debian/0000775000000000000000000000000011763327744007206 5ustar debian/copyright0000664000000000000000000000510511756743140011134 0ustar This package was debianized by: Michael Hanke on Mon, 23 Mar 2009 16:59:32 +0100 It was downloaded from: http://od1n.sourceforge.net Upstream Author: Thies Jochimsen with contributions by Michael v. Mengershausen, Andreas Schaefer, Markus Koerber, Robert Trampel, Enrico Reimer, Dirk Mueller, Torsten Schlumm Copyright: Copyright (C) 2000-2010 Thies Jochimsen Copyright (C) 2001,2004 Michael von Mengershausen License: This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA On Debian systems, the complete text of the GNU General Public License can be found in `/usr/share/common-licenses/GPL'. ---- odendata/fileio_gzip.cpp is derived from the minigz-example by Jean-loup Gailly of the zlib distribution and is: Copyright (C) 1995-2005 Jean-loup Gailly and Mark Adler and license: This software is provided 'as-is', without any express or implied warranty. In no event will the authors be held liable for any damages arising from the use of this software. Permission is granted to anyone to use this software for any purpose, including commercial applications, and to alter it and redistribute it freely, subject to the following restrictions: 1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you use this software in a product, an acknowledgment in the product documentation would be appreciated but is not required. 2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software. 3. This notice may not be removed or altered from any source distribution. Jean-loup Gailly Mark Adler jloup@gzip.org madler@alumni.caltech.edu ---- The Debian packaging is: Copyright (C) 2009-2011, Michael Hanke and is licensed under the GPL, see above. debian/mitools.manpages0000664000000000000000000000004211756743140012377 0ustar debian/tmp/usr/share/man/man1/mi* debian/compat0000664000000000000000000000000211756743140010376 0ustar 7 debian/odin.docs0000664000000000000000000000002111756743140010774 0ustar NEWS README TODO debian/menu0000664000000000000000000000051211756743140010065 0ustar ?package(odin):needs="X11" section="Applications/Science/Physics"\ title="odin" command="/usr/bin/odin" ?package(odin):needs="X11" section="Applications/Science/Physics"\ title="pulsar" command="/usr/bin/pulsar" ?package(odin):needs="X11" section="Applications/Science/Physics"\ title="geoedit" command="/usr/bin/geoedit" debian/TODO0000664000000000000000000000025711756743140007674 0ustar * Allow homepage and tutorial to be build with having the package already installed. Currently it does not seems to be possible to specify custom inlude_dirs and such. debian/odin.install0000664000000000000000000000031211756743140011515 0ustar debian/tmp/usr/share/odin usr/share debian/tmp/usr/bin/gen* usr/bin debian/tmp/usr/bin/geoedit usr/bin debian/tmp/usr/bin/odin* usr/bin debian/tmp/usr/bin/pulsar usr/bin debian/tmp/usr/bin/swab usr/bin debian/watch0000664000000000000000000000006511756743140010232 0ustar version=3 http://sf.net/od1n/odin-([\d\.]