0); try { H5fid = H5.H5Fopen(H5_FILE, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Fopen: openH5file: " + err); } } @After public void closeH5file() throws HDF5LibraryException { if (H5fid > 0) { try {H5.H5Fclose(H5fid);} catch (Exception ex) {} } } @Test public void testH5Lexists() { boolean link_exists = false; try { link_exists = H5.H5Lexists(H5fid, "None", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lexists: " + err); } assertFalse("H5Lexists ",link_exists); try { link_exists = H5.H5Lexists(H5fid, "DS1", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lexists: " + err); } assertTrue("H5Lexists ",link_exists); try { link_exists = H5.H5Lexists(H5fid, "G1/DS2", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lexists: " + err); } assertTrue("H5Lexists ",link_exists); } @Test(expected = HDF5LibraryException.class) public void testH5Lget_info_not_exist() throws Throwable { H5.H5Lget_info(H5fid, "None", HDF5Constants.H5P_DEFAULT); } @Test public void testH5Lget_info_dataset() { H5L_info_t link_info = null; try { link_info = H5.H5Lget_info(H5fid, "DS1", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lget_info: " + err); } assertFalse("H5Lget_info ",link_info==null); assertTrue("H5Lget_info link type",link_info.type==HDF5Constants.H5L_TYPE_HARD); } @Test public void testH5Lget_info_hardlink() { H5L_info_t link_info = null; try { link_info = H5.H5Lget_info(H5fid, "L1", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lget_info: " + err); } assertFalse("H5Lget_info ",link_info==null); assertTrue("H5Lget_info link type",link_info.type==HDF5Constants.H5L_TYPE_HARD); assertTrue("Link Address ",link_info.address_val_size>0); } @Test(expected = HDF5LibraryException.class) public void testH5Lget_info_by_idx_name_not_exist_name() throws Throwable { H5.H5Lget_info_by_idx(H5fid, "None", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, 0, HDF5Constants.H5P_DEFAULT); } @Test(expected = HDF5LibraryException.class) public void testH5Lget_info_by_idx_name_not_exist_create() throws Throwable { H5.H5Lget_info_by_idx(H5fid, "None", HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, 0, HDF5Constants.H5P_DEFAULT); } @Test(expected = HDF5LibraryException.class) public void testH5Lget_info_by_idx_not_exist_name() throws Throwable { H5.H5Lget_info_by_idx(H5fid, "/", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, 5, HDF5Constants.H5P_DEFAULT); } @Test(expected = HDF5LibraryException.class) public void testH5Lget_info_by_idx_not_exist_create() throws Throwable { H5.H5Lget_info_by_idx(H5fid, "/", HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, 5, HDF5Constants.H5P_DEFAULT); } @Test public void testH5Lget_info_by_idx_n0() { H5L_info_t link_info = null; H5L_info_t link_info2 = null; try { link_info = H5.H5Lget_info_by_idx(H5fid, "/", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, 0, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lget_info_by_idx: " + err); } assertFalse("H5Lget_info_by_idx ",link_info==null); assertTrue("H5Lget_info_by_idx link type",link_info.type==HDF5Constants.H5L_TYPE_HARD); try { link_info2 = H5.H5Lget_info(H5fid, "DS1", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lget_info: " + err); } assertTrue("Link Address ",link_info.address_val_size==link_info2.address_val_size); } @Test public void testH5Lget_info_by_idx_n3() { H5L_info_t link_info = null; H5L_info_t link_info2 = null; try { link_info = H5.H5Lget_info_by_idx(H5fid, "/", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, 3, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lget_info_by_idx: " + err); } assertFalse("H5Lget_info_by_idx ",link_info==null); assertTrue("H5Lget_info_by_idx link type",link_info.type==HDF5Constants.H5L_TYPE_HARD); try { link_info2 = H5.H5Lget_info(H5fid, "L1", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lget_info: " + err); } assertTrue("Link Address ",link_info.address_val_size==link_info2.address_val_size); } @Test(expected = HDF5LibraryException.class) public void testH5Lget_name_by_idx_not_exist() throws Throwable { H5.H5Lget_name_by_idx(H5fid, "None", HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, 0, HDF5Constants.H5P_DEFAULT); } @Test public void testH5Lget_name_by_idx_n0() { String link_name = null; try { link_name = H5.H5Lget_name_by_idx(H5fid, "/", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, 0, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lget_name_by_idx: " + err); } assertFalse("H5Lget_name_by_idx ",link_name==null); assertTrue("Link Name ",link_name.compareTo("DS1")==0); } @Test public void testH5Lget_name_by_idx_n3() { String link_name = null; try { link_name = H5.H5Lget_name_by_idx(H5fid, "/", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, 3, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lget_name_by_idx: " + err); } assertFalse("H5Lget_name_by_idx ",link_name==null); assertTrue("Link Name ",link_name.compareTo("L1")==0); } @Test public void testH5Lvisit() { class idata { public String link_name = null; public int link_type = -1; idata(String name, int type) { this.link_name = name; this.link_type = type; } } class H5L_iter_data implements H5L_iterate_t { public ArrayList iterdata = new ArrayList(); } H5L_iterate_t iter_data = new H5L_iter_data(); class H5L_iter_callback implements H5L_iterate_cb { public int callback(int group, String name, H5L_info_t info, H5L_iterate_t op_data) { idata id = new idata(name, info.type); ((H5L_iter_data)op_data).iterdata.add(id); return 0; } } H5L_iterate_cb iter_cb = new H5L_iter_callback(); try { H5.H5Lvisit(H5fid, HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, iter_cb, iter_data); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lvisit: " + err); } assertFalse("H5Lvisit ",((H5L_iter_data)iter_data).iterdata.isEmpty()); assertTrue("H5Lvisit "+((H5L_iter_data)iter_data).iterdata.size(),((H5L_iter_data)iter_data).iterdata.size()==5); assertTrue("H5Lvisit "+(((H5L_iter_data)iter_data).iterdata.get(0)).link_name,(((H5L_iter_data)iter_data).iterdata.get(0)).link_name.compareToIgnoreCase("DS1")==0); assertTrue("H5Lvisit "+(((H5L_iter_data)iter_data).iterdata.get(1)).link_name,(((H5L_iter_data)iter_data).iterdata.get(1)).link_name.compareToIgnoreCase("DT1")==0); assertTrue("H5Lvisit "+(((H5L_iter_data)iter_data).iterdata.get(2)).link_name,(((H5L_iter_data)iter_data).iterdata.get(2)).link_name.compareToIgnoreCase("G1")==0); assertTrue("H5Lvisit "+(((H5L_iter_data)iter_data).iterdata.get(3)).link_name,(((H5L_iter_data)iter_data).iterdata.get(3)).link_name.compareToIgnoreCase("G1/DS2")==0); assertTrue("H5Lvisit "+(((H5L_iter_data)iter_data).iterdata.get(4)).link_name,(((H5L_iter_data)iter_data).iterdata.get(4)).link_name.compareToIgnoreCase("L1")==0); } @Test public void testH5Lvisit_by_name() { class idata { public String link_name = null; public int link_type = -1; idata(String name, int type) { this.link_name = name; this.link_type = type; } } class H5L_iter_data implements H5L_iterate_t { public ArrayList iterdata = new ArrayList(); } H5L_iterate_t iter_data = new H5L_iter_data(); class H5L_iter_callback implements H5L_iterate_cb { public int callback(int group, String name, H5L_info_t info, H5L_iterate_t op_data) { idata id = new idata(name, info.type); ((H5L_iter_data)op_data).iterdata.add(id); return 0; } } H5L_iterate_cb iter_cb = new H5L_iter_callback(); try { H5.H5Lvisit_by_name(H5fid, "G1", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, iter_cb, iter_data, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lvisit_by_name: " + err); } assertFalse("H5Lvisit_by_name ",((H5L_iter_data)iter_data).iterdata.isEmpty()); assertTrue("H5Lvisit_by_name "+((H5L_iter_data)iter_data).iterdata.size(),((H5L_iter_data)iter_data).iterdata.size()==1); assertTrue("H5Lvisit_by_name "+(((H5L_iter_data)iter_data).iterdata.get(0)).link_name,(((H5L_iter_data)iter_data).iterdata.get(0)).link_name.compareToIgnoreCase("DS2")==0); } @Test public void testH5Literate() { class idata { public String link_name = null; public int link_type = -1; idata(String name, int type) { this.link_name = name; this.link_type = type; } } class H5L_iter_data implements H5L_iterate_t { public ArrayList iterdata = new ArrayList(); } H5L_iterate_t iter_data = new H5L_iter_data(); class H5L_iter_callback implements H5L_iterate_cb { public int callback(int group, String name, H5L_info_t info, H5L_iterate_t op_data) { idata id = new idata(name, info.type); ((H5L_iter_data)op_data).iterdata.add(id); return 0; } } H5L_iterate_cb iter_cb = new H5L_iter_callback(); try { H5.H5Literate(H5fid, HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, 0L, iter_cb, iter_data); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Literate: " + err); } assertFalse("H5Literate ",((H5L_iter_data)iter_data).iterdata.isEmpty()); assertTrue("H5Literate "+((H5L_iter_data)iter_data).iterdata.size(),((H5L_iter_data)iter_data).iterdata.size()==4); assertTrue("H5Literate "+(((H5L_iter_data)iter_data).iterdata.get(0)).link_name,(((H5L_iter_data)iter_data).iterdata.get(0)).link_name.compareToIgnoreCase("DS1")==0); assertTrue("H5Literate "+(((H5L_iter_data)iter_data).iterdata.get(1)).link_name,(((H5L_iter_data)iter_data).iterdata.get(1)).link_name.compareToIgnoreCase("DT1")==0); assertTrue("H5Literate "+((idata)((H5L_iter_data)iter_data).iterdata.get(2)).link_name,(((H5L_iter_data)iter_data).iterdata.get(2)).link_name.compareToIgnoreCase("G1")==0); assertTrue("H5Literate "+((idata)((H5L_iter_data)iter_data).iterdata.get(3)).link_name,((idata)((H5L_iter_data)iter_data).iterdata.get(3)).link_name.compareToIgnoreCase("L1")==0); } @Test public void testH5Literate_by_name() { class idata { public String link_name = null; public int link_type = -1; idata(String name, int type) { this.link_name = name; this.link_type = type; } } class H5L_iter_data implements H5L_iterate_t { public ArrayList iterdata = new ArrayList(); } H5L_iterate_t iter_data = new H5L_iter_data(); class H5L_iter_callback implements H5L_iterate_cb { public int callback(int group, String name, H5L_info_t info, H5L_iterate_t op_data) { idata id = new idata(name, info.type); ((H5L_iter_data)op_data).iterdata.add(id); return 0; } } H5L_iterate_cb iter_cb = new H5L_iter_callback(); try { H5.H5Literate_by_name(H5fid, "G1", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, 0L, iter_cb, iter_data, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Literate_by_name: " + err); } assertFalse("H5Literate_by_name ",((H5L_iter_data)iter_data).iterdata.isEmpty()); assertTrue("H5Literate_by_name "+((H5L_iter_data)iter_data).iterdata.size(),((H5L_iter_data)iter_data).iterdata.size()==1); assertTrue("H5Literate_by_name "+((idata)((H5L_iter_data)iter_data).iterdata.get(0)).link_name,((idata)((H5L_iter_data)iter_data).iterdata.get(0)).link_name.compareToIgnoreCase("DS2")==0); } } libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/TestH5Lcreate.java000066400000000000000000001046541256564762100257460ustar00rootroot00000000000000package test.hdf5lib; import static org.junit.Assert.assertFalse; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import java.io.File; import java.util.ArrayList; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.HDF5Constants; import ncsa.hdf.hdf5lib.callbacks.H5L_iterate_cb; import ncsa.hdf.hdf5lib.callbacks.H5L_iterate_t; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import ncsa.hdf.hdf5lib.structs.H5L_info_t; import org.junit.After; import org.junit.Before; import org.junit.Test; @SuppressWarnings("all") public class TestH5Lcreate { private static final String H5_EXTFILE = "test/hdf5lib/h5ex_g_iterate.hdf"; private static final String H5_FILE = "test.h5"; private static final int DIM_X = 4; private static final int DIM_Y = 6; int H5fcpl = -1; int H5fid = -1; int H5dsid = -1; int H5did1 = -1; int H5did2 = -1; int H5gcpl = -1; int H5gid = -1; long[] H5dims = { DIM_X, DIM_Y }; private final void _deleteFile(String filename) { File file = new File(filename); if (file.exists()) { try { file.delete(); } catch (Exception e) { e.printStackTrace(); } } } private final int _createDataset(int fid, int dsid, String name, int dapl) { int did = -1; try { did = H5.H5Dcreate(fid, name, HDF5Constants.H5T_STD_I32BE, dsid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, dapl); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Dcreate: " + err); } assertTrue("TestH5L._createDataset: ",did > 0); return did; } private final int _createGroup(int fid, String name) { int gid = -1; try { H5gcpl = HDF5Constants.H5P_DEFAULT; gid = H5.H5Gcreate(fid, name, HDF5Constants.H5P_DEFAULT, H5gcpl, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gcreate: " + err); } assertTrue("TestH5L._createGroup: ",gid > 0); return gid; } private final void _createHardLink(int fid, int cid, String curname, int did, String dstname, int lcpl, int lapl) { boolean link_exists = false; try { H5.H5Lcreate_hard(cid, curname, did, dstname, lcpl, lapl); H5.H5Fflush(fid, HDF5Constants.H5F_SCOPE_LOCAL); link_exists = H5.H5Lexists(did, dstname, lapl); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lcreate_hard: " + err); } assertTrue("TestH5L._createHardLink ", link_exists); } private final void _createSoftLink(int fid, String curname, int did, String dstname, int lcpl, int lapl) { boolean link_exists = false; try { H5.H5Lcreate_soft(curname, did, dstname, lcpl, lapl); H5.H5Fflush(fid, HDF5Constants.H5F_SCOPE_LOCAL); link_exists = H5.H5Lexists(did, dstname, lapl); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lcreate_soft: " + err); } assertTrue("TestH5L._createSoftLink ", link_exists); } private final void _createExternalLink(int fid, String ext_filename, String curname, int did, String dstname, int lcpl, int lapl) { boolean link_exists = false; try { H5.H5Lcreate_external(ext_filename, curname, did, dstname, lcpl, lapl); H5.H5Fflush(fid, HDF5Constants.H5F_SCOPE_LOCAL); link_exists = H5.H5Lexists(did, dstname, lapl); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lcreate_external: " + err); } assertTrue("TestH5L._createExternalLink ", link_exists); } @Before public void createH5file() throws NullPointerException, HDF5Exception { assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0); try { H5fcpl = H5.H5Pcreate(HDF5Constants.H5P_FILE_CREATE); H5.H5Pset_link_creation_order(H5fcpl, HDF5Constants.H5P_CRT_ORDER_TRACKED+HDF5Constants.H5P_CRT_ORDER_INDEXED); H5fid = H5.H5Fcreate(H5_FILE, HDF5Constants.H5F_ACC_TRUNC, H5fcpl, HDF5Constants.H5P_DEFAULT); H5dsid = H5.H5Screate_simple(2, H5dims, null); H5did1 = _createDataset(H5fid, H5dsid, "DS1", HDF5Constants.H5P_DEFAULT); H5gid = _createGroup(H5fid, "/G1"); H5did2 = _createDataset(H5gid, H5dsid, "DS2", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("TestH5L.createH5file: " + err); } assertTrue("TestH5L.createH5file: H5.H5Fcreate: ",H5fid > 0); assertTrue("TestH5L.createH5file: H5.H5Screate_simple: ",H5dsid > 0); assertTrue("TestH5L.createH5file: H5.H5Gcreate: ",H5gid > 0); H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); } @After public void deleteH5file() throws HDF5LibraryException { if (H5gid > 0) try {H5.H5Gclose(H5gid);} catch (Exception ex) {} if (H5gcpl > 0) try {H5.H5Pclose(H5gcpl);} catch (Exception ex) {} if (H5did2 > 0) try {H5.H5Dclose(H5did2);} catch (Exception ex) {} if (H5dsid > 0) try {H5.H5Sclose(H5dsid);} catch (Exception ex) {} if (H5did1 > 0) try {H5.H5Dclose(H5did1);} catch (Exception ex) {} if (H5fid > 0) try {H5.H5Fclose(H5fid);} catch (Exception ex) {} if (H5fcpl > 0) try {H5.H5Pclose(H5fcpl);} catch (Exception ex) {} _deleteFile(H5_FILE); } @Test public void testH5Lget_info_by_idx_n0_create() { H5L_info_t link_info = null; try { int order = H5.H5Pget_link_creation_order(H5fcpl); assertTrue("creation order :"+order, order == HDF5Constants.H5P_CRT_ORDER_TRACKED+HDF5Constants.H5P_CRT_ORDER_INDEXED); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lget_info_by_idx_n0_create:H5Pget_link_creation_order " + err); } try { link_info = H5.H5Lget_info_by_idx(H5fid, "/", HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, 0, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lget_info_by_idx: " + err); } assertFalse("H5Lget_info_by_idx ", link_info==null); assertTrue("H5Lget_info_by_idx link type", link_info.type==HDF5Constants.H5L_TYPE_HARD); } @Test public void testH5Lget_info_by_idx_n1_create() { H5L_info_t link_info = null; try { int order = H5.H5Pget_link_creation_order(H5fcpl); assertTrue("creation order :"+order, order == HDF5Constants.H5P_CRT_ORDER_TRACKED+HDF5Constants.H5P_CRT_ORDER_INDEXED); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lget_info_by_idx_n1_create:H5Pget_link_creation_order " + err); } try { link_info = H5.H5Lget_info_by_idx(H5fid, "/", HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, 1, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lget_info_by_idx: " + err); } assertFalse("H5Lget_info_by_idx ", link_info==null); assertTrue("H5Lget_info_by_idx link type", link_info.type==HDF5Constants.H5L_TYPE_HARD); } @Test(expected = HDF5LibraryException.class) public void testH5Lcreate_hard_cur_not_exists() throws Throwable { H5.H5Lcreate_hard(H5fid, "None", H5fid, "DS1", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); } @Test public void testH5Lcreate_hard() { try { H5.H5Lcreate_hard(H5fid, "DS1", H5fid, "L1", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); boolean link_exists = H5.H5Lexists(H5fid, "L1", HDF5Constants.H5P_DEFAULT); assertTrue("testH5Lcreate_hard:H5Lexists ", link_exists); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lexists: " + err); } } @Test(expected = HDF5LibraryException.class) public void testH5Lcreate_hard_dst_link_exists() throws Throwable { _createHardLink(H5fid, H5fid, "/G1/DS2", H5fid, "L1", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); H5.H5Lcreate_hard(H5fid, "L1", H5fid, "/G1/DS2", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); } @Test public void testH5Ldelete_hard_link() { _createHardLink(H5fid, H5fid, "/G1/DS2", H5fid, "L1", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); try { H5.H5Ldelete(H5fid, "L1", HDF5Constants.H5P_DEFAULT); H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); boolean link_exists = H5.H5Lexists(H5fid, "L1", HDF5Constants.H5P_DEFAULT); assertFalse("testH5Lcreate_hard:H5Lexists ", link_exists); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lexists: " + err); } } @Test public void testH5Lcreate_soft() { try { H5.H5Lcreate_soft("DS1", H5fid, "L1", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); boolean link_exists = H5.H5Lexists(H5fid, "L1", HDF5Constants.H5P_DEFAULT); assertTrue("testH5Lcreate_soft:H5Lexists ", link_exists); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lexists: " + err); } } @Test(expected = HDF5LibraryException.class) public void testH5Lcreate_soft_dst_link_exists() throws Throwable { _createSoftLink(H5fid, "/G1/DS2", H5fid, "L1", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); H5.H5Lcreate_soft("L1", H5fid, "/G1/DS2", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); } @Test public void testH5Ldelete_soft_link() { _createSoftLink(H5fid, "/G1/DS2", H5fid, "L1", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); try { H5.H5Ldelete(H5fid, "L1", HDF5Constants.H5P_DEFAULT); H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); boolean link_exists = H5.H5Lexists(H5fid, "L1", HDF5Constants.H5P_DEFAULT); assertFalse("testH5Lcreate_soft:H5Lexists ", link_exists); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lexists: " + err); } } @Test public void testH5Lget_info_softlink() { H5L_info_t link_info = null; _createSoftLink(H5fid, "/G1/DS2", H5fid, "L1", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); try { link_info = H5.H5Lget_info(H5fid, "L1", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lget_info: " + err); } assertFalse("H5Lget_info ", link_info==null); assertTrue("H5Lget_info link type", link_info.type==HDF5Constants.H5L_TYPE_SOFT); assertTrue("Link Address ", link_info.address_val_size>0); } @Test public void testH5Lget_val_soft() { String[] link_value = {null, null}; int link_type = -1; _createSoftLink(H5fid, "/G1/DS2", H5fid, "L1", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); try { link_type = H5.H5Lget_val(H5fid, "L1", link_value, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lget_val: " + err); } assertTrue("Link Type", link_type == HDF5Constants.H5L_TYPE_SOFT); assertFalse("H5Lget_val ", link_value[0]==null); assertTrue("Link Value ", link_value[0].compareTo("/G1/DS2")==0); } @Test public void testH5Lcreate_soft_dangle() { try { H5.H5Lcreate_soft("DS3", H5fid, "L2", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); boolean link_exists = H5.H5Lexists(H5fid, "L2", HDF5Constants.H5P_DEFAULT); assertTrue("testH5Lcreate_soft:H5Lexists ", link_exists); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lexists: " + err); } } @Test public void testH5Ldelete_soft_link_dangle() { _createSoftLink(H5fid, "DS3", H5fid, "L2", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); try { H5.H5Ldelete(H5fid, "L2", HDF5Constants.H5P_DEFAULT); H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); boolean link_exists = H5.H5Lexists(H5fid, "L2", HDF5Constants.H5P_DEFAULT); assertFalse("testH5Lcreate_soft:H5Lexists ", link_exists); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lexists: " + err); } } @Test public void testH5Lget_info_softlink_dangle() { H5L_info_t link_info = null; _createSoftLink(H5fid, "DS3", H5fid, "L2", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); try { link_info = H5.H5Lget_info(H5fid, "L2", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lget_info: " + err); } assertFalse("H5Lget_info ", link_info==null); assertTrue("H5Lget_info link type", link_info.type==HDF5Constants.H5L_TYPE_SOFT); assertTrue("Link Address ", link_info.address_val_size>0); } @Test public void testH5Lget_val_dangle() { String[] link_value = {null,null}; int link_type = -1; _createSoftLink(H5fid, "DS3", H5fid, "L2", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); try { link_type = H5.H5Lget_val(H5fid, "L2", link_value, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lget_val: " + err); } assertTrue("Link Type", link_type == HDF5Constants.H5L_TYPE_SOFT); assertFalse("H5Lget_val ", link_value[0]==null); assertTrue("Link Value ", link_value[0].compareTo("DS3")==0); } @Test public void testH5Lcreate_external() { try { H5.H5Lcreate_external(H5_EXTFILE, "DT1", H5fid, "L1", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); boolean link_exists = H5.H5Lexists(H5fid, "L1", HDF5Constants.H5P_DEFAULT); assertTrue("testH5Lcreate_external:H5Lexists ", link_exists); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lexists: " + err); } } @Test public void testH5Lget_info_externallink() { H5L_info_t link_info = null; _createExternalLink(H5fid, H5_EXTFILE, "DT1", H5fid, "L1", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); try { link_info = H5.H5Lget_info(H5fid, "L1", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lget_info: " + err); } assertFalse("H5Lget_info ", link_info==null); assertTrue("H5Lget_info link type", link_info.type==HDF5Constants.H5L_TYPE_EXTERNAL); assertTrue("Link Address ", link_info.address_val_size>0); } @Test public void testH5Lget_val_external(){ String[] link_value = {null,null}; int link_type = -1; _createExternalLink(H5fid, H5_EXTFILE, "DT1", H5fid, "L1", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); try { link_type = H5.H5Lget_val(H5fid, "L1", link_value, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lget_val: " + err); } assertTrue("Link Type", link_type == HDF5Constants.H5L_TYPE_EXTERNAL); assertFalse("H5Lget_val ", link_value[0]==null); assertFalse("H5Lget_val ", link_value[1]==null); assertTrue("Link Value ", link_value[0].compareTo("DT1")==0); } @Test(expected = HDF5LibraryException.class) public void testH5Lcopy_cur_not_exists() throws Throwable { H5.H5Lcopy(H5fid, "None", H5fid, "DS1", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); } @Test public void testH5Lcopy() { try { H5.H5Lcopy(H5fid, "DS1", H5fid, "CPY1", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); boolean link_exists = H5.H5Lexists(H5fid, "CPY1", HDF5Constants.H5P_DEFAULT); assertTrue("testH5Lcopy:H5Lexists ", link_exists); } catch (Throwable err) { err.printStackTrace(); fail("testH5Lcopy:H5Lexists: " + err); } } @Test(expected = HDF5LibraryException.class) public void testH5Lcopy_dst_link_exists() throws Throwable { _createHardLink(H5fid, H5fid, "/G1/DS2", H5fid, "CPY1", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); H5.H5Lcopy(H5fid, "CPY1", H5fid, "/G1/DS2", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); } @Test(expected = HDF5LibraryException.class) public void testH5Lmove_cur_not_exists() throws Throwable { H5.H5Lmove(H5fid, "None", H5fid, "DS1", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); } @Test public void testH5Lmove() { try { H5.H5Lmove(H5fid, "DS1", H5fid, "CPY1", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); boolean link_exists = H5.H5Lexists(H5fid, "CPY1", HDF5Constants.H5P_DEFAULT); assertTrue("testH5Lmove:H5Lexists ", link_exists); link_exists = H5.H5Lexists(H5fid, "DS1", HDF5Constants.H5P_DEFAULT); assertFalse("testH5Lmove:H5Lexists ", link_exists); } catch (Throwable err) { err.printStackTrace(); fail("testH5Lmove:H5Lexists: " + err); } } @Test(expected = HDF5LibraryException.class) public void testH5Lmove_dst_link_exists() throws Throwable { _createHardLink(H5fid, H5fid, "/G1/DS2", H5fid, "CPY1", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); H5.H5Lmove(H5fid, "CPY1", H5fid, "/G1/DS2", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); } @Test(expected = HDF5LibraryException.class) public void testH5Lget_val_by_idx_not_exist_name() throws Throwable { String[] link_value = {null,null}; H5.H5Lget_val_by_idx(H5fid, "None", HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, 0, link_value, HDF5Constants.H5P_DEFAULT); } @Test(expected = HDF5LibraryException.class) public void testH5Lget_val_by_idx_not_exist_create() throws Throwable { String[] link_value = {null,null}; H5.H5Lget_val_by_idx(H5fid, "None", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, 0, link_value, HDF5Constants.H5P_DEFAULT); } @Test public void testH5Lget_val_by_idx_n2_name() { H5L_info_t link_info = null; String[] link_value = {null,null}; int link_type = -1; _createSoftLink(H5fid, "/G1/DS2", H5fid, "LS", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); try { link_info = H5.H5Lget_info_by_idx(H5fid, "/", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, 2, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lget_info_by_idx: " + err); } assertFalse("testH5Lget_val_by_idx_n2 ",link_info==null); assertTrue("testH5Lget_val_by_idx_n2 link type", link_info.type==HDF5Constants.H5L_TYPE_SOFT); try { link_type = H5.H5Lget_val_by_idx(H5fid, "/", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, 2, link_value, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lget_val_by_idx: " + err); } assertTrue("Link Type", link_type == HDF5Constants.H5L_TYPE_SOFT); assertFalse("testH5Lget_val_by_idx_n2 ", link_value[0]==null); assertTrue("testH5Lget_val_by_idx_n2 Link Value ", link_value[0].compareTo("/G1/DS2")==0); } @Test public void testH5Lget_val_by_idx_n2_create() { H5L_info_t link_info = null; String[] link_value = {null,null}; int link_type = -1; try { int order = H5.H5Pget_link_creation_order(H5fcpl); assertTrue("creation order :"+order, order == HDF5Constants.H5P_CRT_ORDER_TRACKED+HDF5Constants.H5P_CRT_ORDER_INDEXED); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lget_val_by_idx_n2_create: H5Pget_link_creation_order " + err); } _createSoftLink(H5fid, "/G1/DS2", H5fid, "LS", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); try { link_info = H5.H5Lget_info_by_idx(H5fid, "/", HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, 2, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lget_info_by_idx: " + err); } assertFalse("testH5Lget_val_by_idx_n2 ", link_info==null); assertTrue("testH5Lget_val_by_idx_n2 link type", link_info.type==HDF5Constants.H5L_TYPE_SOFT); try { link_type = H5.H5Lget_val_by_idx(H5fid, "/", HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, 2, link_value, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lget_val_by_idx: " + err); } assertTrue("Link Type", link_type == HDF5Constants.H5L_TYPE_SOFT); assertFalse("testH5Lget_val_by_idx_n2 ", link_value[0]==null); assertTrue("testH5Lget_val_by_idx_n2 Link Value ", link_value[0].compareTo("/G1/DS2")==0); } @Test public void testH5Lget_val_by_idx_external_name() { H5L_info_t link_info = null; String[] link_value = {null,null}; int link_type = -1; _createExternalLink(H5fid, H5_EXTFILE, "DT1", H5fid, "LE", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); try { link_info = H5.H5Lget_info_by_idx(H5fid, "/", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, 2, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lget_info_by_idx: " + err); } assertFalse("testH5Lget_val_by_idx_ext ", link_info==null); assertTrue("testH5Lget_val_by_idx_ext link type "+link_info.type, link_info.type==HDF5Constants.H5L_TYPE_EXTERNAL); try { link_type = H5.H5Lget_val_by_idx(H5fid, "/", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, 2, link_value, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lget_val_by_idx: " + err); } assertTrue("Link Type", link_type == HDF5Constants.H5L_TYPE_EXTERNAL); assertFalse("testH5Lget_val_by_idx_ext ", link_value[0]==null); assertFalse("testH5Lget_val_by_idx_ext ", link_value[1]==null); assertTrue("testH5Lget_val_by_idx_ext Link Value ", link_value[0].compareTo("DT1")==0); } @Test public void testH5Lget_val_by_idx_external_create() { H5L_info_t link_info = null; String[] link_value = {null,null}; int link_type = -1; _createExternalLink(H5fid, H5_EXTFILE, "DT1", H5fid, "LE", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); try { link_info = H5.H5Lget_info_by_idx(H5fid, "/", HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, 2, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lget_info_by_idx: " + err); } assertFalse("testH5Lget_val_by_idx_ext ", link_info==null); assertTrue("testH5Lget_val_by_idx_ext link type "+link_info.type, link_info.type==HDF5Constants.H5L_TYPE_EXTERNAL); try { link_type = H5.H5Lget_val_by_idx(H5fid, "/", HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, 2, link_value, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lget_val_by_idx: " + err); } assertTrue("Link Type", link_type == HDF5Constants.H5L_TYPE_EXTERNAL); assertFalse("testH5Lget_val_by_idx_ext ", link_value[0]==null); assertFalse("testH5Lget_val_by_idx_ext ", link_value[1]==null); assertTrue("testH5Lget_val_by_idx_ext Link Value ", link_value[0].compareTo("DT1")==0); } @Test(expected = HDF5LibraryException.class) public void testH5Ldelete_by_idx_not_exist_name() throws Throwable { H5.H5Ldelete_by_idx(H5fid, "None", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, 0, HDF5Constants.H5P_DEFAULT); } @Test(expected = HDF5LibraryException.class) public void testH5Ldelete_by_idx_not_exist_create() throws Throwable { H5.H5Ldelete_by_idx(H5fid, "None", HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, 0, HDF5Constants.H5P_DEFAULT); } @Test public void testH5Ldelete_by_idx_n2_name() { H5L_info_t link_info = null; _createSoftLink(H5fid, "/G1/DS2", H5fid, "LS", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); try { link_info = H5.H5Lget_info_by_idx(H5fid, "/", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, 2, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lget_info_by_idx: " + err); } assertFalse("testH5Ldelete_by_idx_n2 ", link_info==null); assertTrue("testH5Ldelete_by_idx_n2 link type", link_info.type==HDF5Constants.H5L_TYPE_SOFT); try { H5.H5Ldelete_by_idx(H5fid, "/", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, 2, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Ldelete_by_idx: " + err); } try { link_info = H5.H5Lget_info_by_idx(H5fid, "/", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, 2, HDF5Constants.H5P_DEFAULT); } catch (HDF5LibraryException err) { link_info = null; } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Ldelete_by_idx: " + err); } assertTrue("testH5Ldelete_by_idx_n2 ",link_info==null); } @Test public void testH5Ldelete_by_idx_n2_create() { H5L_info_t link_info = null; _createSoftLink(H5fid, "/G1/DS2", H5fid, "LS", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); try { link_info = H5.H5Lget_info_by_idx(H5fid, "/", HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, 2, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lget_info_by_idx: " + err); } assertFalse("testH5Ldelete_by_idx_n2 ", link_info==null); assertTrue("testH5Ldelete_by_idx_n2 link type", link_info.type==HDF5Constants.H5L_TYPE_SOFT); try { H5.H5Ldelete_by_idx(H5fid, "/", HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, 2, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Ldelete_by_idx: " + err); } try { link_info = H5.H5Lget_info_by_idx(H5fid, "/", HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, 2, HDF5Constants.H5P_DEFAULT); } catch (HDF5LibraryException err) { link_info = null; } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Ldelete_by_idx: " + err); } assertTrue("testH5Ldelete_by_idx_n2 ",link_info==null); } @Test public void testH5Lvisit_create() { try { int order = H5.H5Pget_link_creation_order(H5fcpl); assertTrue("creation order :"+order, order == HDF5Constants.H5P_CRT_ORDER_TRACKED+HDF5Constants.H5P_CRT_ORDER_INDEXED); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lvisit_create: H5Pget_link_creation_order " + err); } _createHardLink(H5fid, H5fid, "/G1/DS2", H5fid, "CPY1", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); _createExternalLink(H5fid, H5_EXTFILE, "DT1", H5fid, "LE", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); _createSoftLink(H5fid, "/G1/DS2", H5fid, "LS", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); class idata { public String link_name = null; public int link_type = -1; idata(String name, int type) { this.link_name = name; this.link_type = type; } } class H5L_iter_data implements H5L_iterate_t { public ArrayList iterdata = new ArrayList(); } H5L_iterate_t iter_data = new H5L_iter_data(); class H5L_iter_callback implements H5L_iterate_cb { public int callback(int group, String name, H5L_info_t info, H5L_iterate_t op_data) { idata id = new idata(name, info.type); ((H5L_iter_data)op_data).iterdata.add(id); return 0; } } H5L_iterate_cb iter_cb = new H5L_iter_callback(); try { H5.H5Lvisit(H5fid, HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, iter_cb, iter_data); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lvisit: " + err); } assertFalse("H5Lvisit ",((H5L_iter_data)iter_data).iterdata.isEmpty()); assertTrue("H5Lvisit "+((H5L_iter_data)iter_data).iterdata.size(),((H5L_iter_data)iter_data).iterdata.size()==6); assertTrue("H5Lvisit "+((idata)((H5L_iter_data)iter_data).iterdata.get(0)).link_name,((idata)((H5L_iter_data)iter_data).iterdata.get(0)).link_name.compareToIgnoreCase("DS1")==0); assertTrue("H5Lvisit "+((idata)((H5L_iter_data)iter_data).iterdata.get(1)).link_name,((idata)((H5L_iter_data)iter_data).iterdata.get(1)).link_name.compareToIgnoreCase("G1")==0); assertTrue("H5Lvisit "+((idata)((H5L_iter_data)iter_data).iterdata.get(2)).link_name,((idata)((H5L_iter_data)iter_data).iterdata.get(2)).link_name.compareToIgnoreCase("G1/DS2")==0); assertTrue("H5Lvisit "+((idata)((H5L_iter_data)iter_data).iterdata.get(3)).link_name,((idata)((H5L_iter_data)iter_data).iterdata.get(3)).link_name.compareToIgnoreCase("CPY1")==0); assertTrue("H5Lvisit "+((idata)((H5L_iter_data)iter_data).iterdata.get(4)).link_name,((idata)((H5L_iter_data)iter_data).iterdata.get(4)).link_name.compareToIgnoreCase("LE")==0); assertTrue("H5Lvisit "+((idata)((H5L_iter_data)iter_data).iterdata.get(5)).link_name,((idata)((H5L_iter_data)iter_data).iterdata.get(5)).link_name.compareToIgnoreCase("LS")==0); } @Test public void testH5Literate_create() { try { int order = H5.H5Pget_link_creation_order(H5fcpl); assertTrue("creation order :"+order, order == HDF5Constants.H5P_CRT_ORDER_TRACKED+HDF5Constants.H5P_CRT_ORDER_INDEXED); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Literate_create: H5Pget_link_creation_order " + err); } _createHardLink(H5fid, H5fid, "/G1/DS2", H5fid, "CPY1", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); _createExternalLink(H5fid, H5_EXTFILE, "DT1", H5fid, "LE", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); _createSoftLink(H5fid, "/G1/DS2", H5fid, "LS", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); class idata { public String link_name = null; public int link_type = -1; idata(String name, int type) { this.link_name = name; this.link_type = type; } } class H5L_iter_data implements H5L_iterate_t { public ArrayList iterdata = new ArrayList(); } H5L_iterate_t iter_data = new H5L_iter_data(); class H5L_iter_callback implements H5L_iterate_cb { public int callback(int group, String name, H5L_info_t info, H5L_iterate_t op_data) { idata id = new idata(name, info.type); ((H5L_iter_data)op_data).iterdata.add(id); return 0; } } H5L_iterate_cb iter_cb = new H5L_iter_callback(); try { H5.H5Literate(H5fid, HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, 0L, iter_cb, iter_data); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Literate: " + err); } assertFalse("H5Literate ",((H5L_iter_data)iter_data).iterdata.isEmpty()); assertTrue("H5Literate "+((H5L_iter_data)iter_data).iterdata.size(),((H5L_iter_data)iter_data).iterdata.size()==5); assertTrue("H5Literate "+((idata)((H5L_iter_data)iter_data).iterdata.get(0)).link_name,((idata)((H5L_iter_data)iter_data).iterdata.get(0)).link_name.compareToIgnoreCase("DS1")==0); assertTrue("H5Literate "+((idata)((H5L_iter_data)iter_data).iterdata.get(1)).link_name,((idata)((H5L_iter_data)iter_data).iterdata.get(1)).link_name.compareToIgnoreCase("G1")==0); assertTrue("H5Literate "+((idata)((H5L_iter_data)iter_data).iterdata.get(2)).link_name,((idata)((H5L_iter_data)iter_data).iterdata.get(2)).link_name.compareToIgnoreCase("CPY1")==0); assertTrue("H5Literate "+((idata)((H5L_iter_data)iter_data).iterdata.get(3)).link_name,((idata)((H5L_iter_data)iter_data).iterdata.get(3)).link_name.compareToIgnoreCase("LE")==0); assertTrue("H5Literate "+((idata)((H5L_iter_data)iter_data).iterdata.get(4)).link_name,((idata)((H5L_iter_data)iter_data).iterdata.get(4)).link_name.compareToIgnoreCase("LS")==0); } } libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/TestH5Lparams.java000066400000000000000000000154561256564762100257670ustar00rootroot00000000000000package test.hdf5lib; import static org.junit.Assert.assertTrue; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import org.junit.Before; import org.junit.Test; @SuppressWarnings("all") public class TestH5Lparams { @Before public void checkOpenIDs() { assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0); } @Test(expected = HDF5LibraryException.class) public void testH5Lget_val_invalid() throws Throwable { H5.H5Lget_val(-1, "Bogus", null, -1); } @Test(expected = NullPointerException.class) public void testH5Lget_val_null() throws Throwable { H5.H5Lget_val(-1, null, null, 0); } @Test(expected = HDF5LibraryException.class) public void testH5Lexists_invalid() throws Throwable { H5.H5Lexists(-1, "Bogus", -1); } @Test(expected = NullPointerException.class) public void testH5Lexists_null() throws Throwable { H5.H5Lexists(-1, null, 0); } @Test(expected = HDF5LibraryException.class) public void testH5Lget_info_invalid() throws Throwable { H5.H5Lget_info(-1, "Bogus", -1); } @Test(expected = NullPointerException.class) public void testH5Lget_info_null() throws Throwable { H5.H5Lget_info(-1, null, 0); } @Test(expected = HDF5LibraryException.class) public void testH5Lget_info_by_idx_invalid() throws Throwable { H5.H5Lget_info_by_idx(-1, "Bogus", -1, -1, -1L, -1); } @Test(expected = NullPointerException.class) public void testH5Lget_info_by_idx_null() throws Throwable { H5.H5Lget_info_by_idx(-1, null, 0, 0, 0L, 0); } @Test(expected = HDF5LibraryException.class) public void testH5Lget_name_by_idx_invalid() throws Throwable { H5.H5Lget_name_by_idx(-1, "Bogus", -1, -1, -1L, -1); } @Test(expected = NullPointerException.class) public void testH5Lget_name_by_idx_null() throws Throwable { H5.H5Lget_name_by_idx(-1, null, 0, 0, 0L, 0); } @Test(expected = HDF5LibraryException.class) public void testH5Lcreate_hard_invalid() throws Throwable { H5.H5Lcreate_hard(-1, "Bogus", -1, "Bogus", -1, -1); } @Test(expected = NullPointerException.class) public void testH5Lcreate_hard_null_current() throws Throwable { H5.H5Lcreate_hard(-1, null, 0, "Bogus", 0, 0); } @Test(expected = NullPointerException.class) public void testH5Lcreate_hard_null_dest() throws Throwable { H5.H5Lcreate_hard(-1, "Bogus", 0, null, 0, 0); } @Test(expected = HDF5LibraryException.class) public void testH5Ldelete_invalid() throws Throwable { H5.H5Ldelete(-1, "Bogus", -1); } @Test(expected = NullPointerException.class) public void testH5Ldelete_null() throws Throwable { H5.H5Ldelete(-1, null, 0); } @Test(expected = HDF5LibraryException.class) public void testH5Lcreate_soft_invalid() throws Throwable { H5.H5Lcreate_soft( "Bogus", -1, "Bogus", -1, -1); } @Test(expected = NullPointerException.class) public void testH5Lcreate_soft_null_current() throws Throwable { H5.H5Lcreate_soft(null, 0, "Bogus", 0, 0); } @Test(expected = NullPointerException.class) public void testH5Lcreate_soft_null_dest() throws Throwable { H5.H5Lcreate_soft("Bogus", 0, null, 0, 0); } @Test(expected = HDF5LibraryException.class) public void testH5Lcreate_external_invalid() throws Throwable { H5.H5Lcreate_external("PathToFile", "Bogus", -1, "Bogus", -1, -1); } @Test(expected = NullPointerException.class) public void testH5Lcreate_external_null_file() throws Throwable { H5.H5Lcreate_external(null, "Bogus", 0, "Bogus", 0, 0); } @Test(expected = NullPointerException.class) public void testH5Lcreate_external_null_current() throws Throwable { H5.H5Lcreate_external("PathToFile", null, 0, "Bogus", 0, 0); } @Test(expected = NullPointerException.class) public void testH5Lcreate_external_null_dest() throws Throwable { H5.H5Lcreate_external("PathToFile", "Bogus", 0, null, 0, 0); } @Test(expected = HDF5LibraryException.class) public void testH5Lcopy_invalid() throws Throwable { H5.H5Lcopy(-1, "Bogus", -1, "Bogus", -1, -1); } @Test(expected = NullPointerException.class) public void testH5Lcopy_null_current() throws Throwable { H5.H5Lcopy(-1, null, 0, "Bogus", 0, 0); } @Test(expected = NullPointerException.class) public void testH5Lcopy_null_dest() throws Throwable { H5.H5Lcopy(-1, "Bogus", 0, null, 0, 0); } @Test(expected = HDF5LibraryException.class) public void testH5Lmove_invalid() throws Throwable { H5.H5Lmove(-1, "Bogus", -1, "Bogus", -1, -1); } @Test(expected = NullPointerException.class) public void testH5Lmove_null_current() throws Throwable { H5.H5Lmove(-1, null, 0, "Bogus", 0, 0); } @Test(expected = NullPointerException.class) public void testH5Lmove_null_dest() throws Throwable { H5.H5Lmove(-1, "Bogus", 0, null, 0, 0); } @Test(expected = HDF5LibraryException.class) public void testH5Lget_val_by_idx_invalid() throws Throwable { H5.H5Lget_val_by_idx(-1, "Bogus", -1, -1, -1L, null, -1); } @Test(expected = NullPointerException.class) public void testH5Lget_val_by_idx_null() throws Throwable { H5.H5Lget_val_by_idx(-1, null, 0, 0, 0L, null, 0); } @Test(expected = HDF5LibraryException.class) public void testH5Ldelete_by_idx_invalid() throws Throwable { H5.H5Ldelete_by_idx(-1, "Bogus", -1, -1, -1L, -1); } @Test(expected = NullPointerException.class) public void testH5Ldelete_by_idx_null() throws Throwable { H5.H5Ldelete_by_idx(-1, null, 0, 0, 0L, 0); } @Test(expected = NullPointerException.class) public void testH5Lvisit_null() throws Throwable { H5.H5Lvisit(-1, -1, -1, null, null); } @Test(expected = NullPointerException.class) public void testH5Lvisit_by_name_nullname() throws Throwable { H5.H5Lvisit_by_name(-1, null, -1, -1, null, null, -1); } @Test(expected = NullPointerException.class) public void testH5Lvisit_by_name_null() throws Throwable { H5.H5Lvisit_by_name(-1, "Bogus", -1, -1, null, null, -1); } @Test(expected = NullPointerException.class) public void testH5Literate_null() throws Throwable { H5.H5Literate(-1, -1, -1, -1, null, null); } @Test(expected = NullPointerException.class) public void testH5Literate_by_name_nullname() throws Throwable { H5.H5Literate_by_name(-1, null, -1, -1, -1, null, null, -1); } @Test(expected = NullPointerException.class) public void testH5Literate_by_name_null() throws Throwable { H5.H5Literate_by_name(-1, "Bogus", -1, -1, -1, null, null, -1); } } libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/TestH5Obasic.java000066400000000000000000000314721256564762100255640ustar00rootroot00000000000000package test.hdf5lib; import static org.junit.Assert.assertFalse; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import java.util.ArrayList; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.HDF5Constants; import ncsa.hdf.hdf5lib.callbacks.H5O_iterate_cb; import ncsa.hdf.hdf5lib.callbacks.H5O_iterate_t; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import ncsa.hdf.hdf5lib.structs.H5O_info_t; import org.junit.After; import org.junit.Before; import org.junit.Test; @SuppressWarnings("all") public class TestH5Obasic { private static final String H5_FILE = "sourceTest/java/test/hdf5lib/h5ex_g_iterate.hdf"; private static long H5la_ds1 = -1; private static long H5la_l1 = -1; private static long H5la_dt1 = -1; private static long H5la_g1 = -1; int H5fid = -1; @Before public void openH5file() throws HDF5LibraryException, NullPointerException { assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0); try { H5fid = H5.H5Fopen(H5_FILE, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Fopen: openH5file: " + err); } } @After public void closeH5file() throws HDF5LibraryException { if (H5fid > 0) { try {H5.H5Fclose(H5fid);} catch (Exception ex) {} } } @Test(expected = HDF5LibraryException.class) public void testH5Oopen_not_exists() throws Throwable { int oid = -1; oid = H5.H5Oopen(H5fid, "Never_created", HDF5Constants.H5P_DEFAULT); try {H5.H5Oclose(oid);} catch (Exception ex) {} } @Test public void testH5Oget_info_dataset() { int oid = -1; H5O_info_t obj_info = null; try { oid = H5.H5Oopen(H5fid, "DS1", HDF5Constants.H5P_DEFAULT); obj_info = H5.H5Oget_info(oid); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Oget_info: " + err); } assertFalse("H5Oget_info ",obj_info==null); assertTrue("H5Oget_info object type",obj_info.type==HDF5Constants.H5O_TYPE_DATASET); H5la_ds1 = obj_info.addr; try {H5.H5Oclose(oid);} catch (Exception ex) {} } @Test public void testH5Oget_info_hardlink() { int oid = -1; H5O_info_t obj_info = null; try { oid = H5.H5Oopen(H5fid, "L1", HDF5Constants.H5P_DEFAULT); obj_info = H5.H5Oget_info(oid); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Oget_info: " + err); } assertFalse("H5Oget_info ",obj_info==null); assertTrue("H5Oget_info object type",obj_info.type==HDF5Constants.H5O_TYPE_DATASET); H5la_l1 = obj_info.addr; try {H5.H5Oclose(oid);} catch (Exception ex) {} } @Test public void testH5Oget_info_group() { int oid = -1; H5O_info_t obj_info = null; try { oid = H5.H5Oopen(H5fid, "G1", HDF5Constants.H5P_DEFAULT); obj_info = H5.H5Oget_info(oid); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Oget_info: " + err); } assertFalse("H5Oget_info ",obj_info==null); assertTrue("H5Oget_info object type",obj_info.type==HDF5Constants.H5O_TYPE_GROUP); H5la_g1 = obj_info.addr; try {H5.H5Oclose(oid);} catch (Exception ex) {} } @Test public void testH5Oget_info_datatype() { int oid = -1; H5O_info_t obj_info = null; try { oid = H5.H5Oopen(H5fid, "DT1", HDF5Constants.H5P_DEFAULT); obj_info = H5.H5Oget_info(oid); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Oget_info: " + err); } assertFalse("H5Oget_info ",obj_info==null); assertTrue("H5Oget_info object type",obj_info.type==HDF5Constants.H5O_TYPE_NAMED_DATATYPE); H5la_dt1 = obj_info.addr; try {H5.H5Oclose(oid);} catch (Exception ex) {} } @Test(expected = HDF5LibraryException.class) public void testH5Oget_info_by_name_not_exist_name() throws Throwable { H5.H5Oget_info_by_name(H5fid, "None", HDF5Constants.H5P_DEFAULT); } @Test(expected = HDF5LibraryException.class) public void testH5Oget_info_by_name_not_exists() throws Throwable { H5.H5Oget_info_by_name(H5fid, "Bogus", HDF5Constants.H5P_DEFAULT); } @Test public void testH5Oget_info_by_name_dataset() { H5O_info_t obj_info = null; try { obj_info = H5.H5Oget_info_by_name(H5fid, "DS1", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Oget_info: " + err); } assertFalse("H5Oget_info ",obj_info==null); assertTrue("H5Oget_info object type",obj_info.type==HDF5Constants.H5O_TYPE_DATASET); H5la_ds1 = obj_info.addr; } @Test public void testH5Oget_info_by_name_hardlink() { H5O_info_t obj_info = null; try { obj_info = H5.H5Oget_info_by_name(H5fid, "L1", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Oget_info: " + err); } assertFalse("H5Oget_info ",obj_info==null); assertTrue("H5Oget_info object type",obj_info.type==HDF5Constants.H5O_TYPE_DATASET); H5la_l1 = obj_info.addr; } @Test public void testH5Oget_info_by_name_group() { H5O_info_t obj_info = null; try { obj_info = H5.H5Oget_info_by_name(H5fid, "G1", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Oget_info: " + err); } assertFalse("H5Oget_info ",obj_info==null); assertTrue("H5Oget_info object type",obj_info.type==HDF5Constants.H5O_TYPE_GROUP); H5la_g1 = obj_info.addr; } @Test public void testH5Oget_info_by_name_datatype() { H5O_info_t obj_info = null; try { obj_info = H5.H5Oget_info_by_name(H5fid, "DT1", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Oget_info: " + err); } assertFalse("H5Oget_info ",obj_info==null); assertTrue("H5Oget_info object type",obj_info.type==HDF5Constants.H5O_TYPE_NAMED_DATATYPE); H5la_dt1 = obj_info.addr; } @Test(expected = HDF5LibraryException.class) public void testH5Oget_info_by_idx_name_not_exist_name() throws Throwable { H5.H5Oget_info_by_idx(H5fid, "None", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, 0, HDF5Constants.H5P_DEFAULT); } @Test(expected = HDF5LibraryException.class) public void testH5Oget_info_by_idx_name_not_exist_create() throws Throwable { H5.H5Oget_info_by_idx(H5fid, "None", HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, 0, HDF5Constants.H5P_DEFAULT); } @Test(expected = HDF5LibraryException.class) public void testH5Oget_info_by_idx_not_exist_name() throws Throwable { H5.H5Oget_info_by_idx(H5fid, "/", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, 5, HDF5Constants.H5P_DEFAULT); } @Test(expected = HDF5LibraryException.class) public void testH5Oget_info_by_idx_not_exist_create() throws Throwable { H5.H5Oget_info_by_idx(H5fid, "/", HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, 5, HDF5Constants.H5P_DEFAULT); } @Test public void testH5Oget_info_by_idx_n0() { H5O_info_t obj_info = null; try { obj_info = H5.H5Oget_info_by_idx(H5fid, "/", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, 0, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Oget_info_by_idx: " + err); } assertFalse("H5Oget_info_by_idx ",obj_info==null); assertTrue("H5Oget_info_by_idx link type",obj_info.type==HDF5Constants.H5O_TYPE_DATASET); assertTrue("Link Address ",obj_info.addr==H5la_ds1); } @Test public void testH5Oget_info_by_idx_n3() { H5O_info_t obj_info = null; try { obj_info = H5.H5Oget_info_by_idx(H5fid, "/", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, 3, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Oget_info_by_idx: " + err); } assertFalse("H5Oget_info_by_idx ",obj_info==null); assertTrue("H5Oget_info_by_idx link type",obj_info.type==HDF5Constants.H5O_TYPE_DATASET); assertTrue("Link Address ",obj_info.addr==H5la_l1); } @Test public void testH5Ovisit() { class idata { public String link_name = null; public int link_type = -1; idata(String name, int type) { this.link_name = name; this.link_type = type; } } class H5O_iter_data implements H5O_iterate_t { public ArrayList iterdata = new ArrayList(); } H5O_iterate_t iter_data = new H5O_iter_data(); class H5O_iter_callback implements H5O_iterate_cb { public int callback(int group, String name, H5O_info_t info, H5O_iterate_t op_data) { idata id = new idata(name, info.type); ((H5O_iter_data)op_data).iterdata.add(id); return 0; } } H5O_iterate_cb iter_cb = new H5O_iter_callback(); try { H5.H5Ovisit(H5fid, HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, iter_cb, iter_data); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Ovisit: " + err); } assertFalse("H5Ovisit ",((H5O_iter_data)iter_data).iterdata.isEmpty()); assertTrue("H5Ovisit "+((H5O_iter_data)iter_data).iterdata.size(),((H5O_iter_data)iter_data).iterdata.size()==5); assertTrue("H5Ovisit "+(((H5O_iter_data)iter_data).iterdata.get(0)).link_name,(((H5O_iter_data)iter_data).iterdata.get(0)).link_name.compareToIgnoreCase(".")