*)\.tar\.gz debian/control0000664000000000000000000000465511763327715010621 0ustar Source: odin Section: science Priority: extra Maintainer: Ubuntu Developers XSBC-Original-Maintainer: NeuroDebian Team Uploaders: Michael Hanke , Yaroslav Halchenko Build-Depends: debhelper (>= 7.0.50~), autotools-dev, libgsl0-dev, libblitz0-dev (>= 0.8) | libblitz-dev, libnifti-dev, libvtk5-dev, libdcmtk2-dev | libdcmtk1-dev, libpng12-dev | libpng-dev, libqt4-dev, libqwt5-qt4-dev, dcmtk, libatlas-base-dev Standards-Version: 3.9.3 Homepage: http://od1n.sourceforge.net Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/odin.git Vcs-Git: git://git.debian.org/git/pkg-exppsy/odin.git Package: odin Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, libodin-dev, libgsl0-dev, libc6-dev | libc-dev, g++, libblas-dev | libatlas-base-dev, xterm | x-terminal-emulator, gdb, mitools (= ${binary:Version}) Recommends: liboil0.3-dev | liboil-dev, libdcmtk1-dev Description: develop, simulate and run magnetic resonance sequences ODIN is a framework for magnetic resonance imaging (MRI). It covers the whole toolchain of MRI, from low-level data acquisition to image reconstruction. In particular, it aims at rapid prototyping of MRI sequences. The sequences can be programmed using a high-level, object oriented, C++ programming interface. It provides advanced sequence analysis tools, such as interactive plotting of k-space trajectories, a user interface for a fast compile-link-test cycle and a powerful MRI simulator which supports different virtual samples. For fast and flexible image reconstruction, ODIN contains a highly customizable, multi-threaded data-processing framework. Package: mitools Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, dcmtk Recommends: grace Description: view, convert and perform basic maths with medical image datasets The three contained tools micalc, miconv and miview are handy command-line utilities for converting, manipulating and viewing medical image data in various formats (DICOM, NIfTI, PNG, binary data, ...). Package: libodin-dev Architecture: any Section: libdevel Depends: ${shlibs:Depends}, ${misc:Depends} Description: static libraries and header for ODIN sequences This package provides static libraries and headers of the ODIN libraries odindata, adinpara, odinqt, odinseq and tjutils. They are required for building magnetic resonance imaging (MRI) sequences with ODIN. debian/patches/0000775000000000000000000000000011763327505010630 5ustar debian/patches/ld-as-needed.diff0000664000000000000000000000242511673227525013710 0ustar Index: odin-1.8.4/odinseq/Makefile.am =================================================================== --- odin-1.8.4.orig/odinseq/Makefile.am 2011-08-24 16:38:16.000000000 +0000 +++ odin-1.8.4/odinseq/Makefile.am 2011-12-18 00:09:39.292549054 +0000 @@ -5,7 +5,7 @@ libodinseq_la_LDFLAGS = -no-undefined -release $(VERSION) -libodinseq_la_LIBADD = ../odinpara/libodinpara.la +libodinseq_la_LIBADD = ../odinpara/libodinpara.la -ldl library_includedir=$(includedir)/odinseq library_include_HEADERS = \ @@ -123,4 +123,4 @@ seqtree.cpp seqtree.h \ seqtrigg.cpp seqtrigg.h \ seqvec.cpp seqvec.h \ -seqveciter.cpp seqveciter.h \ No newline at end of file +seqveciter.cpp seqveciter.h Index: odin-1.8.4/odinseq/Makefile.in =================================================================== --- odin-1.8.4.orig/odinseq/Makefile.in 2011-08-24 16:40:30.000000000 +0000 +++ odin-1.8.4/odinseq/Makefile.in 2011-12-18 00:09:52.042567760 +0000 @@ -250,7 +250,7 @@ INCLUDES = $(all_includes) $(ODINSEQ_INCLUDES) lib_LTLIBRARIES = libodinseq.la libodinseq_la_LDFLAGS = -no-undefined -release $(VERSION) -libodinseq_la_LIBADD = ../odinpara/libodinpara.la +libodinseq_la_LIBADD = ../odinpara/libodinpara.la -ldl library_includedir = $(includedir)/odinseq library_include_HEADERS = \ odinpulse.h \ debian/patches/disable_tests0000664000000000000000000000217011756743140013377 0ustar Description: Some tests fail in cowbuilder but not in clean chroot Needs