==0); assertTrue("H5Ovisit "+(((H5O_iter_data)iter_data).iterdata.get(1)).link_name,(((H5O_iter_data)iter_data).iterdata.get(1)).link_name.compareToIgnoreCase("DS1")==0); assertTrue("H5Ovisit "+(((H5O_iter_data)iter_data).iterdata.get(2)).link_name,(((H5O_iter_data)iter_data).iterdata.get(2)).link_name.compareToIgnoreCase("DT1")==0); assertTrue("H5Ovisit "+(((H5O_iter_data)iter_data).iterdata.get(3)).link_name,(((H5O_iter_data)iter_data).iterdata.get(3)).link_name.compareToIgnoreCase("G1")==0); assertTrue("H5Ovisit "+(((H5O_iter_data)iter_data).iterdata.get(4)).link_name,(((H5O_iter_data)iter_data).iterdata.get(4)).link_name.compareToIgnoreCase("G1/DS2")==0); // assertTrue("H5Ovisit "+((idata)((H5O_iter_data)iter_data).iterdata.get(5)).link_name,((idata)((H5O_iter_data)iter_data).iterdata.get(5)).link_name.compareToIgnoreCase("L1")==0); } @Test public void testH5Ovisit_by_name() { class idata { public String link_name = null; public int link_type = -1; idata(String name, int type) { this.link_name = name; this.link_type = type; } } class H5O_iter_data implements H5O_iterate_t { public ArrayList iterdata = new ArrayList(); } H5O_iterate_t iter_data = new H5O_iter_data(); class H5O_iter_callback implements H5O_iterate_cb { public int callback(int group, String name, H5O_info_t info, H5O_iterate_t op_data) { idata id = new idata(name, info.type); ((H5O_iter_data)op_data).iterdata.add(id); return 0; } } H5O_iterate_cb iter_cb = new H5O_iter_callback(); try { H5.H5Ovisit_by_name(H5fid, "G1", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, iter_cb, iter_data, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Ovisit_by_name: " + err); } assertFalse("H5Ovisit_by_name ",((H5O_iter_data)iter_data).iterdata.isEmpty()); assertTrue("H5Ovisit_by_name "+((H5O_iter_data)iter_data).iterdata.size(),((H5O_iter_data)iter_data).iterdata.size()==2); assertTrue("H5Ovisit_by_name "+(((H5O_iter_data)iter_data).iterdata.get(0)).link_name,(((H5O_iter_data)iter_data).iterdata.get(0)).link_name.compareToIgnoreCase(".")==0); assertTrue("H5Ovisit_by_name "+(((H5O_iter_data)iter_data).iterdata.get(1)).link_name,(((H5O_iter_data)iter_data).iterdata.get(1)).link_name.compareToIgnoreCase("DS2")==0); } } libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/TestH5Ocopy.java000066400000000000000000000251141256564762100254510ustar00rootroot00000000000000package test.hdf5lib; import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import java.io.File; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.HDF5Constants; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import org.junit.After; import org.junit.Before; import org.junit.Test; @SuppressWarnings("all") public class TestH5Ocopy { private static final String FILENAME = "testRefsattribute.h5"; private static final int DIM_X = 4; private static final int DIM_Y = 6; int H5fid = -1; int H5dsid = -1; int H5did1 = -1; int H5did2 = -1; int H5gcpl = -1; int H5gid = -1; int H5dsid2 = -1; long[] dims = { 2 }; private final void _deleteFile(String filename) { File file = new File(filename); if (file.exists()) { try { file.delete(); } catch (Exception e) { e.printStackTrace(); } } } private final int _createDataset(int fid, int dsid, String name, int dapl) { int did = -1; try { did = H5.H5Dcreate(fid, name, HDF5Constants.H5T_STD_I32BE, dsid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, dapl); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Dcreate: " + err); } assertTrue("TestH5O._createDataset: ",did > 0); return did; } private final int _createGroup(int fid, String name) { int gid = -1; try { H5gcpl = HDF5Constants.H5P_DEFAULT; gid = H5.H5Gcreate(fid, name, HDF5Constants.H5P_DEFAULT, H5gcpl, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gcreate: " + err); } assertTrue("TestH5O._createGroup: ",gid > 0); return gid; } @Before public void createH5file() throws NullPointerException, HDF5Exception { assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0); try { H5fid = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); H5dsid2 = H5.H5Screate(HDF5Constants.H5S_SCALAR); H5did1 = _createDataset(H5fid, H5dsid2, "DS2", HDF5Constants.H5P_DEFAULT); H5dsid = H5.H5Screate_simple(1, dims, null); H5gid = _createGroup(H5fid, "/G1"); H5did2 = _createDataset(H5gid, H5dsid, "DS1", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("TestH5O.createH5file: " + err); } assertTrue("TestH5O.createH5file: H5.H5Fcreate: ",H5fid > 0); assertTrue("TestH5O.createH5file: H5.H5Screate_simple: ",H5dsid > 0); assertTrue("TestH5O.createH5file: H5.H5Gcreate: ",H5gid > 0); H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); } @After public void deleteH5file() throws HDF5LibraryException { if (H5gid > 0) try {H5.H5Gclose(H5gid);} catch (Exception ex) {} if (H5did2 > 0) try {H5.H5Dclose(H5did2);} catch (Exception ex) {} if (H5dsid > 0) try {H5.H5Sclose(H5dsid);} catch (Exception ex) {} if (H5dsid2 > 0) try {H5.H5Sclose(H5dsid2);} catch (Exception ex) {} if (H5did1 > 0) try {H5.H5Dclose(H5did1);} catch (Exception ex) {} if (H5fid > 0) try {H5.H5Fclose(H5fid);} catch (Exception ex) {} _deleteFile(FILENAME); } @Test public void testH5OcopyRefsAttr() { int ocp_plist_id = -1; byte rbuf0[]=null , rbuf1[] = null; byte[] dset_data = new byte[16]; int attribute_id = -1; try{ rbuf0 = H5.H5Rcreate(H5fid, "/G1", HDF5Constants.H5R_OBJECT, -1); rbuf1 = H5.H5Rcreate(H5fid, "DS2", HDF5Constants.H5R_OBJECT, -1); //System.arraycopy(rbuf0, 0, dset_data, 0, 8); System.arraycopy(rbuf1, 0, dset_data, 8, 8); attribute_id = H5.H5Acreate(H5did2, "A1", HDF5Constants.H5T_STD_REF_OBJ, H5dsid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); H5.H5Awrite(attribute_id, HDF5Constants.H5T_STD_REF_OBJ, dset_data); H5.H5Aclose(attribute_id); ocp_plist_id = H5.H5Pcreate(HDF5Constants.H5P_OBJECT_COPY); H5.H5Pset_copy_object(ocp_plist_id, HDF5Constants.H5O_COPY_EXPAND_REFERENCE_FLAG); H5.H5Ocopy(H5fid, ".", H5fid, "CPYREF", ocp_plist_id, HDF5Constants.H5P_DEFAULT); } catch (Exception ex){ fail("testH5OcopyRefsAttr: H5Ocopy failed"); } try{ H5.H5Pclose(ocp_plist_id); } catch (Exception ex){ } } @Test public void testH5OcopyRefsDatasettodiffFile() { int ocp_plist_id = -1; byte rbuf1[] = null; byte[] dset_data = new byte[16]; int dataset_id = -1; try{ rbuf1 = H5.H5Rcreate(H5fid, "DS2", HDF5Constants.H5R_OBJECT, -1); System.arraycopy(rbuf1, 0, dset_data, 8, 8); dataset_id = H5.H5Dcreate(H5fid, "DSREF", HDF5Constants.H5T_STD_REF_OBJ, H5dsid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); H5.H5Dwrite(dataset_id, HDF5Constants.H5T_STD_REF_OBJ, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); H5.H5Dclose(dataset_id); //create new file int H5fid2 = H5.H5Fcreate("copy.h5", HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); H5.H5Fflush(H5fid2, HDF5Constants.H5F_SCOPE_LOCAL); //create object copy property list id and set the flags. ocp_plist_id = H5.H5Pcreate(HDF5Constants.H5P_OBJECT_COPY); H5.H5Pset_copy_object(ocp_plist_id, HDF5Constants.H5O_COPY_EXPAND_REFERENCE_FLAG); //Perform copy function. H5.H5Ocopy(H5fid, ".", H5fid2, "CPYREFD", ocp_plist_id, HDF5Constants.H5P_DEFAULT); //Close file. H5.H5Fclose(H5fid2); } catch (Exception ex){ ex.printStackTrace(); fail("testH5OcopyRefsDatasettodiffFile: H5Ocopy failed"); } try{ H5.H5Pclose(ocp_plist_id); } catch (Exception ex){ } } @Test public void testH5OcopyRefsDatasettosameFile() { int ocp_plist_id = -1; byte rbuf0[]=null , rbuf1[] = null; byte[] dset_data = new byte[16]; int dataset_id = -1; int[] otype = { 1 }; int obj_type = -1; byte[] read_data = new byte[16]; int did = -1; try{ rbuf0 = H5.H5Rcreate(H5fid, "/G1", HDF5Constants.H5R_OBJECT, -1); rbuf1 = H5.H5Rcreate(H5fid, "DS2", HDF5Constants.H5R_OBJECT, -1); System.arraycopy(rbuf0, 0, dset_data, 0, 8); System.arraycopy(rbuf1, 0, dset_data, 8, 8); //Create a dataset and write object references to it. dataset_id = H5.H5Dcreate(H5fid, "DSREF", HDF5Constants.H5T_STD_REF_OBJ, H5dsid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); H5.H5Dwrite(dataset_id, HDF5Constants.H5T_STD_REF_OBJ, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); //Close the dataset. H5.H5Dclose(dataset_id); ocp_plist_id = H5.H5Pcreate(HDF5Constants.H5P_OBJECT_COPY); H5.H5Pset_copy_object(ocp_plist_id, HDF5Constants.H5O_COPY_EXPAND_REFERENCE_FLAG); //Perform copy function. try{ H5.H5Ocopy(H5fid, "DSREF", H5fid, "CPYREFD", ocp_plist_id, HDF5Constants.H5P_DEFAULT); } catch(Exception ex){ fail("testH5OcopyRefsDatasettosameFile: H5Ocopy failed"); } //Open the dataset that has been copied try { did = H5.H5Dopen(H5fid, "DSREF", HDF5Constants.H5P_DEFAULT); } catch (Exception e) { e.printStackTrace(); } //Read the dataset object references in the read_data buffer. H5.H5Dread(did, HDF5Constants.H5T_STD_REF_OBJ, HDF5Constants.H5S_ALL,HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, read_data); System.arraycopy(read_data, 0, rbuf0, 0, 8); System.arraycopy(read_data, 8, rbuf1, 0, 8); //Get the type of object the reference points to. obj_type = H5.H5Rget_obj_type(H5fid, HDF5Constants.H5R_OBJECT, rbuf1, otype); assertEquals(obj_type, HDF5Constants.H5O_TYPE_DATASET); obj_type = H5.H5Rget_obj_type(H5fid, HDF5Constants.H5R_OBJECT, rbuf0, otype); assertEquals(obj_type, HDF5Constants.H5O_TYPE_GROUP); //close the dataset H5.H5Dclose(did); } catch (Exception ex){ ex.printStackTrace(); } try{ H5.H5Pclose(ocp_plist_id); } catch (Exception ex){ } } @Test public void testH5OcopyInvalidRef() { final int _pid_ = HDF5Constants.H5P_DEFAULT; try { int sid = H5.H5Screate_simple(1, new long[] {1}, null); int did = H5.H5Dcreate(H5fid, "Dataset_with_invalid_Ref", HDF5Constants.H5T_NATIVE_INT, sid, _pid_, _pid_, _pid_); int aid = H5.H5Acreate(did, "Invalid_Ref", HDF5Constants.H5T_STD_REF_OBJ, sid, _pid_, _pid_); H5.H5Awrite(aid, HDF5Constants.H5T_STD_REF_OBJ, new long[]{-1}); H5.H5Dclose(did); H5.H5Aclose(aid); H5.H5Sclose(sid); } catch (Exception ex) {} try { int ocp_plist_id = H5.H5Pcreate(HDF5Constants.H5P_OBJECT_COPY); H5.H5Pset_copy_object(ocp_plist_id, HDF5Constants.H5O_COPY_EXPAND_REFERENCE_FLAG); try { H5.H5Ocopy(H5fid, "/Dataset_with_invalid_Ref", H5fid, "/Dataset_with_invalid_Ref_cp", ocp_plist_id, _pid_); } finally { H5.H5Pclose(ocp_plist_id);} } catch (Exception ex) {} } } libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/TestH5Ocreate.java000066400000000000000000000453121256564762100257440ustar00rootroot00000000000000package test.hdf5lib; import static org.junit.Assert.assertFalse; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import java.io.File; import java.util.ArrayList; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.HDF5Constants; import ncsa.hdf.hdf5lib.callbacks.H5O_iterate_cb; import ncsa.hdf.hdf5lib.callbacks.H5O_iterate_t; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import ncsa.hdf.hdf5lib.structs.H5O_info_t; import org.junit.After; import org.junit.Before; import org.junit.Test; @SuppressWarnings("all") public class TestH5Ocreate { private static final String H5_EXTFILE = "sourceTest/java/test/hdf5lib/h5ex_g_iterate.hdf"; private static final String H5_FILE = "test.h5"; private static final int DIM_X = 4; private static final int DIM_Y = 6; int H5fcpl = -1; int H5fid = -1; int H5dsid = -1; int H5did1 = -1; int H5did2 = -1; int H5gcpl = -1; int H5gid = -1; long[] H5dims = { DIM_X, DIM_Y }; private final void _deleteFile(String filename) { File file = new File(filename); if (file.exists()) { try { file.delete(); } catch (Exception e) { e.printStackTrace(); } } } private final int _createDataset(int fid, int dsid, String name, int dapl) { int did = -1; try { did = H5.H5Dcreate(fid, name, HDF5Constants.H5T_STD_I32BE, dsid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, dapl); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Dcreate: " + err); } assertTrue("TestH5O._createDataset: ",did > 0); return did; } private final int _createGroup(int fid, String name) { int gid = -1; try { H5gcpl = HDF5Constants.H5P_DEFAULT; gid = H5.H5Gcreate(fid, name, HDF5Constants.H5P_DEFAULT, H5gcpl, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gcreate: " + err); } assertTrue("TestH5O._createGroup: ",gid > 0); return gid; } private final void _createHardLink(int fid, int cid, String curname, int did, String dstname, int lcpl, int lapl) { boolean link_exists = false; try { H5.H5Lcreate_hard(cid, curname, did, dstname, lcpl, lapl); H5.H5Fflush(fid, HDF5Constants.H5F_SCOPE_LOCAL); link_exists = H5.H5Lexists(did, dstname, lapl); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lcreate_hard: " + err); } assertTrue("TestH5O._createHardLink ", link_exists); } private final void _createSoftLink(int fid, String curname, int did, String dstname, int lcpl, int lapl) { boolean link_exists = false; try { H5.H5Lcreate_soft(curname, did, dstname, lcpl, lapl); H5.H5Fflush(fid, HDF5Constants.H5F_SCOPE_LOCAL); link_exists = H5.H5Lexists(did, dstname, lapl); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lcreate_soft: " + err); } assertTrue("TestH5O._createSoftLink ", link_exists); } private final void _createExternalLink(int fid, String ext_filename, String curname, int did, String dstname, int lcpl, int lapl) { boolean link_exists = false; try { H5.H5Lcreate_external(ext_filename, curname, did, dstname, lcpl, lapl); H5.H5Fflush(fid, HDF5Constants.H5F_SCOPE_LOCAL); link_exists = H5.H5Lexists(did, dstname, lapl); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Lcreate_external: " + err); } assertTrue("TestH5O._createExternalLink ", link_exists); } @Before public void createH5file() throws NullPointerException, HDF5Exception { assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0); try { H5fcpl = H5.H5Pcreate(HDF5Constants.H5P_FILE_CREATE); H5.H5Pset_link_creation_order(H5fcpl, HDF5Constants.H5P_CRT_ORDER_TRACKED+HDF5Constants.H5P_CRT_ORDER_INDEXED); H5fid = H5.H5Fcreate(H5_FILE, HDF5Constants.H5F_ACC_TRUNC, H5fcpl, HDF5Constants.H5P_DEFAULT); H5dsid = H5.H5Screate_simple(2, H5dims, null); H5did1 = _createDataset(H5fid, H5dsid, "DS1", HDF5Constants.H5P_DEFAULT); H5gid = _createGroup(H5fid, "/G1"); H5did2 = _createDataset(H5gid, H5dsid, "DS2", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("TestH5O.createH5file: " + err); } assertTrue("TestH5O.createH5file: H5.H5Fcreate: ",H5fid > 0); assertTrue("TestH5O.createH5file: H5.H5Screate_simple: ",H5dsid > 0); assertTrue("TestH5O.createH5file: H5.H5Gcreate: ",H5gid > 0); H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); } @After public void deleteH5file() throws HDF5LibraryException { if (H5gid > 0) try {H5.H5Gclose(H5gid);} catch (Exception ex) {} if (H5gcpl > 0) try {H5.H5Pclose(H5gcpl);} catch (Exception ex) {} if (H5did2 > 0) try {H5.H5Dclose(H5did2);} catch (Exception ex) {} if (H5dsid > 0) try {H5.H5Sclose(H5dsid);} catch (Exception ex) {} if (H5did1 > 0) try {H5.H5Dclose(H5did1);} catch (Exception ex) {} if (H5fid > 0) try {H5.H5Fclose(H5fid);} catch (Exception ex) {} if (H5fcpl > 0) try {H5.H5Pclose(H5fcpl);} catch (Exception ex) {} _deleteFile(H5_FILE); } @Test(expected = HDF5LibraryException.class) public void testH5Ocopy_cur_not_exists() throws Throwable { H5.H5Ocopy(H5fid, "None", H5fid, "DS1", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); } @Test public void testH5Ocopy() { try { H5.H5Ocopy(H5fid, "DS1", H5fid, "CPY1", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); boolean link_exists = H5.H5Lexists(H5fid, "CPY1", HDF5Constants.H5P_DEFAULT); assertTrue("testH5Ocopy:H5Lexists ",link_exists); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Ocopy: " + err); } } @Test(expected = HDF5LibraryException.class) public void testH5Ocopy_dst_link_exists() throws Throwable { _createHardLink(H5fid, H5fid, "/G1/DS2", H5fid, "CPY1", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); H5.H5Ocopy(H5fid, "CPY1", H5fid, "/G1/DS2", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); } @Test public void testH5Oget_info_by_idx_n0_create() { H5O_info_t obj_info = null; try { int order = H5.H5Pget_link_creation_order(H5fcpl); assertTrue("creation order :"+order, order == HDF5Constants.H5P_CRT_ORDER_TRACKED+HDF5Constants.H5P_CRT_ORDER_INDEXED); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Oget_info_by_idx_n0:H5Pget_link_creation_order " + err); } try { obj_info = H5.H5Oget_info_by_idx(H5fid, "/", HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, 0, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Oget_info_by_idx: " + err); } assertFalse("H5Oget_info_by_idx ", obj_info==null); assertTrue("H5Oget_info_by_idx link type", obj_info.type==HDF5Constants.H5O_TYPE_DATASET); } @Test public void testH5Oget_info_by_idx_n1_create() { H5O_info_t obj_info = null; try { int order = H5.H5Pget_link_creation_order(H5fcpl); assertTrue("creation order :"+order, order == HDF5Constants.H5P_CRT_ORDER_TRACKED+HDF5Constants.H5P_CRT_ORDER_INDEXED); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Oget_info_by_idx_n1:H5Pget_link_creation_order " + err); } try { obj_info = H5.H5Oget_info_by_idx(H5fid, "/", HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, 1, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Oget_info_by_idx: " + err); } assertFalse("H5Oget_info_by_idx ", obj_info==null); assertTrue("H5Oget_info_by_idx link type", obj_info.type==HDF5Constants.H5O_TYPE_GROUP); } @Test public void testH5Oget_info_softlink() { H5O_info_t obj_info = null; _createSoftLink(H5fid, "/G1/DS2", H5fid, "L1", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); try { obj_info = H5.H5Oget_info_by_name(H5fid, "L1", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Oget_info: " + err); } assertFalse("H5Oget_info ", obj_info==null); assertTrue("H5Oget_info link type", obj_info.type==HDF5Constants.H5O_TYPE_DATASET); assertTrue("Link Address ", obj_info.addr>0); } @Test(expected = HDF5LibraryException.class) public void testH5Oget_info_softlink_dangle() throws Throwable { _createSoftLink(H5fid, "DS3", H5fid, "L2", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); H5.H5Oget_info_by_name(H5fid, "L2", HDF5Constants.H5P_DEFAULT); } @Test public void testH5Oget_info_externallink() { H5O_info_t obj_info = null; _createExternalLink(H5fid, H5_EXTFILE, "DT1", H5fid, "L1", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); try { obj_info = H5.H5Oget_info_by_name(H5fid, "L1", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Oget_info: " + err); } assertFalse("H5Oget_info ", obj_info==null); assertTrue("H5Oget_info link type", obj_info.type==HDF5Constants.H5O_TYPE_NAMED_DATATYPE); assertTrue("Link Address ", obj_info.addr>0); } @Test public void testH5Olink() { int oid = -1; H5O_info_t obj_info = null; H5O_info_t dst_obj_info = null; try { oid = H5.H5Oopen(H5fid, "DS1", HDF5Constants.H5P_DEFAULT); obj_info = H5.H5Oget_info(oid); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Oget_info: " + err); } try { H5.H5Olink(oid, H5fid, "CPY1", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Olink: " + err); } try {H5.H5Oclose(oid);} catch (Exception ex) {} assertFalse("H5Oget_info ", obj_info==null); assertTrue("H5Oget_info object type", obj_info.type==HDF5Constants.H5O_TYPE_DATASET); try { dst_obj_info = H5.H5Oget_info_by_name(H5fid, "CPY1", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Oget_info_by_name: " + err); } assertFalse("H5Oget_info ", dst_obj_info==null); assertTrue("H5Oget_info object type", dst_obj_info.type==HDF5Constants.H5O_TYPE_DATASET); } @Test public void testH5Ovisit_create() { try { int order = H5.H5Pget_link_creation_order(H5fcpl); assertTrue("creation order :"+order, order == HDF5Constants.H5P_CRT_ORDER_TRACKED+HDF5Constants.H5P_CRT_ORDER_INDEXED); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Ovisit_create:H5Pget_link_creation_order " + err); } _createHardLink(H5fid, H5fid, "/G1/DS2", H5fid, "CPY1", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); _createExternalLink(H5fid, H5_EXTFILE, "DT1", H5fid, "LE", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); _createSoftLink(H5fid, "/G1/DS2", H5fid, "LS", HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); class idata { public String link_name = null; public int link_type = -1; idata(String name, int type) { this.link_name = name; this.link_type = type; } } class H5O_iter_data implements H5O_iterate_t { public ArrayList iterdata = new ArrayList(); } H5O_iterate_t iter_data = new H5O_iter_data(); class H5O_iter_callback implements H5O_iterate_cb { public int callback(int group, String name, H5O_info_t info, H5O_iterate_t op_data) { idata id = new idata(name, info.type); ((H5O_iter_data)op_data).iterdata.add(id); return 0; } } H5O_iterate_cb iter_cb = new H5O_iter_callback(); try { H5.H5Ovisit(H5fid, HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, iter_cb, iter_data); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Ovisit: " + err); } assertFalse("H5Ovisit ", ((H5O_iter_data)iter_data).iterdata.isEmpty()); assertTrue("H5Ovisit "+((H5O_iter_data)iter_data).iterdata.size(), ((H5O_iter_data)iter_data).iterdata.size()==4); assertTrue("H5Ovisit "+((idata)((H5O_iter_data)iter_data).iterdata.get(0)).link_name, ((idata)((H5O_iter_data)iter_data).iterdata.get(0)).link_name.compareToIgnoreCase(".")