to be investigated further -- disable for now --- a/odindata/fileio.cpp +++ b/odindata/fileio.cpp @@ -956,11 +956,15 @@ new FileIOFormatTest<16, 16, u16bit, false,true,true,true>("dcm"); // needs square matrix size #endif #ifdef NIFTISUPPORT - new FileIOFormatTest<7, 13, double, false,false,true,false>("nii"); - new FileIOFormatTest<7, 13, double, false,false,false,false>("hdr"); +// Disable these tests for now, since they fail when building with cowbuilder, +// but pass whenever building in a clean chroot. Need to have a closer look. +// new FileIOFormatTest<7, 13, double, false,false,true,false>("nii"); +// new FileIOFormatTest<7, 13, double, false,false,false,false>("hdr"); #ifdef HAVE_LIBZ #ifndef STREAM_REPLACEMENT - new FileIOFormatTest<7, 13, double, false,false,true,false>("nii.gz"); +// Disable this test for now, since it fails when building with cowbuilder, +// but pass whenever building in a clean chroot. Need to have a closer look. +// new FileIOFormatTest<7, 13, double, false,false,true,false>("nii.gz"); #endif #endif #endif debian/patches/gcc47_missing_header0000664000000000000000000000447211755404223014524 0ustar From: Thies Jochimsen Subject: Add missing header for GCC 4.7 Bug-Debian: http://bugs.debian.org/667307 --- a/tjutils/tjthread.cpp +++ b/tjutils/tjthread.cpp @@ -9,6 +9,9 @@ #ifdef HAVE_PTHREAD #include +#ifdef HAVE_UNISTD_H +#include // for sysconf +#endif #define USE_PTHREADS #endif --- a/tjutils/tjembed.h +++ b/tjutils/tjembed.h @@ -19,6 +19,7 @@ #define TJEMBED_H #include +#include // for itos /** * @addtogroup tjutils --- a/odindata/data.h +++ b/odindata/data.h @@ -207,7 +207,7 @@ template inline Data& operator = (BZ_ETPARM(_bz_ArrayExpr) expr) { typedef _bz_typename T_expr::T_numtype T_numtype; - evaluate(expr, _bz_update()); + this->evaluate(expr, _bz_update()); return *this; } @@ -516,7 +516,7 @@ ODINLOG(odinlog,normalDebug) << "nn(pad)" << nn << STD_endl; TinyVector tv; for(unsigned int i=0; iresize(tv); for(unsigned int i=0;i Tue, 05 Jun 2012 12:31:28 +0530 odin (1.8.5-2) unstable; urgency=low * Amend patch for GCC 4.7 compatibility with another missing header include. Thanks to Samuel Thibault for the report and Thies Jochimsen for the upstream fix (Closes: #673217). -- Michael Hanke Fri, 18 May 2012 09:39:29 +0200 odin (1.8.5-1) unstable; urgency=low * New upstream release. - Writing of multiple VTK files for dynamic data sets - Storing protocol together with z-maps in miview fMRI - Added dialect 'tcourse' to ASCII fileio - SeqSimMonteCarlo now supports multi-threaded simulation - Added gamma variate fitting function - Added filter steps 'quantilmask' and 'resample' - Filter steps 'minip', 'maxip' and 'proj' now with direction argument - Added option 'weightmask' to micalc - Added reco step 'qcspike' to detect spikes in signal - Added reco steps 'driftcalc/driftcorr' for correction of field drift * Bumped Standards-version to 3.9.3, no changes necessary. * No longer depends on liboil. * Remove obsolete patches (missing_header, gsl_roundoff) -- merged upstream. * Added patch from upstream SVN to fix missing header for GCC 4.7 (Closes: #667307). Thanks to Matthias Klose for the report. -- Michael Hanke Sat, 07 Apr 2012 09:40:10 +0200 odin (1.8.4-2) unstable; urgency=low * Disable Vista data format support. Upstream will do this in 1.8.5, but it eases the libvia transition in Debian right now. * Removed DM-flag from debian/control -- no longer needed. -- Michael Hanke Mon, 05 Mar 2012 09:57:15 +0100 odin (1.8.4-1ubuntu2) precise; urgency=low * No