==0); assertTrue("H5Ovisit "+((idata)((H5O_iter_data)iter_data).iterdata.get(1)).link_name, ((idata)((H5O_iter_data)iter_data).iterdata.get(1)).link_name.compareToIgnoreCase("DS1")==0); assertTrue("H5Ovisit "+((idata)((H5O_iter_data)iter_data).iterdata.get(2)).link_name, ((idata)((H5O_iter_data)iter_data).iterdata.get(2)).link_name.compareToIgnoreCase("G1")==0); assertTrue("H5Ovisit "+((idata)((H5O_iter_data)iter_data).iterdata.get(3)).link_name, ((idata)((H5O_iter_data)iter_data).iterdata.get(3)).link_name.compareToIgnoreCase("G1/DS2")==0); } @Test public void testH5Ocomment() { int oid = -1; String obj_comment = null; try { oid = H5.H5Oopen(H5fid, "DS1", HDF5Constants.H5P_DEFAULT); H5.H5Oset_comment(oid, "Test Comment"); H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Oset_comment: " + err); } try { obj_comment = H5.H5Oget_comment(oid); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Oget_comment: " + err); } try {H5.H5Oclose(oid);} catch (Exception ex) {} assertFalse("H5Oget_comment: ", obj_comment==null); assertTrue("H5Oget_comment: ", obj_comment.compareTo("Test Comment")==0); } @Test public void testH5Ocomment_clear() { int oid = -1; String obj_comment = null; try { oid = H5.H5Oopen(H5fid, "DS1", HDF5Constants.H5P_DEFAULT); H5.H5Oset_comment(oid, "Test Comment"); H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Oset_comment: " + err); } try { obj_comment = H5.H5Oget_comment(oid); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Oget_comment: " + err); } assertFalse("H5Oget_comment: ", obj_comment==null); assertTrue("H5Oget_comment: ", obj_comment.compareTo("Test Comment")==0); try { H5.H5Oset_comment(oid, null); H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Oset_comment: " + err); } try { obj_comment = H5.H5Oget_comment(oid); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Oget_comment: " + err); } try {H5.H5Oclose(oid);} catch (Exception ex) {} assertTrue("H5Oget_comment: ", obj_comment==null); } @Test public void testH5Ocomment_by_name() { String obj_comment = null; try { H5.H5Oset_comment_by_name(H5fid, "DS1", "Test Comment", HDF5Constants.H5P_DEFAULT); H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Oset_comment_by_name: " + err); } try { obj_comment = H5.H5Oget_comment_by_name(H5fid, "DS1", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Oget_comment_by_name: " + err); } assertFalse("H5Oget_comment_by_name: ", obj_comment==null); assertTrue("H5Oget_comment_by_name: ", obj_comment.compareTo("Test Comment")==0); } @Test public void testH5Ocomment_by_name_clear() { String obj_comment = null; try { H5.H5Oset_comment_by_name(H5fid, "DS1", "Test Comment", HDF5Constants.H5P_DEFAULT); H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Oset_comment_by_name: " + err); } try { obj_comment = H5.H5Oget_comment_by_name(H5fid, "DS1", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Oget_comment_by_name: " + err); } assertFalse("H5Oget_comment_by_name: ", obj_comment==null); assertTrue("H5Oget_comment_by_name: ", obj_comment.compareTo("Test Comment")==0); try { H5.H5Oset_comment_by_name(H5fid, "DS1", null, HDF5Constants.H5P_DEFAULT); H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Oset_comment_by_name: " + err); } try { obj_comment = H5.H5Oget_comment_by_name(H5fid, "DS1", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Oget_comment_by_name: " + err); } assertTrue("H5Oget_comment_by_name: ", obj_comment==null); } } libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/TestH5Oparams.java000066400000000000000000000077321256564762100257700ustar00rootroot00000000000000package test.hdf5lib; import static org.junit.Assert.assertTrue; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.HDF5Constants; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import org.junit.Before; import org.junit.Test; public class TestH5Oparams { @Before public void checkOpenIDs() { assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0); } @Test(expected = NullPointerException.class) public void testH5Oopen_null() throws Throwable { H5.H5Oopen(-1, null, 0); } @Test(expected = HDF5LibraryException.class) public void testH5Oopen_invalid() throws Throwable { H5.H5Oopen(-1, "Bogus", 0); } @Test(expected = HDF5LibraryException.class) public void testH5Ocopy_invalid() throws Throwable { H5.H5Ocopy(-1, "Bogus", -1, "Bogus", -1, -1); } @Test(expected = NullPointerException.class) public void testH5Ocopy_null_current() throws Throwable { H5.H5Ocopy(-1, null, 0, "Bogus", 0, 0); } @Test(expected = NullPointerException.class) public void testH5Ocopy_null_dest() throws Throwable { H5.H5Ocopy(-1, "Bogus", 0, null, 0, 0); } @Test(expected = HDF5LibraryException.class) public void testH5Oget_info_invalid() throws Throwable { H5.H5Oget_info(-1); } @Test(expected = NullPointerException.class) public void testH5Oget_info_by_name_null() throws Throwable { H5.H5Oget_info_by_name(-1, null, HDF5Constants.H5P_DEFAULT); } @Test(expected = HDF5LibraryException.class) public void testH5Oget_info_by_name_invalid() throws Throwable { H5.H5Oget_info_by_name(-1, "/testH5Gcreate", HDF5Constants.H5P_DEFAULT); } @Test(expected = HDF5LibraryException.class) public void testH5Oget_info_by_idx_invalid() throws Throwable { H5.H5Oget_info_by_idx(-1, "Bogus", -1, -1, -1L, -1); } @Test(expected = NullPointerException.class) public void testH5Oget_info_by_idx_null() throws Throwable { H5.H5Oget_info_by_idx(-1, null, 0, 0, 0L, 0); } @Test(expected = HDF5LibraryException.class) public void testH5Olink_invalid() throws Throwable { H5.H5Olink(-1, -1, "Bogus", -1, -1); } @Test(expected = NullPointerException.class) public void testH5Olink_null_dest() throws Throwable { H5.H5Olink(-1, 0, null, 0, 0); } @Test(expected = NullPointerException.class) public void testH5Ovisit_null() throws Throwable { H5.H5Ovisit(-1, -1, -1, null, null); } @Test(expected = NullPointerException.class) public void testH5Ovisit_by_name_nullname() throws Throwable { H5.H5Ovisit_by_name(-1, null, -1, -1, null, null, -1); } @Test(expected = NullPointerException.class) public void testH5Ovisit_by_name_null() throws Throwable { H5.H5Ovisit_by_name(-1, "Bogus", -1, -1, null, null, -1); } @Test(expected = HDF5LibraryException.class) @SuppressWarnings("deprecation") public void testH5Oset_comment_invalid() throws Throwable { H5.H5Oset_comment(-1, "Bogus"); } @Test(expected = HDF5LibraryException.class) public void testH5Oget_comment_invalid() throws Throwable { H5.H5Oget_comment(-1); } @Test(expected = HDF5LibraryException.class) @SuppressWarnings("deprecation") public void testH5Oset_comment_by_name_invalid() throws Throwable { H5.H5Oset_comment_by_name(-1, "Bogus", null, -1); } @Test(expected = NullPointerException.class) @SuppressWarnings("deprecation") public void testH5Oset_comment_by_name_null() throws Throwable { H5.H5Oset_comment_by_name(-1, null, null, -1); } @Test(expected = HDF5LibraryException.class) public void testH5Oget_comment_by_name_invalid() throws Throwable { H5.H5Oget_comment_by_name(-1, "Bogus", -1); } @Test(expected = NullPointerException.class) public void testH5Oget_comment_by_name_null() throws Throwable { H5.H5Oget_comment_by_name(-1, null, -1); } } libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/TestH5P.java000066400000000000000000001217461256564762100245670ustar00rootroot00000000000000package test.hdf5lib; import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertFalse; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import java.io.File; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.HDF5Constants; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import org.junit.After; import org.junit.Before; import org.junit.Test; @SuppressWarnings("all") public class TestH5P { private static final String H5_FILE = "test.h5"; private static final int DIM_X = 4; private static final int DIM_Y = 6; long[] H5dims = { DIM_X, DIM_Y }; int H5fid = -1; int H5dsid = -1; int H5did = -1; int lapl_id = -1; int fapl_id = -1; int fcpl_id = -1; int ocpl_id = -1; int ocp_plist_id = -1; int lcpl_id = -1; int plapl_id = -1; int plist_id = -1; int gapl_id = -1; int gcpl_id = -1; int acpl_id = -1; private final void _deleteFile(String filename) { File file = new File(filename); if (file.exists()) { try {file.delete();} catch (SecurityException e) {} } } private final int _createDataset(int fid, int dsid, String name, int dapl) { int did = -1; try { did = H5.H5Dcreate(fid, name, HDF5Constants.H5T_STD_I32BE, dsid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, dapl); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Dcreate: " + err); } assertTrue("TestH5D._createDataset: ", did > 0); return did; } private final void _createH5File(int fcpl, int fapl) { try { H5fid = H5.H5Fcreate(H5_FILE, HDF5Constants.H5F_ACC_TRUNC, fcpl, fapl); H5dsid = H5.H5Screate_simple(2, H5dims, null); H5did = _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("TestH5D.createH5file: " + err); } assertTrue("TestH5D.createH5file: H5.H5Fcreate: ", H5fid > 0); assertTrue("TestH5D.createH5file: H5.H5Screate_simple: ", H5dsid > 0); assertTrue("TestH5D.createH5file: _createDataset: ", H5did > 0); try { H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); } catch (Throwable err) { err.printStackTrace(); } } public void deleteH5file() throws HDF5LibraryException { _deleteFile(H5_FILE); } @Before public void createH5fileProperties() throws NullPointerException, HDF5Exception { assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0); try { lapl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_ACCESS); fapl_id = H5.H5Pcreate(HDF5Constants.H5P_FILE_ACCESS); fcpl_id = H5.H5Pcreate(HDF5Constants.H5P_FILE_CREATE); ocpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE); ocp_plist_id = H5.H5Pcreate(HDF5Constants.H5P_OBJECT_COPY); lcpl_id = H5.H5Pcreate(HDF5Constants.H5P_LINK_CREATE); plapl_id = H5.H5Pcreate(HDF5Constants.H5P_LINK_ACCESS); plist_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_XFER); gapl_id = H5.H5Pcreate(HDF5Constants.H5P_GROUP_ACCESS); gcpl_id = H5.H5Pcreate(HDF5Constants.H5P_GROUP_CREATE); acpl_id = H5.H5Pcreate(HDF5Constants.H5P_ATTRIBUTE_CREATE); } catch (Throwable err) { err.printStackTrace(); fail("TestH5D.createH5file: " + err); } assertTrue(lapl_id > 0); assertTrue(fapl_id > 0); assertTrue(fcpl_id > 0); assertTrue(ocpl_id > 0); assertTrue(ocp_plist_id > 0); assertTrue(lcpl_id > 0); assertTrue(plapl_id>0); assertTrue(plist_id > 0); assertTrue(gapl_id > 0); assertTrue(gcpl_id >0); assertTrue(acpl_id >0); } @After public void deleteH5fileProperties() throws HDF5LibraryException { if (lapl_id >0) try {H5.H5Pclose(lapl_id);} catch (Exception ex) {} if (fapl_id >0) try {H5.H5Pclose(fapl_id);} catch (Exception ex) {} if (fcpl_id >0) try {H5.H5Pclose(fcpl_id);} catch (Exception ex) {} if (ocpl_id >0) try {H5.H5Pclose(ocpl_id);} catch (Exception ex) {} if (ocp_plist_id >0) try {H5.H5Pclose(ocp_plist_id);} catch (Exception ex) {} if (lcpl_id >0) try {H5.H5Pclose(lcpl_id);} catch (Exception ex) {} if (plapl_id >0) try {H5.H5Pclose(plapl_id);} catch (Exception ex) {} if (plist_id >0) try {H5.H5Pclose(plist_id);} catch (Exception ex) {} if (gapl_id >0) try {H5.H5Pclose(gapl_id);} catch (Exception ex) {} if (gcpl_id >0) try {H5.H5Pclose(gcpl_id);} catch (Exception ex) {} if (acpl_id >0) try {H5.H5Pclose(acpl_id);} catch (Exception ex) {} if (H5dsid > 0) try {H5.H5Sclose(H5dsid);} catch (Exception ex) {} if (H5did > 0) try {H5.H5Dclose(H5did);} catch (Exception ex) {} if (H5fid > 0) try {H5.H5Fclose(H5fid);} catch (Exception ex) {} } @Test public void testH5Pget_nlinks() { long nlinks = -1; try { nlinks = (long) H5.H5Pget_nlinks(lapl_id); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Pget_nlinks: " + err); } assertTrue("testH5Pget_nlinks", nlinks > 0); // Check the default value of nlinks. assertEquals(nlinks, 16L); } @Test public void testH5Pset_nlinks() { long nlinks = 20; int ret_val = -1; try { ret_val = H5.H5Pset_nlinks(lapl_id, nlinks); nlinks = (long) H5.H5Pget_nlinks(lapl_id); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Pset_nlinks: " + err); } assertTrue("testH5Pset_nlinks", ret_val >= 0); // Check the value of nlinks retrieved from H5Pget_nlinks function. assertEquals(nlinks, 20L); } @Test(expected = IllegalArgumentException.class) public void testH5Pset_libver_bounds_invalidlow() throws Throwable { H5.H5Pset_libver_bounds(fapl_id, 5, HDF5Constants.H5F_LIBVER_LATEST); } @Test(expected = IllegalArgumentException.class) public void testH5Pset_libver_bounds_invalidhigh() throws Throwable { H5.H5Pset_libver_bounds(fapl_id, HDF5Constants.H5F_LIBVER_LATEST, 5); } @Test public void testH5Pget_link_creation_order() { int crt_order_flags = 0; try { crt_order_flags = H5.H5Pget_link_creation_order(fcpl_id); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_link_creation_order: " + err); } assertTrue("testH5Pget_link_creation_order", crt_order_flags >= 0); } @Test public void testH5Pset_link_creation_order_trackedPLUSindexed() { int ret_val = -1; int crt_order_flags = HDF5Constants.H5P_CRT_ORDER_TRACKED + HDF5Constants.H5P_CRT_ORDER_INDEXED; int crtorderflags = 0; try { ret_val = H5.H5Pset_link_creation_order(fcpl_id, crt_order_flags); crtorderflags = H5.H5Pget_link_creation_order(fcpl_id); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_link_creation_order: " + err); } assertTrue("testH5Pset_link_creation_order_trackedPLUSindexed",ret_val >= 0); assertEquals(crt_order_flags, crtorderflags); } @Test public void testH5Pset_link_creation_order_tracked() { int ret_val = -1; int crtorderflags = 0; try { ret_val = H5.H5Pset_link_creation_order(fcpl_id, HDF5Constants.H5P_CRT_ORDER_TRACKED); crtorderflags = H5.H5Pget_link_creation_order(fcpl_id); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_link_creation_order: " + err); } assertTrue("testH5Pset_link_creation_order_tracked",ret_val >= 0); assertEquals(HDF5Constants.H5P_CRT_ORDER_TRACKED, crtorderflags); } @Test(expected = HDF5LibraryException.class) public void testH5Pset_link_creation_order_invalidvalue() throws Throwable { H5.H5Pset_link_creation_order(fcpl_id, HDF5Constants.H5P_CRT_ORDER_INDEXED); } @Test public void testH5Pget_attr_creation_order() { int crt_order_flags = 0; try { crt_order_flags = H5.H5Pget_attr_creation_order(ocpl_id); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_attr_creation_order: " + err); } assertTrue("testH5Pget_attr_creation_order", crt_order_flags >= 0); } @Test public void testH5Pset_attr_creation_order_trackedPLUSindexed() { int ret_val = -1; int crt_order_flags = HDF5Constants.H5P_CRT_ORDER_TRACKED + HDF5Constants.H5P_CRT_ORDER_INDEXED; int crtorderflags = 0; try { ret_val = H5.H5Pset_attr_creation_order(ocpl_id, crt_order_flags); crtorderflags = H5.H5Pget_attr_creation_order(ocpl_id); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_attr_creation_order: " + err); } assertTrue("testH5Pset_attr_creation_order_trackedPLUSindexed", ret_val >= 0); assertEquals(crt_order_flags, crtorderflags); } @Test public void testH5Pset_attr_creation_order_tracked() { int ret_val = -1; int crtorderflags = 0; try { ret_val = H5.H5Pset_attr_creation_order(ocpl_id, HDF5Constants.H5P_CRT_ORDER_TRACKED); crtorderflags = H5.H5Pget_attr_creation_order(ocpl_id); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_attr_creation_order: " + err); } assertTrue("testH5Pset_attr_creation_order_tracked", ret_val >= 0); assertEquals(HDF5Constants.H5P_CRT_ORDER_TRACKED, crtorderflags); } @Test(expected = HDF5LibraryException.class) public void testH5Pset_attr_creation_order_invalidvalue() throws Throwable { H5.H5Pset_attr_creation_order(ocpl_id, HDF5Constants.H5P_CRT_ORDER_INDEXED); } @Test public void testH5Pset_copy_object() { int cpy_option = -1; try { H5.H5Pset_copy_object(ocp_plist_id, HDF5Constants.H5O_COPY_SHALLOW_HIERARCHY_FLAG); cpy_option = H5.H5Pget_copy_object(ocp_plist_id); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_copy_object: " + err); } assertEquals(HDF5Constants.H5O_COPY_SHALLOW_HIERARCHY_FLAG, cpy_option); try { H5.H5Pset_copy_object(ocp_plist_id, HDF5Constants.H5O_COPY_EXPAND_REFERENCE_FLAG); cpy_option = H5.H5Pget_copy_object(ocp_plist_id); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_copy_object: " + err); } assertEquals(HDF5Constants.H5O_COPY_EXPAND_REFERENCE_FLAG, cpy_option); } @Test(expected = HDF5LibraryException.class) public void testH5Pset_copy_object_invalidobject() throws Throwable { H5.H5Pset_copy_object(HDF5Constants.H5P_DEFAULT, HDF5Constants.H5O_COPY_SHALLOW_HIERARCHY_FLAG); } @Test public void testH5Pset_create_intermediate_group() { int ret_val = -1; try { ret_val = H5.H5Pset_create_intermediate_group(lcpl_id, true); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_create_intermediate_group: " + err); } assertTrue(ret_val>=0); } @Test(expected = HDF5LibraryException.class) public void testH5Pset_create_intermediate_group_invalidobject() throws Throwable { H5.H5Pset_create_intermediate_group(ocp_plist_id, true); } @Test public void testH5Pget_create_intermediate_group() { boolean flag = false; try { H5.H5Pset_create_intermediate_group(lcpl_id, true); flag = H5.H5Pget_create_intermediate_group(lcpl_id); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_create_intermediate_group: " + err); } assertEquals(true, flag); } @Test public void testH5Pget_create_intermediate_group_notcreated() { boolean flag = true; try { flag = H5.H5Pget_create_intermediate_group(lcpl_id); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_create_intermediate_group_notcreated: " + err); } assertEquals(false, flag); } @Test public void testH5Pset_data_transform() { String expression = "(5/9.0)*(x-32)"; int ret_val = -1; try { ret_val= H5.H5Pset_data_transform(plist_id, expression); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_data_transform: " + err); } assertTrue(ret_val>=0); } @Test(expected = NullPointerException.class) public void testH5Pset_data_transform_NullExpression() throws Throwable { H5.H5Pset_data_transform(plist_id, null); } @Test(expected = HDF5LibraryException.class) public void testH5Pset_data_transform_InvalidExpression1() throws Throwable { H5.H5Pset_data_transform(plist_id, ""); } @Test(expected = HDF5LibraryException.class) public void testH5Pset_data_transform_InvalidExpression2() throws Throwable { H5.H5Pset_data_transform(plist_id, "hello"); } @Test public void testH5Pget_data_transform() { String expression = "(5/9.0)*(x-32)"; String [] express = {""}; long express_size = 0; long size = 20; try { H5.H5Pset_data_transform(plist_id, expression); express_size = H5.H5Pget_data_transform(plist_id, express, size); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_data_transform: " + err); } assertTrue(express_size>=0); assertTrue("The data transform expression: ", expression.equals(express[0])); } @Test(expected = HDF5LibraryException.class) public void testH5Pget_data_transform_ExpressionNotSet() throws Throwable { String [] express = {""}; H5.H5Pget_data_transform(plist_id, express, 20); } @Test(expected = IllegalArgumentException.class) public void testH5Pget_data_transform_IllegalSize() throws Throwable { String [] express = {""}; H5.H5Pset_data_transform(plist_id, "(5/9.0)*(x-32)"); H5.H5Pget_data_transform(plist_id, express, 0); } @Test public void testH5Pget_elink_acc_flags() { int get_flags = -1; try { get_flags = H5.H5Pget_elink_acc_flags(gapl_id); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_elink_acc_flags: " + err); } assertTrue("H5Pget_elink_acc_flags", get_flags >= 0); assertEquals(HDF5Constants.H5F_ACC_DEFAULT, get_flags); } @Test public void testH5Pset_elink_acc_flags() { int get_flags = -1; int ret_val = -1; try { ret_val = H5.H5Pset_elink_acc_flags(lapl_id, HDF5Constants.H5F_ACC_RDWR); get_flags = H5.H5Pget_elink_acc_flags(lapl_id); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_elink_acc_flags: " + err); } assertTrue("H5Pset_elink_acc_flags", ret_val >= 0); assertEquals(HDF5Constants.H5F_ACC_RDWR, get_flags); } @Test(expected = IllegalArgumentException.class) public void testH5Pset_elink_acc_flags_InvalidFlag1() throws Throwable { H5.H5Pset_elink_acc_flags(lapl_id, HDF5Constants.H5F_ACC_TRUNC); } @Test(expected = IllegalArgumentException.class) public void testH5Pset_elink_acc_flags_InvalidFlag2() throws Throwable { H5.H5Pset_elink_acc_flags(lapl_id, -1); } @Test public void testH5Pset_link_phase_change() { int ret_val = -1; try { ret_val = H5.H5Pset_link_phase_change(fcpl_id , 2, 2); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_link_phase_change: " + err); } assertTrue("H5Pset_link_phase_change", ret_val >= 0); } @Test(expected = IllegalArgumentException.class) public void testH5Pset_link_phase_change_Highmax_Compact() throws Throwable { H5.H5Pset_link_phase_change(fcpl_id , 70000000, 3); } @Test(expected = IllegalArgumentException.class) public void testH5Pset_link_phase_change_max_compactLESSTHANmin_dense() throws Throwable { H5.H5Pset_link_phase_change(fcpl_id , 5, 6); } @Test public void testH5Pget_link_phase_change() { int ret_val = -1; int[] links = new int[2]; try { ret_val = H5.H5Pget_link_phase_change(fcpl_id, links); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_link_phase_change: " + err); } assertTrue("testH5Pget_link_phase_change", ret_val >= 0); assertEquals("Default value of maximum compact storage", 8, links[0]); assertEquals("Default value of minimum dense storage", 6, links[1]); } @Test public void testH5Pget_link_phase_change_EqualsSet() { int[] links = new int[2]; try { H5.H5Pset_link_phase_change(fcpl_id , 10, 7); H5.H5Pget_link_phase_change(fcpl_id, links); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_link_phase_change_EqualsSet: " + err); } assertEquals("Value of maximum compact storage set", 10, links[0]); assertEquals("Value of minimum dense storage set", 7, links[1]); } @Test(expected = NullPointerException.class) public void testH5Pget_link_phase_change_Null() throws Throwable { H5.H5Pget_link_phase_change(fcpl_id, null); } @Test public void testH5Pget_attr_phase_change() { int ret_val = -1; int[] attributes = new int[2]; try { ret_val = H5.H5Pget_attr_phase_change(ocpl_id, attributes); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_attr_phase_change: " + err); } assertTrue("testH5Pget_attr_phase_change", ret_val >= 0); assertEquals("Default value of the max. no. of attributes stored in compact storage", 8, attributes[0]); assertEquals("Default value of the min. no. of attributes stored in dense storage", 6, attributes[1]); } @Test public void testH5Pget_shared_mesg_phase_change() { int ret_val = -1; int[] size = new int[2]; try { ret_val = H5.H5Pget_shared_mesg_phase_change(fcpl_id, size); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_shared_mesg_phase_change: " + err); } assertTrue("testH5Pget_shared_mesg_phase_change", ret_val >= 0); } @Test public void testH5Pget_shared_mesg_phase_change_EqualsSET() { int[] size = new int[2]; try { H5.H5Pset_shared_mesg_phase_change(fcpl_id,50, 40); H5.H5Pget_shared_mesg_phase_change(fcpl_id, size); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_shared_mesg_phase_change_EqualsSET: " + err); } assertEquals("Value of maximum list set", 50, size[0]); assertEquals("Value of minimum btree set", 40, size[1]); } @Test public void testH5Pset_shared_mesg_phase_change() { int ret_val = -1; try { ret_val = H5.H5Pset_shared_mesg_phase_change(fcpl_id,2, 1); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_shared_mesg_phase_change: " + err); } assertTrue("H5Pset_shared_mesg_phase_change", ret_val >= 0); } @Test(expected = IllegalArgumentException.class) public void testH5PH5Pset_shared_mesg_phase_change_HighMaxlistValue() throws Throwable { H5.H5Pset_shared_mesg_phase_change(fcpl_id, 5001, 4000); } @Test(expected = IllegalArgumentException.class) public void testH5PH5Pset_shared_mesg_phase_change_HighMinbtreeValue() throws Throwable { H5.H5Pset_shared_mesg_phase_change(fcpl_id, 5000, 5001); } @Test(expected = IllegalArgumentException.class) public void testH5PH5Pset_shared_mesg_phase_change_MinbtreeGreaterThanMaxlist() throws Throwable { H5.H5Pset_link_phase_change(fcpl_id , 3, 7); } @Test public void testH5Pget_shared_mesg_nindexes() { int nindexes = -1; try { nindexes = H5.H5Pget_shared_mesg_nindexes(fcpl_id); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_shared_mesg_nindexes: " + err); } assertTrue("H5Pget_shared_mesg_nindexes", nindexes >= 0); } @Test public void testH5Pset_shared_mesg_nindexes() { int nindexes = -1; int ret_val = -1; try { ret_val = H5.H5Pset_shared_mesg_nindexes(fcpl_id, 7); nindexes = H5.H5Pget_shared_mesg_nindexes(fcpl_id); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_shared_mesg_nindexes: " + err); } assertTrue("H5Pset_shared_mesg_nindexes", ret_val >= 0); assertEquals("Value of nindexes is equal to value set",7 ,nindexes); } @Test(expected = IllegalArgumentException.class) public void testH5Pset_shared_mesg_nindexes_InvalidHIGHnindexes()throws Throwable { H5.H5Pset_shared_mesg_nindexes(fcpl_id, 9); } @Test public void testH5Pset_shared_mesg_index() { int ret_val = -1; try { H5.H5Pset_shared_mesg_nindexes(fcpl_id, 2); ret_val = H5.H5Pset_shared_mesg_index(fcpl_id, 0,HDF5Constants.H5O_SHMESG_ATTR_FLAG, 10); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_shared_mesg_index: " + err); } assertTrue("H5Pset_shared_mesg_index", ret_val >= 0); } @Test(expected = IllegalArgumentException.class) public void testH5Pset_shared_mesg_index_Invalid_indexnum() throws Throwable { H5.H5Pset_shared_mesg_index(fcpl_id, 2,HDF5Constants.H5O_SHMESG_ATTR_FLAG, 10); } @Test(expected = IllegalArgumentException.class) public void testH5Pset_shared_mesg_index_InvalidFlag() throws Throwable { H5.H5Pset_shared_mesg_nindexes(fcpl_id, 7); H5.H5Pset_shared_mesg_index(fcpl_id, 2,HDF5Constants.H5O_SHMESG_ALL_FLAG + 1, 10); } @Test public void testH5Pget_shared_mesg_index() { int ret_val = -1; int[] mesg_info = new int[2]; try { H5.H5Pset_shared_mesg_nindexes(fcpl_id, 2); H5.H5Pset_shared_mesg_index(fcpl_id, 0,HDF5Constants.H5O_SHMESG_ATTR_FLAG, 10); ret_val = H5.H5Pget_shared_mesg_index(fcpl_id, 0, mesg_info); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_shared_mesg_index: " + err); } assertTrue("H5Pget_shared_mesg_index", ret_val >= 0); assertEquals("Type of message", HDF5Constants.H5O_SHMESG_ATTR_FLAG, mesg_info[0]); assertEquals("minimum message size", 10, mesg_info[1]); } @Test(expected = IllegalArgumentException.class) public void testH5Pget_shared_mesg_index_Invalid_indexnum() throws Throwable { int[] mesg_info = new int[2]; H5.H5Pget_shared_mesg_index(fcpl_id, 0, mesg_info); } @Test public void testH5Pset_local_heap_size_hint() { int ret_val = -1; try { ret_val = H5.H5Pset_local_heap_size_hint(gcpl_id, 0); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_local_heap_size_hint: " + err); } assertTrue("H5Pset_local_heap_size_hint", ret_val >= 0); } @Test public void testH5Pget_local_heap_size_hint() { long size_hint = -1; try { size_hint = H5.H5Pget_local_heap_size_hint(gcpl_id); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_local_heap_size_hint: " + err); } assertTrue("H5Pget_local_heap_size_hint", size_hint >= 0); } @Test public void testH5Pset_nbit() { int ret_val = -1; try { ret_val = H5.H5Pset_nbit(ocpl_id); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_nbit: " + err); } assertTrue("H5Pset_nbit", ret_val >= 0); } @Test public void testH5Pset_scaleoffset() { int ret_val = -1; int scale_type = HDF5Constants.H5Z_SO_FLOAT_DSCALE; int scale_factor = HDF5Constants.H5Z_SO_INT_MINBITS_DEFAULT; try { ret_val = H5.H5Pset_scaleoffset(ocpl_id, scale_type, scale_factor); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_scaleoffset: " + err); } assertTrue("H5Pset_scaleoffset", ret_val >= 0); } @Test(expected = IllegalArgumentException.class) public void testH5Pset_scaleoffset_Invalidscale_type() throws Throwable { H5.H5Pset_scaleoffset(ocpl_id, 3, 1); } @Test(expected = IllegalArgumentException.class) public void testH5Pset_scaleoffset_Invalidscale_factor() throws Throwable { H5.H5Pset_scaleoffset(ocpl_id, HDF5Constants.H5Z_SO_INT, -1); } @Test public void testH5Pset_est_link_info() { int ret_val = -1; try { ret_val = H5.H5Pset_est_link_info(gcpl_id, 0,10); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_est_link_info: " + err); } assertTrue("H5Pset_est_link_info", ret_val >= 0); } @Test(expected = IllegalArgumentException.class) public void testH5Pset_est_link_info_InvalidValues() throws Throwable { H5.H5Pset_est_link_info(gcpl_id, 100000,10); } @Test public void testH5Pget_est_link_info() { int ret_val = -1; int[] link_info = new int[2]; try { ret_val = H5.H5Pget_est_link_info(gcpl_id, link_info); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_est_link_info: " + err); } assertTrue("H5Pget_est_link_info", ret_val >= 0); } @Test public void testH5Pset_elink_prefix() { int ret_val = -1; String prefix = "tmp"; try { ret_val = H5.H5Pset_elink_prefix(plapl_id, prefix); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_est_link_info: " + err); } assertTrue("H5Pset_elink_prefix", ret_val >= 0); } @Test(expected = NullPointerException.class) public void testH5Pset_elink_prefix_null() throws Throwable{ H5.H5Pset_elink_prefix(plapl_id, null); } @Test public void testH5Pget_elink_prefix() { String prefix = "tmp"; String[] pre = {""}; long prefix_size = 0; try { H5.H5Pset_elink_prefix(plapl_id, prefix); prefix_size = H5.H5Pget_elink_prefix(plapl_id, pre); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_elink_prefix: " + err); } assertTrue(prefix_size>=0); assertTrue("The prefix: ", prefix.equals(pre[0])); } @Test(expected = NullPointerException.class) public void testH5Pget_elink_prefix_null() throws Throwable { H5.H5Pget_elink_prefix(plapl_id, null); } @Test(expected = NullPointerException.class) public void testH5Pget_version_null() throws Throwable { H5.H5Pget_version(fcpl_id, null); } @Test public void testH5Pget_version() { int[] version_info = {255,255,255,255}; try { _createH5File(fcpl_id, fapl_id); H5.H5Pget_version(fcpl_id, version_info); deleteH5file(); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_version: " + err); } assertTrue("super block version: "+version_info[0], version_info[0] == 0); assertTrue("global freelist version: "+version_info[1], version_info[1] == 0); assertTrue("symbol table version: "+version_info[2], version_info[2] == 0); assertTrue("shared object header version: "+version_info[3], version_info[3] == 0); } @Test(expected = NullPointerException.class) public void testH5Pget_userblock_null() throws Throwable { H5.H5Pget_userblock(fcpl_id, null); } @Test public void testH5P_userblock() { int[] version_info = {255,255,255,255}; long[] size = {0}; try { H5.H5Pset_userblock(fcpl_id, 1024); _createH5File(fcpl_id, fapl_id); /* Close FCPL */ H5.H5Pclose(fcpl_id); /* Get the file's dataset creation property list */ fcpl_id = H5.H5Fget_create_plist(H5fid); /* Get the file's version information */ H5.H5Pget_version(fcpl_id, version_info); H5.H5Pget_userblock(fcpl_id, size); deleteH5file(); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_userblock: " + err); } assertTrue("super block version: "+version_info[0], version_info[0] == 0); assertTrue("global freelist version: "+version_info[1], version_info[1] == 0); assertTrue("symbol table version: "+version_info[2], version_info[2] == 0); assertTrue("shared object header version: "+version_info[3], version_info[3] == 0); assertTrue("user block size: "+size[0], size[0] == 1024); } @Test(expected = NullPointerException.class) public void testH5Pget_sizes_null() throws Throwable { H5.H5Pget_sizes(fcpl_id, null); } @Test public void testH5P_sizes() { int[] version_info = {255,255,255,255}; long[] size = {0,0}; try { H5.H5Pset_sizes(fcpl_id, 4, 8); _createH5File(fcpl_id, fapl_id); /* Close FCPL */ H5.H5Pclose(fcpl_id); /* Get the file's dataset creation property list */ fcpl_id = H5.H5Fget_create_plist(H5fid); /* Get the file's version information */ H5.H5Pget_version(fcpl_id, version_info); H5.H5Pget_sizes(fcpl_id, size); deleteH5file(); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_sizes: " + err); } assertTrue("super block version: "+version_info[0], version_info[0] == 0); assertTrue("global freelist version: "+version_info[1], version_info[1] == 0); assertTrue("symbol table version: "+version_info[2], version_info[2] == 0); assertTrue("shared object header version: "+version_info[3], version_info[3] == 0); assertTrue("sizeof_addr size: "+size[0], size[0] == 4); assertTrue("sizeof_size size: "+size[1], size[1] == 8); } @Test(expected = NullPointerException.class) public void testH5Pget_sym_k_null() throws Throwable { H5.H5Pget_sym_k(fcpl_id, null); } @Test public void testH5P_sym_k() { int[] version_info = {255,255,255,255}; int[] size = {0,0}; try { H5.H5Pset_sym_k(fcpl_id, 32, 8); _createH5File(fcpl_id, fapl_id); /* Close FCPL */ H5.H5Pclose(fcpl_id); /* Get the file's dataset creation property list */ fcpl_id = H5.H5Fget_create_plist(H5fid); /* Get the file's version information */ H5.H5Pget_version(fcpl_id, version_info); H5.H5Pget_sym_k(fcpl_id, size); deleteH5file(); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_sym_k: " + err); } assertTrue("super block version: "+version_info[0], version_info[0] == 0); assertTrue("global freelist version: "+version_info[1], version_info[1] == 0); assertTrue("symbol table version: "+version_info[2], version_info[2] == 0); assertTrue("shared object header version: "+version_info[3], version_info[3] == 0); assertTrue("symbol table tree rank: "+size[0], size[0] == 32); assertTrue("symbol table node size: "+size[1], size[1] == 8); } @Test(expected = NullPointerException.class) public void testH5Pget_istore_k_null() throws Throwable { H5.H5Pget_istore_k(fcpl_id, null); } @Test public void testH5P_istore_k() { int[] version_info = {255,255,255,255}; int[] size = {0}; try { H5.H5Pset_istore_k(fcpl_id, 64); _createH5File(fcpl_id, fapl_id); /* Close FCPL */ H5.H5Pclose(fcpl_id); /* Get the file's dataset creation property list */ fcpl_id = H5.H5Fget_create_plist(H5fid); /* Get the file's version information */ H5.H5Pget_version(fcpl_id, version_info); H5.H5Pget_istore_k(fcpl_id, size); deleteH5file(); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_sym_k: " + err); } assertTrue("super block version: "+version_info[0], version_info[0] == 1); assertTrue("global freelist version: "+version_info[1], version_info[1] == 0); assertTrue("symbol table version: "+version_info[2], version_info[2] == 0); assertTrue("shared object header version: "+version_info[3], version_info[3] == 0); assertTrue("chunked storage b-tree 1/2-rank: "+size[0], size[0] == 64); } @Test public void testH5P_obj_track_times() { boolean default_ret_val = false; boolean ret_val = true; try { default_ret_val = H5.H5Pget_obj_track_times(ocpl_id); H5.H5Pset_obj_track_times(ocpl_id, false); ret_val = H5.H5Pget_obj_track_times(ocpl_id); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_obj_track_times: " + err); } assertTrue("H5Pget_obj_track_times default", default_ret_val); assertFalse("H5Pget_obj_track_times", ret_val); } @Test public void testH5Pget_char_encoding() { int char_encoding = 0; try { char_encoding = H5.H5Pget_char_encoding(acpl_id); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_char_encoding: " + err); } assertTrue("testH5Pget_char_encoding", char_encoding == HDF5Constants.H5T_CSET_ASCII); try { H5.H5Pset_char_encoding(acpl_id, HDF5Constants.H5T_CSET_UTF8); char_encoding = H5.H5Pget_char_encoding(acpl_id); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_char_encoding: " + err); } assertTrue("testH5Pget_char_encoding", char_encoding == HDF5Constants.H5T_CSET_UTF8); } @Test public void testH5P_fill_time() { int[] fill_time = {0}; try { H5.H5Pget_fill_time(ocpl_id, fill_time); assertTrue("fill_time: "+fill_time[0], fill_time[0] == HDF5Constants.H5D_FILL_TIME_IFSET); H5.H5Pset_fill_time(ocpl_id, HDF5Constants.H5D_FILL_TIME_ALLOC); H5.H5Pget_fill_time(ocpl_id, fill_time); assertTrue("fill_time: "+fill_time[0], fill_time[0] == HDF5Constants.H5D_FILL_TIME_ALLOC); H5.H5Pset_fill_time(ocpl_id, HDF5Constants.H5D_FILL_TIME_NEVER); H5.H5Pget_fill_time(ocpl_id, fill_time); assertTrue("fill_time: "+fill_time[0], fill_time[0] == HDF5Constants.H5D_FILL_TIME_NEVER); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_fill_time: " + err); } } @Test public void testH5P_alloc_time() { int[] alloc_time = {0}; try { H5.H5Pget_alloc_time(ocpl_id, alloc_time); assertTrue("alloc_time: "+alloc_time[0], alloc_time[0] == HDF5Constants.H5D_ALLOC_TIME_LATE); H5.H5Pset_alloc_time(ocpl_id, HDF5Constants.H5D_ALLOC_TIME_EARLY); H5.H5Pget_alloc_time(ocpl_id, alloc_time); assertTrue("alloc_time: "+alloc_time[0], alloc_time[0] == HDF5Constants.H5D_ALLOC_TIME_EARLY); H5.H5Pset_alloc_time(ocpl_id, HDF5Constants.H5D_ALLOC_TIME_INCR); H5.H5Pget_alloc_time(ocpl_id, alloc_time); assertTrue("alloc_time: "+alloc_time[0], alloc_time[0] == HDF5Constants.H5D_ALLOC_TIME_INCR); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_alloc_time: " + err); } } @Test public void testH5P_fill_value() { int[] fill_value = {-1}; int[] fill_value_status = {-1}; try { H5.H5Pfill_value_defined(ocpl_id, fill_value_status); assertTrue("fill_value_status: "+fill_value_status[0], fill_value_status[0] == HDF5Constants.H5D_FILL_VALUE_DEFAULT); H5.H5Pget_fill_value(ocpl_id, HDF5Constants.H5T_NATIVE_INT, fill_value); assertTrue("fill_value: "+fill_value[0], fill_value[0] == 0); fill_value[0] = 255; H5.H5Pset_fill_value(ocpl_id, HDF5Constants.H5T_NATIVE_INT, fill_value); H5.H5Pget_fill_value(ocpl_id, HDF5Constants.H5T_NATIVE_INT, fill_value); assertTrue("fill_value: "+fill_value[0], fill_value[0] == 255); H5.H5Pfill_value_defined(ocpl_id, fill_value_status); assertTrue("fill_value_status: "+fill_value_status[0], fill_value_status[0] == HDF5Constants.H5D_FILL_VALUE_USER_DEFINED); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_fill_value: " + err); } } @Test public void testH5P_layout() { int layout_type = -1; try { layout_type = H5.H5Pget_layout(ocpl_id); assertTrue("layout: "+layout_type, layout_type == HDF5Constants.H5D_CONTIGUOUS); H5.H5Pset_layout(ocpl_id, HDF5Constants.H5D_COMPACT); layout_type = H5.H5Pget_layout(ocpl_id); assertTrue("layout: "+layout_type, layout_type == HDF5Constants.H5D_COMPACT); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_layout: " + err); } } @Test public void testH5P_chunk() { long[] chunk_size = {0,0}; long[] chunk_new_size = {2,3}; int layout_type = -1; try { H5.H5Pset_chunk(ocpl_id, 2, chunk_new_size); H5.H5Pget_chunk(ocpl_id, 2, chunk_size); assertTrue("chunk: "+chunk_size[0], chunk_size[0] == chunk_new_size[0]); assertTrue("chunk: "+chunk_size[1], chunk_size[1] == chunk_new_size[1]); layout_type = H5.H5Pget_layout(ocpl_id); assertTrue("layout: "+layout_type, layout_type == HDF5Constants.H5D_CHUNKED); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_chunk: " + err); } } } libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/TestH5PData.java000066400000000000000000000143731256564762100253560ustar00rootroot00000000000000package test.hdf5lib; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import java.io.File; import java.text.DecimalFormat; import java.text.NumberFormat; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.HDF5Constants; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import org.junit.After; import org.junit.Before; import org.junit.Test; public class TestH5PData { private static final String H5_FILE = "test.h5"; private static final int DIM_X = 12; private static final int DIM_Y = 18; int H5fid = -1; int H5dsid = -1; int H5did = -1; int plist_id = -1; long[] H5dims = { DIM_X, DIM_Y }; double windchillF[][] = {{36.0, 31.0, 25.0, 19.0, 13.0, 7.0, 1.0, -5.0, -11.0, -16.0, -22.0, -28.0, -34.0, -40.0, -46.0, -52.0, -57.0, -63.0}, {34.0, 27.0, 21.0, 15.0, 9.0, 3.0, -4.0, -10.0, -16.0, -22.0, -28.0, -35.0, -41.0, -47.0, -53.0, -59.0, -66.0, -72.0}, {32.0, 25.0, 19.0, 13.0, 6.0, 0.0, -7.0, -13.0, -19.0, -26.0, -32.0, -39.0, -45.0, -51.0, -58.0, -64.0, -71.0, -77.0}, {30.0, 24.0, 17.0, 11.0, 4.0, -2.0, -9.0, -15.0, -22.0, -29.0, -35.0, -42.0, -48.0, -55.0, -61.0, -68.0, -74.0, -81.0}, {29.0, 23.0, 16.0, 9.0, 3.0, -4.0, -11.0, -17.0, -24.0, -31.0, -37.0, -44.0, -51.0, -58.0, -64.0, -71.0, -78.0, -84.0}, {28.0, 22.0, 15.0, 8.0, 1.0, -5.0, -12.0, -19.0, -26.0, -33.0, -39.0, -46.0, -53.0, -60.0, -67.0, -73.0, -80.0, -87.0}, {28.0, 21.0, 14.0, 7.0, 0.0, -7.0, -14.0, -21.0, -27.0, -34.0, -41.0, -48.0, -55.0, -62.0, -69.0, -76.0, -82.0, -89.0}, {27.0, 20.0, 13.0, 6.0, -1.0, -8.0, -15.0, -22.0, -29.0, -36.0, -43.0, -50.0, -57.0, -64.0, -71.0, -78.0, -84.0, -91.0}, {26.0, 19.0, 12.0, 5.0, -2.0, -9.0, -16.0, -23.0, -30.0, -37.0, -44.0, -51.0, -58.0, -65.0, -72.0, -79.0, -86.0, -93.0}, {26.0, 19.0, 12.0, 4.0, -3.0, -10.0, -17.0, -24.0, -31.0, -38.0, -45.0, -52.0, -60.0, -67.0, -74.0, -81.0, -88.0, -95.0}, {25.0, 18.0, 11.0, 4.0, -3.0, -11.0, -18.0, -25.0, -32.0, -39.0, -46.0, -54.0, -61.0, -68.0, -75.0, -82.0, -89.0, -97.0}, {25.0, 17.0, 10.0, 3.0, -4.0, -11.0, -19.0, -26.0, -33.0, -40.0, -48.0, -55.0, -62.0, -69.0, -76.0, -84.0, -91.0, -98.0} }; private final void _deleteFile(String filename) { File file = new File(filename); if (file.exists()) { try {file.delete();} catch (SecurityException e) {} } } private final int _createFloatDataset(int fid, int dsid, String name, int dapl) { int did = -1; try { did = H5.H5Dcreate(fid, name, HDF5Constants.H5T_NATIVE_FLOAT, dsid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, dapl); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Dcreate: " + err); } assertTrue("TestH5D._createFloatDataset: ", did > 0); return did; } @Before public void createH5file() throws NullPointerException, HDF5Exception { assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0); try { H5fid = H5.H5Fcreate(H5_FILE, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); H5dsid = H5.H5Screate_simple(2, H5dims, null); H5did = _createFloatDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT); plist_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_XFER); } catch (Throwable err) { err.printStackTrace(); fail("TestH5D.createH5file: " + err); } assertTrue("TestH5D.createH5file: H5.H5Fcreate: ",H5fid > 0); assertTrue("TestH5D.createH5file: H5.H5Screate_simple: ",H5dsid > 0); assertTrue("TestH5D.createH5file: _createFloatDataset: ",H5did > 0); assertTrue(plist_id > 0); H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); } @After public void deleteH5file() throws HDF5LibraryException { if (H5dsid > 0) try {H5.H5Sclose(H5dsid);} catch (Exception ex) {} if (H5did > 0) try {H5.H5Dclose(H5did);} catch (Exception ex) {} if (H5fid > 0) try {H5.H5Fclose(H5fid);} catch (Exception ex) {} _deleteFile(H5_FILE); if (plist_id > 0) try {H5.H5Pclose(plist_id);} catch (Exception ex) {} } @Test public void testH5Pdata_transform() { String f_to_c = "(5/9.0)*(x-32)"; double windchillFread[][] = new double[DIM_X][DIM_Y]; double windchillC; NumberFormat formatter = new DecimalFormat("#0.000"); try { H5.H5Pset_data_transform(plist_id, f_to_c); H5.H5Dwrite(H5did, HDF5Constants.H5T_NATIVE_DOUBLE, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, plist_id, windchillF); H5.H5Dread(H5did, HDF5Constants.H5T_NATIVE_DOUBLE, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, windchillFread); } catch (Throwable err) { err.printStackTrace(); fail("H5Pdata_transform: " + err); } for(int row = 0; row < DIM_X; row++) for(int col = 0; col < DIM_Y; col++) { windchillC = (5/9.0)*(windchillF[row][col]-32); String Cstr = formatter.format(windchillC); String Fread = formatter.format(windchillFread[row][col]); assertTrue("H5Pdata_transform: <"+row+","+col+">"+Fread+"="+Cstr, Fread.compareTo(Cstr)==0); } } @Test public void testH5P_buffer() { long default_size = 0; long size = 0; try { default_size = H5.H5Pget_buffer_size(plist_id); H5.H5Pset_buffer_size(plist_id, DIM_X*DIM_Y); size = H5.H5Pget_buffer_size(plist_id); } catch (Throwable err) { err.printStackTrace(); fail("H5P_buffer: " + err); } assertTrue("H5P_buffer default: "+default_size, default_size==1024*1024); assertTrue("H5P_buffer default: "+size, size==DIM_X*DIM_Y); } } libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/TestH5Pfapl.java000066400000000000000000001507721256564762100254330ustar00rootroot00000000000000package test.hdf5lib; import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import java.io.File; import java.text.DecimalFormat; import java.text.NumberFormat; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.HDF5Constants; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import ncsa.hdf.hdf5lib.structs.H5AC_cache_config_t; import org.junit.After; import org.junit.Before; import org.junit.Test; @SuppressWarnings("all") public class TestH5Pfapl { private static final String H5_FILE = "test.h5"; private static final String H5_LOG_FILE = "test.log"; private static final String H5_FAMILY_FILE = "test%05d"; private static final String H5_MULTI_FILE = "testmulti"; private static char MULTI_LETTERS[] = {'X','s','b','r','g','l','o'}; private static final int DIM_X = 4; private static final int DIM_Y = 6; private static final int DIMF_X = 12; private static final int DIMF_Y = 18; int H5fid = -1; int H5dsid = -1; int H5did = -1; int H5Fdsid = -1; int H5Fdid = -1; long[] H5dims = { DIM_X, DIM_Y }; int fapl_id = -1; int plapl_id = -1; int dapl_id = -1; int multi_dxplid = -1; int plist_id = -1; int btplist_id = -1; long[] H5Fdims = { DIMF_X, DIMF_Y }; double windchillF[][] = {{36.0, 31.0, 25.0, 19.0, 13.0, 7.0, 1.0, -5.0, -11.0, -16.0, -22.0, -28.0, -34.0, -40.0, -46.0, -52.0, -57.0, -63.0}, {34.0, 27.0, 21.0, 15.0, 9.0, 3.0, -4.0, -10.0, -16.0, -22.0, -28.0, -35.0, -41.0, -47.0, -53.0, -59.0, -66.0, -72.0}, {32.0, 25.0, 19.0, 13.0, 6.0, 0.0, -7.0, -13.0, -19.0, -26.0, -32.0, -39.0, -45.0, -51.0, -58.0, -64.0, -71.0, -77.0}, {30.0, 24.0, 17.0, 11.0, 4.0, -2.0, -9.0, -15.0, -22.0, -29.0, -35.0, -42.0, -48.0, -55.0, -61.0, -68.0, -74.0, -81.0}, {29.0, 23.0, 16.0, 9.0, 3.0, -4.0, -11.0, -17.0, -24.0, -31.0, -37.0, -44.0, -51.0, -58.0, -64.0, -71.0, -78.0, -84.0}, {28.0, 22.0, 15.0, 8.0, 1.0, -5.0, -12.0, -19.0, -26.0, -33.0, -39.0, -46.0, -53.0, -60.0, -67.0, -73.0, -80.0, -87.0}, {28.0, 21.0, 14.0, 7.0, 0.0, -7.0, -14.0, -21.0, -27.0, -34.0, -41.0, -48.0, -55.0, -62.0, -69.0, -76.0, -82.0, -89.0}, {27.0, 20.0, 13.0, 6.0, -1.0, -8.0, -15.0, -22.0, -29.0, -36.0, -43.0, -50.0, -57.0, -64.0, -71.0, -78.0, -84.0, -91.0}, {26.0, 19.0, 12.0, 5.0, -2.0, -9.0, -16.0, -23.0, -30.0, -37.0, -44.0, -51.0, -58.0, -65.0, -72.0, -79.0, -86.0, -93.0}, {26.0, 19.0, 12.0, 4.0, -3.0, -10.0, -17.0, -24.0, -31.0, -38.0, -45.0, -52.0, -60.0, -67.0, -74.0, -81.0, -88.0, -95.0}, {25.0, 18.0, 11.0, 4.0, -3.0, -11.0, -18.0, -25.0, -32.0, -39.0, -46.0, -54.0, -61.0, -68.0, -75.0, -82.0, -89.0, -97.0}, {25.0, 17.0, 10.0, 3.0, -4.0, -11.0, -19.0, -26.0, -33.0, -40.0, -48.0, -55.0, -62.0, -69.0, -76.0, -84.0, -91.0, -98.0} }; private final void _deleteFile(String filename) { File file = null; try { file = new File(filename); } catch (Throwable err) {} if (file.exists()) { try {file.delete();} catch (SecurityException e) {} } } private final void _deleteLogFile() { File file = null; try { file = new File(H5_LOG_FILE); } catch (Throwable err) {} if (file.exists()) { try {file.delete();} catch (SecurityException e) {} } } private final void _deleteFamilyFile() { File file = null; for(int indx = 0; ;indx++) { java.text.DecimalFormat myFormat = new java.text.DecimalFormat("00000"); try { file = new File("test"+myFormat.format(new Integer(indx))+".h5"); } catch (Throwable err) {} if (file.exists()) { try {file.delete();} catch (SecurityException e) {} } else return; } } private final void _deleteMultiFile() { File file = null; for(int indx = 1;indx<7;indx++) { try { file = new File(H5_MULTI_FILE+"-"+MULTI_LETTERS[indx]+".h5"); } catch (Throwable err) {} if (file.exists()) { try {file.delete();} catch (SecurityException e) {} } } } private final int _createDataset(int fid, int dsid, String name, int dapl) { int did = -1; try { did = H5.H5Dcreate(fid, name, HDF5Constants.H5T_STD_I32BE, dsid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, dapl); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Dcreate: " + err); } assertTrue("TestH5D._createDataset: ", did > 0); return did; } private final void _createFloatDataset() { try { H5Fdsid = H5.H5Screate_simple(2, H5Fdims, null); H5Fdid = H5.H5Dcreate(H5fid, "dsfloat", HDF5Constants.H5T_NATIVE_FLOAT, H5Fdsid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Dcreate: " + err); } assertTrue("TestH5D._createFloatDataset: ", H5Fdid > 0); try { H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); } catch (Throwable err) { err.printStackTrace(); } } private final void _createH5multiFileDS() { try { H5did = _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("TestH5D.createH5file: " + err); } assertTrue("TestH5D.createH5file: _createDataset: ", H5did > 0); try { H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); } catch (Throwable err) { err.printStackTrace(); } } private final void _createH5File(int fapl) { try { H5fid = H5.H5Fcreate(H5_FILE, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, fapl); H5dsid = H5.H5Screate_simple(2, H5dims, null); H5did = _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("TestH5D.createH5file: " + err); } assertTrue("TestH5D.createH5file: H5.H5Fcreate: ", H5fid > 0); assertTrue("TestH5D.createH5file: H5.H5Screate_simple: ", H5dsid > 0); assertTrue("TestH5D.createH5file: _createDataset: ", H5did > 0); try { H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); } catch (Throwable err) { err.printStackTrace(); } } private final void _createH5familyFile(int fapl) { try { H5fid = H5.H5Fcreate(H5_FAMILY_FILE+".h5", HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, fapl); H5dsid = H5.H5Screate_simple(2, H5dims, null); H5did = _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("TestH5D.createH5file: " + err); } assertTrue("TestH5D.createH5file: H5.H5Fcreate: ", H5fid > 0); assertTrue("TestH5D.createH5file: H5.H5Screate_simple: ", H5dsid > 0); assertTrue("TestH5D.createH5file: _createDataset: ", H5did > 0); try { H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); } catch (Throwable err) { err.printStackTrace(); } } private final void _createH5multiFile(int fapl) { try { H5fid = H5.H5Fcreate(H5_MULTI_FILE, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, fapl); H5dsid = H5.H5Screate_simple(2, H5dims, null); } catch (Throwable err) { err.printStackTrace(); fail("TestH5D.createH5file: " + err); } assertTrue("TestH5D.createH5file: H5.H5Fcreate: ", H5fid > 0); assertTrue("TestH5D.createH5file: H5.H5Screate_simple: ", H5dsid > 0); try { H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); } catch (Throwable err) { err.printStackTrace(); } } public void deleteH5file() { _deleteFile(H5_FILE); } public void deleteH5familyfile() { _deleteFamilyFile(); } public void deleteH5multifile() { _deleteMultiFile(); } @Before public void createFileAccess() throws NullPointerException, HDF5Exception { assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0); try { fapl_id = H5.H5Pcreate(HDF5Constants.H5P_FILE_ACCESS); } catch (Throwable err) { err.printStackTrace(); fail("TestH5D.createFileAccess: " + err); } assertTrue(fapl_id > 0); try { plapl_id = H5.H5Pcreate(HDF5Constants.H5P_LINK_ACCESS); } catch (Throwable err) { err.printStackTrace(); fail("TestH5D.createFileAccess: " + err); } assertTrue(plapl_id > 0); try { multi_dxplid = H5.H5Pcreate(HDF5Constants.H5P_DATASET_XFER); plist_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_XFER); btplist_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_XFER); dapl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_ACCESS); } catch (Throwable err) { err.printStackTrace(); fail("TestH5D.createFileAccess: " + err); } assertTrue(multi_dxplid > 0); assertTrue(plist_id > 0); assertTrue(btplist_id > 0); assertTrue(dapl_id > 0); } @After public void deleteFileAccess() throws HDF5LibraryException { if (fapl_id > 0) try {H5.H5Pclose(fapl_id);} catch (Exception ex) {} if (plapl_id > 0) try {H5.H5Pclose(plapl_id);} catch (Exception ex) {} if (dapl_id > 0) try {H5.H5Pclose(dapl_id);} catch (Exception ex) {} if (plist_id > 0) try {H5.H5Pclose(plist_id);} catch (Exception ex) {} if (btplist_id > 0) try {H5.H5Pclose(btplist_id);} catch (Exception ex) {} if (multi_dxplid > 0) try {H5.H5Pclose(multi_dxplid);} catch (Exception ex) {} if (H5Fdsid > 0) try {H5.H5Sclose(H5Fdsid);} catch (Exception ex) {} if (H5Fdid > 0) try {H5.H5Dclose(H5Fdid);} catch (Exception ex) {} if (H5dsid > 0) try {H5.H5Sclose(H5dsid);} catch (Exception ex) {} if (H5did > 0) try {H5.H5Dclose(H5did);} catch (Exception ex) {} if (H5fid > 0) try {H5.H5Fclose(H5fid);} catch (Exception ex) {} } @Test public void testH5Pget_libver_bounds() { int ret_val = -1; int[] libver = new int[2]; try { ret_val = H5.H5Pget_libver_bounds(fapl_id, libver); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_libver_bounds: " + err); } assertTrue("testH5Pget_libver_bounds", ret_val >= 0); // Check the Earliest Version if the library assertEquals(HDF5Constants.H5F_LIBVER_EARLIEST, libver[0]); // Check the Latest Version if the library assertEquals(HDF5Constants.H5F_LIBVER_LATEST, libver[1]); } @Test public void testH5Pset_libver_bounds() { int ret_val = -1; int low = HDF5Constants.H5F_LIBVER_EARLIEST; int high = HDF5Constants.H5F_LIBVER_LATEST; int[] libver = new int[2]; try { ret_val = H5.H5Pset_libver_bounds(fapl_id, low, high); H5.H5Pget_libver_bounds(fapl_id, libver); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_libver_bounds: " + err); } assertTrue("testH5Pset_libver_bounds", ret_val >= 0); // Check the Earliest Version if the library assertEquals(HDF5Constants.H5F_LIBVER_EARLIEST, libver[0]); // Check the Latest Version if the library assertEquals(HDF5Constants.H5F_LIBVER_LATEST, libver[1]); } @Test(expected = HDF5LibraryException.class) public void testH5Pset_elink_fapl_NegativeID() throws Throwable { H5.H5Pset_elink_fapl(-1, fapl_id ); } @Test public void testH5Pset_elink_fapl() { int ret_val = -1; try { ret_val = H5.H5Pset_elink_fapl(plapl_id, fapl_id ); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_elink_fapl: " + err); } assertTrue("H5Pset_elink_fapl", ret_val >= 0); } @Test public void testH5Pget_elink_fapl() { int ret_val_id = -1; try { ret_val_id = H5.H5Pget_elink_fapl(plapl_id); assertTrue("H5Pget_elink_fapl", ret_val_id >= 0); assertEquals(HDF5Constants.H5P_DEFAULT, ret_val_id ); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_elink_fapl: " + err); } finally { if (ret_val_id > 0) try {H5.H5Pclose(ret_val_id);} catch (Exception ex) {} } } @Test public void testH5P_elink_fapl() { int ret_val_id = -1; try { H5.H5Pset_elink_fapl(plapl_id, fapl_id ); ret_val_id = H5.H5Pget_elink_fapl(plapl_id); assertTrue("H5P_elink_fapl", ret_val_id >= 0); } catch (Throwable