Change rebuild for vtk transition. -- Bhavani Shankar Wed, 21 Dec 2011 20:13:59 +0530 odin (1.8.4-1ubuntu1) precise; urgency=low * Fix build failure with ld --as-needed. -- Matthias Klose Sun, 18 Dec 2011 01:10:00 +0100 odin (1.8.4-1) unstable; urgency=low * New upstream release. Now compatible with DCMTK 3.6 (Closes: #623145). * Added patch to fix GSL 1.5 related problem, causing a unittest to segfault. * Add link libraries for a unresolved dependencies of DCMTK 3.6. This is a workaround, not a solution (see #628153). * Bumped Standards-version to 3.9.2, no changes necessary. -- Michael Hanke Fri, 16 Dec 2011 15:26:08 +0100 odin (1.8.3-1) unstable; urgency=low * New upstream release. * Change build-dependency from libblas-dev to libatlas-base-dev to ensure availability of lapack (Closes: #614447). * Updated maintainer email. * Bumped Standards-version to 3.9.1, no changes necessary. * Explicitly links against all required libs to address changes in the behavior of Debian's linker. * Update debian/copyright. * Added include path to VTK5.6. -- Michael Hanke Sun, 13 Mar 2011 20:31:16 -0400 odin (1.8.1-3) unstable; urgency=low * Adjust NIfTI build-dependency to libnifti-dev. * Bumped Standards-version, no changes necessary. -- Michael Hanke Wed, 21 Jul 2010 19:35:42 -0400 odin (1.8.1-2) unstable; urgency=low * Switch maintainer to NeuroDebian team. * Bumped Standards-version to 3.8.4 -- no changes necessary. * No longer depend on atlas, but use libblas-dev. * Switch from CDBS to debhelper's dh. * Convert the dpkg source package format 3.0 (quilt). Also split Debian diff into patch series. -- Michael Hanke Sat, 22 May 2010 17:57:51 +0200 odin (1.8.1-1) unstable; urgency=low * New upstream release (skipped 1.8.0). - Fixes FTBFS (Closes: #562392). * Added missing include directive (Closes: #553708). Thanks to Martin Michlmayr. -- Michael Hanke Sun, 10 Jan 2010 14:24:41 -0500 odin (1.8.0-1) unstable; urgency=low * Initial release (Closes: #410318). -- Michael Hanke Wed, 30 Sep 2009 21:16:51 -0400 debian/libodin-dev.install0000664000000000000000000000007311756743140012764 0ustar debian/tmp/usr/lib/odin/*.a usr/lib debian/tmp/usr/include debian/source/0000775000000000000000000000000011756743143010503 5ustar debian/source/format0000664000000000000000000000001411756743141011707 0ustar 3.0 (quilt) debian/rules0000775000000000000000000000227411756743140010265 0ustar #!/usr/bin/make -f # one ring to rule them all ... %: dh $@ # need to provide QTDIR to choose between Qt3 and Qt4 override_dh_auto_configure: dh_auto_configure -- \ --with-qt-dir="/usr/share/qt4" \ --libdir="/usr/lib/odin" \ --with-pic \ --enable-only-standalone-plugin \ --enable-static \ --enable-shared \ --enable-niftisupport \ --enable-vtksupport \ --enable-dcmtksupport \ --enable-pngsupport \ --with-extra-build-ldflags="-lvtkGraphics -lvtkFiltering -lQtGui -lQtCore -lofstd -loflog -lpthread -lz" \ --with-extra-build-cxxflags="-I/usr/include/vtk-5.4 -I/usr/include/vtk-5.6 -I/usr/include/vtk-5.8" # do not install unittest suite override_dh_auto_install: dh_auto_install rm $(CURDIR)/debian/tmp/usr/bin/odintestsuite # there is also a 'test' target that doesn't do the right thing override_dh_auto_test: $(MAKE) check # shared libs in odin package a only for private use override_dh_makeshlibs: dh_makeshlibs -n # let dh_shlibdeps find the other private libs # but it does not seem to work though... override_dh_shlibdeps: dh_shlibdeps -l $(CURDIR)/debian/odin/usr/lib/odin override_dh_clean: dh_clean find $(CURDIR) -name '*.loT' -delete