err) { err.printStackTrace(); fail("H5P_elink_fapl: " + err); } finally { if (ret_val_id > 0) try {H5.H5Pclose(ret_val_id);} catch (Exception ex) {} } } @Test public void testH5P_elink_file_cache_size() { int elink_fapl_id = -1; int efc_size = 0; try { H5.H5Pset_elink_fapl(plapl_id, fapl_id ); elink_fapl_id = H5.H5Pget_elink_fapl(plapl_id); assertTrue("H5P_elink_file_cache_size", elink_fapl_id >= 0); try { efc_size = H5.H5Pget_elink_file_cache_size(elink_fapl_id); assertTrue("H5P_elink_file_cache_size default", efc_size == 0); } catch (UnsupportedOperationException err) { System.out.println(err.getMessage()); } try { efc_size = 8; H5.H5Pset_elink_file_cache_size(elink_fapl_id, efc_size); efc_size = H5.H5Pget_elink_file_cache_size(elink_fapl_id); assertTrue("H5P_elink_file_cache_size 8", efc_size == 8); } catch (UnsupportedOperationException err) { System.out.println(err.getMessage()); } } catch (Throwable err) { err.printStackTrace(); fail("H5P_elink_file_cache_size: " + err); } finally { if (elink_fapl_id > 0) try {H5.H5Pclose(elink_fapl_id);} catch (Exception ex) {} } } @Test public void testH5P_btree_ratios() { double[] left = {0.1}; double[] middle = {0.5}; double[] right = {0.7}; try { H5.H5Pset_btree_ratios(plist_id, left[0], middle[0], right[0]); H5.H5Pget_btree_ratios(plist_id, left, middle, right); assertTrue("H5P_btree_ratios", left[0] == 0.1); } catch (Throwable err) { err.printStackTrace(); fail("H5P_btree_ratios: " + err); } } @Test public void testH5P_edc_check() { int ret_val_id = -1; try { ret_val_id = H5.H5Pget_edc_check(plist_id); assertTrue("H5P_edc_check", ret_val_id == HDF5Constants.H5Z_ENABLE_EDC); H5.H5Pset_edc_check(plist_id, HDF5Constants.H5Z_DISABLE_EDC); ret_val_id = H5.H5Pget_edc_check(plist_id); assertTrue("H5P_edc_check", ret_val_id == HDF5Constants.H5Z_DISABLE_EDC); } catch (Throwable err) { err.printStackTrace(); fail("H5P_edc_check: " + err); } } @Test public void testH5P_fclose_degree() { int ret_val_id = -1; try { ret_val_id = H5.H5Pget_fclose_degree(fapl_id); assertTrue("H5Pget_fclose_degree default", ret_val_id == HDF5Constants.H5F_CLOSE_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5P_fclose_degree: default " + err); } try { H5.H5Pset_fclose_degree(fapl_id, HDF5Constants.H5F_CLOSE_STRONG); ret_val_id = H5.H5Pget_fclose_degree(fapl_id); assertTrue("H5Pget_fclose_degree", ret_val_id == HDF5Constants.H5F_CLOSE_STRONG); } catch (Throwable err) { err.printStackTrace(); fail("H5P_fclose_degree: H5F_CLOSE_STRONG " + err); } try { H5.H5Pset_fclose_degree(fapl_id, HDF5Constants.H5F_CLOSE_SEMI); ret_val_id = H5.H5Pget_fclose_degree(fapl_id); assertTrue("H5Pget_fclose_degree", ret_val_id == HDF5Constants.H5F_CLOSE_SEMI); } catch (Throwable err) { err.printStackTrace(); fail("H5P_fclose_degree: H5F_CLOSE_SEMI " + err); } } @Test public void testH5P_alignment() { long[] align = {0,0}; try { H5.H5Pget_alignment(fapl_id, align); assertTrue("H5P_alignment threshold default", align[0] == 1); assertTrue("H5P_alignment alignment default", align[1] == 1); } catch (Throwable err) { err.printStackTrace(); fail("H5P_alignment: default " + err); } try { align[0] = 1024; align[1] = 2048; H5.H5Pset_alignment(fapl_id, align[0], align[1]); H5.H5Pget_alignment(fapl_id, align); assertTrue("H5P_alignment threshold", align[0] == 1024); assertTrue("H5P_alignment alignment", align[1] == 2048); } catch (Throwable err) { err.printStackTrace(); fail("H5P_alignment: " + err); } } @Test public void testH5P_meta_block_size() { long meta_size = 0; try { meta_size = H5.H5Pget_meta_block_size(fapl_id); assertTrue("H5P_meta_block_size default", meta_size == 2048); } catch (Throwable err) { err.printStackTrace(); fail("H5P_meta_block_size: default " + err); } try { meta_size = 4096; H5.H5Pset_meta_block_size(fapl_id, meta_size); meta_size = H5.H5Pget_meta_block_size(fapl_id); assertTrue("H5P_meta_block_size 4096", meta_size == 4096); } catch (Throwable err) { err.printStackTrace(); fail("H5P_meta_block_size: " + err); } } @Test public void testH5P_small_data_block_size() { long[] align = {0}; try { H5.H5Pget_small_data_block_size(fapl_id, align); assertTrue("H5P_small_data_block_size default", align[0] == 2048); } catch (Throwable err) { err.printStackTrace(); fail("H5P_small_data_block_size: default " + err); } try { align[0] = 4096; H5.H5Pset_small_data_block_size(fapl_id, align[0]); H5.H5Pget_small_data_block_size(fapl_id, align); assertTrue("H5P_small_data_block_size 4096", align[0] == 4096); } catch (Throwable err) { err.printStackTrace(); fail("H5P_small_data_block_size: " + err); } } @Test public void testH5P_hyper_vector_size() { long[] align = {0}; try { H5.H5Pget_hyper_vector_size(plist_id, align); assertTrue("H5P_hyper_vector_size default", align[0] == 1024); } catch (Throwable err) { err.printStackTrace(); fail("H5P_hyper_vector_size: default " + err); } try { align[0] = 4096; H5.H5Pset_hyper_vector_size(plist_id, align[0]); H5.H5Pget_hyper_vector_size(plist_id, align); assertTrue("H5P_hyper_vector_size 4096", align[0] == 4096); } catch (Throwable err) { err.printStackTrace(); fail("H5P_hyper_vector_size: " + err); } } @Test public void testH5P_cache() { long[] rdcc_nelmts = {0}; long[] rdcc_nbytes = {0}; double[] rdcc_w0 = {0}; try { H5.H5Pget_cache(fapl_id, null, rdcc_nelmts, rdcc_nbytes, rdcc_w0); assertTrue("H5P_cache default", rdcc_nelmts[0] == 521); assertTrue("H5P_cache default", rdcc_nbytes[0] == (1024*1024)); assertTrue("H5P_cache default", rdcc_w0[0] == 0.75); } catch (Throwable err) { err.printStackTrace(); fail("H5P_cache: default " + err); } try { rdcc_nelmts[0] = 4096; H5.H5Pset_cache(fapl_id, 0, rdcc_nelmts[0], rdcc_nbytes[0], rdcc_w0[0]); H5.H5Pget_cache(fapl_id, null, rdcc_nelmts, rdcc_nbytes, rdcc_w0); assertTrue("H5P_cache 4096", rdcc_nelmts[0] == 4096); } catch (Throwable err) { err.printStackTrace(); fail("H5P_cache: " + err); } } @Test public void testH5P_chunk_cache() { long[] rdcc_nslots = {0}; long[] rdcc_nbytes = {0}; double[] rdcc_w0 = {0}; try { H5.H5Pget_chunk_cache(dapl_id, rdcc_nslots, rdcc_nbytes, rdcc_w0); assertTrue("H5P_chunk_cache default", rdcc_nslots[0] == 521); assertTrue("H5P_chunk_cache default", rdcc_nbytes[0] == (1024*1024)); assertTrue("H5P_chunk_cache default", rdcc_w0[0] == 0.75); } catch (Throwable err) { err.printStackTrace(); fail("H5P_chunk_cache: default " + err); } try { rdcc_nslots[0] = 4096; H5.H5Pset_chunk_cache(dapl_id, rdcc_nslots[0], rdcc_nbytes[0], rdcc_w0[0]); H5.H5Pget_chunk_cache(dapl_id, rdcc_nslots, rdcc_nbytes, rdcc_w0); assertTrue("H5P_chunk_cache 4096", rdcc_nslots[0] == 4096); } catch (Throwable err) { err.printStackTrace(); fail("H5P_chunk_cache: " + err); } } @Test public void testH5P_sieve_buf_size() { long buf_size = 0; try { buf_size = H5.H5Pget_sieve_buf_size(fapl_id); assertTrue("H5P_sieve_buf_size default", buf_size == (64*1024)); } catch (Throwable err) { err.printStackTrace(); fail("H5P_sieve_buf_size: default " + err); } try { buf_size = 4096; H5.H5Pset_sieve_buf_size(fapl_id, buf_size); buf_size = H5.H5Pget_sieve_buf_size(fapl_id); assertTrue("H5P_sieve_buf_size 4096", buf_size == 4096); } catch (Throwable err) { err.printStackTrace(); fail("H5P_sieve_buf_size: " + err); } } @Test public void testH5P_gc_references() { boolean ret_val_id = false; try { H5.H5Pset_gc_references(fapl_id, true); ret_val_id = H5.H5Pget_gcreferences(fapl_id); assertTrue("H5P_gc_references", ret_val_id); } catch (Throwable err) { err.printStackTrace(); fail("H5P_gc_references: " + err); } } @Test public void testH5Pget_mdc_config() { H5AC_cache_config_t cache_config = null; try { cache_config = H5.H5Pget_mdc_config(fapl_id); assertTrue("H5Pget_mdc_config", cache_config.version==HDF5Constants.H5AC_CURR_CACHE_CONFIG_VERSION); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_mdc_config: " + err); } } @Test public void testH5Pset_mdc_config() { H5AC_cache_config_t cache_config = null; try { cache_config = H5.H5Pget_mdc_config(fapl_id); assertTrue("H5Pset_mdc_config", cache_config.version==HDF5Constants.H5AC_CURR_CACHE_CONFIG_VERSION); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_mdc_config: " + err); } try { cache_config.decr_mode = HDF5Constants.H5C_decr_off; H5.H5Pset_mdc_config(fapl_id, cache_config); cache_config = H5.H5Pget_mdc_config(fapl_id); assertTrue("H5Pset_mdc_config", cache_config.version==HDF5Constants.H5AC_CURR_CACHE_CONFIG_VERSION); assertTrue("H5Pset_mdc_config", cache_config.decr_mode==HDF5Constants.H5C_decr_off); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_mdc_config: " + err); } } @Test public void testH5P_fapl_core() { if (HDF5Constants.H5FD_CORE < 0) return; try { H5.H5Pset_fapl_core(fapl_id, 4096, false); int driver_type = H5.H5Pget_driver(fapl_id); assertTrue("H5Pget_driver: core = "+ driver_type, HDF5Constants.H5FD_CORE==driver_type); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_fapl_core: " + err); } try { long[] increment = {-1}; boolean[] backingstore = {true}; H5.H5Pget_fapl_core(fapl_id, increment, backingstore); assertTrue("H5Pget_fapl_core: increment="+increment[0], increment[0]==4096); assertTrue("H5Pget_fapl_core: backingstore="+backingstore[0], !backingstore[0]); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_fapl_core: " + err); } } @Test public void testH5P_fapl_family() { if (HDF5Constants.H5FD_FAMILY < 0) return; try { H5.H5Pset_fapl_family(fapl_id, 1024, HDF5Constants.H5P_DEFAULT); int driver_type = H5.H5Pget_driver(fapl_id); assertTrue("H5Pget_driver: family = "+ driver_type, HDF5Constants.H5FD_FAMILY==driver_type); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_fapl_family: " + err); } try { long[] member_size = {0}; int[] member_fapl = {-1}; H5.H5Pget_fapl_family(fapl_id, member_size, member_fapl); assertTrue("H5Pget_fapl_family: member_size="+member_size[0], member_size[0]==1024); assertTrue("H5Pget_fapl_family: member_fapl ", H5.H5P_equal(member_fapl[0], HDF5Constants.H5P_FILE_ACCESS_DEFAULT)); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_fapl_family: " + err); } _createH5familyFile(fapl_id); deleteH5familyfile(); } @Test public void testH5P_family_offset() { if (HDF5Constants.H5FD_FAMILY < 0) return; try { H5.H5Pset_fapl_family(fapl_id, 1024, HDF5Constants.H5P_DEFAULT); int driver_type = H5.H5Pget_driver(fapl_id); assertTrue("H5Pget_driver: family = "+ driver_type, HDF5Constants.H5FD_FAMILY==driver_type); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_fapl_family: " + err); } _createH5familyFile(fapl_id); long family_offset = 512; try { H5.H5Pset_family_offset(fapl_id, family_offset); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_fapl_family: " + err); } try { long offset = H5.H5Pget_family_offset(fapl_id); assertTrue("H5Pget_fapl_family: offset="+offset, offset==family_offset); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_fapl_family: " + err); } deleteH5familyfile(); } @Test public void testH5Pset_fapl_sec2() { if (HDF5Constants.H5FD_SEC2 < 0) return; try { H5.H5Pset_fapl_sec2(fapl_id); int driver_type = H5.H5Pget_driver(fapl_id); assertTrue("H5Pget_driver: sec2 = "+ driver_type, HDF5Constants.H5FD_SEC2==driver_type); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_fapl_sec2: " + err); } _createH5File(fapl_id); deleteH5file(); } @Test public void testH5Pset_fapl_stdio() { if (HDF5Constants.H5FD_STDIO < 0) return; try { H5.H5Pset_fapl_stdio(fapl_id); int driver_type = H5.H5Pget_driver(fapl_id); assertTrue("H5Pget_driver: stdio = "+ driver_type, HDF5Constants.H5FD_STDIO==driver_type); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_fapl_stdio: " + err); } _createH5File(fapl_id); deleteH5file(); } @Test public void testH5Pset_fapl_log() { if (HDF5Constants.H5FD_LOG < 0) return; try { long log_flags = HDF5Constants.H5FD_LOG_LOC_IO; H5.H5Pset_fapl_log(fapl_id, H5_LOG_FILE, log_flags, 1024); int driver_type = H5.H5Pget_driver(fapl_id); assertTrue("H5Pget_driver: log = "+ driver_type, HDF5Constants.H5FD_LOG==driver_type); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_fapl_log: " + err); } _createH5File(fapl_id); deleteH5file(); _deleteLogFile(); } @Test public void testH5P_fapl_muti_nulls() { if (HDF5Constants.H5FD_MULTI < 0) return; int[] member_map = null; int[] member_fapl = null; String[] member_name = null; long[] member_addr = null; try { H5.H5Pset_fapl_multi(fapl_id, member_map, member_fapl, member_name, member_addr, true); int driver_type = H5.H5Pget_driver(fapl_id); assertTrue("H5Pget_driver: muti = "+ driver_type, HDF5Constants.H5FD_MULTI==driver_type); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_fapl_muti: " + err); } try { boolean relax = H5.H5Pget_fapl_multi(fapl_id, member_map, member_fapl, member_name, member_addr); assertTrue("H5Pget_fapl_muti: relax ", relax); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_fapl_muti: " + err); } _createH5multiFile(fapl_id); deleteH5multifile(); } @Test public void testH5P_fapl_muti_defaults() { if (HDF5Constants.H5FD_MULTI < 0) return; long HADDRMAX = HDF5Constants.H5FD_DEFAULT_HADDR_SIZE; int[] member_map = null; int[] member_fapl = null; String[] member_name = null; long[] member_addr = null; try { H5.H5Pset_fapl_multi(fapl_id, member_map, member_fapl, member_name, member_addr, true); int driver_type = H5.H5Pget_driver(fapl_id); assertTrue("H5Pget_driver: muti = "+ driver_type, HDF5Constants.H5FD_MULTI==driver_type); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_fapl_muti: " + err); } try { member_map = new int[HDF5Constants.H5FD_MEM_NTYPES]; member_fapl = new int[HDF5Constants.H5FD_MEM_NTYPES]; member_name = new String[HDF5Constants.H5FD_MEM_NTYPES]; member_addr = new long[HDF5Constants.H5FD_MEM_NTYPES]; boolean relax = H5.H5Pget_fapl_multi(fapl_id, member_map, member_fapl, member_name, member_addr); assertTrue("H5Pget_fapl_muti: relax ", relax); assertTrue("H5Pget_fapl_muti: member_map="+member_map[HDF5Constants.H5FD_MEM_DEFAULT], member_map[HDF5Constants.H5FD_MEM_DEFAULT] == HDF5Constants.H5FD_MEM_DEFAULT); assertTrue("H5Pget_fapl_muti: member_fapl ", H5.H5P_equal(member_fapl[HDF5Constants.H5FD_MEM_DEFAULT], HDF5Constants.H5P_FILE_ACCESS_DEFAULT)); assertTrue("H5Pget_fapl_muti: member_name="+member_name[HDF5Constants.H5FD_MEM_DEFAULT], member_name[HDF5Constants.H5FD_MEM_DEFAULT].compareTo("%s-X.h5")==0); assertTrue("H5Pget_fapl_muti: member_name="+member_name[HDF5Constants.H5FD_MEM_SUPER], member_name[HDF5Constants.H5FD_MEM_SUPER].compareTo("%s-s.h5")==0); assertTrue("H5Pget_fapl_muti: member_name="+member_name[HDF5Constants.H5FD_MEM_BTREE], member_name[HDF5Constants.H5FD_MEM_BTREE].compareTo("%s-b.h5")==0); assertTrue("H5Pget_fapl_muti: member_name="+member_name[HDF5Constants.H5FD_MEM_DRAW], member_name[HDF5Constants.H5FD_MEM_DRAW].compareTo("%s-r.h5")==0); assertTrue("H5Pget_fapl_muti: member_addr="+member_addr[HDF5Constants.H5FD_MEM_DEFAULT], member_addr[HDF5Constants.H5FD_MEM_DEFAULT] == 0); assertTrue("H5Pget_fapl_muti: member_addr="+member_addr[HDF5Constants.H5FD_MEM_SUPER], member_addr[HDF5Constants.H5FD_MEM_SUPER] == 0); assertTrue("H5Pget_fapl_muti: member_addr="+member_addr[HDF5Constants.H5FD_MEM_BTREE]+"<>"+HADDRMAX, member_addr[HDF5Constants.H5FD_MEM_BTREE] == HADDRMAX); assertTrue("H5Pget_fapl_muti: member_addr="+member_addr[HDF5Constants.H5FD_MEM_DRAW], member_addr[HDF5Constants.H5FD_MEM_DRAW] == (HADDRMAX-1)); assertTrue("H5Pget_fapl_muti: member_addr="+member_addr[HDF5Constants.H5FD_MEM_GHEAP], member_addr[HDF5Constants.H5FD_MEM_GHEAP] == (HADDRMAX-1)); assertTrue("H5Pget_fapl_muti: member_addr="+member_addr[HDF5Constants.H5FD_MEM_LHEAP], member_addr[HDF5Constants.H5FD_MEM_LHEAP] == (HADDRMAX-1)); assertTrue("H5Pget_fapl_muti: member_addr="+member_addr[HDF5Constants.H5FD_MEM_OHDR], member_addr[HDF5Constants.H5FD_MEM_OHDR] == (HADDRMAX-2)); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_fapl_muti: " + err); } _createH5multiFile(fapl_id); _createH5multiFileDS(); deleteH5multifile(); } @Test public void testH5P_fapl_muti() { if (HDF5Constants.H5FD_MULTI < 0) return; long HADDRMAX = HDF5Constants.H5FD_DEFAULT_HADDR_SIZE; int[] member_map = new int[HDF5Constants.H5FD_MEM_NTYPES]; int[] member_fapl = new int[HDF5Constants.H5FD_MEM_NTYPES]; String[] member_name = new String[HDF5Constants.H5FD_MEM_NTYPES]; long[] member_addr = new long[HDF5Constants.H5FD_MEM_NTYPES]; for(int mt=HDF5Constants.H5FD_MEM_DEFAULT; mt= HADDRMAX/4 || file_size <= HADDRMAX/2); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_fapl_muti:H5Fget_filesize " + err); } _createH5multiFileDS(); deleteH5multifile(); File file = new File(H5_MULTI_FILE+"-super.h5"); if (file.exists()) { try { file.delete(); } catch (SecurityException e) { ;// e.printStackTrace(); } } file = new File(H5_MULTI_FILE+"-btree.h5"); if (file.exists()) { try { file.delete(); } catch (SecurityException e) { ;// e.printStackTrace(); } } file = new File(H5_MULTI_FILE+"-draw.h5"); if (file.exists()) { try { file.delete(); } catch (SecurityException e) { ;// e.printStackTrace(); } } file = new File(H5_MULTI_FILE+"-gheap.h5"); if (file.exists()) { try { file.delete(); } catch (SecurityException e) { ;// e.printStackTrace(); } } } @Test public void testH5P_fapl_split() { if (HDF5Constants.H5FD_MULTI < 0) return; try { H5.H5Pset_fapl_split(fapl_id, "-meta.h5", HDF5Constants.H5P_DEFAULT, "-raw.h5", HDF5Constants.H5P_DEFAULT); int driver_type = H5.H5Pget_driver(fapl_id); assertTrue("H5Pget_driver: split = "+ driver_type, HDF5Constants.H5FD_MULTI==driver_type); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_fapl_split: " + err); } try { int[] member_map = new int[HDF5Constants.H5FD_MEM_NTYPES]; int[] member_fapl = new int[HDF5Constants.H5FD_MEM_NTYPES]; String[] member_name = new String[HDF5Constants.H5FD_MEM_NTYPES]; long[] member_addr = new long[HDF5Constants.H5FD_MEM_NTYPES]; boolean relax = H5.H5Pget_fapl_multi(fapl_id, member_map, member_fapl, member_name, member_addr); assertTrue("H5Pget_fapl_multi: relax ", relax); assertTrue("H5Pget_fapl_multi: member_name="+member_name[HDF5Constants.H5FD_MEM_SUPER], member_name[HDF5Constants.H5FD_MEM_SUPER].compareTo("%s-meta.h5")==0); assertTrue("H5Pget_fapl_multi: member_name="+member_name[HDF5Constants.H5FD_MEM_DRAW], member_name[HDF5Constants.H5FD_MEM_DRAW].compareTo("%s-raw.h5")==0); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_fapl_split: " + err); } _createH5multiFile(fapl_id); deleteH5multifile(); File file = new File(H5_MULTI_FILE+"-meta.h5"); if (file.exists()) { try { file.delete(); } catch (SecurityException e) { ;// e.printStackTrace(); } } file = new File(H5_MULTI_FILE+"-raw.h5"); if (file.exists()) { try { file.delete(); } catch (SecurityException e) { ;// e.printStackTrace(); } } } @Test public void testH5P_fapl_direct() { if (HDF5Constants.H5FD_DIRECT < 0) return; try { H5.H5Pset_fapl_direct(fapl_id, 1024, 4096, 8*4096); int driver_type = H5.H5Pget_driver(fapl_id); assertTrue("H5Pget_driver: direct = "+ driver_type, HDF5Constants.H5FD_DIRECT==driver_type); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_fapl_direct: " + err); } try { long[] params = {-1, -1, -1}; H5.H5Pget_fapl_direct(fapl_id, params); assertTrue("H5Pget_fapl_direct: alignment="+params[0], params[0]==1024); assertTrue("H5Pget_fapl_direct: block_size="+params[1], params[1]==4096); assertTrue("H5Pget_fapl_direct: cbuf_size="+params[2], params[2]==8*4096); } catch (Throwable err) { err.printStackTrace(); fail("H5Pget_fapl_direct: " + err); } _createH5File(fapl_id); deleteH5file(); } @Test public void testH5Pset_fapl_windows() { if (HDF5Constants.H5FD_WINDOWS < 0) return; try { H5.H5Pset_fapl_windows(fapl_id); int driver_type = H5.H5Pget_driver(fapl_id); assertTrue("H5Pget_driver: windows = "+ driver_type, HDF5Constants.H5FD_WINDOWS==driver_type); } catch (Throwable err) { err.printStackTrace(); fail("H5Pset_fapl_windows: " + err); } _createH5File(fapl_id); deleteH5file(); } @Test public void testH5Pmulti_transform() { if (HDF5Constants.H5FD_MULTI < 0) return; String f_to_c = "(5/9.0)*(x-32)"; double windchillFread[][] = new double[DIMF_X][DIMF_Y]; double windchillC; NumberFormat formatter = new DecimalFormat("#0.000"); long HADDRMAX = HDF5Constants.H5FD_DEFAULT_HADDR_SIZE; int[] member_map = new int[HDF5Constants.H5FD_MEM_NTYPES]; int[] member_fapl = new int[HDF5Constants.H5FD_MEM_NTYPES]; String[] member_name = new String[HDF5Constants.H5FD_MEM_NTYPES]; long[] member_addr = new long[HDF5Constants.H5FD_MEM_NTYPES]; int[] member_dxpl = new int[HDF5Constants.H5FD_MEM_NTYPES]; try { H5.H5Pset_data_transform(plist_id, f_to_c); H5.H5Pset_btree_ratios(btplist_id, 0.1, 0.5, 0.7); } catch (Throwable err) { err.printStackTrace(); fail("H5Pdata_transform: " + err); } for(int mt=HDF5Constants.H5FD_MEM_DEFAULT; mt= HADDRMAX/4 || file_size <= HADDRMAX/2); _createH5multiFileDS(); _createFloatDataset(); } catch (Throwable err) { err.printStackTrace(); fail("H5Pdata_transform: " + err); } try { H5.H5Dwrite(H5Fdid, HDF5Constants.H5T_NATIVE_DOUBLE, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, member_dxpl[HDF5Constants.H5FD_MEM_DRAW], windchillF); H5.H5Dread(H5Fdid, HDF5Constants.H5T_NATIVE_DOUBLE, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, windchillFread); } catch (Throwable err) { err.printStackTrace(); fail("H5Pdata_transform: " + err); } for(int row = 0; row < DIMF_X; row++) { for(int col = 0; col < DIMF_Y; col++) { windchillC = (5/9.0)*(windchillF[row][col]-32); String Cstr = formatter.format(windchillC); String Fread = formatter.format(windchillFread[row][col]); assertTrue("H5Pdata_transform: <"+row+","+col+">"+Fread+"="+Cstr, Fread.compareTo(Cstr)==0); } } deleteH5multifile(); File file = new File(H5_MULTI_FILE+"-super.h5"); if (file.exists()) { try { file.delete(); } catch (SecurityException e) { ;// e.printStackTrace(); } } file = new File(H5_MULTI_FILE+"-btree.h5"); if (file.exists()) { try { file.delete(); } catch (SecurityException e) { ;// e.printStackTrace(); } } file = new File(H5_MULTI_FILE+"-draw.h5"); if (file.exists()) { try { file.delete(); } catch (SecurityException e) { ;// e.printStackTrace(); } } file = new File(H5_MULTI_FILE+"-gheap.h5"); if (file.exists()) { try { file.delete(); } catch (SecurityException e) { ;// e.printStackTrace(); } } } } libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/TestH5R.java000066400000000000000000000252111256564762100245570ustar00rootroot00000000000000package test.hdf5lib; import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertNotNull; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import java.io.File; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.HDF5Constants; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import org.junit.After; import org.junit.Before; import org.junit.Test; @SuppressWarnings("all") public class TestH5R { private static final String H5_FILE = "testH5R.h5"; private static final int DIM_X = 4; private static final int DIM_Y = 6; int H5fid = -1; int H5dsid = -1; int H5did = -1; int H5gid = -1; int H5did2 = -1; long[] H5dims = { DIM_X, DIM_Y }; private final void _deleteFile(String filename) { File file = null; try { file = new File(filename); } catch (Throwable err) {} if (file.exists()) { try {file.delete();} catch (SecurityException e) {} } } private final int _createDataset(int fid, int dsid, String name, int dapl) { int did = -1; try { did = H5.H5Dcreate(fid, name, HDF5Constants.H5T_STD_I32BE, dsid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, dapl); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Dcreate: " + err); } assertTrue("TestH5R._createDataset: ",did > 0); return did; } private final int _createGroup(int fid, String name) { int gid = -1; try { gid = H5.H5Gcreate(fid, name, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gcreate: " + err); } assertTrue("TestH5R._createGroup: ",gid > 0); return gid; } @Before public void createH5file() throws NullPointerException, HDF5Exception { assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0); try { H5fid = H5.H5Fcreate(H5_FILE, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); H5dsid = H5.H5Screate_simple(2, H5dims, null); H5gid = _createGroup(H5fid, "Group1"); H5did2 = _createDataset(H5gid, H5dsid, "dset2", HDF5Constants.H5P_DEFAULT); H5did = _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("TestH5D.createH5file: " + err); } assertTrue("TestH5D.createH5file: H5.H5Fcreate: ",H5fid > 0); assertTrue("TestH5D.createH5file: H5.H5Screate_simple: ",H5dsid > 0); assertTrue("TestH5D.createH5file: _createDataset: ",H5did > 0); H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); } @After public void deleteH5file() throws HDF5LibraryException { if (H5dsid > 0) try {H5.H5Sclose(H5dsid);} catch (Exception ex) {} if (H5did > 0) try {H5.H5Dclose(H5did);} catch (Exception ex) {} if (H5fid > 0) try {H5.H5Fclose(H5fid);} catch (Exception ex) {} if (H5gid > 0) try {H5.H5Gclose(H5gid);} catch (Exception ex) {} if (H5did2 > 0) try {H5.H5Dclose(H5did2);} catch (Exception ex) {} _deleteFile(H5_FILE); } @Test public void testH5Rget_name() { int loc_id=H5fid; int ref_type=HDF5Constants.H5R_OBJECT; long ret_val=-1; byte[] ref=null; String[] name= {""}; String objName = "/dset"; try { ref = H5.H5Rcreate(H5fid, objName, ref_type, -1); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Rget_name:H5Rcreate " + err); } try { ret_val = H5.H5Rget_name(loc_id, ref_type, ref, name, 16); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Rget_name: " + err); } assertTrue("testH5Rget_name: H5Rget_name", ret_val>0); assertTrue("The name of the object: ", objName.equals(name[0])); } @Test public void testH5Rget_obj_type2() { int ref_type=HDF5Constants.H5R_OBJECT; byte[] ref=null; String objName = "/dset"; int obj_type = -1;; int[] otype = { 1 }; try { ref = H5.H5Rcreate(H5fid, objName, ref_type, -1); } catch(Throwable err) { err.printStackTrace(); } try { obj_type = H5.H5Rget_obj_type(H5fid, HDF5Constants.H5R_OBJECT, ref, otype); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Rget_obj_type2: " + err); } assertEquals(obj_type, HDF5Constants.H5O_TYPE_DATASET); } @Test public void testH5Rcreate_refobj() { byte[] ref = null; try { ref = H5.H5Rcreate(H5fid, "/dset", HDF5Constants.H5R_OBJECT, -1); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Rcreate: " + err); } assertNotNull(ref); } @Test public void testH5Rcreate_regionrefobj() { byte[] ref = null; try { ref = H5.H5Rcreate(H5fid, "/dset", HDF5Constants.H5R_DATASET_REGION, H5dsid); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Rcreate: " + err); } assertNotNull(ref); } @Test public void testH5Rdereference() { byte[] ref1 = null; byte[] ref2 = null; int dataset_id = -1; int group_id = -1; try { //Create reference on dataset ref1 = H5.H5Rcreate(H5fid, "/dset", HDF5Constants.H5R_DATASET_REGION, H5dsid); dataset_id= H5.H5Rdereference(H5fid, HDF5Constants.H5R_DATASET_REGION, ref1); //Create reference on group ref2 = H5.H5Rcreate(H5gid, "/Group1", HDF5Constants.H5R_OBJECT, -1); group_id= H5.H5Rdereference(H5gid, HDF5Constants.H5R_OBJECT, ref2); assertNotNull(ref1); assertNotNull(ref2); assertTrue(dataset_id>=0); assertTrue(group_id>=0); } catch (Throwable err) { err.printStackTrace(); fail("TestH5Rdereference " + err); } finally { try {H5.H5Dclose(dataset_id);} catch (Exception ex) {} try {H5.H5Gclose(group_id);} catch (Exception ex) {} } } @Test public void testH5Rget_region() { byte[] ref = null; int dsid = -1; try { ref = H5.H5Rcreate(H5fid, "/dset", HDF5Constants.H5R_DATASET_REGION, H5dsid); dsid = H5.H5Rget_region(H5fid, HDF5Constants.H5R_DATASET_REGION, ref); assertNotNull(ref); assertTrue(dsid>=0); } catch (Throwable err) { err.printStackTrace(); fail("TestH5Rget_region: " + err); } finally { try {H5.H5Sclose(dsid);} catch (Exception ex) {} } } @Test(expected = IllegalArgumentException.class) public void testH5Rget_name_Invalidreftype() throws Throwable { byte[] ref = null; String[] name= {""}; ref = H5.H5Rcreate(H5fid, "/dset", HDF5Constants.H5R_OBJECT, -1); H5.H5Rget_name(H5fid, HDF5Constants.H5R_DATASET_REGION, ref, name, 16); } @Test(expected = NullPointerException.class) public void testH5Rget_name_NULLreference() throws Throwable { byte[] ref = null; String[] name= {""}; H5.H5Rget_name(H5fid, HDF5Constants.H5R_OBJECT, ref, name, 16); } @Test(expected = HDF5LibraryException.class) public void testH5Rget_obj_type2_Invalidreftype() throws Throwable { byte[] ref = null; int[] otype = { 1 }; ref = H5.H5Rcreate(H5fid, "/dset", HDF5Constants.H5R_OBJECT, -1); H5.H5Rget_obj_type(H5fid, HDF5Constants.H5R_DATASET_REGION, ref, otype); } @Test(expected = HDF5LibraryException.class) public void testH5Rcreate_InvalidObjectName() throws Throwable { H5.H5Rcreate(H5fid, "/GROUPS", HDF5Constants.H5R_OBJECT, -1); } @Test(expected = HDF5LibraryException.class) public void testH5Rcreate_Invalidspace_id() throws Throwable { H5.H5Rcreate(H5fid, "/dset", HDF5Constants.H5R_DATASET_REGION, -1); } @Test(expected = IllegalArgumentException.class) public void testH5Rcreate_Invalidreftype() throws Throwable { H5.H5Rcreate(H5fid, "/dset", HDF5Constants.H5R_BADTYPE, -1); } @Test(expected = IllegalArgumentException.class) public void testH5Rgetregion_Invalidreftype() throws Throwable { byte[] ref = null; ref = H5.H5Rcreate(H5fid, "/dset", HDF5Constants.H5R_OBJECT, H5dsid); H5.H5Rget_region(H5fid, HDF5Constants.H5R_DATASET_REGION, ref); } @Test(expected = IllegalArgumentException.class) public void testH5Rgetregion_Badreferencetype() throws Throwable { byte[] ref = null; ref = H5.H5Rcreate(H5fid, "/dset", HDF5Constants.H5R_OBJECT, H5dsid); H5.H5Rget_region(H5fid, HDF5Constants.H5R_OBJECT, ref); } @Test(expected = NullPointerException.class) public void testH5Rgetregion_Nullreference() throws Throwable { byte[] ref = null; H5.H5Rget_region(H5fid, HDF5Constants.H5R_DATASET_REGION, ref); } @Test(expected = NullPointerException.class) public void testH5Rdereference_Nullreference() throws Throwable { byte[] ref = null; H5.H5Rdereference(H5did2, HDF5Constants.H5R_OBJECT, ref); } @Test(expected = IllegalArgumentException.class) public void testH5Rdereference_Invalidreference() throws Throwable { byte[] ref1 = null; byte[] ref2 = null; ref1 = H5.H5Rcreate(H5fid, "/dset", HDF5Constants.H5R_DATASET_REGION, H5dsid); ref2 = H5.H5Rcreate(H5gid, "/Group1", HDF5Constants.H5R_OBJECT, -1); H5.H5Rdereference(H5gid, HDF5Constants.H5R_OBJECT, ref1); } } libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/TestH5S.java000066400000000000000000000445611256564762100245710ustar00rootroot00000000000000/** * */ package test.hdf5lib; import static org.junit.Assert.assertFalse; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.HDF5Constants; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import org.junit.After; import org.junit.Before; import org.junit.Test; public class TestH5S { int H5sid = -1; int H5rank = 2; long H5dims[] = {5, 5}; long H5maxdims[] = {10, 10}; @Before public void createH5file() throws NullPointerException, HDF5Exception { assertTrue("H5 open ids is 0", H5.getOpenIDCount()==0); H5sid = H5.H5Screate_simple(H5rank, H5dims, H5maxdims); assertTrue("H5.H5Screate_simple_extent", H5sid > 0); } @After public void deleteH5file() throws HDF5LibraryException { if (H5sid > 0) { try {H5.H5Sclose(H5sid);} catch (Exception ex) {} } } @Test public void testH5Sget_simple_extent_ndims() { int read_rank = -1; try { read_rank = H5.H5Sget_simple_extent_ndims(H5sid); assertTrue("H5.H5Sget_simple_extent_ndims", H5rank == read_rank); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Sget_simple_extent_ndims: " + err); } } @Test public void testH5Sget_simple_extent_dims_null() { int read_rank = -1; try { read_rank = H5.H5Sget_simple_extent_dims(H5sid, null, null); assertTrue("H5.H5Sget_simple_extent_dims", H5rank == read_rank); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Sget_simple_extent_dims: " + err); } } @Test public void testH5Sget_simple_extent_dims() { int read_rank = -1; long dims[] = {5, 5}; long maxdims[] = {10, 10}; try { read_rank = H5.H5Sget_simple_extent_dims(H5sid, dims, maxdims); assertTrue("H5.H5Sget_simple_extent_dims", H5rank == read_rank); assertTrue("H5.H5Sget_simple_extent_dims:dims", H5dims[0] == dims[0]); assertTrue("H5.H5Sget_simple_extent_dims:maxdims", H5maxdims[0] == maxdims[0]); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Sget_simple_extent_dims: " + err); } } @Test public void testH5Sget_simple_extent_npoints() { long num_elements = -1; try { num_elements = H5.H5Sget_simple_extent_npoints(H5sid); assertTrue("H5.H5Sget_simple_extent_npoints", (H5dims[0]*H5dims[1]) == num_elements); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Sget_simple_extent_npoints: " + err); } } @Test public void testH5Sget_simple_extent_type() { int read_type = -1; try { read_type = H5.H5Sget_simple_extent_type(H5sid); assertTrue("H5.H5Sget_simple_extent_type", HDF5Constants.H5S_SIMPLE == read_type); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Sget_simple_extent_type: " + err); } } @Test public void testH5Sis_simple() { boolean result = false; try { result = H5.H5Sis_simple(H5sid); assertTrue("H5.H5Sis_simple", result); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Sis_simple: " + err); } } @Test public void testH5Sset_extent_simple() { long num_elements = -1; try { H5.H5Sset_extent_simple(H5sid, H5rank, H5maxdims, H5maxdims); num_elements = H5.H5Sget_simple_extent_npoints(H5sid); assertTrue("H5.H5Sget_simple_extent_npoints", (H5maxdims[0]*H5maxdims[1]) == num_elements); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Sset_extent_simple: " + err); } } @Test public void testH5Sget_select_type() { int read_type = -1; try { read_type = H5.H5Sget_select_type(H5sid); assertTrue("H5.H5Sget_select_type", HDF5Constants.H5S_SEL_ALL == read_type); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Sset_extent_none: " + err); } } @Test public void testH5Sset_extent_none() { int read_type = -1; try { H5.H5Sset_extent_none(H5sid); read_type = H5.H5Sget_simple_extent_type(H5sid); assertTrue("H5.H5Sget_simple_extent_type: "+read_type, HDF5Constants.H5S_NO_CLASS == read_type); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Sset_extent_none: " + err); } } @Test public void testH5Scopy() { int sid = -1; int read_rank = -1; try { sid = H5.H5Scopy(H5sid); assertTrue("H5.H5Sis_simple", sid > 0); read_rank = H5.H5Sget_simple_extent_ndims(sid); assertTrue("H5.H5Screate_simple_extent_ndims", H5rank == read_rank); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Scopy: " + err); } finally { try {H5.H5Sclose(sid);} catch (Exception ex) {} } } @Test public void testH5Sextent_copy() { int sid = -1; int class_type = -1; try { sid = H5.H5Screate(HDF5Constants.H5S_NULL); assertTrue("H5.H5Screate_null", sid > 0); H5.H5Sextent_copy(sid, H5sid); class_type = H5.H5Sget_simple_extent_type(sid); assertTrue("H5.H5Screate_null: type", class_type == HDF5Constants.H5S_SIMPLE); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Sextent_copy: " + err); } finally { try {H5.H5Sclose(sid);} catch (Exception ex) {} } } @Test public void testH5Sextent_equal() { int sid = -1; boolean result = false; try { sid = H5.H5Screate(HDF5Constants.H5S_NULL); assertTrue("H5.H5Screate_null",sid > 0); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Screate: null " + err); } try { result = H5.H5Sextent_equal(sid, H5sid); assertFalse("H5.testH5Sextent_equal",result); H5.H5Sextent_copy(sid, H5sid); result = H5.H5Sextent_equal(sid, H5sid); assertTrue("H5.testH5Sextent_equal", result); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Sextent_copy " + err); } finally { try {H5.H5Sclose(sid);} catch (Exception ex) {} } } @Test public void testH5Sencode_decode_null_dataspace() { int sid = -1; int decoded_sid = -1; byte[] null_sbuf = null; boolean result = false; try { sid = H5.H5Screate(HDF5Constants.H5S_NULL); assertTrue("H5.H5Screate_null", sid > 0); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Screate: null " + err); } try { null_sbuf = H5.H5Sencode(sid); assertFalse("H5.testH5Sencode", null_sbuf==null); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Sencode " + err); } finally { if(null_sbuf == null) { try {H5.H5Sclose(sid);} catch (Exception ex) {} } } try { decoded_sid = H5.H5Sdecode(null_sbuf); assertTrue("H5.testH5Sdecode", decoded_sid>0); result = H5.H5Sextent_equal(sid, decoded_sid); assertTrue("H5.testH5Sextent_equal", result); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Sdecode " + err); } finally { try {H5.H5Sclose(decoded_sid);} catch (Exception ex) {} try {H5.H5Sclose(sid);} catch (Exception ex) {} } } @Test public void testH5Sencode_decode_scalar_dataspace() { int sid = -1; int decoded_sid = -1; byte[] scalar_sbuf = null; boolean result = false; int iresult = -1; long lresult = -1; try { sid = H5.H5Screate(HDF5Constants.H5S_SCALAR); assertTrue("H5.H5Screate_null", sid > 0); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Screate: null " + err); } try { scalar_sbuf = H5.H5Sencode(sid); assertFalse("H5.testH5Sencode", scalar_sbuf==null); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Sencode " + err); } finally { if(scalar_sbuf == null) { try {H5.H5Sclose(sid);} catch (Exception ex) {} } } try { decoded_sid = H5.H5Sdecode(scalar_sbuf); assertTrue("H5.testH5Sdecode", decoded_sid>0); result = H5.H5Sextent_equal(sid, decoded_sid); assertTrue("H5.testH5Sextent_equal", result); /* Verify decoded dataspace */ lresult = H5.H5Sget_simple_extent_npoints(decoded_sid); assertTrue("H5.testH5Sget_simple_extent_npoints", lresult==1); iresult = H5.H5Sget_simple_extent_ndims(decoded_sid); assertTrue("H5.testH5Sget_simple_extent_ndims", iresult==0); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Sdecode " + err); } finally { try {H5.H5Sclose(decoded_sid);} catch (Exception ex) {} try {H5.H5Sclose(sid);} catch (Exception ex) {} } } @Test public void testH5Sselect_none() { int read_type = -1; try { H5.H5Sselect_none(H5sid); read_type = H5.H5Sget_select_type(H5sid); assertTrue("H5.H5Sget_select_type: "+read_type, HDF5Constants.H5S_SEL_NONE == read_type); H5.H5Sselect_all(H5sid); read_type = H5.H5Sget_select_type(H5sid); assertTrue("H5.H5Sget_select_type: "+read_type, HDF5Constants.H5S_SEL_ALL == read_type); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Sset_extent_none: " + err); } } @Test public void testH5Sget_select_npoints() { long coord[][] = {{0,1},{2,4},{5,6}}; /* Coordinates for point selection */ long num_elements = -1; try { H5.H5Sselect_elements(H5sid, HDF5Constants.H5S_SELECT_SET, 3, coord); num_elements = H5.H5Sget_select_npoints(H5sid); assertTrue("H5.H5Sget_select_npoints: "+num_elements, 3 == num_elements); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Sget_select_npoints: " + err); } } @Test(expected = IllegalArgumentException.class) public void testH5Sget_select_elem_pointlist_invalid() throws Throwable { long coord[][] = {{0,1},{2,4},{5,6}}; /* Coordinates for point selection */ long getcoord[] = {-1,-1}; /* Coordinates for get point selection */ try { H5.H5Sselect_elements(H5sid, HDF5Constants.H5S_SELECT_SET, 3, coord); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Sget_select_elem_pointlist: " + err); } H5.H5Sget_select_elem_pointlist(H5sid, 0, 3, getcoord); } @Test public void testH5Sget_select_elem_pointlist() { long coord[][] = {{0,1},{2,3},{4,5}}; /* Coordinates for point selection */ long getcoord[] = {-1,-1,-1,-1,-1,-1}; /* Coordinates for get point selection */ try { H5.H5Sselect_elements(H5sid, HDF5Constants.H5S_SELECT_SET, 3, coord); H5.H5Sget_select_elem_pointlist(H5sid, 0, 3, getcoord); assertTrue("H5.H5Sget_select_elem_pointlist", coord[0][0] == getcoord[0]); assertTrue("H5.H5Sget_select_elem_pointlist", coord[0][1] == getcoord[1]); assertTrue("H5.H5Sget_select_elem_pointlist", coord[1][0] == getcoord[2]); assertTrue("H5.H5Sget_select_elem_pointlist", coord[1][1] == getcoord[3]); assertTrue("H5.H5Sget_select_elem_pointlist", coord[2][0] == getcoord[4]); assertTrue("H5.H5Sget_select_elem_pointlist", coord[2][1] == getcoord[5]); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Sget_select_elem_pointlist: " + err); } } @Test public void testH5Sget_select_bounds() { long lowbounds[] = {-1,-1}; long hibounds[] = {-1,-1}; try { H5.H5Sget_select_bounds(H5sid, lowbounds, hibounds); assertTrue("H5.H5Sget_select_bounds", 0 == lowbounds[0]); assertTrue("H5.H5Sget_select_bounds", 0 == lowbounds[1]); assertTrue("H5.H5Sget_select_bounds", (H5dims[0]-1) == hibounds[0]); assertTrue("H5.H5Sget_select_bounds", (H5dims[1]-1) == hibounds[1]); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Sget_select_bounds: " + err); } } @Test public void testH5Soffset_simple() { long coord[][] = {{2,2},{2,4},{4,2},{4,4}}; /* Coordinates for point selection */ long lowbounds[] = {-1,-1}; long hibounds[] = {-1,-1}; try { H5.H5Sselect_elements(H5sid, HDF5Constants.H5S_SELECT_SET, 4, coord); H5.H5Sget_select_bounds(H5sid, lowbounds, hibounds); assertTrue("H5.H5Sget_select_bounds", 2 == lowbounds[0]); assertTrue("H5.H5Sget_select_bounds", 2 == lowbounds[1]); assertTrue("H5.H5Sget_select_bounds", (H5dims[0]-1) == hibounds[0]); assertTrue("H5.H5Sget_select_bounds", (H5dims[1]-1) == hibounds[1]); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Sget_select_bounds: " + err); } try { long offset[] = {-1,-1}; H5.H5Soffset_simple(H5sid, offset); H5.H5Sget_select_bounds(H5sid, lowbounds, hibounds); assertTrue("H5.H5Sget_select_bounds", 1 == lowbounds[0]); assertTrue("H5.H5Sget_select_bounds", 1 == lowbounds[1]); assertTrue("H5.H5Sget_select_bounds", (H5dims[0]-2) == hibounds[0]); assertTrue("H5.H5Sget_select_bounds", (H5dims[1]-2) == hibounds[1]); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Soffset_simple: " + err); } } @Test public void testH5Sget_select_hyper() { int space1 = -1; long start[] = {0,0}; long stride[] = {1,1}; long count[] = {1,1}; long block[] = {4,4}; long nblocks; // Number of hyperslab blocks long blocks[] = {-1, -1, -1, -1, -1, -1, -1, -1}; // List of blocks try { // Copy "all" selection & space space1 = H5.H5Scopy(H5sid); assertTrue("H5.H5Scopy", H5sid > 0); // 'AND' "all" selection with another hyperslab H5.H5Sselect_hyperslab(space1, HDF5Constants.H5S_SELECT_AND, start, stride, count, block); // Verify that there is only one block nblocks = H5.H5Sget_select_hyper_nblocks(space1); assertTrue("H5Sget_select_hyper_nblocks", nblocks == 1); // Retrieve the block defined H5.H5Sget_select_hyper_blocklist(space1, 0, nblocks, blocks); // Verify that the correct block is defined assertTrue("H5.H5Sget_select_hyper_blocklist", start[0] == blocks[0]); assertTrue("H5.H5Sget_select_hyper_blocklist", start[1] == blocks[1]); assertTrue("H5.H5Sget_select_hyper_blocklist", (block[0]-1) == blocks[2]); assertTrue("H5.H5Sget_select_hyper_blocklist", (block[1]-1) == blocks[3]); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Sget_select_bounds: " + err); } finally { try {H5.H5Sclose(space1);} catch (Exception ex) {} } } @Test public void testH5Sget_select_valid() { int space1 = -1; long start[] = {1,0}; long stride[] = {1,1}; long count[] = {2,3}; long block[] = {1,1}; long offset[] = {0,0}; // Offset of selection try { // Copy "all" selection & space space1 = H5.H5Scopy(H5sid); assertTrue("H5.H5Scopy", H5sid > 0); // 'AND' "all" selection with another hyperslab H5.H5Sselect_hyperslab(space1, HDF5Constants.H5S_SELECT_SET, start, stride, count, block); // Check a valid offset offset[0]=-1; offset[1]=0; H5.H5Soffset_simple(space1, offset); assertTrue("H5Sselect_valid", H5.H5Sselect_valid(space1)); // Check an invalid offset offset[0]=10; offset[1]=0; H5.H5Soffset_simple(space1, offset); assertFalse("H5Sselect_valid", H5.H5Sselect_valid(space1)); /* Reset offset */ offset[0]=0; offset[1]=0; H5.H5Soffset_simple(space1, offset); assertTrue("H5Sselect_valid", H5.H5Sselect_valid(space1)); } catch (Throwable err) { err.printStackTrace(); fail("testH5Sget_select_valid: " + err); } finally { try {H5.H5Sclose(space1);} catch (Exception ex) {} } } } libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/TestH5Sbasic.java000066400000000000000000000154721256564762100255720ustar00rootroot00000000000000/** * */ package test.hdf5lib; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.HDF5Constants; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import org.junit.Before; import org.junit.Test; @SuppressWarnings("all") public class TestH5Sbasic { @Before public void checkOpenIDs() { assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0); } @Test(expected = HDF5LibraryException.class) public void testH5Screate_invalid() throws Throwable { H5.H5Screate(-1); } @Test(expected = HDF5LibraryException.class) public void testH5Sget_simple_extent_type_invalid() throws Throwable { H5.H5Sget_simple_extent_type(-1); } @Test public void testH5Screate_scalar() { int sid = -1; int class_type = -1; try { sid = H5.H5Screate(HDF5Constants.H5S_SCALAR); assertTrue("H5.H5Screate_scalar",sid > 0); class_type = H5.H5Sget_simple_extent_type(sid); assertTrue("H5.H5Screate_scalar: type",class_type == HDF5Constants.H5S_SCALAR); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Screate: " + err); } finally { try {H5.H5Sclose(sid);} catch (Exception ex) {} } } @Test public void testH5Screate_null() { int sid = -1; int class_type = -1; try { sid = H5.H5Screate(HDF5Constants.H5S_NULL); assertTrue("H5.H5Screate_null", sid > 0); class_type = H5.H5Sget_simple_extent_type(sid); assertTrue("H5.H5Screate_null: type", class_type == HDF5Constants.H5S_NULL); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Screate: " + err); } finally { try {H5.H5Sclose(sid);} catch (Exception ex) {} } } @Test(expected = NullPointerException.class) public void testH5Screate_simple_dims_null() throws Throwable { H5.H5Screate_simple(2, (long[])null, null); } @Test(expected = IllegalArgumentException.class) public void testH5Screate_simple_rank_invalid() throws Throwable { long dims[] = {5, 5}; H5.H5Screate_simple(-1, dims, null); } @Test(expected = IllegalArgumentException.class) public void testH5Screate_simple_dims_invalid() throws Throwable { long dims[] = {2, 2}; H5.H5Screate_simple(5, dims, null); } @Test(expected = HDF5LibraryException.class) public void testH5Screate_simple_dims_exceed() throws Throwable { long dims[] = {0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20, 21,22,23,24,25,26,27,28,29,30,31,32,33,35}; H5.H5Screate_simple(35, dims, null); } //H5Screate_simple was changed to allow a dim of 0 // @Ignore(expected = HDF5LibraryException.class) // public void testH5Screate_simple_dims_zero() { // long dims[] = {0, 0}; // H5.H5Screate_simple(2, dims, null); // } @Test public void testH5Screate_simple() { int sid = -1; int class_type = -1; int rank = 2; long dims[] = {5, 5}; long maxdims[] = {10, 10}; try { sid = H5.H5Screate_simple(rank, dims, maxdims); assertTrue("H5.H5Screate_simple", sid > 0); class_type = H5.H5Sget_simple_extent_type(sid); assertTrue("H5.H5Screate_simple: type", class_type == HDF5Constants.H5S_SIMPLE); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Screate_simple: " + err); } finally { try {H5.H5Sclose(sid);} catch (Exception ex) {} } } @Test public void testH5Screate_simple_unlimted() { int sid = -1; int class_type = -1; int rank = 2; long dims[] = {5, 5}; long maxdims[] = {HDF5Constants.H5S_UNLIMITED, HDF5Constants.H5S_UNLIMITED}; try { sid = H5.H5Screate_simple(rank, dims, maxdims); assertTrue("H5.H5Screate_simple", sid > 0); class_type = H5.H5Sget_simple_extent_type(sid); assertTrue("H5.H5Screate_simple: type", class_type == HDF5Constants.H5S_SIMPLE); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Screate_simple: " + err); } finally { try {H5.H5Sclose(sid);} catch (Exception ex) {} } } @Test public void testH5Screate_simple_unlimted_1d() { int sid = -1; int class_type = -1; int rank = 1; long dims[] = {5}; long maxdims[] = {HDF5Constants.H5S_UNLIMITED}; try { sid = H5.H5Screate_simple(rank, dims, maxdims); assertTrue("H5.H5Screate_simple", sid > 0); class_type = H5.H5Sget_simple_extent_type(sid); assertTrue("H5.H5Screate_simple: type", class_type == HDF5Constants.H5S_SIMPLE); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Screate_simple: " + err); } finally { try {H5.H5Sclose(sid);} catch (Exception ex) {} } } @Test public void testH5Screate_simple_max_default() { int sid = -1; int rank = 2; long dims[] = {5, 5}; try { sid = H5.H5Screate_simple(rank, dims, null); assertTrue("H5.H5Screate_simple_max_default", sid > 0); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Screate_simple: " + err); } finally { try {H5.H5Sclose(sid);} catch (Exception ex) {} } } @Test public void testH5Screate_simple_extent() { int sid = -1; int rank = 2; long dims[] = {5, 5}; long maxdims[] = {10, 10}; try { sid = H5.H5Screate(HDF5Constants.H5S_SIMPLE); assertTrue("H5.H5Screate_simple_extent",sid > 0); H5.H5Sset_extent_simple(sid, rank, dims, maxdims); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Screate: " + err); } finally { try {H5.H5Sclose(sid);} catch (Exception ex) {} } } @Test(expected = IllegalArgumentException.class) public void testH5Sencode_invalid() throws Throwable { H5.H5Sencode(-1); } @Test(expected = NullPointerException.class) public void testH5Sdecode_null() throws Throwable { H5.H5Sdecode(null); } } libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/TestH5T.java000066400000000000000000000366431256564762100245740ustar00rootroot00000000000000package test.hdf5lib; import static org.junit.Assert.assertFalse; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import java.io.File; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.HDF5Constants; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import org.junit.After; import org.junit.Before; import org.junit.Test; @SuppressWarnings("all") public class TestH5T { private static final String H5_FILE = "test.h5"; int H5fid = -1; int H5strdid = -1; private final void _deleteFile(String filename) { File file = null; try { file = new File(filename); } catch (Throwable err) {} if (file.exists()) { try {file.delete();} catch (SecurityException e) {} } } @Before public void createH5file() throws NullPointerException, HDF5Exception { assertTrue("H5 open ids is 0", H5.getOpenIDCount()==0); H5fid = H5.H5Fcreate(H5_FILE, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); assertTrue("H5.H5Fcreate", H5fid > 0); H5strdid = H5.H5Tcopy(HDF5Constants.H5T_C_S1); assertTrue("H5.H5Tcopy", H5strdid > 0); H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); } @After public void deleteH5file() throws HDF5LibraryException { if (H5strdid >= 0) try {H5.H5Tclose(H5strdid);} catch (Exception ex) {} if (H5fid > 0) try {H5.H5Fclose(H5fid);} catch (Exception ex) {} _deleteFile(H5_FILE); } @Test(expected = HDF5LibraryException.class) public void testH5Tequal_type_error() throws Throwable { H5.H5Tequal(HDF5Constants.H5T_INTEGER, H5strdid); } @Test public void testH5Tget_class() { try { int result = H5.H5Tget_class(H5strdid); assertTrue("H5.H5Tget_class", result > 0); String class_name = H5.H5Tget_class_name(result); assertTrue("H5.H5Tget_class", class_name.compareTo("H5T_STRING")==0); } catch (Throwable err) { err.printStackTrace(); fail("testH5Tget_class: " + err); } } @Test public void testH5Tget_size() { long dt_size = -1; try { dt_size = H5.H5Tget_size(H5strdid); } catch (Throwable err) { err.printStackTrace(); fail("testH5Tget_size:H5.H5Tget_size " + err); } assertTrue("testH5Tget_size", dt_size > 0); } @Test public void testH5Tset_size() { long dt_size = 5; try { H5.H5Tset_size(H5strdid, dt_size); } catch (Throwable err) { err.printStackTrace(); fail("testH5Tset_size:H5.H5Tset_size " + err); } try { dt_size = H5.H5Tget_size(H5strdid); } catch (Throwable err) { err.printStackTrace(); fail("testH5Tget_size:H5.H5Tget_size " + err); } assertTrue("testH5Tget_size", dt_size == 5); } @Test public void testH5Tarray_create() { int filetype_id = -1; long[] adims = { 3, 5 }; try { filetype_id = H5.H5Tarray_create(HDF5Constants.H5T_STD_I64LE, 2, adims); assertTrue("testH5Tarray_create", filetype_id > 0); } catch (Throwable err) { err.printStackTrace(); fail("testH5Tarray_create.H5Tarray_create " + err); } finally { if (filetype_id >= 0) try {H5.H5Tclose(filetype_id);} catch (Exception ex) {} } } @Test public void testH5Tget_array_ndims() { int filetype_id = -1; int ndims = 0; long[] adims = { 3, 5 }; try { filetype_id = H5.H5Tarray_create(HDF5Constants.H5T_STD_I64LE, 2, adims); } catch (Throwable err) { err.printStackTrace(); fail("testH5Tarray_create.H5Tarray_create " + err); } assertTrue("testH5Tget_array_ndims:H5Tarray_create", filetype_id > 0); try { ndims = H5.H5Tget_array_ndims(filetype_id); assertTrue("testH5Tget_array_ndims", ndims == 2); } catch (Throwable err) { err.printStackTrace(); fail("testH5Tget_array_ndims.H5Tget_array_ndims " + err); } finally { if (filetype_id >= 0) try {H5.H5Tclose(filetype_id);} catch (Exception ex) {} } } @Test public void testH5Tget_array_dims() { int filetype_id = -1; int ndims = 0; long[] adims = { 3, 5 }; long[] rdims = new long[2]; try { filetype_id = H5.H5Tarray_create(HDF5Constants.H5T_STD_I64LE, 2, adims); } catch (Throwable err) { err.printStackTrace(); fail("testH5Tarray_create.H5Tarray_create " + err); } assertTrue("testH5Tget_array_dims:H5Tarray_create", filetype_id > 0); try { ndims = H5.H5Tget_array_dims(filetype_id, rdims); assertTrue("testH5Tget_array_dims", ndims == 2); assertTrue("testH5Tget_array_dims", adims[0] == rdims[0]); assertTrue("testH5Tget_array_dims", adims[1] == rdims[1]); } catch (Throwable err) { err.printStackTrace(); fail("testH5Tget_array_dims.H5Tget_array_dims " + err); } finally { if (filetype_id >= 0) try {H5.H5Tclose(filetype_id);} catch (Exception ex) {} } } @Test public void testH5Tenum_functions() { int filetype_id =-1; String enum_type ="Enum_type"; byte[] enum_val = new byte[1]; String enum_name = null; // Create a enumerate datatype try { filetype_id = H5.H5Tcreate(HDF5Constants.H5T_ENUM, (long)1); } catch (Throwable err) { err.printStackTrace(); fail("testH5Tenum_functions:H5Tcreate " + err); } assertTrue("testH5Tenum_functions:H5Tcreate", filetype_id > 0); try { enum_val[0]=10; H5.H5Tenum_insert(filetype_id, "RED", enum_val); enum_val[0]=11; H5.H5Tenum_insert(filetype_id, "GREEN", enum_val); enum_val[0]=12; H5.H5Tenum_insert(filetype_id, "BLUE", enum_val); enum_val[0]=13; H5.H5Tenum_insert(filetype_id, "ORANGE", enum_val); enum_val[0]=14; H5.H5Tenum_insert(filetype_id, "YELLOW", enum_val); // Query member number and member index by member name, for enumeration type. assertTrue("Can't get member number", H5.H5Tget_nmembers(filetype_id) == 5); assertTrue("Can't get correct index number", H5.H5Tget_member_index(filetype_id, "ORANGE") == 3); // Commit enumeration datatype and close it */ H5.H5Tcommit(H5fid, enum_type, filetype_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); H5.H5Tclose(filetype_id); // Open the dataytpe for query filetype_id = H5.H5Topen(H5fid, enum_type, HDF5Constants.H5P_DEFAULT); assertTrue("testH5Tenum_functions:H5Tcreate", filetype_id > 0); // Query member number and member index by member name, for enumeration type assertTrue("Can't get member number", H5.H5Tget_nmembers(filetype_id) == 5); assertTrue("Can't get correct index number", H5.H5Tget_member_index(filetype_id, "ORANGE") == 3); // Query member value by member name, for enumeration type H5.H5Tenum_valueof (filetype_id, "ORANGE", enum_val); assertTrue("Incorrect value for enum member", enum_val[0]==13); // Query member value by member index, for enumeration type H5.H5Tget_member_value (filetype_id, 2, enum_val); assertTrue("Incorrect value for enum member", enum_val[0]==12); // Query member name by member value, for enumeration type enum_val[0] = 14; enum_name = H5.H5Tenum_nameof(filetype_id, enum_val, 16); assertTrue("Incorrect name for enum member", enum_name.compareTo("YELLOW")==0); } catch (Throwable err) { err.printStackTrace(); fail("testH5Tenum_functions:query " + err); } finally { if (filetype_id >= 0) try {H5.H5Tclose(filetype_id);} catch (Exception ex) {} } } @Test public void testH5Tenum_create_functions() { int filetype_id = -1; byte[] enum_val = new byte[1]; // Create a enumerate datatype try { filetype_id = H5.H5Tenum_create(HDF5Constants.H5T_NATIVE_INT); } catch (Throwable err) { err.printStackTrace(); fail("testH5Tenum_create_functions:H5Tcreate " + err); } assertTrue("testH5Tenum_create_functions:H5Tcreate", filetype_id > 0); try { enum_val[0]=10; H5.H5Tenum_insert(filetype_id, "RED", enum_val); enum_val[0]=11; H5.H5Tenum_insert(filetype_id, "GREEN", enum_val); enum_val[0]=12; H5.H5Tenum_insert(filetype_id, "BLUE", enum_val); enum_val[0]=13; H5.H5Tenum_insert(filetype_id, "ORANGE", enum_val); enum_val[0]=14; H5.H5Tenum_insert(filetype_id, "YELLOW", enum_val); // Query member number and member index by member name, for enumeration type. assertTrue("Can't get member number", H5.H5Tget_nmembers(filetype_id) == 5); assertTrue("Can't get correct index number", H5.H5Tget_member_index(filetype_id, "ORANGE") == 3); } catch (Throwable err) { err.printStackTrace(); fail("testH5Tenum_create_functions:H5Tget_nmembers " + err); } finally { if (filetype_id >= 0) try {H5.H5Tclose(filetype_id);} catch (Exception ex) {} } } @Test public void testH5Topaque_functions() { int filetype_id = -1; String opaque_name = null; // Create a enumerate datatype try { filetype_id = H5.H5Tcreate(HDF5Constants.H5T_OPAQUE, (long)4); } catch (Throwable err) { err.printStackTrace(); fail("testH5Topaque_functions:H5Tcreate " + err); } assertTrue("testH5Topaque_functions:H5Tcreate", filetype_id > 0); try { H5.H5Tset_tag(filetype_id, "opaque type"); opaque_name = H5.H5Tget_tag(filetype_id); assertTrue("Incorrect tag for opaque type", opaque_name.compareTo("opaque type")==0); } catch (Throwable err) { err.printStackTrace(); fail("testH5Topaque_functions:H5Tset_get_tag " + err); } finally { if (filetype_id >= 0) try {H5.H5Tclose(filetype_id);} catch (Exception ex) {} } } @Test public void testH5Tvlen_create() { int filetype_id = -1; try { filetype_id = H5.H5Tvlen_create(HDF5Constants.H5T_C_S1); assertTrue("testH5Tvlen_create", filetype_id > 0); } catch (Throwable err) { err.printStackTrace(); fail("testH5Tvlen_create.H5Tvlen_create " + err); } finally { if (filetype_id >= 0) try {H5.H5Tclose(filetype_id);} catch (Exception ex) {} } } @Test public void testH5Tis_variable_str() { int filetype_id = -1; try { filetype_id = H5.H5Tcopy(HDF5Constants.H5T_C_S1); assertTrue("testH5Tis_variable_str", filetype_id > 0); // Convert to variable-length string H5.H5Tset_size(filetype_id, HDF5Constants.H5T_VARIABLE); // Check if datatype is VL string int vlclass = H5.H5Tget_class(filetype_id); assertTrue("testH5Tis_variable_str:H5Tget_class", vlclass == HDF5Constants.H5T_STRING); assertTrue("testH5Tis_variable_str:H5Tis_variable_str", H5.H5Tis_variable_str(filetype_id)); // Verify that the class detects as a string assertTrue("testH5Tis_variable_str:H5Tdetect_class", H5.H5Tdetect_class(filetype_id, HDF5Constants.H5T_STRING)); } catch (Throwable err) { err.printStackTrace(); fail("testH5Tis_variable_str.H5Tis_variable_str " + err); } finally { if (filetype_id >= 0) try {H5.H5Tclose(filetype_id);} catch (Exception ex) {} } } @Test public void testH5Tcompound_functions() { int filetype_id =-1; // Create a enumerate datatype try { filetype_id = H5.H5Tcreate(HDF5Constants.H5T_COMPOUND, (long)16); } catch (Throwable err) { err.printStackTrace(); fail("testH5Tcompound_functions:H5Tcreate " + err); } assertTrue("testH5Tcompound_functions:H5Tcreate", filetype_id > 0); try { H5.H5Tinsert(filetype_id, "Lon", 0, HDF5Constants.H5T_NATIVE_DOUBLE); H5.H5Tinsert(filetype_id, "Lat", 8, HDF5Constants.H5T_NATIVE_DOUBLE); // Query member number and member index by member name, for enumeration type. assertTrue("Can't get member number", H5.H5Tget_nmembers(filetype_id) == 2); assertTrue("Can't get correct index number", H5.H5Tget_member_index(filetype_id, "Lat") == 1); // We started to support this function for compound type in 1.8.6 release. int order = H5.H5Tget_order(filetype_id); assertFalse("Can't get order for compound type.", order == HDF5Constants.H5T_ORDER_ERROR); assertTrue("Wrong order for this type.", (order == HDF5Constants.H5T_ORDER_LE) || (order == HDF5Constants.H5T_ORDER_BE)); // Make certain that the correct classes can be detected assertTrue("Can't get correct class", H5.H5Tdetect_class(filetype_id, HDF5Constants.H5T_COMPOUND)); assertTrue("Can't get correct class", H5.H5Tdetect_class(filetype_id, HDF5Constants.H5T_FLOAT)); // Make certain that an incorrect class is not detected assertFalse("Can get incorrect class", H5.H5Tdetect_class(filetype_id, HDF5Constants.H5T_TIME)); // Query member name by member index String index_name = H5.H5Tget_member_name (filetype_id, 0); assertTrue("Incorrect name for member index", index_name.compareTo("Lon")==0); // Query member offset by member no long index_offset = H5.H5Tget_member_offset (filetype_id, 1); assertTrue("Incorrect offset for member no", index_offset == 8); // Query member type by member index int index_type = H5.H5Tget_member_type (filetype_id, 0); assertTrue("Incorrect type for member index", H5.H5Tequal(HDF5Constants.H5T_NATIVE_DOUBLE, index_type)); if (index_type >= 0) try {H5.H5Tclose(index_type);} catch (Exception ex) {} } catch (Throwable err) { err.printStackTrace(); fail("testH5Tcompound_functions:query " + err); } finally { if (filetype_id >= 0) try {H5.H5Tclose(filetype_id);} catch (Exception ex) {} } } } libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/TestH5Tbasic.java000066400000000000000000000102621256564762100255630ustar00rootroot00000000000000package test.hdf5lib; import static org.junit.Assert.assertFalse; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.HDF5Constants; import org.junit.Before; import org.junit.Test; public class TestH5Tbasic { @Before public void checkOpenIDs() { assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0); } @Test public void testH5Tcopy() { int H5strdid = -1; try { H5strdid = H5.H5Tcopy(HDF5Constants.H5T_C_S1); assertTrue("H5.H5Tcopy",H5strdid > 0); } catch (Throwable err) { err.printStackTrace(); fail("testH5Tcopy: " + err); } finally { if (H5strdid >= 0) try {H5.H5Tclose(H5strdid);} catch (Exception ex) {} } } @Test public void testH5Tequal() { int H5strdid = -1; try { H5strdid = H5.H5Tcopy(HDF5Constants.H5T_C_S1); assertTrue("H5.H5Tcopy",H5strdid > 0); boolean teq = H5.H5Tequal(HDF5Constants.H5T_C_S1, H5strdid); assertTrue("H5.H5Tequal",teq); } catch (Throwable err) { err.printStackTrace(); fail("testH5Tequal: " + err); } finally { if (H5strdid >= 0) try {H5.H5Tclose(H5strdid);} catch (Exception ex) {} } } @Test public void testH5Tequal_not() { int H5strdid = -1; try { H5strdid = H5.H5Tcopy(HDF5Constants.H5T_STD_U64LE); assertTrue("H5.H5Tcopy",H5strdid > 0); boolean teq = H5.H5Tequal(HDF5Constants.H5T_IEEE_F32BE, H5strdid); assertFalse("H5.H5Tequal",teq); } catch (Throwable err) { err.printStackTrace(); fail("testH5Tequal_not: " + err); } finally { if (H5strdid >= 0) try {H5.H5Tclose(H5strdid);} catch (Exception ex) {} } } @Test public void testH5Tconvert() { String[] strs = {"a1234","b1234"}; int srcLen = 5; int dstLen = 10; int srcId = -1; int dstId = -1; int dimSize = strs.length; byte[] buf = new byte[dimSize*dstLen]; for (int i=0; i 0); H5.H5Tset_size(H5strdid, (long)5); assertTrue(HDF5Constants.H5T_ORDER_NONE == H5.H5Tget_order(H5strdid)); H5.H5Tset_order(H5strdid, HDF5Constants.H5T_ORDER_NONE); assertTrue(HDF5Constants.H5T_ORDER_NONE == H5.H5Tget_order(H5strdid)); assertTrue(5 == H5.H5Tget_size(H5strdid)); // Variable length string H5.H5Tset_size(H5strdid, HDF5Constants.H5T_VARIABLE); H5.H5Tset_order(H5strdid, HDF5Constants.H5T_ORDER_BE); assertTrue(HDF5Constants.H5T_ORDER_BE == H5.H5Tget_order(H5strdid)); } catch (Throwable err) { err.printStackTrace(); fail("testH5Torder: " + err); } finally { if (H5strdid >= 0) try {H5.H5Tclose(H5strdid);} catch (Exception ex) {} } } } libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/TestH5Tparams.java000066400000000000000000000256401256564762100257730ustar00rootroot00000000000000package test.hdf5lib; import static org.junit.Assert.assertTrue; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import org.junit.Before; import org.junit.Test; public class TestH5Tparams { @Before public void checkOpenIDs() { assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0); } @Test(expected = HDF5LibraryException.class) public void testH5Tcopy_invalid() throws Throwable { H5.H5Tcopy(-1); } @Test(expected = HDF5LibraryException.class) public void testH5Tequal_invalid() throws Throwable { H5.H5Tequal(-1, -1); } @Test(expected = HDF5LibraryException.class) public void testH5Tlock_invalid() throws Throwable { H5.H5Tlock(-1); } @Test(expected = HDF5LibraryException.class) public void testH5Tget_class_invalid() throws Throwable { H5.H5Tget_class(-1); } @Test(expected = HDF5LibraryException.class) public void testH5Tget_size_invalid() throws Throwable { H5.H5Tget_size(-1); } @Test(expected = HDF5LibraryException.class) public void testH5Tget_size_long_invalid() throws Throwable { H5.H5Tget_size_long(-1); } @Test(expected = HDF5LibraryException.class) public void testH5Tset_size_invalid() throws Throwable { H5.H5Tset_size(-1, 0); } @Test(expected = HDF5LibraryException.class) public void testH5Tget_order_invalid() throws Throwable { H5.H5Tget_order(-1); } @Test(expected = HDF5LibraryException.class) public void testH5Tset_order_invalid() throws Throwable { H5.H5Tset_order(-1, 0); } @Test(expected = HDF5LibraryException.class) public void testH5Tget_precision_invalid() throws Throwable { H5.H5Tget_precision(-1); } @Test(expected = HDF5LibraryException.class) public void testH5Tget_precision_long_invalid() throws Throwable { H5.H5Tget_precision_long(-1); } @Test(expected = HDF5LibraryException.class) public void testH5Tset_precision_invalid() throws Throwable { H5.H5Tset_precision(-1, 0); } @Test(expected = HDF5LibraryException.class) public void testH5Tget_offset_invalid() throws Throwable { H5.H5Tget_offset(-1); } @Test(expected = HDF5LibraryException.class) public void testH5Tset_offset_invalid() throws Throwable { H5.H5Tset_offset(-1, 0); } @Test(expected = HDF5LibraryException.class) public void testH5Tcreate_invalid() throws Throwable { H5.H5Tcreate(-1, 0); } @Test(expected = NullPointerException.class) public void testH5Topen_null() throws Throwable { H5.H5Topen(-1, null, 0); } @Test(expected = HDF5LibraryException.class) public void testH5Topen_invalid() throws Throwable { H5.H5Topen(-1, "Bogus", 0); } @Test(expected = NullPointerException.class) public void testH5Tcommit_null() throws Throwable { H5.H5Tcommit(-1, null, 0, -1, -1, -1); } @Test(expected = HDF5LibraryException.class) public void testH5Tcommit_invalid() throws Throwable { H5.H5Tcommit(-1, "Bogus", -1, -1, -1, -1); } @Test(expected = NullPointerException.class) public void testH5Tget_pad_null() throws Throwable { H5.H5Tget_pad(-1, null); } @Test(expected = HDF5LibraryException.class) public void testH5Tget_pad_invalid() throws Throwable { int[] pad = new int[2]; H5.H5Tget_pad(-1, pad); } @Test(expected = HDF5LibraryException.class) public void testH5Tset_pad_invalid() throws Throwable { H5.H5Tset_pad(-1, -1, -1); } @Test(expected = HDF5LibraryException.class) public void testH5Tget_sign_invalid() throws Throwable { H5.H5Tget_sign(-1); } @Test(expected = HDF5LibraryException.class) public void testH5Tset_sign_invalid() throws Throwable { H5.H5Tset_sign(-1, 0); } @Test(expected = NullPointerException.class) public void testH5Tget_fields_null() throws Throwable { H5.H5Tget_fields(-1, (long[])null); } @Test(expected = IllegalArgumentException.class) public void testH5Tget_fields_length_invalid() throws Throwable { long[] fields = new long[2]; H5.H5Tget_fields(-1, fields); } @Test(expected = HDF5LibraryException.class) public void testH5Tget_fields_invalid() throws Throwable { long[] fields = new long[5]; H5.H5Tget_fields(-1, fields); } @Test(expected = HDF5LibraryException.class) public void testH5Tset_fields_invalid() throws Throwable { H5.H5Tset_fields(-1, -1, -1, -1, -1, -1); } @Test(expected = HDF5LibraryException.class) public void testH5Tget_ebias_invalid() throws Throwable { H5.H5Tget_ebias(-1); } @Test(expected = HDF5LibraryException.class) public void testH5Tget_ebias_long_invalid() throws Throwable { H5.H5Tget_ebias_long(-1); } @Test(expected = HDF5LibraryException.class) public void testH5Tset_ebias_invalid() throws Throwable { H5.H5Tset_ebias(-1, 0); } @Test(expected = HDF5LibraryException.class) public void testH5Tget_norm_invalid() throws Throwable { H5.H5Tget_norm(-1); } @Test(expected = HDF5LibraryException.class) public void testH5Tset_norm_invalid() throws Throwable { H5.H5Tset_norm(-1, 0); } @Test(expected = HDF5LibraryException.class) public void testH5Tget_inpad_invalid() throws Throwable { H5.H5Tget_inpad(-1); } @Test(expected = HDF5LibraryException.class) public void testH5Tset_inpad_invalid() throws Throwable { H5.H5Tset_inpad(-1, 0); } @Test(expected = HDF5LibraryException.class) public void testH5Tget_cset_invalid() throws Throwable { H5.H5Tget_cset(-1); } @Test(expected = HDF5LibraryException.class) public void testH5Tset_cset_invalid() throws Throwable { H5.H5Tset_cset(-1, 0); } @Test(expected = HDF5LibraryException.class) public void testH5Tget_strpad_invalid() throws Throwable { H5.H5Tget_strpad(-1); } @Test(expected = HDF5LibraryException.class) public void testH5Tset_strpad_invalid() throws Throwable { H5.H5Tset_strpad(-1, 0); } @Test(expected = HDF5LibraryException.class) public void testH5Tget_nmembers_invalid() throws Throwable { H5.H5Tget_nmembers(-1); } @Test(expected = NullPointerException.class) public void testH5Tget_member_index_null() throws Throwable { H5.H5Tget_member_index(-1, null); } @Test(expected = HDF5LibraryException.class) public void testH5Tget_member_index_invalid() throws Throwable { H5.H5Tget_member_index(-1, "Bogus"); } @Test(expected = HDF5LibraryException.class) public void testH5Tget_member_type_invalid() throws Throwable { H5.H5Tget_member_type(-1, -1); } @Test(expected = HDF5LibraryException.class) public void testH5Tget_member_class_invalid() throws Throwable { H5.H5Tget_member_class(-1, -1); } @Test(expected = NullPointerException.class) public void testH5Tinsert_null() throws Throwable { H5.H5Tinsert(-1, null, 0, 0); } @Test(expected = HDF5LibraryException.class) public void testH5Tinsert_invalid() throws Throwable { H5.H5Tinsert(-1, "Bogus", 0, 0); } @Test(expected = HDF5LibraryException.class) public void testH5Tpack_invalid() throws Throwable { H5.H5Tpack(-1); } @Test(expected = HDF5LibraryException.class) public void testH5Tvlen_create_invalid() throws Throwable { H5.H5Tvlen_create(-1); } @Test(expected = NullPointerException.class) public void testH5Tset_tag_null() throws Throwable { H5.H5Tset_tag(-1, null); } @Test(expected = HDF5LibraryException.class) public void testH5Tset_tag_invalid() throws Throwable { H5.H5Tset_tag(-1, "Bogus"); } @Test(expected = HDF5LibraryException.class) public void testH5Tget_super_invalid() throws Throwable { H5.H5Tget_super(-1); } @Test(expected = HDF5LibraryException.class) public void testH5Tenum_create_invalid() throws Throwable { H5.H5Tenum_create(-1); } @Test(expected = NullPointerException.class) public void testH5Tenum_insert_name_null() throws Throwable { H5.H5Tenum_insert(-1, null, (byte[])null); } @Test(expected = NullPointerException.class) public void testH5Tenum_insert_null() throws Throwable { H5.H5Tenum_insert(-1, "bogus", (byte[])null); } @Test(expected = HDF5LibraryException.class) public void testH5Tenum_insert_invalid() throws Throwable { byte[] enumtype = new byte[2]; H5.H5Tenum_insert(-1, "bogus", enumtype); } @Test(expected = IllegalArgumentException.class) public void testH5Tenum_nameof_invalid_size() throws Throwable { H5.H5Tenum_nameof(-1, null, -1); } @Test(expected = NullPointerException.class) public void testH5Tenum_nameof_value_null() throws Throwable { H5.H5Tenum_nameof(-1, null, 1); } @Test(expected = HDF5LibraryException.class) public void testH5Tenum_nameof_invalid() throws Throwable { byte[] btype = new byte[2]; H5.H5Tenum_nameof(-1, btype, 1); } @Test(expected = NullPointerException.class) public void testH5Tenum_valueof_name_null() throws Throwable { H5.H5Tenum_valueof(-1, null, (byte[])null); } @Test(expected = NullPointerException.class) public void testH5Tenum_valueof_null() throws Throwable { H5.H5Tenum_valueof(-1, "bogus", (byte[])null); } @Test(expected = HDF5LibraryException.class) public void testH5Tenum_valueof_invalid() throws Throwable { byte[] btype = new byte[2]; H5.H5Tenum_valueof(-1, "bogus", btype); } @Test(expected = NullPointerException.class) public void testH5Tget_member_value_null() throws Throwable { H5.H5Tget_member_value(-1, -1, (byte[])null); } @Test(expected = HDF5LibraryException.class) public void testH5Tget_member_value_invalid() throws Throwable { byte[] btype = new byte[2]; H5.H5Tget_member_value(-1, -1, btype); } @Test(expected = IllegalArgumentException.class) public void testH5Tarray_create_invalid() throws Throwable { H5.H5Tarray_create(-1, -1, null); } @Test(expected = NullPointerException.class) public void testH5Tarray_create_value_null() throws Throwable { H5.H5Tarray_create(-1, 1, null); } @Test(expected = HDF5LibraryException.class) public void testH5Tget_array_ndims_invalid() throws Throwable { H5.H5Tget_array_ndims(-1); } @Test(expected = NullPointerException.class) public void testH5Tget_array_dims_null() throws Throwable { H5.H5Tget_array_dims(-1, null); } @Test(expected = HDF5LibraryException.class) public void testH5Tget_native_type_invalid() throws Throwable { H5.H5Tget_native_type(-1); } } libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/TestH5Z.java000066400000000000000000000074471256564762100246020ustar00rootroot00000000000000package test.hdf5lib; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.HDF5Constants; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import org.junit.Test; public class TestH5Z { @Test public void testH5Zfilter_avail() { try { int filter_found = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_DEFLATE); assertTrue("H5.H5Zfilter_avail", filter_found > 0); filter_found = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_FLETCHER32); assertTrue("H5.H5Zfilter_avail", filter_found > 0); filter_found = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_NBIT); assertTrue("H5.H5Zfilter_avail", filter_found > 0); filter_found = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_SCALEOFFSET); assertTrue("H5.H5Zfilter_avail", filter_found > 0); filter_found = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_SHUFFLE); assertTrue("H5.H5Zfilter_avail", filter_found > 0); /* filter_found = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_SZIP); assertTrue("H5.H5Zfilter_avail", filter_found > 0); */ } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Zfilter_avail " + err); } } @Test public void testH5Zget_filter_info() { try { int filter_flag = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_DEFLATE); assertTrue("H5.H5Zget_filter_info", (filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) > 0); assertTrue("H5.H5Zget_filter_info", (filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) > 0); filter_flag = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_FLETCHER32); assertTrue("H5.H5Zget_filter_info", (filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) > 0); assertTrue("H5.H5Zget_filter_info", (filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) > 0); filter_flag = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_NBIT); assertTrue("H5.H5Zget_filter_info", (filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) > 0); assertTrue("H5.H5Zget_filter_info", (filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) > 0); filter_flag = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_SCALEOFFSET); assertTrue("H5.H5Zget_filter_info", (filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) > 0); assertTrue("H5.H5Zget_filter_info", (filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) > 0); filter_flag = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_SHUFFLE); assertTrue("H5.H5Zget_filter_info", (filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) > 0); assertTrue("H5.H5Zget_filter_info", (filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) > 0); /* filter_flag = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_SZIP); assertTrue("H5.H5Zget_filter_info", (filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) > 0); assertTrue("H5.H5Zget_filter_info", (filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) > 0); */ } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Zget_filter_info " + err); } } @Test(expected = HDF5LibraryException.class) public void testH5Zunregister_predefined() throws Throwable { int filter_found = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_SHUFFLE); assertTrue("H5.H5Zfilter_avail", filter_found > 0); H5.H5Zunregister(HDF5Constants.H5Z_FILTER_SHUFFLE); } } libsis-jhdf5-java-14.12.1/sourceTest/java/test/hdf5lib/h5ex_g_iterate.hdf000066400000000000000000000055601256564762100260420ustar00rootroot00000000000000‰HDF  ÿÿÿÿÿÿÿÿp ÿÿÿÿÿÿÿÿ €`HEAP(€G1DS1DT1L1ØTREEÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ@  €`HEAP P TREEÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ  ðÐSNODˆ¨ðÐ ø ( ÿÿÿÿÿÿÿÿƒüNHh@  ( ˜ÍüNHhSNODøDS2libsis-jhdf5-java-14.12.1/sourceTest/java/tests.xml000066400000000000000000000004321256564762100220440ustar00rootroot00000000000000